TY - JOUR
AB - The plant-signaling molecule auxin triggers fast and slow cellular responses across land plants and algae. The nuclear auxin pathway mediates gene expression and controls growth and development in land plants, but this pathway is absent from algal sister groups. Several components of rapid responses have been identified in Arabidopsis, but it is unknown if these are part of a conserved mechanism. We recently identified a fast, proteome-wide phosphorylation response to auxin. Here, we show that this response occurs across 5 land plant and algal species and converges on a core group of shared targets. We found conserved rapid physiological responses to auxin in the same species and identified rapidly accelerated fibrosarcoma (RAF)-like protein kinases as central mediators of auxin-triggered phosphorylation across species. Genetic analysis connects this kinase to both auxin-triggered protein phosphorylation and rapid cellular response, thus identifying an ancient mechanism for fast auxin responses in the green lineage.
AU - Kuhn, Andre
AU - Roosjen, Mark
AU - Mutte, Sumanth
AU - Dubey, Shiv Mani
AU - Carrillo Carrasco, Vanessa Polet
AU - Boeren, Sjef
AU - Monzer, Aline
AU - Koehorst, Jasper
AU - Kohchi, Takayuki
AU - Nishihama, Ryuichi
AU - Fendrych, Matyas
AU - Sprakel, Joris
AU - Friml, Jiří
AU - Weijers, Dolf
ID - 14826
IS - 1
JF - Cell
KW - General Biochemistry
KW - Genetics and Molecular Biology
SN - 0092-8674
TI - RAF-like protein kinases mediate a deeply conserved, rapid auxin response
VL - 187
ER -
TY - JOUR
AB - Bacteria divide by binary fission. The protein machine responsible for this process is the divisome, a transient assembly of more than 30 proteins in and on the surface of the cytoplasmic membrane. Together, they constrict the cell envelope and remodel the peptidoglycan layer to eventually split the cell into two. For Escherichia coli, most molecular players involved in this process have probably been identified, but obtaining the quantitative information needed for a mechanistic understanding can often not be achieved from experiments in vivo alone. Since the discovery of the Z-ring more than 30 years ago, in vitro reconstitution experiments have been crucial to shed light on molecular processes normally hidden in the complex environment of the living cell. In this review, we summarize how rebuilding the divisome from purified components – or at least parts of it - have been instrumental to obtain the detailed mechanistic understanding of the bacterial cell division machinery that we have today.
AU - Radler, Philipp
AU - Loose, Martin
ID - 14834
IS - 1
JF - European Journal of Cell Biology
KW - Cell Biology
KW - General Medicine
KW - Histology
KW - Pathology and Forensic Medicine
SN - 0171-9335
TI - A dynamic duo: Understanding the roles of FtsZ and FtsA for Escherichia coli cell division through in vitro approaches
VL - 103
ER -
TY - JOUR
AB - Elaborate sexual signals are thought to have evolved and be maintained to serve as honest indicators of signaller quality. One measure of quality is health, which can be affected by parasite infection. Cnemaspis mysoriensis is a diurnal gecko that is often infested with ectoparasites in the wild, and males of this species express visual (coloured gular patches) and chemical (femoral gland secretions) traits that receivers could assess during social interactions. In this paper, we tested whether ectoparasites affect individual health, and whether signal quality is an indicator of ectoparasite levels. In wild lizards, we found that ectoparasite level was negatively correlated with body condition in both sexes. Moreover, some characteristics of both visual and chemical traits in males were strongly associated with ectoparasite levels. Specifically, males with higher ectoparasite levels had yellow gular patches with lower brightness and chroma, and chemical secretions with a lower proportion of aromatic compounds. We then determined whether ectoparasite levels in males influence female behaviour. Using sequential choice trials, wherein females were provided with either the visual or the chemical signals of wild-caught males that varied in ectoparasite level, we found that only chemical secretions evoked an elevated female response towards less parasitised males. Simultaneous choice trials in which females were exposed to the chemical secretions from males that varied in parasite level further confirmed a preference for males with lower parasites loads. Overall, we find that although health (body condition) or ectoparasite load can be honestly advertised through multiple modalities, the parasite-mediated female response is exclusively driven by chemical signals.
AU - Pal, Arka
AU - Joshi, Mihir
AU - Thaker, Maria
ID - 14850
IS - 1
JF - Journal of Experimental Biology
KW - Insect Science
KW - Molecular Biology
KW - Animal Science and Zoology
KW - Aquatic Science
KW - Physiology
KW - Ecology
KW - Evolution
KW - Behavior and Systematics
SN - 1477-9145
TI - Too much information? Males convey parasite levels using more signal modalities than females utilise
VL - 227
ER -
TY - JOUR
AB - The GNOM (GN) Guanine nucleotide Exchange Factor for ARF small GTPases (ARF-GEF) is among the best studied trafficking regulators in plants, playing crucial and unique developmental roles in patterning and polarity. The current models place GN at the Golgi apparatus (GA), where it mediates secretion/recycling, and at the plasma membrane (PM) presumably contributing to clathrin-mediated endocytosis (CME). The mechanistic basis of the developmental function of GN, distinct from the other ARF-GEFs including its closest homologue GNOM-LIKE1 (GNL1), remains elusive. Insights from this study largely extend the current notions of GN function. We show that GN, but not GNL1, localizes to the cell periphery at long-lived structures distinct from clathrin-coated pits, while CME and secretion proceed normally in gn knockouts. The functional GN mutant variant GNfewerroots, absent from the GA, suggests that the cell periphery is the major site of GN action responsible for its developmental function. Following inhibition by Brefeldin A, GN, but not GNL1, relocates to the PM likely on exocytic vesicles, suggesting selective molecular associations en route to the cell periphery. A study of GN-GNL1 chimeric ARF-GEFs indicates that all GN domains contribute to the specific GN function in a partially redundant manner. Together, this study offers significant steps toward the elucidation of the mechanism underlying unique cellular and development functions of GNOM.
AU - Adamowski, Maciek
AU - Matijevic, Ivana
AU - Friml, Jiří
ID - 15033
JF - eLife
KW - General Immunology and Microbiology
KW - General Biochemistry
KW - Genetics and Molecular Biology
KW - General Medicine
KW - General Neuroscience
SN - 2050-084X
TI - Developmental patterning function of GNOM ARF-GEF mediated from the cell periphery
VL - 13
ER -
TY - JOUR
AB - Poxviruses are among the largest double-stranded DNA viruses, with members such as variola virus, monkeypox virus and the vaccination strain vaccinia virus (VACV). Knowledge about the structural proteins that form the viral core has remained sparse. While major core proteins have been annotated via indirect experimental evidence, their structures have remained elusive and they could not be assigned to individual core features. Hence, which proteins constitute which layers of the core, such as the palisade layer and the inner core wall, has remained enigmatic. Here we show, using a multi-modal cryo-electron microscopy (cryo-EM) approach in combination with AlphaFold molecular modeling, that trimers formed by the cleavage product of VACV protein A10 are the key component of the palisade layer. This allows us to place previously obtained descriptions of protein interactions within the core wall into perspective and to provide a detailed model of poxvirus core architecture. Importantly, we show that interactions within A10 trimers are likely generalizable over members of orthopox- and parapoxviruses.
AU - Datler, Julia
AU - Hansen, Jesse
AU - Thader, Andreas
AU - Schlögl, Alois
AU - Bauer, Lukas W
AU - Hodirnau, Victor-Valentin
AU - Schur, Florian KM
ID - 14979
JF - Nature Structural & Molecular Biology
KW - Molecular Biology
KW - Structural Biology
SN - 1545-9993
TI - Multi-modal cryo-EM reveals trimers of protein A10 to form the palisade layer in poxvirus cores
ER -
TY - THES
AB - This thesis consists of four distinct pieces of work within theoretical biology, with two themes in common: the concept of optimization in biological systems, and the use of information-theoretic tools to quantify biological stochasticity and statistical uncertainty.
Chapter 2 develops a statistical framework for studying biological systems which we believe to be optimized for a particular utility function, such as retinal neurons conveying information about visual stimuli. We formalize such beliefs as maximum-entropy Bayesian priors, constrained by the expected utility. We explore how such priors aid inference of system parameters with limited data and enable optimality hypothesis testing: is the utility higher than by chance?
Chapter 3 examines the ultimate biological optimization process: evolution by natural selection. As some individuals survive and reproduce more successfully than others, populations evolve towards fitter genotypes and phenotypes. We formalize this as accumulation of genetic information, and use population genetics theory to study how much such information can be accumulated per generation and maintained in the face of random mutation and genetic drift. We identify the population size and fitness variance as the key quantities that control information accumulation and maintenance.
Chapter 4 reuses the concept of genetic information from Chapter 3, but from a different perspective: we ask how much genetic information organisms actually need, in particular in the context of gene regulation. For example, how much information is needed to bind transcription factors at correct locations within the genome? Population genetics provides us with a refined answer: with an increasing population size, populations achieve higher fitness by maintaining more genetic information. Moreover, regulatory parameters experience selection pressure to optimize the fitness-information trade-off, i.e. minimize the information needed for a given fitness. This provides an evolutionary derivation of the optimization priors introduced in Chapter 2.
Chapter 5 proves an upper bound on mutual information between a signal and a communication channel output (such as neural activity). Mutual information is an important utility measure for biological systems, but its practical use can be difficult due to the large dimensionality of many biological channels. Sometimes, a lower bound on mutual information is computed by replacing the high-dimensional channel outputs with decodes (signal estimates). Our result provides a corresponding upper bound, provided that the decodes are the maximum posterior estimates of the signal.
AU - Hledik, Michal
ID - 15020
KW - Theoretical biology
KW - Optimality
KW - Evolution
KW - Information
SN - 2663 - 337X
TI - Genetic information and biological optimization
ER -
TY - JOUR
AB - Probing the dynamics of aromatic side chains provides important insights into the behavior of a protein because flips of aromatic rings in a protein’s hydrophobic core report on breathing motion involving a large part of the protein. Inherently invisible to crystallography, aromatic motions have been primarily studied by solution NMR. The question how packing of proteins in crystals affects ring flips has, thus, remained largely unexplored. Here we apply magic-angle spinning NMR, advanced phenylalanine 1H-13C/2H isotope labeling and MD simulation to a protein in three different crystal packing environments to shed light onto possible impact of packing on ring flips. The flips of the two Phe residues in ubiquitin, both surface exposed, appear remarkably conserved in the different crystal forms, even though the intermolecular packing is quite different: Phe4 flips on a ca. 10–20 ns time scale, and Phe45 are broadened in all crystals, presumably due to µs motion. Our findings suggest that intramolecular influences are more important for ring flips than intermolecular (packing) effects.
AU - Gauto, Diego F.
AU - Lebedenko, Olga O.
AU - Becker, Lea Marie
AU - Ayala, Isabel
AU - Lichtenecker, Roman
AU - Skrynnikov, Nikolai R.
AU - Schanda, Paul
ID - 12114
JF - Journal of Structural Biology: X
KW - Structural Biology
SN - 2590-1524
TI - Aromatic ring flips in differently packed ubiquitin protein crystals from MAS NMR and MD
VL - 7
ER -
TY - JOUR
AB - Small GTPases play essential roles in the organization of eukaryotic cells. In recent years, it has become clear that their intracellular functions result from intricate biochemical networks of the GTPase and their regulators that dynamically bind to a membrane surface. Due to the inherent complexities of their interactions, however, revealing the underlying mechanisms of action is often difficult to achieve from in vivo studies. This review summarizes in vitro reconstitution approaches developed to obtain a better mechanistic understanding of how small GTPase activities are regulated in space and time.
AU - Loose, Martin
AU - Auer, Albert
AU - Brognara, Gabriel
AU - Budiman, Hanifatul R
AU - Kowalski, Lukasz M
AU - Matijevic, Ivana
ID - 12163
IS - 6
JF - FEBS Letters
KW - Cell Biology
KW - Genetics
KW - Molecular Biology
KW - Biochemistry
KW - Structural Biology
KW - Biophysics
SN - 0014-5793
TI - In vitro reconstitution of small GTPase regulation
VL - 597
ER -
TY - JOUR
AB - Characterizing and controlling entanglement in quantum materials is crucial for the development of next-generation quantum technologies. However, defining a quantifiable figure of merit for entanglement in macroscopic solids is theoretically and experimentally challenging. At equilibrium the presence of entanglement can be diagnosed by extracting entanglement witnesses from spectroscopic observables and a nonequilibrium extension of this method could lead to the discovery of novel dynamical phenomena. Here, we propose a systematic approach to quantify the time-dependent quantum Fisher information and entanglement depth of transient states of quantum materials with time-resolved resonant inelastic x-ray scattering. Using a quarter-filled extended Hubbard model as an example, we benchmark the efficiency of this approach and predict a light-enhanced many-body entanglement due to the proximity to a phase boundary. Our work sets the stage for experimentally witnessing and controlling entanglement in light-driven quantum materials via ultrafast spectroscopic measurements.
AU - Hales, Jordyn
AU - Bajpai, Utkarsh
AU - Liu, Tongtong
AU - Baykusheva, Denitsa Rangelova
AU - Li, Mingda
AU - Mitrano, Matteo
AU - Wang, Yao
ID - 13989
JF - Nature Communications
KW - General Physics and Astronomy
KW - General Biochemistry
KW - Genetics and Molecular Biology
KW - General Chemistry
KW - Multidisciplinary
TI - Witnessing light-driven entanglement using time-resolved resonant inelastic X-ray scattering
VL - 14
ER -
TY - JOUR
AB - The study of RNAs has become one of the most influential research fields in contemporary biology and biomedicine. In the last few years, new sequencing technologies have produced an explosion of new and exciting discoveries in the field but have also given rise to many open questions. Defining these questions, together with old, long-standing gaps in our knowledge, is the spirit of this article. The breadth of topics within RNA biology research is vast, and every aspect of the biology of these molecules contains countless exciting open questions. Here, we asked 12 groups to discuss their most compelling question among some plant RNA biology topics. The following vignettes cover RNA alternative splicing; RNA dynamics; RNA translation; RNA structures; R-loops; epitranscriptomics; long non-coding RNAs; small RNA production and their functions in crops; small RNAs during gametogenesis and in cross-kingdom RNA interference; and RNA-directed DNA methylation. In each section, we will present the current state-of-the-art in plant RNA biology research before asking the questions that will surely motivate future discoveries in the field. We hope this article will spark a debate about the future perspective on RNA biology and provoke novel reflections in the reader.
AU - Manavella, Pablo A
AU - Godoy Herz, Micaela A
AU - Kornblihtt, Alberto R
AU - Sorenson, Reed
AU - Sieburth, Leslie E
AU - Nakaminami, Kentaro
AU - Seki, Motoaki
AU - Ding, Yiliang
AU - Sun, Qianwen
AU - Kang, Hunseung
AU - Ariel, Federico D
AU - Crespi, Martin
AU - Giudicatti, Axel J
AU - Cai, Qiang
AU - Jin, Hailing
AU - Feng, Xiaoqi
AU - Qi, Yijun
AU - Pikaard, Craig S
ID - 12669
IS - 6
JF - The Plant Cell
KW - Cell Biology
KW - Plant Science
SN - 1040-4651
TI - Beyond transcription: compelling open questions in plant RNA biology
VL - 35
ER -
TY - JOUR
AB - Muscle degeneration is the most prevalent cause for frailty and dependency in inherited diseases and ageing. Elucidation of pathophysiological mechanisms, as well as effective treatments for muscle diseases, represents an important goal in improving human health. Here, we show that the lipid synthesis enzyme phosphatidylethanolamine cytidyltransferase (PCYT2/ECT) is critical to muscle health. Human deficiency in PCYT2 causes a severe disease with failure to thrive and progressive weakness. pcyt2-mutant zebrafish and muscle-specific Pcyt2-knockout mice recapitulate the participant phenotypes, with failure to thrive, progressive muscle weakness and accelerated ageing. Mechanistically, muscle Pcyt2 deficiency affects cellular bioenergetics and membrane lipid bilayer structure and stability. PCYT2 activity declines in ageing muscles of mice and humans, and adeno-associated virus-based delivery of PCYT2 ameliorates muscle weakness in Pcyt2-knockout and old mice, offering a therapy for individuals with a rare disease and muscle ageing. Thus, PCYT2 plays a fundamental and conserved role in vertebrate muscle health, linking PCYT2 and PCYT2-synthesized lipids to severe muscle dystrophy and ageing.
AU - Cikes, Domagoj
AU - Elsayad, Kareem
AU - Sezgin, Erdinc
AU - Koitai, Erika
AU - Ferenc, Torma
AU - Orthofer, Michael
AU - Yarwood, Rebecca
AU - Heinz, Leonhard X.
AU - Sedlyarov, Vitaly
AU - Darwish-Miranda, Nasser
AU - Taylor, Adrian
AU - Grapentine, Sophie
AU - al-Murshedi, Fathiya
AU - Abot, Anne
AU - Weidinger, Adelheid
AU - Kutchukian, Candice
AU - Sanchez, Colline
AU - Cronin, Shane J. F.
AU - Novatchkova, Maria
AU - Kavirayani, Anoop
AU - Schuetz, Thomas
AU - Haubner, Bernhard
AU - Haas, Lisa
AU - Hagelkruys, Astrid
AU - Jackowski, Suzanne
AU - Kozlov, Andrey
AU - Jacquemond, Vincent
AU - Knauf, Claude
AU - Superti-Furga, Giulio
AU - Rullman, Eric
AU - Gustafsson, Thomas
AU - McDermot, John
AU - Lowe, Martin
AU - Radak, Zsolt
AU - Chamberlain, Jeffrey S.
AU - Bakovic, Marica
AU - Banka, Siddharth
AU - Penninger, Josef M.
ID - 12747
JF - Nature Metabolism
KW - Cell Biology
KW - Physiology (medical)
KW - Endocrinology
KW - Diabetes and Metabolism
KW - Internal Medicine
SN - 2522-5812
TI - PCYT2-regulated lipid biosynthesis is critical to muscle health and ageing
VL - 5
ER -
TY - JOUR
AB - Background: Biallelic variants in OGDHL, encoding part of the α-ketoglutarate dehydrogenase complex, have been associated with highly heterogeneous neurological and neurodevelopmental disorders. However, the validity of this association remains to be confirmed. A second OGDHL patient cohort was recruited to carefully assess the gene-disease relationship.
Methods: Using an unbiased genotype-first approach, we screened large, multiethnic aggregated sequencing datasets worldwide for biallelic OGDHL variants. We used CRISPR/Cas9 to generate zebrafish knockouts of ogdhl, ogdh paralogs, and dhtkd1 to investigate functional relationships and impact during development. Functional complementation with patient variant transcripts was conducted to systematically assess protein functionality as a readout for pathogenicity.
Results: A cohort of 14 individuals from 12 unrelated families exhibited highly variable clinical phenotypes, with the majority of them presenting at least one additional variant, potentially accounting for a blended phenotype and complicating phenotypic understanding. We also uncovered extreme clinical heterogeneity and high allele frequencies, occasionally incompatible with a fully penetrant recessive disorder. Human cDNA of previously described and new variants were tested in an ogdhl zebrafish knockout model, adding functional evidence for variant reclassification. We disclosed evidence of hypomorphic alleles as well as a loss-of-function variant without deleterious effects in zebrafish variant testing also showing discordant familial segregation, challenging the relationship of OGDHL as a conventional Mendelian gene. Going further, we uncovered evidence for a complex compensatory relationship among OGDH, OGDHL, and DHTKD1 isoenzymes that are associated with neurodevelopmental disorders and exhibit complex transcriptional compensation patterns with partial functional redundancy.
Conclusions: Based on the results of genetic, clinical, and functional studies, we formed three hypotheses in which to frame observations: biallelic OGDHL variants lead to a highly variable monogenic disorder, variants in OGDHL are following a complex pattern of inheritance, or they may not be causative at all. Our study further highlights the continuing challenges of assessing the validity of reported disease-gene associations and effects of variants identified in these genes. This is particularly more complicated in making genetic diagnoses based on identification of variants in genes presenting a highly heterogenous phenotype such as “OGDHL-related disorders”.
AU - Lin, Sheng-Jia
AU - Vona, Barbara
AU - Lau, Tracy
AU - Huang, Kevin
AU - Zaki, Maha S.
AU - Aldeen, Huda Shujaa
AU - Karimiani, Ehsan Ghayoor
AU - Rocca, Clarissa
AU - Noureldeen, Mahmoud M.
AU - Saad, Ahmed K.
AU - Petree, Cassidy
AU - Bartolomaeus, Tobias
AU - Abou Jamra, Rami
AU - Zifarelli, Giovanni
AU - Gotkhindikar, Aditi
AU - Wentzensen, Ingrid M.
AU - Liao, Mingjuan
AU - Cork, Emalyn Elise
AU - Varshney, Pratishtha
AU - Hashemi, Narges
AU - Mohammadi, Mohammad Hasan
AU - Rad, Aboulfazl
AU - Neira, Juanita
AU - Toosi, Mehran Beiraghi
AU - Knopp, Cordula
AU - Kurth, Ingo
AU - Challman, Thomas D.
AU - Smith, Rebecca
AU - Abdalla, Asmahan
AU - Haaf, Thomas
AU - Suri, Mohnish
AU - Joshi, Manali
AU - Chung, Wendy K.
AU - Moreno-De-Luca, Andres
AU - Houlden, Henry
AU - Maroofian, Reza
AU - Varshney, Gaurav K.
ID - 14639
JF - Genome Medicine
KW - Genetics (clinical)
KW - Genetics
KW - Molecular Biology
KW - Molecular Medicine
SN - 1756-994X
TI - Evaluating the association of biallelic OGDHL variants with significant phenotypic heterogeneity
VL - 15
ER -
TY - JOUR
AB - The regulatory architecture of gene expression is known to differ substantially between sexes in Drosophila, but most studies performed
so far used whole-body data and only single crosses, which may have limited their scope to detect patterns that are robust across tissues
and biological replicates. Here, we use allele-specific gene expression of parental and reciprocal hybrid crosses between 6 Drosophila
melanogaster inbred lines to quantify cis- and trans-regulatory variation in heads and gonads of both sexes separately across 3 replicate
crosses. Our results suggest that female and male heads, as well as ovaries, have a similar regulatory architecture. On the other hand,
testes display more and substantially different cis-regulatory effects, suggesting that sex differences in the regulatory architecture that
have been previously observed may largely derive from testis-specific effects. We also examine the difference in cis-regulatory variation
of genes across different levels of sex bias in gonads and heads. Consistent with the idea that intersex correlations constrain expression
and can lead to sexual antagonism, we find more cis variation in unbiased and moderately biased genes in heads. In ovaries, reduced cis
variation is observed for male-biased genes, suggesting that cis variants acting on these genes in males do not lead to changes in ovary
expression. Finally, we examine the dominance patterns of gene expression and find that sex- and tissue-specific patterns of inheritance
as well as trans-regulatory variation are highly variable across biological crosses, although these were performed in highly controlled
experimental conditions. This highlights the importance of using various genetic backgrounds to infer generalizable patterns.
AU - Puixeu Sala, Gemma
AU - Macon, Ariana
AU - Vicoso, Beatriz
ID - 14077
IS - 8
JF - G3: Genes, Genomes, Genetics
KW - Genetics (clinical)
KW - Genetics
KW - Molecular Biology
SN - 2160-1836
TI - Sex-specific estimation of cis and trans regulation of gene expression in heads and gonads of Drosophila melanogaster
VL - 13
ER -
TY - JOUR
AB - Mosaic analysis with double markers (MADM) technology enables the generation of genetic mosaic tissue in mice and high-resolution phenotyping at the individual cell level. Here, we present a protocol for isolating MADM-labeled cells with high yield for downstream molecular analyses using fluorescence-activated cell sorting (FACS). We describe steps for generating MADM-labeled mice, perfusion, single-cell suspension, and debris removal. We then detail procedures for cell sorting by FACS and downstream analysis. This protocol is suitable for embryonic to adult mice.
For complete details on the use and execution of this protocol, please refer to Contreras et al. (2021).1
AU - Amberg, Nicole
AU - Cheung, Giselle T
AU - Hippenmeyer, Simon
ID - 14683
IS - 1
JF - STAR Protocols
KW - General Immunology and Microbiology
KW - General Biochemistry
KW - Genetics and Molecular Biology
KW - General Neuroscience
SN - 2666-1667
TI - Protocol for sorting cells from mouse brains labeled with mosaic analysis with double markers by flow cytometry
VL - 5
ER -
TY - JOUR
AB - Autocrine signaling pathways regulated by RAPID ALKALINIZATION FACTORs (RALFs) control cell wall integrity during pollen tube germination and growth in Arabidopsis (Arabidopsis thaliana). To investigate the role of pollen-specific RALFs in another plant species, we combined gene expression data with phylogenetic and biochemical studies to identify candidate orthologs in maize (Zea mays). We show that Clade IB ZmRALF2/3 mutations, but not Clade III ZmRALF1/5 mutations, cause cell wall instability in the sub-apical region of the growing pollen tube. ZmRALF2/3 are mainly located in the cell wall and are partially able to complement the pollen germination defect of their Arabidopsis orthologs AtRALF4/19. Mutations in ZmRALF2/3 compromise pectin distribution patterns leading to altered cell wall organization and thickness culminating in pollen tube burst. Clade IB, but not Clade III ZmRALFs, strongly interact as ligands with the pollen-specific Catharanthus roseus RLK1-like (CrRLK1L) receptor kinases Zea mays FERONIA-like (ZmFERL) 4/7/9, LORELEI-like glycosylphosphatidylinositol-anchor (LLG) proteins Zea mays LLG 1 and 2 (ZmLLG1/2) and Zea mays pollen extension-like (PEX) cell wall proteins ZmPEX2/4. Notably, ZmFERL4 outcompetes ZmLLG2 and ZmPEX2 outcompetes ZmFERL4 for ZmRALF2 binding. Based on these data, we suggest that Clade IB RALFs act in a dual role as cell wall components and extracellular sensors to regulate cell wall integrity and thickness during pollen tube growth in maize and probably other plants.
AU - Zhou, Liang-Zi
AU - Wang, Lele
AU - Chen, Xia
AU - Ge, Zengxiang
AU - Mergner, Julia
AU - Li, Xingli
AU - Küster, Bernhard
AU - Längst, Gernot
AU - Qu, Li-Jia
AU - Dresselhaus, Thomas
ID - 14726
JF - The Plant Cell
KW - Cell Biology
KW - Plant Science
SN - 1040-4651
TI - The RALF signaling pathway regulates cell wall integrity during pollen tube growth in maize
ER -
TY - JOUR
AB - Chromosomal rearrangements (CRs) have been known since almost the beginning of genetics.
While an important role for CRs in speciation has been suggested, evidence primarily stems
from theoretical and empirical studies focusing on the microevolutionary level (i.e., on taxon
pairs where speciation is often incomplete). Although the role of CRs in eukaryotic speciation at
a macroevolutionary level has been supported by associations between species diversity and
rates of evolution of CRs across phylogenies, these findings are limited to a restricted range of
CRs and taxa. Now that more broadly applicable and precise CR detection approaches have
become available, we address the challenges in filling some of the conceptual and empirical
gaps between micro- and macroevolutionary studies on the role of CRs in speciation. We
synthesize what is known about the macroevolutionary impact of CRs and suggest new research avenues to overcome the pitfalls of previous studies to gain a more comprehensive understanding of the evolutionary significance of CRs in speciation across the tree of life.
AU - Lucek, Kay
AU - Giménez, Mabel D.
AU - Joron, Mathieu
AU - Rafajlović, Marina
AU - Searle, Jeremy B.
AU - Walden, Nora
AU - Westram, Anja M
AU - Faria, Rui
ID - 14742
IS - 11
JF - Cold Spring Harbor Perspectives in Biology
KW - General Biochemistry
KW - Genetics and Molecular Biology
SN - 1943-0264
TI - The impact of chromosomal rearrangements in speciation: From micro- to macroevolution
VL - 15
ER -
TY - JOUR
AB - We developed LIONESS, a technology that leverages improvements to optical super-resolution microscopy and prior information on sample structure via machine learning to overcome the limitations (in 3D-resolution, signal-to-noise ratio and light exposure) of optical microscopy of living biological specimens. LIONESS enables dense reconstruction of living brain tissue and morphodynamics visualization at the nanoscale.
AU - Danzl, Johann G
AU - Velicky, Philipp
ID - 14770
IS - 8
JF - Nature Methods
KW - Cell Biology
KW - Molecular Biology
KW - Biochemistry
KW - Biotechnology
SN - 1548-7091
TI - LIONESS enables 4D nanoscale reconstruction of living brain tissue
VL - 20
ER -
TY - JOUR
AB - Morphogen gradients impart positional information to cells in a homogenous tissue field. Fgf8a, a highly conserved growth factor, has been proposed to act as a morphogen during zebrafish gastrulation. However, technical limitations have so far prevented direct visualization of the endogenous Fgf8a gradient and confirmation of its morphogenic activity. Here, we monitor Fgf8a propagation in the developing neural plate using a CRISPR/Cas9-mediated EGFP knock-in at the endogenous fgf8a locus. By combining sensitive imaging with single-molecule fluorescence correlation spectroscopy, we demonstrate that Fgf8a, which is produced at the embryonic margin, propagates by diffusion through the extracellular space and forms a graded distribution towards the animal pole. Overlaying the Fgf8a gradient curve with expression profiles of its downstream targets determines the precise input-output relationship of Fgf8a-mediated patterning. Manipulation of the extracellular Fgf8a levels alters the signaling outcome, thus establishing Fgf8a as a bona fide morphogen during zebrafish gastrulation. Furthermore, by hindering Fgf8a diffusion, we demonstrate that extracellular diffusion of the protein from the source is crucial for it to achieve its morphogenic potential.
AU - Harish, Rohit K
AU - Gupta, Mansi
AU - Zöller, Daniela
AU - Hartmann, Hella
AU - Gheisari, Ali
AU - Machate, Anja
AU - Hans, Stefan
AU - Brand, Michael
ID - 14774
IS - 19
JF - Development
KW - Developmental Biology
KW - Molecular Biology
SN - 0950-1991
TI - Real-time monitoring of an endogenous Fgf8a gradient attests to its role as a morphogen during zebrafish gastrulation
VL - 150
ER -
TY - JOUR
AB - Soluble chaperones residing in the endoplasmic reticulum (ER) play vitally important roles in folding and quality control of newly synthesized proteins that transiently pass through the ER en route to their final destinations. These soluble residents of the ER are themselves endowed with an ER retrieval signal that enables the cell to bring the escaped residents back from the Golgi. Here, by using purified proteins, we showed that Nicotiana tabacum phytaspase, a plant aspartate-specific protease, introduces two breaks at the C-terminus of the N. tabacum ER resident calreticulin-3. These cleavages resulted in removal of either a dipeptide or a hexapeptide from the C-terminus of calreticulin-3 encompassing part or all of the ER retrieval signal. Consistently, expression of the calreticulin-3 derivative mimicking the phytaspase cleavage product in Nicotiana benthamiana cells demonstrated loss of the ER accumulation of the protein. Notably, upon its escape from the ER, calreticulin-3 was further processed by an unknown protease(s) to generate the free N-terminal (N) domain of calreticulin-3, which was ultimately secreted into the apoplast. Our study thus identified a specific proteolytic enzyme capable of precise detachment of the ER retrieval signal from a plant ER resident protein, with implications for the further fate of the escaped resident.
AU - Teplova, Anastasiia
AU - Pigidanov, Artemii A.
AU - Serebryakova, Marina V.
AU - Golyshev, Sergei A.
AU - Galiullina, Raisa A.
AU - Chichkova, Nina V.
AU - Vartapetian, Andrey B.
ID - 14776
IS - 22
JF - International Journal of Molecular Sciences
KW - Inorganic Chemistry
KW - Organic Chemistry
KW - Physical and Theoretical Chemistry
KW - Computer Science Applications
KW - Spectroscopy
KW - Molecular Biology
KW - General Medicine
KW - Catalysis
SN - 1422-0067
TI - Phytaspase Is capable of detaching the endoplasmic reticulum retrieval signal from tobacco calreticulin-3
VL - 24
ER -
TY - JOUR
AB - Germ granules, condensates of phase-separated RNA and protein, are organelles that are essential for germline development in different organisms. The patterning of the granules and their relevance for germ cell fate are not fully understood. Combining three-dimensional in vivo structural and functional analyses, we study the dynamic spatial organization of molecules within zebrafish germ granules. We find that the localization of RNA molecules to the periphery of the granules, where ribosomes are localized, depends on translational activity at this location. In addition, we find that the vertebrate-specific Dead end (Dnd1) protein is essential for nanos3 RNA localization at the condensates’ periphery. Accordingly, in the absence of Dnd1, or when translation is inhibited, nanos3 RNA translocates into the granule interior, away from the ribosomes, a process that is correlated with the loss of germ cell fate. These findings highlight the relevance of sub-granule compartmentalization for post-transcriptional control and its importance for preserving germ cell totipotency.
AU - Westerich, Kim Joana
AU - Tarbashevich, Katsiaryna
AU - Schick, Jan
AU - Gupta, Antra
AU - Zhu, Mingzhao
AU - Hull, Kenneth
AU - Romo, Daniel
AU - Zeuschner, Dagmar
AU - Goudarzi, Mohammad
AU - Gross-Thebing, Theresa
AU - Raz, Erez
ID - 14781
IS - 17
JF - Developmental Cell
KW - Developmental Biology
KW - Cell Biology
KW - General Biochemistry
KW - Genetics and Molecular Biology
KW - Molecular Biology
SN - 1534-5807
TI - Spatial organization and function of RNA molecules within phase-separated condensates in zebrafish are controlled by Dnd1
VL - 58
ER -
TY - JOUR
AB - Eukaryotic cells use clathrin-mediated endocytosis to take up a large range of extracellular cargo. During endocytosis, a clathrin coat forms on the plasma membrane, but it remains controversial when and how it is remodeled into a spherical vesicle.
Here, we use 3D superresolution microscopy to determine the precise geometry of the clathrin coat at large numbers of endocytic sites. Through pseudo-temporal sorting, we determine the average trajectory of clathrin remodeling during endocytosis. We find that clathrin coats assemble first on flat membranes to 50% of the coat area before they become rapidly and continuously bent, and this mechanism is confirmed in three cell lines. We introduce the cooperative curvature model, which is based on positive feedback for curvature generation. It accurately describes the measured shapes and dynamics of the clathrin coat and could represent a general mechanism for clathrin coat remodeling on the plasma membrane.
AU - Mund, Markus
AU - Tschanz, Aline
AU - Wu, Yu-Le
AU - Frey, Felix F
AU - Mehl, Johanna L.
AU - Kaksonen, Marko
AU - Avinoam, Ori
AU - Schwarz, Ulrich S.
AU - Ries, Jonas
ID - 14788
IS - 3
JF - Journal of Cell Biology
KW - Cell Biology
SN - 0021-9525
TI - Clathrin coats partially preassemble and subsequently bend during endocytosis
VL - 222
ER -
TY - JOUR
AB - Homeostatic balance in the intestinal epithelium relies on a fast cellular turnover, which is coordinated by an intricate interplay between biochemical signalling, mechanical forces and organ geometry. We review recent modelling approaches that have been developed to understand different facets of this remarkable homeostatic equilibrium. Existing models offer different, albeit complementary, perspectives on the problem. First, biomechanical models aim to explain the local and global mechanical stresses driving cell renewal as well as tissue shape maintenance. Second, compartmental models provide insights into the conditions necessary to keep a constant flow of cells with well-defined ratios of cell types, and how perturbations can lead to an unbalance of relative compartment sizes. A third family of models address, at the cellular level, the nature and regulation of stem fate choices that are necessary to fuel cellular turnover. We also review how these different approaches are starting to be integrated together across scales, to provide quantitative predictions and new conceptual frameworks to think about the dynamics of cell renewal in complex tissues.
AU - Corominas-Murtra, Bernat
AU - Hannezo, Edouard B
ID - 12162
JF - Seminars in Cell & Developmental Biology
KW - Cell Biology
KW - Developmental Biology
SN - 1084-9521
TI - Modelling the dynamics of mammalian gut homeostasis
VL - 150-151
ER -
TY - JOUR
AB - Understanding complex living systems, which are fundamentally constrained by physical phenomena, requires combining experimental data with theoretical physical and mathematical models. To develop such models, collaborations between experimental cell biologists and theoreticians are increasingly important but these two groups often face challenges achieving mutual understanding. To help navigate these challenges, this Perspective discusses different modelling approaches, including bottom-up hypothesis-driven and top-down data-driven models, and highlights their strengths and applications. Using cell mechanics as an example, we explore the integration of specific physical models with experimental data from the molecular, cellular and tissue level up to multiscale input. We also emphasize the importance of constraining model complexity and outline strategies for crosstalk between experimental design and model development. Furthermore, we highlight how physical models can provide conceptual insights and produce unifying and generalizable frameworks for biological phenomena. Overall, this Perspective aims to promote fruitful collaborations that advance our understanding of complex biological systems.
AU - Schwayer, Cornelia
AU - Brückner, David
ID - 14827
IS - 24
JF - Journal of Cell Science
KW - Cell Biology
SN - 0021-9533
TI - Connecting theory and experiment in cell and tissue mechanics
VL - 136
ER -
TY - JOUR
AB - Little is known about the critical metabolic changes that neural cells have to undergo during development and how temporary shifts in this program can influence brain circuitries and behavior. Inspired by the discovery that mutations in SLC7A5, a transporter of metabolically essential large neutral amino acids (LNAAs), lead to autism, we employed metabolomic profiling to study the metabolic states of the cerebral cortex across different developmental stages. We found that the forebrain undergoes significant metabolic remodeling throughout development, with certain groups of metabolites showing stage-specific changes, but what are the consequences of perturbing this metabolic program? By manipulating Slc7a5 expression in neural cells, we found that the metabolism of LNAAs and lipids are interconnected in the cortex. Deletion of Slc7a5 in neurons affects the postnatal metabolic state, leading to a shift in lipid metabolism. Additionally, it causes stage- and cell-type-specific alterations in neuronal activity patterns, resulting in a long-term circuit dysfunction.
AU - Knaus, Lisa
AU - Basilico, Bernadette
AU - Malzl, Daniel
AU - Gerykova Bujalkova, Maria
AU - Smogavec, Mateja
AU - Schwarz, Lena A.
AU - Gorkiewicz, Sarah
AU - Amberg, Nicole
AU - Pauler, Florian
AU - Knittl-Frank, Christian
AU - Tassinari, Marianna
AU - Maulide, Nuno
AU - Rülicke, Thomas
AU - Menche, Jörg
AU - Hippenmeyer, Simon
AU - Novarino, Gaia
ID - 12802
IS - 9
JF - Cell
KW - General Biochemistry
KW - Genetics and Molecular Biology
SN - 0092-8674
TI - Large neutral amino acid levels tune perinatal neuronal excitability and survival
VL - 186
ER -
TY - JOUR
AB - Many insects carry an ancient X chromosome - the Drosophila Muller element F - that likely predates their origin. Interestingly, the X has undergone turnover in multiple fly species (Diptera) after being conserved for more than 450 MY. The long evolutionary distance between Diptera and other sequenced insect clades makes it difficult to infer what could have contributed to this sudden increase in rate of turnover. Here, we produce the first genome and transcriptome of a long overlooked sister-order to Diptera: Mecoptera. We compare the scorpionfly Panorpa cognata X-chromosome gene content, expression, and structure, to that of several dipteran species as well as more distantly-related insect orders (Orthoptera and Blattodea). We find high conservation of gene content between the mecopteran X and the dipteran Muller F element, as well as several shared biological features, such as the presence of dosage compensation and a low amount of genetic diversity, consistent with a low recombination rate. However, the two homologous X chromosomes differ strikingly in their size and number of genes they carry. Our results therefore support a common ancestry of the mecopteran and ancestral dipteran X chromosomes, and suggest that Muller element F shrank in size and gene content after the split of Diptera and Mecoptera, which may have contributed to its turnover in dipteran insects.
AU - Lasne, Clementine
AU - Elkrewi, Marwan N
AU - Toups, Melissa A
AU - Layana Franco, Lorena Alexandra
AU - Macon, Ariana
AU - Vicoso, Beatriz
ID - 14613
IS - 12
JF - Molecular Biology and Evolution
KW - Genetics
KW - Molecular Biology
KW - Ecology
KW - Evolution
KW - Behavior and Systematics
SN - 0737-4038
TI - The scorpionfly (Panorpa cognata) genome highlights conserved and derived features of the peculiar dipteran X chromosome
VL - 40
ER -
TY - JOUR
AB - The genomic binding sites of the transcription factor (TF) and tumor suppressor p53 are unusually diverse with regard to their chromatin features, including histone modifications, raising the possibility that the local chromatin environment can contextualize p53 regulation. Here, we show that epigenetic characteristics of closed chromatin, such as DNA methylation, do not influence the binding of p53 across the genome. Instead, the ability of p53 to open chromatin and activate its target genes is locally restricted by its cofactor Trim24. Trim24 binds to both p53 and unmethylated histone 3 lysine 4 (H3K4), thereby preferentially localizing to those p53 sites that reside in closed chromatin, whereas it is deterred from accessible chromatin by H3K4 methylation. The presence of Trim24 increases cell viability upon stress and enables p53 to affect gene expression as a function of the local chromatin state. These findings link H3K4 methylation to p53 function and illustrate how specificity in chromatin can be achieved, not by TF-intrinsic sensitivity to histone modifications, but by employing chromatin-sensitive cofactors that locally modulate TF function.
AU - Isbel, Luke
AU - Iskar, Murat
AU - Durdu, Sevi
AU - Weiss, Joscha
AU - Grand, Ralph S.
AU - Hietter-Pfeiffer, Eric
AU - Kozicka, Zuzanna
AU - Michael, Alicia
AU - Burger, Lukas
AU - Thomä, Nicolas H.
AU - Schübeler, Dirk
ID - 15149
IS - 7
JF - Nature Structural & Molecular Biology
KW - Molecular Biology
KW - Structural Biology
SN - 1545-9993
TI - Readout of histone methylation by Trim24 locally restricts chromatin opening by p53
VL - 30
ER -
TY - THES
AB - The extracellular matrix (ECM) is a hydrated and complex three-dimensional network consisting of proteins, polysaccharides, and water. It provides structural scaffolding for the cells embedded within it and is essential in regulating numerous physiological processes, including cell migration and proliferation, wound healing, and stem cell fate.
Despite extensive study, detailed structural knowledge of ECM components in physiologically relevant conditions is still rudimentary. This is due to methodological limitations in specimen preparation protocols which are incompatible with keeping large samples, such as the ECM, in their native state for subsequent imaging. Conventional electron microscopy (EM) techniques rely on fixation, dehydration, contrasting, and sectioning. This results in the alteration of a highly hydrated environment and the potential introduction of artifacts. Other structural biology techniques, such as nuclear magnetic resonance (NMR) spectroscopy and X-ray crystallography, allow high-resolution analysis of protein structures but only work on homogenous and purified samples, hence lacking contextual information. Currently, no approach exists for the ultrastructural and structural study of extracellular components under native conditions in a physiological, 3D environment.
In this thesis, I have developed a workflow that allows for the ultrastructural analysis of the ECM in near-native conditions at molecular resolution. The developments I introduced include implementing a novel specimen preparation workflow for cell-derived matrices (CDMs) to render them compatible with ion-beam milling and subsequent high-resolution cryo-electron tomography (ET).
To this end, I have established protocols to generate CDMs grown over several weeks on EM grids that are compatible with downstream cryo-EM sample preparation and imaging techniques. Characterization of these ECMs confirmed that they contain essential ECM components such as collagen I, collagen VI, and fibronectin I in high abundance and hence represent a bona fide biologically-relevant sample. I successfully optimized vitrification of these specimens by testing various vitrification techniques and cryoprotectants.
In order to obtain high-resolution molecular insights into the ultrastructure and organization of CDMs, I established cryo-focused ion beam scanning electron microscopy (FIBSEM) on these challenging and complex specimens. I explored different approaches for the creation of thin cryo-lamellae by FIB milling and succeeded in optimizing the cryo-lift-out technique, resulting in high-quality lamellae of approximately 200 nm thickness.
High-resolution Cryo-ET of these lamellae revealed for the first time the architecture of native CDM in the context of matrix-secreting cells. This allowed for the in situ visualization of fibrillar matrix proteins such as collagen, laying the foundation for future structural and ultrastructural characterization of these proteins in their near-native environment.
In summary, in this thesis, I present a novel workflow that combines state-of-the-art cryo-EM specimen preparation and imaging technologies to permit characterization of the ECM, an important tissue component in higher organisms. This innovative and highly versatile workflow will enable addressing far-reaching questions on ECM architecture, composition, and reciprocal ECM-cell interactions.
AU - Zens, Bettina
ID - 12491
KW - cryo-EM
KW - cryo-ET
KW - FIB milling
KW - method development
KW - FIBSEM
KW - extracellular matrix
KW - ECM
KW - cell-derived matrices
KW - CDMs
KW - cell culture
KW - high pressure freezing
KW - HPF
KW - structural biology
KW - tomography
KW - collagen
SN - 2663-337X
TI - Ultrastructural characterization of natively preserved extracellular matrix by cryo-electron tomography
ER -
TY - JOUR
AB - Nuclear pore complexes (NPCs) bridge the nucleus and the cytoplasm and are indispensable for crucial cellular activities, such as bidirectional molecular trafficking and gene transcription regulation. The discovery of long-lived proteins (LLPs) in NPCs from postmitotic cells raises the exciting possibility that the maintenance of NPC integrity might play an inherent role in lifelong cell function. Age-dependent deterioration of NPCs and loss of nuclear integrity have been linked to age-related decline in postmitotic cell function and degenerative diseases. In this review, we discuss our current understanding of NPC maintenance in proliferating and postmitotic cells, and how malfunction of nucleoporins (Nups) might contribute to the pathogenesis of various neurodegenerative and cardiovascular diseases.
AU - Liu, Jinqiang
AU - HETZER, Martin W
ID - 11051
IS - 3
JF - Trends in Cell Biology
KW - Cell Biology
SN - 0962-8924
TI - Nuclear pore complex maintenance and implications for age-related diseases
VL - 32
ER -
TY - JOUR
AB - Objective: MazF is a sequence-specific endoribonuclease-toxin of the MazEF toxin–antitoxin system. MazF cleaves single-stranded ribonucleic acid (RNA) regions at adenine–cytosine–adenine (ACA) sequences in the bacterium Escherichia coli. The MazEF system has been used in various biotechnology and synthetic biology applications. In this study, we infer how ectopic mazF overexpression affects production of heterologous proteins. To this end, we quantified the levels of fluorescent proteins expressed in E. coli from reporters translated from the ACA-containing or ACA-less messenger RNAs (mRNAs). Additionally, we addressed the impact of the 5′-untranslated region of these reporter mRNAs under the same conditions by comparing expression from mRNAs that comprise (canonical mRNA) or lack this region (leaderless mRNA).
Results: Flow cytometry analysis indicates that during mazF overexpression, fluorescent proteins are translated from the canonical as well as leaderless mRNAs. Our analysis further indicates that longer mazF overexpression generally increases the concentration of fluorescent proteins translated from ACA-less mRNAs, however it also substantially increases bacterial population heterogeneity. Finally, our results suggest that the strength and duration of mazF overexpression should be optimized for each experimental setup, to maximize the heterologous protein production and minimize the amount of phenotypic heterogeneity in bacterial populations, which is unfavorable in biotechnological processes.
AU - Nikolic, Nela
AU - Sauert, Martina
AU - Albanese, Tanino G.
AU - Moll, Isabella
ID - 11713
JF - BMC Research Notes
KW - General Biochemistry
KW - Genetics and Molecular Biology
KW - General Medicine
SN - 1756-0500
TI - Quantifying heterologous gene expression during ectopic MazF production in Escherichia coli
VL - 15
ER -
TY - JOUR
AB - Models of transcriptional regulation that assume equilibrium binding of transcription factors have been less successful at predicting gene expression from sequence in eukaryotes than in bacteria. This could be due to the non-equilibrium nature of eukaryotic regulation. Unfortunately, the space of possible non-equilibrium mechanisms is vast and predominantly uninteresting. The key question is therefore how this space can be navigated efficiently, to focus on mechanisms and models that are biologically relevant. In this review, we advocate for the normative role of theory—theory that prescribes rather than just describes—in providing such a focus. Theory should expand its remit beyond inferring mechanistic models from data, towards identifying non-equilibrium gene regulatory schemes that may have been evolutionarily selected, despite their energy consumption, because they are precise, reliable, fast, or otherwise outperform regulation at equilibrium. We illustrate our reasoning by toy examples for which we provide simulation code.
AU - Zoller, Benjamin
AU - Gregor, Thomas
AU - Tkačik, Gašper
ID - 12156
IS - 9
JF - Current Opinion in Systems Biology
KW - Applied Mathematics
KW - Computer Science Applications
KW - Drug Discovery
KW - General Biochemistry
KW - Genetics and Molecular Biology
KW - Modeling and Simulation
SN - 2452-3100
TI - Eukaryotic gene regulation at equilibrium, or non?
VL - 31
ER -
TY - JOUR
AB - DNA methylation plays essential homeostatic functions in eukaryotic genomes. In animals, DNA methylation is also developmentally regulated and, in turn, regulates development. In the past two decades, huge research effort has endorsed the understanding that DNA methylation plays a similar role in plant development, especially during sexual reproduction. The power of whole-genome sequencing and cell isolation techniques, as well as bioinformatics tools, have enabled recent studies to reveal dynamic changes in DNA methylation during germline development. Furthermore, the combination of these technological advances with genetics, developmental biology and cell biology tools has revealed functional methylation reprogramming events that control gene and transposon activities in flowering plant germlines. In this review, we discuss the major advances in our knowledge of DNA methylation dynamics during male and female germline development in flowering plants.
AU - He, Shengbo
AU - Feng, Xiaoqi
ID - 12670
IS - 12
JF - Journal of Integrative Plant Biology
KW - Plant Science
KW - General Biochemistry
KW - Genetics and Molecular Biology
KW - Biochemistry
SN - 1672-9072
TI - DNA methylation dynamics during germline development
VL - 64
ER -
TY - JOUR
AB - The potential of energy filtering and direct electron detection for cryo-electron microscopy (cryo-EM) has been well documented. Here, we assess the performance of recently introduced hardware for cryo-electron tomography (cryo-ET) and subtomogram averaging (STA), an increasingly popular structural determination method for complex 3D specimens. We acquired cryo-ET datasets of EIAV virus-like particles (VLPs) on two contemporary cryo-EM systems equipped with different energy filters and direct electron detectors (DED), specifically a Krios G4, equipped with a cold field emission gun (CFEG), Thermo Fisher Scientific Selectris X energy filter, and a Falcon 4 DED; and a Krios G3i, with a Schottky field emission gun (XFEG), a Gatan Bioquantum energy filter, and a K3 DED. We performed constrained cross-correlation-based STA on equally sized datasets acquired on the respective systems. The resulting EIAV CA hexamer reconstructions show that both systems perform comparably in the 4–6 Å resolution range based on Fourier-Shell correlation (FSC). In addition, by employing a recently introduced multiparticle refinement approach, we obtained a reconstruction of the EIAV CA hexamer at 2.9 Å. Our results demonstrate the potential of the new generation of energy filters and DEDs for STA, and the effects of using different processing pipelines on their STA outcomes.
AU - Obr, Martin
AU - Hagen, Wim J.H.
AU - Dick, Robert A.
AU - Yu, Lingbo
AU - Kotecha, Abhay
AU - Schur, Florian KM
ID - 11155
IS - 2
JF - Journal of Structural Biology
KW - Structural Biology
SN - 1047-8477
TI - Exploring high-resolution cryo-ET and subtomogram averaging capabilities of contemporary DEDs
VL - 214
ER -
TY - JOUR
AB - Complex I is one of the major respiratory complexes, conserved from bacteria to mammals. It oxidises NADH, reduces quinone and pumps protons across the membrane, thus playing a central role in the oxidative energy metabolism. In this review we discuss our current state of understanding the structure of complex I from various species of mammals, plants, fungi, and bacteria, as well as of several complex I-related proteins. By comparing the structural evidence from these systems in different redox states and data from mutagenesis and molecular simulations, we formulate the mechanisms of electron transfer and proton pumping and explain how they are conformationally and electrostatically coupled. Finally, we discuss the structural basis of the deactivation phenomenon in mammalian complex I.
AU - Kampjut, Domen
AU - Sazanov, Leonid A
ID - 11167
JF - Current Opinion in Structural Biology
KW - Molecular Biology
KW - Structural Biology
SN - 0959-440X
TI - Structure of respiratory complex I – An emerging blueprint for the mechanism
VL - 74
ER -
TY - JOUR
AB - One hallmark of plant cells is their cell wall. They protect cells against the environment and high turgor and mediate morphogenesis through the dynamics of their mechanical and chemical properties. The walls are a complex polysaccharidic structure. Although their biochemical composition is well known, how the different components organize in the volume of the cell wall and interact with each other is not well understood and yet is key to the wall’s mechanical properties. To investigate the ultrastructure of the plant cell wall, we imaged the walls of onion (Allium cepa) bulbs in a near-native state via cryo-focused ion beam milling (cryo-FIB milling) and cryo-electron tomography (cryo-ET). This allowed the high-resolution visualization of cellulose fibers in situ. We reveal the coexistence of dense fiber fields bathed in a reticulated matrix we termed “meshing,” which is more abundant at the inner surface of the cell wall. The fibers adopted a regular bimodal angular distribution at all depths in the cell wall and bundled according to their orientation, creating layers within the cell wall. Concomitantly, employing homogalacturonan (HG)-specific enzymatic digestion, we observed changes in the meshing, suggesting that it is—at least in part—composed of HG pectins. We propose the following model for the construction of the abaxial epidermal primary cell wall: the cell deposits successive layers of cellulose fibers at −45° and +45° relative to the cell’s long axis and secretes the surrounding HG-rich meshing proximal to the plasma membrane, which then migrates to more distal regions of the cell wall.
AU - Nicolas, William J.
AU - Fäßler, Florian
AU - Dutka, Przemysław
AU - Schur, Florian KM
AU - Jensen, Grant
AU - Meyerowitz, Elliot
ID - 11351
IS - 11
JF - Current Biology
KW - General Agricultural and Biological Sciences
KW - General Biochemistry
KW - Genetics and Molecular Biology
SN - 0960-9822
TI - Cryo-electron tomography of the onion cell wall shows bimodally oriented cellulose fibers and reticulated homogalacturonan networks
VL - 32
ER -
TY - JOUR
AB - Background: Proper cerebral cortical development depends on the tightly orchestrated migration of newly born neurons from the inner ventricular and subventricular zones to the outer cortical plate. Any disturbance in this process during prenatal stages may lead to neuronal migration disorders (NMDs), which can vary in extent from focal to global. Furthermore, NMDs show a substantial comorbidity with other neurodevelopmental disorders, notably autism spectrum disorders (ASDs). Our previous work demonstrated focal neuronal migration defects in mice carrying loss-of-function alleles of the recognized autism risk gene WDFY3. However, the cellular origins of these defects in Wdfy3 mutant mice remain elusive and uncovering it will provide critical insight into WDFY3-dependent disease pathology.
Methods: Here, in an effort to untangle the origins of NMDs in Wdfy3lacZ mice, we employed mosaic analysis with double markers (MADM). MADM technology enabled us to genetically distinctly track and phenotypically analyze mutant and wild-type cells concomitantly in vivo using immunofluorescent techniques.
Results: We revealed a cell autonomous requirement of WDFY3 for accurate laminar positioning of cortical projection neurons and elimination of mispositioned cells during early postnatal life. In addition, we identified significant deviations in dendritic arborization, as well as synaptic density and morphology between wild type, heterozygous, and homozygous Wdfy3 mutant neurons in Wdfy3-MADM reporter mice at postnatal stages.
Limitations: While Wdfy3 mutant mice have provided valuable insight into prenatal aspects of ASD pathology that remain inaccessible to investigation in humans, like most animal models, they do not a perfectly replicate all aspects of human ASD biology. The lack of human data makes it indeterminate whether morphological deviations described here apply to ASD patients or some of the other neurodevelopmental conditions associated with WDFY3 mutation.
Conclusions: Our genetic approach revealed several cell autonomous requirements of WDFY3 in neuronal development that could underlie the pathogenic mechanisms of WDFY3-related neurodevelopmental conditions. The results are also consistent with findings in other ASD animal models and patients and suggest an important role for WDFY3 in regulating neuronal function and interconnectivity in postnatal life.
AU - Schaaf, Zachary A.
AU - Tat, Lyvin
AU - Cannizzaro, Noemi
AU - Green, Ralph
AU - Rülicke, Thomas
AU - Hippenmeyer, Simon
AU - Zarbalis, Konstantinos S.
ID - 11460
JF - Molecular Autism
KW - Psychiatry and Mental health
KW - Developmental Biology
KW - Developmental Neuroscience
KW - Molecular Biology
SN - 2040-2392
TI - WDFY3 mutation alters laminar position and morphology of cortical neurons
VL - 13
ER -
TY - JOUR
AB - Studies of protein fitness landscapes reveal biophysical constraints guiding protein evolution and empower prediction of functional proteins. However, generalisation of these findings is limited due to scarceness of systematic data on fitness landscapes of proteins with a defined evolutionary relationship. We characterized the fitness peaks of four orthologous fluorescent proteins with a broad range of sequence divergence. While two of the four studied fitness peaks were sharp, the other two were considerably flatter, being almost entirely free of epistatic interactions. Mutationally robust proteins, characterized by a flat fitness peak, were not optimal templates for machine-learning-driven protein design – instead, predictions were more accurate for fragile proteins with epistatic landscapes. Our work paves insights for practical application of fitness landscape heterogeneity in protein engineering.
AU - Gonzalez Somermeyer, Louisa
AU - Fleiss, Aubin
AU - Mishin, Alexander S
AU - Bozhanova, Nina G
AU - Igolkina, Anna A
AU - Meiler, Jens
AU - Alaball Pujol, Maria-Elisenda
AU - Putintseva, Ekaterina V
AU - Sarkisyan, Karen S
AU - Kondrashov, Fyodor
ID - 11448
JF - eLife
KW - General Immunology and Microbiology
KW - General Biochemistry
KW - Genetics and Molecular Biology
KW - General Medicine
KW - General Neuroscience
SN - 2050-084X
TI - Heterogeneity of the GFP fitness landscape and data-driven protein design
VL - 11
ER -
TY - JOUR
AB - Empirical essays of fitness landscapes suggest that they may be rugged, that is having multiple fitness peaks. Such fitness landscapes, those that have multiple peaks, necessarily have special local structures, called reciprocal sign epistasis (Poelwijk et al. in J Theor Biol 272:141–144, 2011). Here, we investigate the quantitative relationship between the number of fitness peaks and the number of reciprocal sign epistatic interactions. Previously, it has been shown (Poelwijk et al. in J Theor Biol 272:141–144, 2011) that pairwise reciprocal sign epistasis is a necessary but not sufficient condition for the existence of multiple peaks. Applying discrete Morse theory, which to our knowledge has never been used in this context, we extend this result by giving the minimal number of reciprocal sign epistatic interactions required to create a given number of peaks.
AU - Saona Urmeneta, Raimundo J
AU - Kondrashov, Fyodor
AU - Khudiakova, Kseniia
ID - 11447
IS - 8
JF - Bulletin of Mathematical Biology
KW - Computational Theory and Mathematics
KW - General Agricultural and Biological Sciences
KW - Pharmacology
KW - General Environmental Science
KW - General Biochemistry
KW - Genetics and Molecular Biology
KW - General Mathematics
KW - Immunology
KW - General Neuroscience
SN - 0092-8240
TI - Relation between the number of peaks and the number of reciprocal sign epistatic interactions
VL - 84
ER -
TY - JOUR
AB - Local adaptation leads to differences between populations within a species. In many systems, similar environmental contrasts occur repeatedly, sometimes driving parallel phenotypic evolution. Understanding the genomic basis of local adaptation and parallel evolution is a major goal of evolutionary genomics. It is now known that by preventing the break-up of favourable combinations of alleles across multiple loci, genetic architectures that reduce recombination, like chromosomal inversions, can make an important contribution to local adaptation. However, little is known about whether inversions also contribute disproportionately to parallel evolution. Our aim here is to highlight this knowledge gap, to showcase existing studies, and to illustrate the differences between genomic architectures with and without inversions using simple models. We predict that by generating stronger effective selection, inversions can sometimes speed up the parallel adaptive process or enable parallel adaptation where it would be impossible otherwise, but this is highly dependent on the spatial setting. We highlight that further empirical work is needed, in particular to cover a broader taxonomic range and to understand the relative importance of inversions compared to genomic regions without inversions.
AU - Westram, Anja M
AU - Faria, Rui
AU - Johannesson, Kerstin
AU - Butlin, Roger
AU - Barton, Nicholas H
ID - 11546
IS - 1856
JF - Philosophical Transactions of the Royal Society B: Biological Sciences
KW - General Agricultural and Biological Sciences
KW - General Biochemistry
KW - Genetics and Molecular Biology
SN - 0962-8436
TI - Inversions and parallel evolution
VL - 377
ER -
TY - JOUR
AB - Progress in structural membrane biology has been significantly accelerated by the ongoing 'Resolution Revolution' in cryo electron microscopy (cryo-EM). In particular, structure determination by single particle analysis has evolved into the most powerful method for atomic model building of multisubunit membrane protein complexes. This has created an ever increasing demand in cryo-EM machine time, which to satisfy is in need of new and affordable cryo electron microscopes. Here, we review our experience in using the JEOL CRYO ARM 200 prototype for the structure determination by single particle analysis of three different multisubunit membrane complexes: the Thermus thermophilus V-type ATPase VO complex, the Thermosynechococcus elongatus photosystem I monomer and the flagellar motor LP-ring from Salmonella enterica.
AU - Gerle, Christoph
AU - Kishikawa, Jun-ichi
AU - Yamaguchi, Tomoko
AU - Nakanishi, Atsuko
AU - Çoruh, Mehmet Orkun
AU - Makino, Fumiaki
AU - Miyata, Tomoko
AU - Kawamoto, Akihiro
AU - Yokoyama, Ken
AU - Namba, Keiichi
AU - Kurisu, Genji
AU - Kato, Takayuki
ID - 11648
IS - 5
JF - Microscopy
KW - Radiology
KW - Nuclear Medicine and imaging
KW - Instrumentation
KW - Structural Biology
SN - 2050-5698
TI - Structures of multisubunit membrane complexes with the CRYO ARM 200
VL - 71
ER -
TY - JOUR
AB - The mammalian hippocampal formation (HF) plays a key role in several higher brain functions, such as spatial coding, learning and memory. Its simple circuit architecture is often viewed as a trisynaptic loop, processing input originating from the superficial layers of the entorhinal cortex (EC) and sending it back to its deeper layers. Here, we show that excitatory neurons in layer 6b of the mouse EC project to all sub-regions comprising the HF and receive input from the CA1, thalamus and claustrum. Furthermore, their output is characterized by unique slow-decaying excitatory postsynaptic currents capable of driving plateau-like potentials in their postsynaptic targets. Optogenetic inhibition of the EC-6b pathway affects spatial coding in CA1 pyramidal neurons, while cell ablation impairs not only acquisition of new spatial memories, but also degradation of previously acquired ones. Our results provide evidence of a functional role for cortical layer 6b neurons in the adult brain.
AU - Ben Simon, Yoav
AU - Käfer, Karola
AU - Velicky, Philipp
AU - Csicsvari, Jozsef L
AU - Danzl, Johann G
AU - Jonas, Peter M
ID - 11951
JF - Nature Communications
KW - General Physics and Astronomy
KW - General Biochemistry
KW - Genetics and Molecular Biology
KW - General Chemistry
KW - Multidisciplinary
SN - 2041-1723
TI - A direct excitatory projection from entorhinal layer 6b neurons to the hippocampus contributes to spatial coding and memory
VL - 13
ER -
TY - JOUR
AB - Transcription of the ribosomal RNA precursor by RNA polymerase (Pol) I is a major determinant of cellular growth, and dysregulation is observed in many cancer types. Here, we present the purification of human Pol I from cells carrying a genomic GFP fusion on the largest subunit allowing the structural and functional analysis of the enzyme across species. In contrast to yeast, human Pol I carries a single-subunit stalk, and in vitro transcription indicates a reduced proofreading activity. Determination of the human Pol I cryo-EM reconstruction in a close-to-native state rationalizes the effects of disease-associated mutations and uncovers an additional domain that is built into the sequence of Pol I subunit RPA1. This “dock II” domain resembles a truncated HMG box incapable of DNA binding which may serve as a downstream transcription factor–binding platform in metazoans. Biochemical analysis, in situ modelling, and ChIP data indicate that Topoisomerase 2a can be recruited to Pol I via the domain and cooperates with the HMG box domain–containing factor UBF. These adaptations of the metazoan Pol I transcription system may allow efficient release of positive DNA supercoils accumulating downstream of the transcription bubble.
AU - Daiß, Julia L
AU - Pilsl, Michael
AU - Straub, Kristina
AU - Bleckmann, Andrea
AU - Höcherl, Mona
AU - Heiss, Florian B
AU - Abascal-Palacios, Guillermo
AU - Ramsay, Ewan P
AU - Tluckova, Katarina
AU - Mars, Jean-Clement
AU - Fürtges, Torben
AU - Bruckmann, Astrid
AU - Rudack, Till
AU - Bernecky, Carrie A
AU - Lamour, Valérie
AU - Panov, Konstantin
AU - Vannini, Alessandro
AU - Moss, Tom
AU - Engel, Christoph
ID - 12051
IS - 11
JF - Life Science Alliance
KW - Health
KW - Toxicology and Mutagenesis
KW - Plant Science
KW - Biochemistry
KW - Genetics and Molecular Biology (miscellaneous)
KW - Ecology
SN - 2575-1077
TI - The human RNA polymerase I structure reveals an HMG-like docking domain specific to metazoans
VL - 5
ER -
TY - JOUR
AB - Autophagosomes are double-membraned vesicles that traffic harmful or unwanted cellular macromolecules to the vacuole for recycling. Although autophagosome biogenesis has been extensively studied, autophagosome maturation, i.e., delivery and fusion with the vacuole, remains largely unknown in plants. Here, we have identified an autophagy adaptor, CFS1, that directly interacts with the autophagosome marker ATG8 and localizes on both membranes of the autophagosome. Autophagosomes form normally in Arabidopsis thaliana cfs1 mutants, but their delivery to the vacuole is disrupted. CFS1’s function is evolutionarily conserved in plants, as it also localizes to the autophagosomes and plays a role in autophagic flux in the liverwort Marchantia polymorpha. CFS1 regulates autophagic flux by bridging autophagosomes with the multivesicular body-localized ESCRT-I component VPS23A, leading to the formation of amphisomes. Similar to CFS1-ATG8 interaction, disrupting the CFS1-VPS23A interaction blocks autophagic flux and renders plants sensitive to nitrogen starvation. Altogether, our results reveal a conserved vacuolar sorting hub that regulates autophagic flux in plants.
AU - Zhao, Jierui
AU - Bui, Mai Thu
AU - Ma, Juncai
AU - Künzl, Fabian
AU - Picchianti, Lorenzo
AU - De La Concepcion, Juan Carlos
AU - Chen, Yixuan
AU - Petsangouraki, Sofia
AU - Mohseni, Azadeh
AU - García-Leon, Marta
AU - Gomez, Marta Salas
AU - Giannini, Caterina
AU - Gwennogan, Dubois
AU - Kobylinska, Roksolana
AU - Clavel, Marion
AU - Schellmann, Swen
AU - Jaillais, Yvon
AU - Friml, Jiří
AU - Kang, Byung-Ho
AU - Dagdas, Yasin
ID - 12121
IS - 12
JF - Journal of Cell Biology
KW - Cell Biology
SN - 0021-9525
TI - Plant autophagosomes mature into amphisomes prior to their delivery to the central vacuole
VL - 221
ER -
TY - JOUR
AB - Germline determination is essential for species survival and evolution in multicellular organisms. In most flowering plants, formation of the female germline is initiated with specification of one megaspore mother cell (MMC) in each ovule; however, the molecular mechanism underlying this key event remains unclear. Here we report that spatially restricted auxin signaling promotes MMC fate in Arabidopsis. Our results show that the microRNA160 (miR160) targeted gene ARF17 (AUXIN RESPONSE FACTOR17) is required for promoting MMC specification by genetically interacting with the SPL/NZZ (SPOROCYTELESS/NOZZLE) gene. Alterations of auxin signaling cause formation of supernumerary MMCs in an ARF17- and SPL/NZZ-dependent manner. Furthermore, miR160 and ARF17 are indispensable for attaining a normal auxin maximum at the ovule apex via modulating the expression domain of PIN1 (PIN-FORMED1) auxin transporter. Our findings elucidate the mechanism by which auxin signaling promotes the acquisition of female germline cell fate in plants.
AU - Huang, Jian
AU - Zhao, Lei
AU - Malik, Shikha
AU - Gentile, Benjamin R.
AU - Xiong, Va
AU - Arazi, Tzahi
AU - Owen, Heather A.
AU - Friml, Jiří
AU - Zhao, Dazhong
ID - 12130
JF - Nature Communications
KW - General Physics and Astronomy
KW - General Biochemistry
KW - Genetics and Molecular Biology
KW - General Chemistry
KW - Multidisciplinary
SN - 2041-1723
TI - Specification of female germline by microRNA orchestrated auxin signaling in Arabidopsis
VL - 13
ER -
TY - JOUR
AB - MicroRNA (miRNA) and RNA interference (RNAi) pathways rely on small RNAs produced by Dicer endonucleases. Mammalian Dicer primarily supports the essential gene-regulating miRNA pathway, but how it is specifically adapted to miRNA biogenesis is unknown. We show that the adaptation entails a unique structural role of Dicer’s DExD/H helicase domain. Although mice tolerate loss of its putative ATPase function, the complete absence of the domain is lethal because it assures high-fidelity miRNA biogenesis. Structures of murine Dicer⋅miRNA precursor complexes revealed that the DExD/H domain has a helicase-unrelated structural function. It locks Dicer in a closed state, which facilitates miRNA precursor selection. Transition to a cleavage-competent open state is stimulated by Dicer-binding protein TARBP2. Absence of the DExD/H domain or its mutations unlocks the closed state, reduces substrate selectivity, and activates RNAi. Thus, the DExD/H domain structurally contributes to mammalian miRNA biogenesis and underlies mechanistical partitioning of miRNA and RNAi pathways.
AU - Zapletal, David
AU - Taborska, Eliska
AU - Pasulka, Josef
AU - Malik, Radek
AU - Kubicek, Karel
AU - Zanova, Martina
AU - Much, Christian
AU - Sebesta, Marek
AU - Buccheri, Valeria
AU - Horvat, Filip
AU - Jenickova, Irena
AU - Prochazkova, Michaela
AU - Prochazka, Jan
AU - Pinkas, Matyas
AU - Novacek, Jiri
AU - Joseph, Diego F.
AU - Sedlacek, Radislav
AU - Bernecky, Carrie A
AU - O’Carroll, Dónal
AU - Stefl, Richard
AU - Svoboda, Petr
ID - 12143
IS - 21
JF - Molecular Cell
KW - Cell Biology
KW - Molecular Biology
SN - 1097-2765
TI - Structural and functional basis of mammalian microRNA biogenesis by Dicer
VL - 82
ER -
TY - JOUR
AB - ESCRT-III filaments are composite cytoskeletal polymers that can constrict and cut cell membranes from the inside of the membrane neck. Membrane-bound ESCRT-III filaments undergo a series of dramatic composition and geometry changes in the presence of an ATP-consuming Vps4 enzyme, which causes stepwise changes in the membrane morphology. We set out to understand the physical mechanisms involved in translating the changes in ESCRT-III polymer composition into membrane deformation. We have built a coarse-grained model in which ESCRT-III polymers of different geometries and mechanical properties are allowed to copolymerise and bind to a deformable membrane. By modelling ATP-driven stepwise depolymerisation of specific polymers, we identify mechanical regimes in which changes in filament composition trigger the associated membrane transition from a flat to a buckled state, and then to a tubule state that eventually undergoes scission to release a small cargo-loaded vesicle. We then characterise how the location and kinetics of polymer loss affects the extent of membrane deformation and the efficiency of membrane neck scission. Our results identify the near-minimal mechanical conditions for the operation of shape-shifting composite polymers that sever membrane necks.
AU - Jiang, Xiuyun
AU - Harker-Kirschneck, Lena
AU - Vanhille-Campos, Christian Eduardo
AU - Pfitzner, Anna-Katharina
AU - Lominadze, Elene
AU - Roux, Aurélien
AU - Baum, Buzz
AU - Šarić, Anđela
ID - 12152
IS - 10
JF - PLOS Computational Biology
KW - Computational Theory and Mathematics
KW - Cellular and Molecular Neuroscience
KW - Genetics
KW - Molecular Biology
KW - Ecology
KW - Modeling and Simulation
KW - Ecology
KW - Evolution
KW - Behavior and Systematics
SN - 1553-7358
TI - Modelling membrane reshaping by staged polymerization of ESCRT-III filaments
VL - 18
ER -
TY - JOUR
AB - Polygenic adaptation is thought to be ubiquitous, yet remains poorly understood. Here, we model this process analytically, in the plausible setting of a highly polygenic, quantitative trait that experiences a sudden shift in the fitness optimum. We show how the mean phenotype changes over time, depending on the effect sizes of loci that contribute to variance in the trait, and characterize the allele dynamics at these loci. Notably, we describe the two phases of the allele dynamics: The first is a rapid phase, in which directional selection introduces small frequency differences between alleles whose effects are aligned with or opposed to the shift, ultimately leading to small differences in their probability of fixation during a second, longer phase, governed by stabilizing selection. As we discuss, key results should hold in more general settings and have important implications for efforts to identify the genetic basis of adaptation in humans and other species.
AU - Hayward, Laura
AU - Sella, Guy
ID - 12157
JF - eLife
KW - General Immunology and Microbiology
KW - General Biochemistry
KW - Genetics and Molecular Biology
KW - General Medicine
KW - General Neuroscience
TI - Polygenic adaptation after a sudden change in environment
VL - 11
ER -
TY - JOUR
AB - The inadequate understanding of the mechanisms that reversibly convert molecular sulfur (S) into lithium sulfide (Li2S) via soluble polysulfides (PSs) formation impedes the development of high-performance lithium-sulfur (Li-S) batteries with non-aqueous electrolyte solutions. Here, we use operando small and wide angle X-ray scattering and operando small angle neutron scattering (SANS) measurements to track the nucleation, growth and dissolution of solid deposits from atomic to sub-micron scales during real-time Li-S cell operation. In particular, stochastic modelling based on the SANS data allows quantifying the nanoscale phase evolution during battery cycling. We show that next to nano-crystalline Li2S the deposit comprises solid short-chain PSs particles. The analysis of the experimental data suggests that initially, Li2S2 precipitates from the solution and then is partially converted via solid-state electroreduction to Li2S. We further demonstrate that mass transport, rather than electron transport through a thin passivating film, limits the discharge capacity and rate performance in Li-S cells.
AU - Prehal, Christian
AU - von Mentlen, Jean-Marc
AU - Drvarič Talian, Sara
AU - Vizintin, Alen
AU - Dominko, Robert
AU - Amenitsch, Heinz
AU - Porcar, Lionel
AU - Freunberger, Stefan Alexander
AU - Wood, Vanessa
ID - 12208
JF - Nature Communications
KW - General Physics and Astronomy
KW - General Biochemistry
KW - Genetics and Molecular Biology
KW - General Chemistry
KW - Multidisciplinary
SN - 2041-1723
TI - On the nanoscale structural evolution of solid discharge products in lithium-sulfur batteries using operando scattering
VL - 13
ER -
TY - JOUR
AB - The development dynamics and self-organization of glandular branched epithelia is of utmost importance for our understanding of diverse processes ranging from normal tissue growth to the growth of cancerous tissues. Using single primary murine pancreatic ductal adenocarcinoma (PDAC) cells embedded in a collagen matrix and adapted media supplementation, we generate organoids that self-organize into highly branched structures displaying a seamless lumen connecting terminal end buds, replicating in vivo PDAC architecture. We identify distinct morphogenesis phases, each characterized by a unique pattern of cell invasion, matrix deformation, protein expression, and respective molecular dependencies. We propose a minimal theoretical model of a branching and proliferating tissue, capturing the dynamics of the first phases. Observing the interaction of morphogenesis, mechanical environment and gene expression in vitro sets a benchmark for the understanding of self-organization processes governing complex organoid structure formation processes and branching morphogenesis.
AU - Randriamanantsoa, S.
AU - Papargyriou, A.
AU - Maurer, H. C.
AU - Peschke, K.
AU - Schuster, M.
AU - Zecchin, G.
AU - Steiger, K.
AU - Öllinger, R.
AU - Saur, D.
AU - Scheel, C.
AU - Rad, R.
AU - Hannezo, Edouard B
AU - Reichert, M.
AU - Bausch, A. R.
ID - 12217
JF - Nature Communications
KW - General Physics and Astronomy
KW - General Biochemistry
KW - Genetics and Molecular Biology
KW - General Chemistry
KW - Multidisciplinary
SN - 2041-1723
TI - Spatiotemporal dynamics of self-organized branching in pancreas-derived organoids
VL - 13
ER -
TY - JOUR
AB - Muskelin (Mkln1) is implicated in neuronal function, regulating plasma membrane receptor trafficking. However, its influence on intrinsic brain activity and corresponding behavioral processes remains unclear. Here we show that murine Mkln1 knockout causes non-habituating locomotor activity, increased exploratory drive, and decreased locomotor response to amphetamine. Muskelin deficiency impairs social novelty detection while promoting the retention of spatial reference memory and fear extinction recall. This is strongly mirrored in either weaker or stronger resting-state functional connectivity between critical circuits mediating locomotor exploration and cognition. We show that Mkln1 deletion alters dendrite branching and spine structure, coinciding with enhanced AMPAR-mediated synaptic transmission but selective impairment in synaptic potentiation maintenance. We identify muskelin at excitatory synapses and highlight its role in regulating dendritic spine actin stability. Our findings point to aberrant spine actin modulation and changes in glutamatergic synaptic function as critical mechanisms that contribute to the neurobehavioral phenotype arising from Mkln1 ablation.
AU - Muhia, Mary W
AU - YuanXiang, PingAn
AU - Sedlacik, Jan
AU - Schwarz, Jürgen R.
AU - Heisler, Frank F.
AU - Gromova, Kira V.
AU - Thies, Edda
AU - Breiden, Petra
AU - Pechmann, Yvonne
AU - Kreutz, Michael R.
AU - Kneussel, Matthias
ID - 12224
JF - Communications Biology
KW - General Agricultural and Biological Sciences
KW - General Biochemistry
KW - Genetics and Molecular Biology
KW - Medicine (miscellaneous)
SN - 2399-3642
TI - Muskelin regulates actin-dependent synaptic changes and intrinsic brain activity relevant to behavioral and cognitive processes
VL - 5
ER -
TY - JOUR
AB - Ventral tail bending, which is transient but pronounced, is found in many chordate embryos and constitutes an interesting model of how tissue interactions control embryo shape. Here, we identify one key upstream regulator of ventral tail bending in embryos of the ascidian Ciona. We show that during the early tailbud stages, ventral epidermal cells exhibit a boat-shaped morphology (boat cell) with a narrow apical surface where phosphorylated myosin light chain (pMLC) accumulates. We further show that interfering with the function of the BMP ligand Admp led to pMLC localizing to the basal instead of the apical side of ventral epidermal cells and a reduced number of boat cells. Finally, we show that cutting ventral epidermal midline cells at their apex using an ultraviolet laser relaxed ventral tail bending. Based on these results, we propose a previously unreported function for Admp in localizing pMLC to the apical side of ventral epidermal cells, which causes the tail to bend ventrally by resisting antero-posterior notochord extension at the ventral side of the tail.
AU - Kogure, Yuki S.
AU - Muraoka, Hiromochi
AU - Koizumi, Wataru C.
AU - Gelin-alessi, Raphaël
AU - Godard, Benoit G
AU - Oka, Kotaro
AU - Heisenberg, Carl-Philipp J
AU - Hotta, Kohji
ID - 12231
IS - 21
JF - Development
KW - Developmental Biology
KW - Molecular Biology
SN - 0950-1991
TI - Admp regulates tail bending by controlling ventral epidermal cell polarity via phosphorylated myosin localization in Ciona
VL - 149
ER -
TY - JOUR
AB - Biological systems are the sum of their dynamic three-dimensional (3D) parts. Therefore, it is critical to study biological structures in 3D and at high resolution to gain insights into their physiological functions. Electron microscopy of metal replicas of unroofed cells and isolated organelles has been a key technique to visualize intracellular structures at nanometer resolution. However, many of these methods require specialized equipment and personnel to complete them. Here, we present novel accessible methods to analyze biological structures in unroofed cells and biochemically isolated organelles in 3D and at nanometer resolution, focusing on Arabidopsis clathrin-coated vesicles (CCVs). While CCVs are essential trafficking organelles, their detailed structural information is lacking due to their poor preservation when observed via classical electron microscopy protocols experiments. First, we establish a method to visualize CCVs in unroofed cells using scanning transmission electron microscopy tomography, providing sufficient resolution to define the clathrin coat arrangements. Critically, the samples are prepared directly on electron microscopy grids, removing the requirement to use extremely corrosive acids, thereby enabling the use of this method in any electron microscopy lab. Secondly, we demonstrate that this standardized sample preparation allows the direct comparison of isolated CCV samples with those visualized in cells. Finally, to facilitate the high-throughput and robust screening of metal replicated samples, we provide a deep learning analysis method to screen the “pseudo 3D” morphologies of CCVs imaged with 2D modalities. Collectively, our work establishes accessible ways to examine the 3D structure of biological samples and provide novel insights into the structure of plant CCVs.
AU - Johnson, Alexander J
AU - Kaufmann, Walter
AU - Sommer, Christoph M
AU - Costanzo, Tommaso
AU - Dahhan, Dana A.
AU - Bednarek, Sebastian Y.
AU - Friml, Jiří
ID - 12239
IS - 10
JF - Molecular Plant
KW - Plant Science
KW - Molecular Biology
SN - 1674-2052
TI - Three-dimensional visualization of planta clathrin-coated vesicles at ultrastructural resolution
VL - 15
ER -
TY - JOUR
AB - MicroRNAs (miRs) have an important role in tuning dynamic gene expression. However, the mechanism by which they are quantitatively controlled is unknown. We show that the amount of mature miR-9, a key regulator of neuronal development, increases during zebrafish neurogenesis in a sharp stepwise manner. We characterize the spatiotemporal profile of seven distinct microRNA primary transcripts (pri-mir)-9s that produce the same mature miR-9 and show that they are sequentially expressed during hindbrain neurogenesis. Expression of late-onset pri-mir-9-1 is added on to, rather than replacing, the expression of early onset pri-mir-9-4 and -9-5 in single cells. CRISPR/Cas9 mutation of the late-onset pri-mir-9-1 prevents the developmental increase of mature miR-9, reduces late neuronal differentiation and fails to downregulate Her6 at late stages. Mathematical modelling shows that an adaptive network containing Her6 is insensitive to linear increases in miR-9 but responds to stepwise increases of miR-9. We suggest that a sharp stepwise increase of mature miR-9 is created by sequential and additive temporal activation of distinct loci. This may be a strategy to overcome adaptation and facilitate a transition of Her6 to a new dynamic regime or steady state.
AU - Soto, Ximena
AU - Burton, Joshua
AU - Manning, Cerys S.
AU - Minchington, Thomas
AU - Lea, Robert
AU - Lee, Jessica
AU - Kursawe, Jochen
AU - Rattray, Magnus
AU - Papalopulu, Nancy
ID - 12245
IS - 19
JF - Development
KW - Developmental Biology
KW - Molecular Biology
SN - 0950-1991
TI - Sequential and additive expression of miR-9 precursors control timing of neurogenesis
VL - 149
ER -
TY - JOUR
AB - Upon the initiation of collective cell migration, the cells at the free edge are specified as leader cells; however, the mechanism underlying the leader cell specification remains elusive. Here, we show that lamellipodial extension after the release from mechanical confinement causes sustained extracellular signal-regulated kinase (ERK) activation and underlies the leader cell specification. Live-imaging of Madin-Darby canine kidney (MDCK) cells and mouse epidermis through the use of Förster resonance energy transfer (FRET)-based biosensors showed that leader cells exhibit sustained ERK activation in a hepatocyte growth factor (HGF)-dependent manner. Meanwhile, follower cells exhibit oscillatory ERK activation waves in an epidermal growth factor (EGF) signaling-dependent manner. Lamellipodial extension at the free edge increases the cellular sensitivity to HGF. The HGF-dependent ERK activation, in turn, promotes lamellipodial extension, thereby forming a positive feedback loop between cell extension and ERK activation and specifying the cells at the free edge as the leader cells. Our findings show that the integration of physical and biochemical cues underlies the leader cell specification during collective cell migration.
AU - Hino, Naoya
AU - Matsuda, Kimiya
AU - Jikko, Yuya
AU - Maryu, Gembu
AU - Sakai, Katsuya
AU - Imamura, Ryu
AU - Tsukiji, Shinya
AU - Aoki, Kazuhiro
AU - Terai, Kenta
AU - Hirashima, Tsuyoshi
AU - Trepat, Xavier
AU - Matsuda, Michiyuki
ID - 12238
IS - 19
JF - Developmental Cell
KW - Developmental Biology
KW - Cell Biology
KW - General Biochemistry
KW - Genetics and Molecular Biology
KW - Molecular Biology
SN - 1534-5807
TI - A feedback loop between lamellipodial extension and HGF-ERK signaling specifies leader cells during collective cell migration
VL - 57
ER -
TY - JOUR
AB - Dose–response relationships are a general concept for quantitatively describing biological systems across multiple scales, from the molecular to the whole-cell level. A clinically relevant example is the bacterial growth response to antibiotics, which is routinely characterized by dose–response curves. The shape of the dose–response curve varies drastically between antibiotics and plays a key role in treatment, drug interactions, and resistance evolution. However, the mechanisms shaping the dose–response curve remain largely unclear. Here, we show in Escherichia coli that the distinctively shallow dose–response curve of the antibiotic trimethoprim is caused by a negative growth-mediated feedback loop: Trimethoprim slows growth, which in turn weakens the effect of this antibiotic. At the molecular level, this feedback is caused by the upregulation of the drug target dihydrofolate reductase (FolA/DHFR). We show that this upregulation is not a specific response to trimethoprim but follows a universal trend line that depends primarily on the growth rate, irrespective of its cause. Rewiring the feedback loop alters the dose–response curve in a predictable manner, which we corroborate using a mathematical model of cellular resource allocation and growth. Our results indicate that growth-mediated feedback loops may shape drug responses more generally and could be exploited to design evolutionary traps that enable selection against drug resistance.
AU - Angermayr, Andreas
AU - Pang, Tin Yau
AU - Chevereau, Guillaume
AU - Mitosch, Karin
AU - Lercher, Martin J
AU - Bollenbach, Mark Tobias
ID - 12261
IS - 9
JF - Molecular Systems Biology
KW - Applied Mathematics
KW - Computational Theory and Mathematics
KW - General Agricultural and Biological Sciences
KW - General Immunology and Microbiology
KW - General Biochemistry
KW - Genetics and Molecular Biology
KW - Information Systems
TI - Growth‐mediated negative feedback shapes quantitative antibiotic response
VL - 18
ER -
TY - JOUR
AB - The AAA-ATPase Drg1 is a key factor in eukaryotic ribosome biogenesis that initiates cytoplasmic maturation of the large ribosomal subunit. Drg1 releases the shuttling maturation factor Rlp24 from pre-60S particles shortly after nuclear export, a strict requirement for downstream maturation. The molecular mechanism of release remained elusive. Here, we report a series of cryo-EM structures that captured the extraction of Rlp24 from pre-60S particles by Saccharomyces cerevisiae Drg1. These structures reveal that Arx1 and the eukaryote-specific rRNA expansion segment ES27 form a joint docking platform that positions Drg1 for efficient extraction of Rlp24 from the pre-ribosome. The tips of the Drg1 N domains thereby guide the Rlp24 C terminus into the central pore of the Drg1 hexamer, enabling extraction by a hand-over-hand translocation mechanism. Our results uncover substrate recognition and processing by Drg1 step by step and provide a comprehensive mechanistic picture of the conserved modus operandi of AAA-ATPases.
AU - Prattes, Michael
AU - Grishkovskaya, Irina
AU - Hodirnau, Victor-Valentin
AU - Hetzmannseder, Christina
AU - Zisser, Gertrude
AU - Sailer, Carolin
AU - Kargas, Vasileios
AU - Loibl, Mathias
AU - Gerhalter, Magdalena
AU - Kofler, Lisa
AU - Warren, Alan J.
AU - Stengel, Florian
AU - Haselbach, David
AU - Bergler, Helmut
ID - 12262
IS - 9
JF - Nature Structural & Molecular Biology
KW - Molecular Biology
KW - Structural Biology
SN - 1545-9993
TI - Visualizing maturation factor extraction from the nascent ribosome by the AAA-ATPase Drg1
VL - 29
ER -
TY - JOUR
AB - To understand the function of neuronal circuits, it is crucial to disentangle the connectivity patterns within the network. However, most tools currently used to explore connectivity have low throughput, low selectivity, or limited accessibility. Here, we report the development of an improved packaging system for the production of the highly neurotropic RVdGenvA-CVS-N2c rabies viral vectors, yielding titers orders of magnitude higher with no background contamination, at a fraction of the production time, while preserving the efficiency of transsynaptic labeling. Along with the production pipeline, we developed suites of ‘starter’ AAV and bicistronic RVdG-CVS-N2c vectors, enabling retrograde labeling from a wide range of neuronal populations, tailored for diverse experimental requirements. We demonstrate the power and flexibility of the new system by uncovering hidden local and distal inhibitory connections in the mouse hippocampal formation and by imaging the functional properties of a cortical microcircuit across weeks. Our novel production pipeline provides a convenient approach to generate new rabies vectors, while our toolkit flexibly and efficiently expands the current capacity to label, manipulate and image the neuronal activity of interconnected neuronal circuits in vitro and in vivo.
AU - Sumser, Anton L
AU - Jösch, Maximilian A
AU - Jonas, Peter M
AU - Ben Simon, Yoav
ID - 12288
JF - eLife
KW - General Immunology and Microbiology
KW - General Biochemistry
KW - Genetics and Molecular Biology
KW - General Medicine
KW - General Neuroscience
TI - Fast, high-throughput production of improved rabies viral vectors for specific, efficient and versatile transsynaptic retrograde labeling
VL - 11
ER -
TY - JOUR
AB - In repeated interactions, players can use strategies that respond to the outcome of previous rounds. Much of the existing literature on direct reciprocity assumes that all competing individuals use the same strategy space. Here, we study both learning and evolutionary dynamics of players that differ in the strategy space they explore. We focus on the infinitely repeated donation game and compare three natural strategy spaces: memory-1 strategies, which consider the last moves of both players, reactive strategies, which respond to the last move of the co-player, and unconditional strategies. These three strategy spaces differ in the memory capacity that is needed. We compute the long term average payoff that is achieved in a pairwise learning process. We find that smaller strategy spaces can dominate larger ones. For weak selection, unconditional players dominate both reactive and memory-1 players. For intermediate selection, reactive players dominate memory-1 players. Only for strong selection and low cost-to-benefit ratio, memory-1 players dominate the others. We observe that the supergame between strategy spaces can be a social dilemma: maximum payoff is achieved if both players explore a larger strategy space, but smaller strategy spaces dominate.
AU - Schmid, Laura
AU - Hilbe, Christian
AU - Chatterjee, Krishnendu
AU - Nowak, Martin
ID - 12280
IS - 6
JF - PLOS Computational Biology
KW - Computational Theory and Mathematics
KW - Cellular and Molecular Neuroscience
KW - Genetics
KW - Molecular Biology
KW - Ecology
KW - Modeling and Simulation
KW - Ecology
KW - Evolution
KW - Behavior and Systematics
TI - Direct reciprocity between individuals that use different strategy spaces
VL - 18
ER -
TY - JOUR
AB - Neurons extend axons to form the complex circuitry of the mature brain. This depends on the coordinated response and continuous remodelling of the microtubule and F-actin networks in the axonal growth cone. Growth cone architecture remains poorly understood at nanoscales. We therefore investigated mouse hippocampal neuron growth cones using cryo-electron tomography to directly visualise their three-dimensional subcellular architecture with molecular detail. Our data showed that the hexagonal arrays of actin bundles that form filopodia penetrate and terminate deep within the growth cone interior. We directly observed the modulation of these and other growth cone actin bundles by alteration of individual F-actin helical structures. Microtubules with blunt, slightly flared or gently curved ends predominated in the growth cone, frequently contained lumenal particles and exhibited lattice defects. Investigation of the effect of absence of doublecortin, a neurodevelopmental cytoskeleton regulator, on growth cone cytoskeleton showed no major anomalies in overall growth cone organisation or in F-actin subpopulations. However, our data suggested that microtubules sustained more structural defects, highlighting the importance of microtubule integrity during growth cone migration.
AU - Atherton, Joseph
AU - Stouffer, Melissa A
AU - Francis, Fiona
AU - Moores, Carolyn A.
ID - 12283
IS - 7
JF - Journal of Cell Science
KW - Cell Biology
SN - 0021-9533
TI - Visualising the cytoskeletal machinery in neuronal growth cones using cryo-electron tomography
VL - 135
ER -
TY - JOUR
AB - Centrosomes play a crucial role during immune cell interactions and initiation of the immune response. In proliferating cells, centrosome numbers are tightly controlled and generally limited to one in G1 and two prior to mitosis. Defects in regulating centrosome numbers have been associated with cell transformation and tumorigenesis. Here, we report the emergence of extra centrosomes in leukocytes during immune activation. Upon antigen encounter, dendritic cells pass through incomplete mitosis and arrest in the subsequent G1 phase leading to tetraploid cells with accumulated centrosomes. In addition, cell stimulation increases expression of polo-like kinase 2, resulting in diploid cells with two centrosomes in G1-arrested cells. During cell migration, centrosomes tightly cluster and act as functional microtubule-organizing centers allowing for increased persistent locomotion along gradients of chemotactic cues. Moreover, dendritic cells with extra centrosomes display enhanced secretion of inflammatory cytokines and optimized T cell responses. Together, these results demonstrate a previously unappreciated role of extra centrosomes for regular cell and tissue homeostasis.
AU - Weier, Ann-Kathrin
AU - Homrich, Mirka
AU - Ebbinghaus, Stephanie
AU - Juda, Pavel
AU - Miková, Eliška
AU - Hauschild, Robert
AU - Zhang, Lili
AU - Quast, Thomas
AU - Mass, Elvira
AU - Schlitzer, Andreas
AU - Kolanus, Waldemar
AU - Burgdorf, Sven
AU - Gruß, Oliver J.
AU - Hons, Miroslav
AU - Wieser, Stefan
AU - Kiermaier, Eva
ID - 12122
IS - 12
JF - Journal of Cell Biology
KW - Cell Biology
SN - 0021-9525
TI - Multiple centrosomes enhance migration and immune cell effector functions of mature dendritic cells
VL - 221
ER -
TY - JOUR
AB - N-glycans are molecularly diverse sugars borne by over 70% of proteins transiting the secretory pathway and have been implicated in protein folding, stability, and localization. Mutations in genes important for N-glycosylation result in congenital disorders of glycosylation that are often associated with intellectual disability. Here, we show that structurally distinct N-glycans regulate an extracellular protein complex involved in the patterning of somatosensory dendrites in Caenorhabditis elegans. Specifically, aman-2/Golgi alpha-mannosidase II, a conserved key enzyme in the biosynthesis of specific N-glycans, regulates the activity of the Menorin adhesion complex without obviously affecting the protein stability and localization of its components. AMAN-2 functions cell-autonomously to allow for decoration of the neuronal transmembrane receptor DMA-1/LRR-TM with the correct set of high-mannose/hybrid/paucimannose N-glycans. Moreover, distinct types of N-glycans on specific N-glycosylation sites regulate DMA-1/LRR-TM receptor function, which, together with three other extracellular proteins, forms the Menorin adhesion complex. In summary, specific N-glycan structures regulate dendrite patterning by coordinating the activity of an extracellular adhesion complex, suggesting that the molecular diversity of N-glycans can contribute to developmental specificity in the nervous system.
AU - Rahman, Maisha
AU - Ramirez, Nelson
AU - Diaz‐Balzac, Carlos A
AU - Bülow, Hannes E
ID - 12275
IS - 7
JF - EMBO Reports
KW - Genetics
KW - Molecular Biology
KW - Biochemistry
SN - 1469-221X
TI - Specific N-glycans regulate an extracellular adhesion complex during somatosensory dendrite patterning
VL - 23
ER -
TY - JOUR
AB - Plant root architecture flexibly adapts to changing nitrate (NO3−) availability in the soil; however, the underlying molecular mechanism of this adaptive development remains under-studied. To explore the regulation of NO3−-mediated root growth, we screened for low-nitrate-resistant mutant (lonr) and identified mutants that were defective in the NAC transcription factor NAC075 (lonr1) as being less sensitive to low NO3− in terms of primary root growth. We show that NAC075 is a mobile transcription factor relocating from the root stele tissues to the endodermis based on NO3− availability. Under low-NO3− availability, the kinase CBL-interacting protein kinase 1 (CIPK1) is activated, and it phosphorylates NAC075, restricting its movement from the stele, which leads to the transcriptional regulation of downstream target WRKY53, consequently leading to adapted root architecture. Our work thus identifies an adaptive mechanism involving translocation of transcription factor based on nutrient availability and leading to cell-specific reprogramming of plant root growth.
AU - Xiao, Huixin
AU - Hu, Yumei
AU - Wang, Yaping
AU - Cheng, Jinkui
AU - Wang, Jinyi
AU - Chen, Guojingwei
AU - Li, Qian
AU - Wang, Shuwei
AU - Wang, Yalu
AU - Wang, Shao-Shuai
AU - Wang, Yi
AU - Xuan, Wei
AU - Li, Zhen
AU - Guo, Yan
AU - Gong, Zhizhong
AU - Friml, Jiří
AU - Zhang, Jing
ID - 12120
IS - 23
JF - Developmental Cell
KW - Developmental Biology
KW - Cell Biology
KW - General Biochemistry
KW - Genetics and Molecular Biology
KW - Molecular Biology
SN - 1534-5807
TI - Nitrate availability controls translocation of the transcription factor NAC075 for cell-type-specific reprogramming of root growth
VL - 57
ER -
TY - JOUR
AB - To understand how potential gene manipulations affect in vitro microglia, we provide a set of short protocols to evaluate microglia identity and function. We detail steps for immunostaining to determine microglia identity. We describe three functional assays for microglia: phagocytosis, calcium response following ATP stimulation, and cytokine expression upon inflammatory stimuli. We apply these protocols to human induced-pluripotent-stem-cell (hiPSC)-derived microglia, but they can be also applied to other in vitro microglial models including primary mouse microglia.
For complete details on the use and execution of this protocol, please refer to Bartalska et al. (2022).1
AU - Hübschmann, Verena
AU - Korkut, Medina
AU - Siegert, Sandra
ID - 12117
IS - 4
JF - STAR Protocols
KW - General Immunology and Microbiology
KW - General Biochemistry
KW - Genetics and Molecular Biology
KW - General Neuroscience
SN - 2666-1667
TI - Assessing human iPSC-derived microglia identity and function by immunostaining, phagocytosis, calcium activity, and inflammation assay
VL - 3
ER -
TY - JOUR
AB - Reading, interpreting and crawling along gradients of chemotactic cues is one of the most complex questions in cell biology. In this issue, Georgantzoglou et al. (2022. J. Cell. Biol.https://doi.org/10.1083/jcb.202103207) use in vivo models to map the temporal sequence of how neutrophils respond to an acutely arising gradient of chemoattractant.
AU - Stopp, Julian A
AU - Sixt, Michael K
ID - 12272
IS - 8
JF - Journal of Cell Biology
KW - Cell Biology
SN - 0021-9525
TI - Plan your trip before you leave: The neutrophils’ search-and-run journey
VL - 221
ER -
TY - JOUR
AB - A species distributed across diverse environments may adapt to local conditions. We ask how quickly such a species changes its range in response to changed conditions. Szép et al. (Szép E, Sachdeva H, Barton NH. 2021 Polygenic local adaptation in metapopulations: a stochastic eco-evolutionary model. Evolution75, 1030–1045 (doi:10.1111/evo.14210)) used the infinite island model to find the stationary distribution of allele frequencies and deme sizes. We extend this to find how a metapopulation responds to changes in carrying capacity, selection strength, or migration rate when deme sizes are fixed. We further develop a ‘fixed-state’ approximation. Under this approximation, polymorphism is only possible for a narrow range of habitat proportions when selection is weak compared to drift, but for a much wider range otherwise. When rates of selection or migration relative to drift change in a single deme of the metapopulation, the population takes a time of order m−1 to reach the new equilibrium. However, even with many loci, there can be substantial fluctuations in net adaptation, because at each locus, alleles randomly get lost or fixed. Thus, in a finite metapopulation, variation may gradually be lost by chance, even if it would persist in an infinite metapopulation. When conditions change across the whole metapopulation, there can be rapid change, which is predicted well by the fixed-state approximation. This work helps towards an understanding of how metapopulations extend their range across diverse environments.
This article is part of the theme issue ‘Species’ ranges in the face of changing environments (Part II)’.
AU - Barton, Nicholas H
AU - Olusanya, Oluwafunmilola O
ID - 10787
IS - 1848
JF - Philosophical Transactions of the Royal Society B: Biological Sciences
KW - General Agricultural and Biological Sciences
KW - General Biochemistry
KW - Genetics and Molecular Biology
SN - 0962-8436
TI - The response of a metapopulation to a changing environment
VL - 377
ER -
TY - JOUR
AB - The actin-homologue FtsA is essential for E. coli cell division, as it links FtsZ filaments in the Z-ring to transmembrane proteins. FtsA is thought to initiate cell constriction by switching from an inactive polymeric to an active monomeric conformation, which recruits downstream proteins and stabilizes the Z-ring. However, direct biochemical evidence for this mechanism is missing. Here, we use reconstitution experiments and quantitative fluorescence microscopy to study divisome activation in vitro. By comparing wild-type FtsA with FtsA R286W, we find that this hyperactive mutant outperforms FtsA WT in replicating FtsZ treadmilling dynamics, FtsZ filament stabilization and recruitment of FtsN. We could attribute these differences to a faster exchange and denser packing of FtsA R286W below FtsZ filaments. Using FRET microscopy, we also find that FtsN binding promotes FtsA self-interaction. We propose that in the active divisome FtsA and FtsN exist as a dynamic copolymer that follows treadmilling filaments of FtsZ.
AU - Radler, Philipp
AU - Baranova, Natalia S.
AU - Dos Santos Caldas, Paulo R
AU - Sommer, Christoph M
AU - Lopez Pelegrin, Maria D
AU - Michalik, David
AU - Loose, Martin
ID - 11373
JF - Nature Communications
KW - General Physics and Astronomy
KW - General Biochemistry
KW - Genetics and Molecular Biology
KW - General Chemistry
SN - 2041-1723
TI - In vitro reconstitution of Escherichia coli divisome activation
VL - 13
ER -
TY - JOUR
AB - Mutations in the chromodomain helicase DNA-binding 8 (CHD8) gene are a frequent cause of autism spectrum disorder (ASD). While its phenotypic spectrum often encompasses macrocephaly, implicating cortical abnormalities, how CHD8 haploinsufficiency affects neurodevelopmental is unclear. Here, employing human cerebral organoids, we find that CHD8 haploinsufficiency disrupted neurodevelopmental trajectories with an accelerated and delayed generation of, respectively, inhibitory and excitatory neurons that yields, at days 60 and 120, symmetrically opposite expansions in their proportions. This imbalance is consistent with an enlargement of cerebral organoids as an in vitro correlate of patients’ macrocephaly. Through an isogenic design of patient-specific mutations and mosaic organoids, we define genotype-phenotype relationships and uncover their cell-autonomous nature. Our results define cell-type-specific CHD8-dependent molecular defects related to an abnormal program of proliferation and alternative splicing. By identifying cell-type-specific effects of CHD8 mutations, our study uncovers reproducible developmental alterations that may be employed for neurodevelopmental disease modeling.
AU - Villa, Carlo Emanuele
AU - Cheroni, Cristina
AU - Dotter, Christoph
AU - López-Tóbon, Alejandro
AU - Oliveira, Bárbara
AU - Sacco, Roberto
AU - Yahya, Aysan Çerağ
AU - Morandell, Jasmin
AU - Gabriele, Michele
AU - Tavakoli, Mojtaba
AU - Lyudchik, Julia
AU - Sommer, Christoph M
AU - Gabitto, Mariano
AU - Danzl, Johann G
AU - Testa, Giuseppe
AU - Novarino, Gaia
ID - 11160
IS - 1
JF - Cell Reports
KW - General Biochemistry
KW - Genetics and Molecular Biology
SN - 2211-1247
TI - CHD8 haploinsufficiency links autism to transient alterations in excitatory and inhibitory trajectories
VL - 39
ER -
TY - JOUR
AB - The T cell receptor (TCR) pathway receives, processes, and amplifies the signal from pathogenic antigens to the activation of T cells. Although major components in this pathway have been identified, the knowledge on how individual components cooperate to effectively transduce signals remains limited. Phase separation emerges as a biophysical principle in organizing signaling molecules into liquid-like condensates. Here, we report that phospholipase Cγ1 (PLCγ1) promotes phase separation of LAT, a key adaptor protein in the TCR pathway. PLCγ1 directly cross-links LAT through its two SH2 domains. PLCγ1 also protects LAT from dephosphorylation by the phosphatase CD45 and promotes LAT-dependent ERK activation and SLP76 phosphorylation. Intriguingly, a nonmonotonic effect of PLCγ1 on LAT clustering was discovered. Computer simulations, based on patchy particles, revealed how the cluster size is regulated by protein compositions. Together, these results define a critical function of PLCγ1 in promoting phase separation of the LAT complex and TCR signal transduction.
AU - Zeng, Longhui
AU - Palaia, Ivan
AU - Šarić, Anđela
AU - Su, Xiaolei
ID - 10337
IS - 6
JF - Journal of Cell Biology
KW - cell biology
SN - 0021-9525
TI - PLCγ1 promotes phase separation of T cell signaling components
VL - 220
ER -
TY - JOUR
AB - In order to combat molecular damage, most cellular proteins undergo rapid turnover. We have previously identified large nuclear protein assemblies that can persist for years in post-mitotic tissues and are subject to age-related decline. Here, we report that mitochondria can be long lived in the mouse brain and reveal that specific mitochondrial proteins have half-lives longer than the average proteome. These mitochondrial long-lived proteins (mitoLLPs) are core components of the electron transport chain (ETC) and display increased longevity in respiratory supercomplexes. We find that COX7C, a mitoLLP that forms a stable contact site between complexes I and IV, is required for complex IV and supercomplex assembly. Remarkably, even upon depletion of COX7C transcripts, ETC function is maintained for days, effectively uncoupling mitochondrial function from ongoing transcription of its mitoLLPs. Our results suggest that modulating protein longevity within the ETC is critical for mitochondrial proteome maintenance and the robustness of mitochondrial function.
AU - Krishna, Shefali
AU - Arrojo e Drigo, Rafael
AU - Capitanio, Juliana S.
AU - Ramachandra, Ranjan
AU - Ellisman, Mark
AU - HETZER, Martin W
ID - 11052
IS - 21
JF - Developmental Cell
KW - Developmental Biology
KW - Cell Biology
KW - General Biochemistry
KW - Genetics and Molecular Biology
KW - Molecular Biology
SN - 1534-5807
TI - Identification of long-lived proteins in the mitochondria reveals increased stability of the electron transport chain
VL - 56
ER -
TY - JOUR
AB - Glaciers in High Mountain Asia generate meltwater that supports the water needs of 250 million people, but current knowledge of annual accumulation and ablation is limited to sparse field measurements biased in location and glacier size. Here, we present altitudinally-resolved specific mass balances (surface, internal, and basal combined) for 5527 glaciers in High Mountain Asia for 2000–2016, derived by correcting observed glacier thinning patterns for mass redistribution due to ice flow. We find that 41% of glaciers accumulated mass over less than 20% of their area, and only 60% ± 10% of regional annual ablation was compensated by accumulation. Even without 21st century warming, 21% ± 1% of ice volume will be lost by 2100 due to current climatic-geometric imbalance, representing a reduction in glacier ablation into rivers of 28% ± 1%. The ablation of glaciers in the Himalayas and Tien Shan was mostly unsustainable and ice volume in these regions will reduce by at least 30% by 2100. The most important and vulnerable glacier-fed river basins (Amu Darya, Indus, Syr Darya, Tarim Interior) were supplied with >50% sustainable glacier ablation but will see long-term reductions in ice mass and glacier meltwater supply regardless of the Karakoram Anomaly.
AU - Miles, Evan
AU - McCarthy, Michael
AU - Dehecq, Amaury
AU - Kneib, Marin
AU - Fugger, Stefan
AU - Pellicciotti, Francesca
ID - 12585
JF - Nature Communications
KW - General Physics and Astronomy
KW - General Biochemistry
KW - Genetics and Molecular Biology
KW - General Chemistry
KW - Multidisciplinary
SN - 2041-1723
TI - Health and sustainability of glaciers in High Mountain Asia
VL - 12
ER -
TY - JOUR
AB - Self-assembly of nanoparticles can be mediated by polymers, but has so far led almost exclusively to nanoparticle aggregates that are amorphous. Here, we employed Coulombic interactions to generate a range of composite materials from mixtures of charged nanoparticles and oppositely charged polymers. The assembly behavior of these nanoparticle/polymer composites depends on their order of addition: polymers added to nanoparticles give rise to stable aggregates, but nanoparticles added to polymers disassemble the initially formed aggregates. The amorphous aggregates were transformed into crystalline ones by transiently increasing the ionic strength of the solution. The morphology of the resulting crystals depended on the length of the polymer: short polymer chains mediated the self-assembly of nanoparticles into strongly faceted crystals, whereas long chains led to pseudospherical nanoparticle/polymer assemblies, within which the crystalline order of nanoparticles was retained.
AU - Bian, Tong
AU - Klajn, Rafal
ID - 13356
IS - 1
JF - Annals of the New York Academy of Sciences
KW - History and Philosophy of Science
KW - General Biochemistry
KW - Genetics and Molecular Biology
KW - General Neuroscience
SN - 0077-8923
TI - Morphology control in crystalline nanoparticle–polymer aggregates
VL - 1505
ER -
TY - JOUR
AB - During development, a single cell is transformed into a highly complex organism through progressive cell division, specification and rearrangement. An important prerequisite for the emergence of patterns within the developing organism is to establish asymmetries at various scales, ranging from individual cells to the entire embryo, eventually giving rise to the different body structures. This becomes especially apparent during gastrulation, when the earliest major lineage restriction events lead to the formation of the different germ layers. Traditionally, the unfolding of the developmental program from symmetry breaking to germ layer formation has been studied by dissecting the contributions of different signaling pathways and cellular rearrangements in the in vivo context of intact embryos. Recent efforts, using the intrinsic capacity of embryonic stem cells to self-assemble and generate embryo-like structures de novo, have opened new avenues for understanding the many ways by which an embryo can be built and the influence of extrinsic factors therein. Here, we discuss and compare divergent and conserved strategies leading to germ layer formation in embryos as compared to in vitro systems, their upstream molecular cascades and the role of extrinsic factors in this process.
AU - Schauer, Alexandra
AU - Heisenberg, Carl-Philipp J
ID - 8966
JF - Developmental Biology
KW - Developmental Biology
KW - Cell Biology
KW - Molecular Biology
SN - 0012-1606
TI - Reassembling gastrulation
VL - 474
ER -
TY - JOUR
AB - Genomic imprinting is an epigenetic mechanism that results in parental allele-specific expression of ~1% of all genes in mouse and human. Imprinted genes are key developmental regulators and play pivotal roles in many biological processes such as nutrient transfer from the mother to offspring and neuronal development. Imprinted genes are also involved in human disease, including neurodevelopmental disorders, and often occur in clusters that are regulated by a common imprint control region (ICR). In extra-embryonic tissues ICRs can act over large distances, with the largest surrounding Igf2r spanning over 10 million base-pairs. Besides classical imprinted expression that shows near exclusive maternal or paternal expression, widespread biased imprinted expression has been identified mainly in brain. In this review we discuss recent developments mapping cell type specific imprinted expression in extra-embryonic tissues and neocortex in the mouse. We highlight the advantages of using an inducible uniparental chromosome disomy (UPD) system to generate cells carrying either two maternal or two paternal copies of a specific chromosome to analyze the functional consequences of genomic imprinting. Mosaic Analysis with Double Markers (MADM) allows fluorescent labeling and concomitant induction of UPD sparsely in specific cell types, and thus to over-express or suppress all imprinted genes on that chromosome. To illustrate the utility of this technique, we explain how MADM-induced UPD revealed new insights about the function of the well-studied Cdkn1c imprinted gene, and how MADM-induced UPDs led to identification of highly cell type specific phenotypes related to perturbed imprinted expression in the mouse neocortex. Finally, we give an outlook on how MADM could be used to probe cell type specific imprinted expression in other tissues in mouse, particularly in extra-embryonic tissues.
AU - Pauler, Florian
AU - Hudson, Quanah
AU - Laukoter, Susanne
AU - Hippenmeyer, Simon
ID - 9188
IS - 5
JF - Neurochemistry International
KW - Cell Biology
KW - Cellular and Molecular Neuroscience
SN - 0197-0186
TI - Inducible uniparental chromosome disomy to probe genomic imprinting at single-cell level in brain and beyond
VL - 145
ER -
TY - JOUR
AB - We report the complete analysis of a deterministic model of deleterious mutations and negative selection against them at two haploid loci without recombination. As long as mutation is a weaker force than selection, mutant alleles remain rare at the only stable equilibrium, and otherwise, a variety of dynamics are possible. If the mutation-free genotype is absent, generally the only stable equilibrium is the one that corresponds to fixation of the mutant allele at the locus where it is less deleterious. This result suggests that fixation of a deleterious allele that follows a click of the Muller’s ratchet is governed by natural selection, instead of random drift.
AU - Khudiakova, Kseniia
AU - Neretina, Tatiana Yu.
AU - Kondrashov, Alexey S.
ID - 9387
JF - Journal of Theoretical Biology
KW - General Biochemistry
KW - Genetics and Molecular Biology
KW - Modelling and Simulation
KW - Statistics and Probability
KW - General Immunology and Microbiology
KW - Applied Mathematics
KW - General Agricultural and Biological Sciences
KW - General Medicine
SN - 0022-5193
TI - Two linked loci under mutation-selection balance and Muller’s ratchet
VL - 524
ER -
TY - JOUR
AB - Inositol hexakisphosphate (IP6) is an assembly cofactor for HIV-1. We report here that IP6 is also used for assembly of Rous sarcoma virus (RSV), a retrovirus from a different genus. IP6 is ~100-fold more potent at promoting RSV mature capsid protein (CA) assembly than observed for HIV-1 and removal of IP6 in cells reduces infectivity by 100-fold. Here, visualized by cryo-electron tomography and subtomogram averaging, mature capsid-like particles show an IP6-like density in the CA hexamer, coordinated by rings of six lysines and six arginines. Phosphate and IP6 have opposing effects on CA in vitro assembly, inducing formation of T = 1 icosahedrons and tubes, respectively, implying that phosphate promotes pentamer and IP6 hexamer formation. Subtomogram averaging and classification optimized for analysis of pleomorphic retrovirus particles reveal that the heterogeneity of mature RSV CA polyhedrons results from an unexpected, intrinsic CA hexamer flexibility. In contrast, the CA pentamer forms rigid units organizing the local architecture. These different features of hexamers and pentamers determine the structural mechanism to form CA polyhedrons of variable shape in mature RSV particles.
AU - Obr, Martin
AU - Ricana, Clifton L.
AU - Nikulin, Nadia
AU - Feathers, Jon-Philip R.
AU - Klanschnig, Marco
AU - Thader, Andreas
AU - Johnson, Marc C.
AU - Vogt, Volker M.
AU - Schur, Florian KM
AU - Dick, Robert A.
ID - 9431
IS - 1
JF - Nature Communications
KW - General Biochemistry
KW - Genetics and Molecular Biology
KW - General Physics and Astronomy
KW - General Chemistry
TI - Structure of the mature Rous sarcoma virus lattice reveals a role for IP6 in the formation of the capsid hexamer
VL - 12
ER -
TY - JOUR
AB - The hexameric AAA-ATPase Drg1 is a key factor in eukaryotic ribosome biogenesis and initiates cytoplasmic maturation of the large ribosomal subunit by releasing the shuttling maturation factor Rlp24. Drg1 monomers contain two AAA-domains (D1 and D2) that act in a concerted manner. Rlp24 release is inhibited by the drug diazaborine which blocks ATP hydrolysis in D2. The mode of inhibition was unknown. Here we show the first cryo-EM structure of Drg1 revealing the inhibitory mechanism. Diazaborine forms a covalent bond to the 2′-OH of the nucleotide in D2, explaining its specificity for this site. As a consequence, the D2 domain is locked in a rigid, inactive state, stalling the whole Drg1 hexamer. Resistance mechanisms identified include abolished drug binding and altered positioning of the nucleotide. Our results suggest nucleotide-modifying compounds as potential novel inhibitors for AAA-ATPases.
AU - Prattes, Michael
AU - Grishkovskaya, Irina
AU - Hodirnau, Victor-Valentin
AU - Rössler, Ingrid
AU - Klein, Isabella
AU - Hetzmannseder, Christina
AU - Zisser, Gertrude
AU - Gruber, Christian C.
AU - Gruber, Karl
AU - Haselbach, David
AU - Bergler, Helmut
ID - 9540
IS - 1
JF - Nature Communications
KW - General Biochemistry
KW - Genetics and Molecular Biology
KW - General Physics and Astronomy
KW - General Chemistry
TI - Structural basis for inhibition of the AAA-ATPase Drg1 by diazaborine
VL - 12
ER -
TY - JOUR
AB - The hippocampal mossy fiber synapse is a key synapse of the trisynaptic circuit. Post-tetanic potentiation (PTP) is the most powerful form of plasticity at this synaptic connection. It is widely believed that mossy fiber PTP is an entirely presynaptic phenomenon, implying that PTP induction is input-specific, and requires neither activity of multiple inputs nor stimulation of postsynaptic neurons. To directly test cooperativity and associativity, we made paired recordings between single mossy fiber terminals and postsynaptic CA3 pyramidal neurons in rat brain slices. By stimulating non-overlapping mossy fiber inputs converging onto single CA3 neurons, we confirm that PTP is input-specific and non-cooperative. Unexpectedly, mossy fiber PTP exhibits anti-associative induction properties. EPSCs show only minimal PTP after combined pre- and postsynaptic high-frequency stimulation with intact postsynaptic Ca2+ signaling, but marked PTP in the absence of postsynaptic spiking and after suppression of postsynaptic Ca2+ signaling (10 mM EGTA). PTP is largely recovered by inhibitors of voltage-gated R- and L-type Ca2+ channels, group II mGluRs, and vacuolar-type H+-ATPase, suggesting the involvement of retrograde vesicular glutamate signaling. Transsynaptic regulation of PTP extends the repertoire of synaptic computations, implementing a brake on mossy fiber detonation and a “smart teacher” function of hippocampal mossy fiber synapses.
AU - Vandael, David H
AU - Okamoto, Yuji
AU - Jonas, Peter M
ID - 9778
IS - 1
JF - Nature Communications
KW - general physics and astronomy
KW - general biochemistry
KW - genetics and molecular biology
KW - general chemistry
SN - 2041-1723
TI - Transsynaptic modulation of presynaptic short-term plasticity in hippocampal mossy fiber synapses
VL - 12
ER -
TY - JOUR
AB - The C-terminal domain (CTD) of the largest subunit of RNA polymerase II (Pol II) is a regulatory hub for transcription and RNA processing. Here, we identify PHD-finger protein 3 (PHF3) as a regulator of transcription and mRNA stability that docks onto Pol II CTD through its SPOC domain. We characterize SPOC as a CTD reader domain that preferentially binds two phosphorylated Serine-2 marks in adjacent CTD repeats. PHF3 drives liquid-liquid phase separation of phosphorylated Pol II, colocalizes with Pol II clusters and tracks with Pol II across the length of genes. PHF3 knock-out or SPOC deletion in human cells results in increased Pol II stalling, reduced elongation rate and an increase in mRNA stability, with marked derepression of neuronal genes. Key neuronal genes are aberrantly expressed in Phf3 knock-out mouse embryonic stem cells, resulting in impaired neuronal differentiation. Our data suggest that PHF3 acts as a prominent effector of neuronal gene regulation by bridging transcription with mRNA decay.
AU - Appel, Lisa-Marie
AU - Franke, Vedran
AU - Bruno, Melania
AU - Grishkovskaya, Irina
AU - Kasiliauskaite, Aiste
AU - Kaufmann, Tanja
AU - Schoeberl, Ursula E.
AU - Puchinger, Martin G.
AU - Kostrhon, Sebastian
AU - Ebenwaldner, Carmen
AU - Sebesta, Marek
AU - Beltzung, Etienne
AU - Mechtler, Karl
AU - Lin, Gen
AU - Vlasova, Anna
AU - Leeb, Martin
AU - Pavri, Rushad
AU - Stark, Alexander
AU - Akalin, Altuna
AU - Stefl, Richard
AU - Bernecky, Carrie A
AU - Djinovic-Carugo, Kristina
AU - Slade, Dea
ID - 10163
IS - 1
JF - Nature Communications
KW - general physics and astronomy
KW - general biochemistry
KW - genetics and molecular biology
KW - general chemistry
TI - PHF3 regulates neuronal gene expression through the Pol II CTD reader domain SPOC
VL - 12
ER -
TY - JOUR
AB - De novo protein synthesis is required for synapse modifications underlying stable memory encoding. Yet neurons are highly compartmentalized cells and how protein synthesis can be regulated at the synapse level is unknown. Here, we characterize neuronal signaling complexes formed by the postsynaptic scaffold GIT1, the mechanistic target of rapamycin (mTOR) kinase, and Raptor that couple synaptic stimuli to mTOR-dependent protein synthesis; and identify NMDA receptors containing GluN3A subunits as key negative regulators of GIT1 binding to mTOR. Disruption of GIT1/mTOR complexes by enhancing GluN3A expression or silencing GIT1 inhibits synaptic mTOR activation and restricts the mTOR-dependent translation of specific activity-regulated mRNAs. Conversely, GluN3A removal enables complex formation, potentiates mTOR-dependent protein synthesis, and facilitates the consolidation of associative and spatial memories in mice. The memory enhancement becomes evident with light or spaced training, can be achieved by selectively deleting GluN3A from excitatory neurons during adulthood, and does not compromise other aspects of cognition such as memory flexibility or extinction. Our findings provide mechanistic insight into synaptic translational control and reveal a potentially selective target for cognitive enhancement.
AU - Conde-Dusman, María J
AU - Dey, Partha N
AU - Elía-Zudaire, Óscar
AU - Garcia Rabaneda, Luis E
AU - García-Lira, Carmen
AU - Grand, Teddy
AU - Briz, Victor
AU - Velasco, Eric R
AU - Andero Galí, Raül
AU - Niñerola, Sergio
AU - Barco, Angel
AU - Paoletti, Pierre
AU - Wesseling, John F
AU - Gardoni, Fabrizio
AU - Tavalin, Steven J
AU - Perez-Otaño, Isabel
ID - 10301
JF - eLife
KW - general immunology and microbiology
KW - general biochemistry
KW - genetics and molecular biology
KW - general medicine
KW - general neuroscience
SN - 2050-084X
TI - Control of protein synthesis and memory by GluN3A-NMDA receptors through inhibition of GIT1/mTORC1 assembly
VL - 10
ER -
TY - JOUR
AB - A high-resolution structure of trimeric cyanobacterial Photosystem I (PSI) from Thermosynechococcus elongatus was reported as the first atomic model of PSI almost 20 years ago. However, the monomeric PSI structure has not yet been reported despite long-standing interest in its structure and extensive spectroscopic characterization of the loss of red chlorophylls upon monomerization. Here, we describe the structure of monomeric PSI from Thermosynechococcus elongatus BP-1. Comparison with the trimer structure gave detailed insights into monomerization-induced changes in both the central trimerization domain and the peripheral regions of the complex. Monomerization-induced loss of red chlorophylls is assigned to a cluster of chlorophylls adjacent to PsaX. Based on our findings, we propose a role of PsaX in the stabilization of red chlorophylls and that lipids of the surrounding membrane present a major source of thermal energy for uphill excitation energy transfer from red chlorophylls to P700.
AU - Çoruh, Mehmet Orkun
AU - Frank, Anna
AU - Tanaka, Hideaki
AU - Kawamoto, Akihiro
AU - El-Mohsnawy, Eithar
AU - Kato, Takayuki
AU - Namba, Keiichi
AU - Gerle, Christoph
AU - Nowaczyk, Marc M.
AU - Kurisu, Genji
ID - 10310
IS - 1
JF - Communications Biology
KW - general agricultural and biological Sciences
KW - general biochemistry
KW - genetics and molecular biology
KW - medicine (miscellaneous)
SN - 2399-3642
TI - Cryo-EM structure of a functional monomeric Photosystem I from Thermosynechococcus elongatus reveals red chlorophyll cluster
VL - 4
ER -
TY - JOUR
AB - Flowering plants utilize small RNA molecules to guide DNA methyltransferases to genomic sequences. This RNA-directed DNA methylation (RdDM) pathway preferentially targets euchromatic transposable elements. However, RdDM is thought to be recruited by methylation of histone H3 at lysine 9 (H3K9me), a hallmark of heterochromatin. How RdDM is targeted to euchromatin despite an affinity for H3K9me is unclear. Here we show that loss of histone H1 enhances heterochromatic RdDM, preferentially at nucleosome linker DNA. Surprisingly, this does not require SHH1, the RdDM component that binds H3K9me. Furthermore, H3K9me is dispensable for RdDM, as is CG DNA methylation. Instead, we find that non-CG methylation is specifically associated with small RNA biogenesis, and without H1 small RNA production quantitatively expands to non-CG methylated loci. Our results demonstrate that H1 enforces the separation of euchromatic and heterochromatic DNA methylation pathways by excluding the small RNA-generating branch of RdDM from non-CG methylated heterochromatin.
AU - Choi, Jaemyung
AU - Lyons, David B
AU - Zilberman, Daniel
ID - 10533
JF - eLife
KW - genetics and molecular biology
SN - 2050-084X
TI - Histone H1 prevents non-CG methylation-mediated small RNA biogenesis in Arabidopsis heterochromatin
VL - 10
ER -
TY - JOUR
AB - Hematopoietic-specific protein 1 (Hem1) is an essential subunit of the WAVE regulatory complex (WRC) in immune cells. WRC is crucial for Arp2/3 complex activation and the protrusion of branched actin filament networks. Moreover, Hem1 loss of function in immune cells causes autoimmune diseases in humans. Here, we show that genetic removal of Hem1 in macrophages diminishes frequency and efficacy of phagocytosis as well as phagocytic cup formation in addition to defects in lamellipodial protrusion and migration. Moreover, Hem1-null macrophages displayed strong defects in cell adhesion despite unaltered podosome formation and concomitant extracellular matrix degradation. Specifically, dynamics of both adhesion and de-adhesion as well as concomitant phosphorylation of paxillin and focal adhesion kinase (FAK) were significantly compromised. Accordingly, disruption of WRC function in non-hematopoietic cells coincided with both defects in adhesion turnover and altered FAK and paxillin phosphorylation. Consistently, platelets exhibited reduced adhesion and diminished integrin αIIbβ3 activation upon WRC removal. Interestingly, adhesion phenotypes, but not lamellipodia formation, were partially rescued by small molecule activation of FAK. A full rescue of the phenotype, including lamellipodia formation, required not only the presence of WRCs but also their binding to and activation by Rac. Collectively, our results uncover that WRC impacts on integrin-dependent processes in a FAK-dependent manner, controlling formation and dismantling of adhesions, relevant for properly grabbing onto extracellular surfaces and particles during cell edge expansion, like in migration or phagocytosis.
AU - Stahnke, Stephanie
AU - Döring, Hermann
AU - Kusch, Charly
AU - de Gorter, David J.J.
AU - Dütting, Sebastian
AU - Guledani, Aleks
AU - Pleines, Irina
AU - Schnoor, Michael
AU - Sixt, Michael K
AU - Geffers, Robert
AU - Rohde, Manfred
AU - Müsken, Mathias
AU - Kage, Frieda
AU - Steffen, Anika
AU - Faix, Jan
AU - Nieswandt, Bernhard
AU - Rottner, Klemens
AU - Stradal, Theresia E.B.
ID - 10834
IS - 10
JF - Current Biology
KW - General Agricultural and Biological Sciences
KW - General Biochemistry
KW - Genetics and Molecular Biology
SN - 0960-9822
TI - Loss of Hem1 disrupts macrophage function and impacts migration, phagocytosis, and integrin-mediated adhesion
VL - 31
ER -
TY - JOUR
AB - A precise quantitative description of the ultrastructural characteristics underlying biological mechanisms is often key to their understanding. This is particularly true for dynamic extra- and intracellular filamentous assemblies, playing a role in cell motility, cell integrity, cytokinesis, tissue formation and maintenance. For example, genetic manipulation or modulation of actin regulatory proteins frequently manifests in changes of the morphology, dynamics, and ultrastructural architecture of actin filament-rich cell peripheral structures, such as lamellipodia or filopodia. However, the observed ultrastructural effects often remain subtle and require sufficiently large datasets for appropriate quantitative analysis. The acquisition of such large datasets has been enabled by recent advances in high-throughput cryo-electron tomography (cryo-ET) methods. This also necessitates the development of complementary approaches to maximize the extraction of relevant biological information. We have developed a computational toolbox for the semi-automatic quantification of segmented and vectorized filamentous networks from pre-processed cryo-electron tomograms, facilitating the analysis and cross-comparison of multiple experimental conditions. GUI-based components simplify the processing of data and allow users to obtain a large number of ultrastructural parameters describing filamentous assemblies. We demonstrate the feasibility of this workflow by analyzing cryo-ET data of untreated and chemically perturbed branched actin filament networks and that of parallel actin filament arrays. In principle, the computational toolbox presented here is applicable for data analysis comprising any type of filaments in regular (i.e. parallel) or random arrangement. We show that it can ease the identification of key differences between experimental groups and facilitate the in-depth analysis of ultrastructural data in a time-efficient manner.
AU - Dimchev, Georgi A
AU - Amiri, Behnam
AU - Fäßler, Florian
AU - Falcke, Martin
AU - Schur, Florian KM
ID - 10290
IS - 4
JF - Journal of Structural Biology
KW - Structural Biology
SN - 1047-8477
TI - Computational toolbox for ultrastructural quantitative analysis of filament networks in cryo-ET data
VL - 213
ER -
TY - JOUR
AB - Phenomenological relations such as Ohm’s or Fourier’s law have a venerable history in physics but are still scarce in biology. This situation restrains predictive theory. Here, we build on bacterial “growth laws,” which capture physiological feedback between translation and cell growth, to construct a minimal biophysical model for the combined action of ribosome-targeting antibiotics. Our model predicts drug interactions like antagonism or synergy solely from responses to individual drugs. We provide analytical results for limiting cases, which agree well with numerical results. We systematically refine the model by including direct physical interactions of different antibiotics on the ribosome. In a limiting case, our model provides a mechanistic underpinning for recent predictions of higher-order interactions that were derived using entropy maximization. We further refine the model to include the effects of antibiotics that mimic starvation and the presence of resistance genes. We describe the impact of a starvation-mimicking antibiotic on drug interactions analytically and verify it experimentally. Our extended model suggests a change in the type of drug interaction that depends on the strength of resistance, which challenges established rescaling paradigms. We experimentally show that the presence of unregulated resistance genes can lead to altered drug interaction, which agrees with the prediction of the model. While minimal, the model is readily adaptable and opens the door to predicting interactions of second and higher-order in a broad range of biological systems.
AU - Kavcic, Bor
AU - Tkačik, Gašper
AU - Bollenbach, Tobias
ID - 8997
JF - PLOS Computational Biology
KW - Modelling and Simulation
KW - Genetics
KW - Molecular Biology
KW - Antibiotics
KW - Drug interactions
SN - 1553-7358
TI - Minimal biophysical model of combined antibiotic action
VL - 17
ER -
TY - JOUR
AB - Gene expression levels are influenced by multiple coexisting molecular mechanisms. Some of these interactions such as those of transcription factors and promoters have been studied extensively. However, predicting phenotypes of gene regulatory networks (GRNs) remains a major challenge. Here, we use a well-defined synthetic GRN to study in Escherichia coli how network phenotypes depend on local genetic context, i.e. the genetic neighborhood of a transcription factor and its relative position. We show that one GRN with fixed topology can display not only quantitatively but also qualitatively different phenotypes, depending solely on the local genetic context of its components. Transcriptional read-through is the main molecular mechanism that places one transcriptional unit (TU) within two separate regulons without the need for complex regulatory sequences. We propose that relative order of individual TUs, with its potential for combinatorial complexity, plays an important role in shaping phenotypes of GRNs.
AU - Nagy-Staron, Anna A
AU - Tomasek, Kathrin
AU - Caruso Carter, Caroline
AU - Sonnleitner, Elisabeth
AU - Kavcic, Bor
AU - Paixão, Tiago
AU - Guet, Calin C
ID - 9283
JF - eLife
KW - Genetics and Molecular Biology
SN - 2050-084X
TI - Local genetic context shapes the function of a gene regulatory network
VL - 10
ER -
TY - JOUR
AB - Eukaryotic DNA-binding proteins operate in the context of chromatin, where nucleosomes are the elementary building blocks. Nucleosomal DNA is wrapped around a histone core, thereby rendering a large fraction of the DNA surface inaccessible to DNA-binding proteins. Nevertheless, first responders in DNA repair and sequence-specific transcription factors bind DNA target sites obstructed by chromatin. While early studies examined protein binding to histone-free DNA, it is only now beginning to emerge how DNA sequences are interrogated on nucleosomes. These readout strategies range from the release of nucleosomal DNA from histones, to rotational/translation register shifts of the DNA motif, and nucleosome-specific DNA binding modes that differ from those observed on naked DNA. Since DNA motif engagement on nucleosomes strongly depends on position and orientation, we argue that motif location and nucleosome positioning co-determine protein access to DNA in transcription and DNA repair.
AU - Michael, Alicia
AU - Thomä, Nicolas H.
ID - 15151
IS - 14
JF - Cell
KW - General Biochemistry
KW - Genetics and Molecular Biology
SN - 0092-8674
TI - Reading the chromatinized genome
VL - 184
ER -
TY - JOUR
AB - De novo loss of function mutations in the ubiquitin ligase-encoding gene Cullin3 lead to autism spectrum disorder (ASD). In mouse, constitutive haploinsufficiency leads to motor coordination deficits as well as ASD-relevant social and cognitive impairments. However, induction of Cul3 haploinsufficiency later in life does not lead to ASD-relevant behaviors, pointing to an important role of Cul3 during a critical developmental window. Here we show that Cul3 is essential to regulate neuronal migration and, therefore, constitutive Cul3 heterozygous mutant mice display cortical lamination abnormalities. At the molecular level, we found that Cul3 controls neuronal migration by tightly regulating the amount of Plastin3 (Pls3), a previously unrecognized player of neural migration. Furthermore, we found that Pls3 cell-autonomously regulates cell migration by regulating actin cytoskeleton organization, and its levels are inversely proportional to neural migration speed. Finally, we provide evidence that cellular phenotypes associated with autism-linked gene haploinsufficiency can be rescued by transcriptional activation of the intact allele in vitro, offering a proof of concept for a potential therapeutic approach for ASDs.
AU - Morandell, Jasmin
AU - Schwarz, Lena A
AU - Basilico, Bernadette
AU - Tasciyan, Saren
AU - Dimchev, Georgi A
AU - Nicolas, Armel
AU - Sommer, Christoph M
AU - Kreuzinger, Caroline
AU - Dotter, Christoph
AU - Knaus, Lisa
AU - Dobler, Zoe
AU - Cacci, Emanuele
AU - Schur, Florian KM
AU - Danzl, Johann G
AU - Novarino, Gaia
ID - 9429
IS - 1
JF - Nature Communications
KW - General Biochemistry
KW - Genetics and Molecular Biology
TI - Cul3 regulates cytoskeleton protein homeostasis and cell migration during a critical window of brain development
VL - 12
ER -
TY - JOUR
AB - The endosomal sorting complex required for transport-III (ESCRT-III) catalyzes membrane fission from within membrane necks, a process that is essential for many cellular functions, from cell division to lysosome degradation and autophagy. How it breaks membranes, though, remains unknown. Here, we characterize a sequential polymerization of ESCRT-III subunits that, driven by a recruitment cascade and by continuous subunit-turnover powered by the ATPase Vps4, induces membrane deformation and fission. During this process, the exchange of Vps24 for Did2 induces a tilt in the polymer-membrane interface, which triggers transition from flat spiral polymers to helical filament to drive the formation of membrane protrusions, and ends with the formation of a highly constricted Did2-Ist1 co-polymer that we show is competent to promote fission when bound on the inside of membrane necks. Overall, our results suggest a mechanism of stepwise changes in ESCRT-III filament structure and mechanical properties via exchange of the filament subunits to catalyze ESCRT-III activity.
AU - Pfitzner, Anna-Katharina
AU - Mercier, Vincent
AU - Jiang, Xiuyun
AU - Moser von Filseck, Joachim
AU - Baum, Buzz
AU - Šarić, Anđela
AU - Roux, Aurélien
ID - 10348
IS - 5
JF - Cell
KW - general biochemistry
KW - genetics and molecular biology
SN - 0092-8674
TI - An ESCRT-III polymerization sequence drives membrane deformation and fission
VL - 182
ER -
TY - JOUR
AB - Aging of the circulatory system correlates with the pathogenesis of a large spectrum of diseases. However, it is largely unknown which factors drive the age-dependent or pathological decline of the vasculature and how vascular defects relate to tissue aging. The goal of the study is to design a multianalytical approach to identify how the cellular microenvironment (i.e., fibroblasts) and serum from healthy donors of different ages or Alzheimer disease (AD) patients can modulate the functionality of organ-specific vascular endothelial cells (VECs). Long-living human microvascular networks embedding VECs and fibroblasts from skin biopsies are generated. RNA-seq, secretome analyses, and microfluidic assays demonstrate that fibroblasts from young donors restore the functionality of aged endothelial cells, an effect also achieved by serum from young donors. New biomarkers of vascular aging are validated in human biopsies and it is shown that young serum induces angiopoietin-like-4, which can restore compromised vascular barriers. This strategy is then employed to characterize transcriptional/functional changes induced on the blood–brain barrier by AD serum, demonstrating the importance of PTP4A3 in the regulation of permeability. Features of vascular degeneration during aging and AD are recapitulated, and a tool to identify novel biomarkers that can be exploited to develop future therapeutics modulating vascular function is established.
AU - Bersini, Simone
AU - Arrojo e Drigo, Rafael
AU - Huang, Ling
AU - Shokhirev, Maxim N.
AU - HETZER, Martin W
ID - 11056
IS - 5
JF - Advanced Biosystems
KW - General Biochemistry
KW - Genetics and Molecular Biology
KW - Biomedical Engineering
KW - Biomaterials
SN - 2366-7478
TI - Transcriptional and functional changes of the human microvasculature during physiological aging and Alzheimer disease
VL - 4
ER -
TY - JOUR
AB - Vascular dysfunctions are a common feature of multiple age-related diseases. However, modeling healthy and pathological aging of the human vasculature represents an unresolved experimental challenge. Here, we generated induced vascular endothelial cells (iVECs) and smooth muscle cells (iSMCs) by direct reprogramming of healthy human fibroblasts from donors of different ages and Hutchinson-Gilford Progeria Syndrome (HGPS) patients. iVECs induced from old donors revealed upregulation of GSTM1 and PALD1, genes linked to oxidative stress, inflammation and endothelial junction stability, as vascular aging markers. A functional assay performed on PALD1 KD VECs demonstrated a recovery in vascular permeability. We found that iSMCs from HGPS donors overexpressed bone morphogenetic protein (BMP)−4, which plays a key role in both vascular calcification and endothelial barrier damage observed in HGPS. Strikingly, BMP4 concentrations are higher in serum from HGPS vs. age-matched mice. Furthermore, targeting BMP4 with blocking antibody recovered the functionality of the vascular barrier in vitro, hence representing a potential future therapeutic strategy to limit cardiovascular dysfunction in HGPS. These results show that iVECs and iSMCs retain disease-related signatures, allowing modeling of vascular aging and HGPS in vitro.
AU - Bersini, Simone
AU - Schulte, Roberta
AU - Huang, Ling
AU - Tsai, Hannah
AU - HETZER, Martin W
ID - 11055
JF - eLife
KW - General Immunology and Microbiology
KW - General Biochemistry
KW - Genetics and Molecular Biology
KW - General Medicine
KW - General Neuroscience
SN - 2050-084X
TI - Direct reprogramming of human smooth muscle and vascular endothelial cells reveals defects associated with aging and Hutchinson-Gilford progeria syndrome
VL - 9
ER -
TY - JOUR
AB - During mitosis, transcription of genomic DNA is dramatically reduced, before it is reactivated during nuclear reformation in anaphase/telophase. Many aspects of the underlying principles that mediate transcriptional memory and reactivation in the daughter cells remain unclear. Here, we used ChIP-seq on synchronized cells at different stages after mitosis to generate genome-wide maps of histone modifications. Combined with EU-RNA-seq and Hi-C analyses, we found that during prometaphase, promoters, enhancers, and insulators retain H3K4me3 and H3K4me1, while losing H3K27ac. Enhancers globally retaining mitotic H3K4me1 or locally retaining mitotic H3K27ac are associated with cell type-specific genes and their transcription factors for rapid transcriptional activation. As cells exit mitosis, promoters regain H3K27ac, which correlates with transcriptional reactivation. Insulators also gain H3K27ac and CCCTC-binding factor (CTCF) in anaphase/telophase. This increase of H3K27ac in anaphase/telophase is required for posttranscriptional activation and may play a role in the establishment of topologically associating domains (TADs). Together, our results suggest that the genome is reorganized in a sequential order, in which histone methylations occur first in prometaphase, histone acetylation, and CTCF in anaphase/telophase, transcription in cytokinesis, and long-range chromatin interactions in early G1. We thus provide insights into the histone modification landscape that allows faithful reestablishment of the transcriptional program and TADs during cell division.
AU - Kang, Hyeseon
AU - Shokhirev, Maxim N.
AU - Xu, Zhichao
AU - Chandran, Sahaana
AU - Dixon, Jesse R.
AU - HETZER, Martin W
ID - 11057
IS - 13-14
JF - Genes & Development
KW - Developmental Biology
KW - Genetics
SN - 0890-9369
TI - Dynamic regulation of histone modifications and long-range chromosomal interactions during postmitotic transcriptional reactivation
VL - 34
ER -
TY - JOUR
AB - Nucleoporin 93 (Nup93) expression inversely correlates with the survival of triple-negative breast cancer patients. However, our knowledge of Nup93 function in breast cancer besides its role as structural component of the nuclear pore complex is not understood. Combination of functional assays and genetic analyses suggested that chromatin interaction of Nup93 partially modulates the expression of genes associated with actin cytoskeleton remodeling and epithelial to mesenchymal transition, resulting in impaired invasion of triple-negative, claudin-low breast cancer cells. Nup93 depletion induced stress fiber formation associated with reduced cell migration/proliferation and impaired expression of mesenchymal-like genes. Silencing LIMCH1, a gene responsible for actin cytoskeleton remodeling and up-regulated upon Nup93 depletion, partially restored the invasive phenotype of cancer cells. Loss of Nup93 led to significant defects in tumor establishment/propagation in vivo, whereas patient samples revealed that high Nup93 and low LIMCH1 expression correlate with late tumor stage. Our approach identified Nup93 as contributor of triple-negative, claudin-low breast cancer cell invasion and paves the way to study the role of nuclear envelope proteins during breast cancer tumorigenesis.
AU - Bersini, Simone
AU - Lytle, Nikki K
AU - Schulte, Roberta
AU - Huang, Ling
AU - Wahl, Geoffrey M
AU - HETZER, Martin W
ID - 11058
IS - 1
JF - Life Science Alliance
KW - Health
KW - Toxicology and Mutagenesis
KW - Plant Science
KW - Biochemistry
KW - Genetics and Molecular Biology (miscellaneous)
KW - Ecology
SN - 2575-1077
TI - Nup93 regulates breast tumor growth by modulating cell proliferation and actin cytoskeleton remodeling
VL - 3
ER -
TY - JOUR
AB - Background: The mitochondrial pyruvate carrier (MPC) plays a central role in energy metabolism by transporting pyruvate across the inner mitochondrial membrane. Its heterodimeric composition and homology to SWEET and semiSWEET transporters set the MPC apart from the canonical mitochondrial carrier family (named MCF or SLC25). The import of the canonical carriers is mediated by the carrier translocase of the inner membrane (TIM22) pathway and is dependent on their structure, which features an even number of transmembrane segments and both termini in the intermembrane space. The import pathway of MPC proteins has not been elucidated. The odd number of transmembrane segments and positioning of the N-terminus in the matrix argues against an import via the TIM22 carrier pathway but favors an import via the flexible presequence pathway.
Results: Here, we systematically analyzed the import pathways of Mpc2 and Mpc3 and report that, contrary to an expected import via the flexible presequence pathway, yeast MPC proteins with an odd number of transmembrane segments and matrix-exposed N-terminus are imported by the carrier pathway, using the receptor Tom70, small TIM chaperones, and the TIM22 complex. The TIM9·10 complex chaperones MPC proteins through the mitochondrial intermembrane space using conserved hydrophobic motifs that are also required for the interaction with canonical carrier proteins.
Conclusions: The carrier pathway can import paired and non-paired transmembrane helices and translocate N-termini to either side of the mitochondrial inner membrane, revealing an unexpected versatility of the mitochondrial import pathway for non-cleavable inner membrane proteins.
AU - Rampelt, Heike
AU - Sucec, Iva
AU - Bersch, Beate
AU - Horten, Patrick
AU - Perschil, Inge
AU - Martinou, Jean-Claude
AU - van der Laan, Martin
AU - Wiedemann, Nils
AU - Schanda, Paul
AU - Pfanner, Nikolaus
ID - 8402
JF - BMC Biology
KW - Biotechnology
KW - Plant Science
KW - General Biochemistry
KW - Genetics and Molecular Biology
KW - Developmental Biology
KW - Cell Biology
KW - Physiology
KW - Ecology
KW - Evolution
KW - Behavior and Systematics
KW - Structural Biology
KW - General Agricultural and Biological Sciences
SN - 1741-7007
TI - The mitochondrial carrier pathway transports non-canonical substrates with an odd number of transmembrane segments
VL - 18
ER -
TY - JOUR
AB - Meiotic crossovers (COs) are important for reshuffling genetic information between homologous chromosomes and they are essential for their correct segregation. COs are unevenly distributed along chromosomes and the underlying mechanisms controlling CO localization are not well understood. We previously showed that meiotic COs are mis-localized in the absence of AXR1, an enzyme involved in the neddylation/rubylation protein modification pathway in Arabidopsis thaliana. Here, we report that in axr1-/-, male meiocytes show a strong defect in chromosome pairing whereas the formation of the telomere bouquet is not affected. COs are also redistributed towards subtelomeric chromosomal ends where they frequently form clusters, in contrast to large central regions depleted in recombination. The CO suppressed regions correlate with DNA hypermethylation of transposable elements (TEs) in the CHH context in axr1-/- meiocytes. Through examining somatic methylomes, we found axr1-/- affects DNA methylation in a plant, causing hypermethylation in all sequence contexts (CG, CHG and CHH) in TEs. Impairment of the main pathways involved in DNA methylation is epistatic over axr1-/- for DNA methylation in somatic cells but does not restore regular chromosome segregation during meiosis. Collectively, our findings reveal that the neddylation pathway not only regulates hormonal perception and CO distribution but is also, directly or indirectly, a major limiting pathway of TE DNA methylation in somatic cells.
AU - Christophorou, Nicolas
AU - She, Wenjing
AU - Long, Jincheng
AU - Hurel, Aurélie
AU - Beaubiat, Sébastien
AU - Idir, Yassir
AU - Tagliaro-Jahns, Marina
AU - Chambon, Aurélie
AU - Solier, Victor
AU - Vezon, Daniel
AU - Grelon, Mathilde
AU - Feng, Xiaoqi
AU - Bouché, Nicolas
AU - Mézard, Christine
ID - 12189
IS - 6
JF - PLOS Genetics
KW - Cancer Research
KW - Genetics (clinical)
KW - Genetics
KW - Molecular Biology
KW - Ecology
KW - Evolution
KW - Behavior and Systematics
SN - 1553-7404
TI - AXR1 affects DNA methylation independently of its role in regulating meiotic crossover localization
VL - 16
ER -
TY - JOUR
AB - Practical quantum networks require low-loss and noise-resilient optical interconnects as well as non-Gaussian resources for entanglement distillation and distributed quantum computation. The latter could be provided by superconducting circuits but existing solutions to interface the microwave and optical domains lack either scalability or efficiency, and in most cases the conversion noise is not known. In this work we utilize the unique opportunities of silicon photonics, cavity optomechanics and superconducting circuits to demonstrate a fully integrated, coherent transducer interfacing the microwave X and the telecom S bands with a total (internal) bidirectional transduction efficiency of 1.2% (135%) at millikelvin temperatures. The coupling relies solely on the radiation pressure interaction mediated by the femtometer-scale motion of two silicon nanobeams reaching a Vπ as low as 16 μV for sub-nanowatt pump powers. Without the associated optomechanical gain, we achieve a total (internal) pure conversion efficiency of up to 0.019% (1.6%), relevant for future noise-free operation on this qubit-compatible platform.
AU - Arnold, Georg M
AU - Wulf, Matthias
AU - Barzanjeh, Shabir
AU - Redchenko, Elena
AU - Rueda Sanchez, Alfredo R
AU - Hease, William J
AU - Hassani, Farid
AU - Fink, Johannes M
ID - 8529
JF - Nature Communications
KW - General Biochemistry
KW - Genetics and Molecular Biology
KW - General Physics and Astronomy
KW - General Chemistry
SN - 2041-1723
TI - Converting microwave and telecom photons with a silicon photonic nanomechanical interface
VL - 11
ER -
TY - JOUR
AB - Glioblastoma is the most malignant cancer in the brain and currently incurable. It is urgent to identify effective targets for this lethal disease. Inhibition of such targets should suppress the growth of cancer cells and, ideally also precancerous cells for early prevention, but minimally affect their normal counterparts. Using genetic mouse models with neural stem cells (NSCs) or oligodendrocyte precursor cells (OPCs) as the cells‐of‐origin/mutation, it is shown that the susceptibility of cells within the development hierarchy of glioma to the knockout of insulin‐like growth factor I receptor (IGF1R) is determined not only by their oncogenic states, but also by their cell identities/states. Knockout of IGF1R selectively disrupts the growth of mutant and transformed, but not normal OPCs, or NSCs. The desirable outcome of IGF1R knockout on cell growth requires the mutant cells to commit to the OPC identity regardless of its development hierarchical status. At the molecular level, oncogenic mutations reprogram the cellular network of OPCs and force them to depend more on IGF1R for their growth. A new‐generation brain‐penetrable, orally available IGF1R inhibitor harnessing tumor OPCs in the brain is also developed. The findings reveal the cellular window of IGF1R targeting and establish IGF1R as an effective target for the prevention and treatment of glioblastoma.
AU - Tian, Anhao
AU - Kang, Bo
AU - Li, Baizhou
AU - Qiu, Biying
AU - Jiang, Wenhong
AU - Shao, Fangjie
AU - Gao, Qingqing
AU - Liu, Rui
AU - Cai, Chengwei
AU - Jing, Rui
AU - Wang, Wei
AU - Chen, Pengxiang
AU - Liang, Qinghui
AU - Bao, Lili
AU - Man, Jianghong
AU - Wang, Yan
AU - Shi, Yu
AU - Li, Jin
AU - Yang, Minmin
AU - Wang, Lisha
AU - Zhang, Jianmin
AU - Hippenmeyer, Simon
AU - Zhu, Junming
AU - Bian, Xiuwu
AU - Wang, Ying‐Jie
AU - Liu, Chong
ID - 8592
IS - 21
JF - Advanced Science
KW - General Engineering
KW - General Physics and Astronomy
KW - General Materials Science
KW - Medicine (miscellaneous)
KW - General Chemical Engineering
KW - Biochemistry
KW - Genetics and Molecular Biology (miscellaneous)
SN - 2198-3844
TI - Oncogenic state and cell identity combinatorially dictate the susceptibility of cells within glioma development hierarchy to IGF1R targeting
VL - 7
ER -
TY - JOUR
AB - Aqueous iodine based electrochemical energy storage is considered a potential candidate to improve sustainability and performance of current battery and supercapacitor technology. It harnesses the redox activity of iodide, iodine, and polyiodide species in the confined geometry of nanoporous carbon electrodes. However, current descriptions of the electrochemical reaction mechanism to interconvert these species are elusive. Here we show that electrochemical oxidation of iodide in nanoporous carbons forms persistent solid iodine deposits. Confinement slows down dissolution into triiodide and pentaiodide, responsible for otherwise significant self-discharge via shuttling. The main tools for these insights are in situ Raman spectroscopy and in situ small and wide-angle X-ray scattering (in situ SAXS/WAXS). In situ Raman confirms the reversible formation of triiodide and pentaiodide. In situ SAXS/WAXS indicates remarkable amounts of solid iodine deposited in the carbon nanopores. Combined with stochastic modeling, in situ SAXS allows quantifying the solid iodine volume fraction and visualizing the iodine structure on 3D lattice models at the sub-nanometer scale. Based on the derived mechanism, we demonstrate strategies for improved iodine pore filling capacity and prevention of self-discharge, applicable to hybrid supercapacitors and batteries.
AU - Prehal, Christian
AU - Fitzek, Harald
AU - Kothleitner, Gerald
AU - Presser, Volker
AU - Gollas, Bernhard
AU - Freunberger, Stefan Alexander
AU - Abbas, Qamar
ID - 8568
JF - Nature Communications
KW - General Biochemistry
KW - Genetics and Molecular Biology
KW - General Physics and Astronomy
KW - General Chemistry
SN - 2041-1723
TI - Persistent and reversible solid iodine electrodeposition in nanoporous carbons
VL - 11
ER -
TY - JOUR
AB - Understanding the conformational sampling of translation-arrested ribosome nascent chain complexes is key to understand co-translational folding. Up to now, coupling of cysteine oxidation, disulfide bond formation and structure formation in nascent chains has remained elusive. Here, we investigate the eye-lens protein γB-crystallin in the ribosomal exit tunnel. Using mass spectrometry, theoretical simulations, dynamic nuclear polarization-enhanced solid-state nuclear magnetic resonance and cryo-electron microscopy, we show that thiol groups of cysteine residues undergo S-glutathionylation and S-nitrosylation and form non-native disulfide bonds. Thus, covalent modification chemistry occurs already prior to nascent chain release as the ribosome exit tunnel provides sufficient space even for disulfide bond formation which can guide protein folding.
AU - Schulte, Linda
AU - Mao, Jiafei
AU - Reitz, Julian
AU - Sreeramulu, Sridhar
AU - Kudlinzki, Denis
AU - Hodirnau, Victor-Valentin
AU - Meier-Credo, Jakob
AU - Saxena, Krishna
AU - Buhr, Florian
AU - Langer, Julian D.
AU - Blackledge, Martin
AU - Frangakis, Achilleas S.
AU - Glaubitz, Clemens
AU - Schwalbe, Harald
ID - 8744
JF - Nature Communications
KW - General Biochemistry
KW - Genetics and Molecular Biology
KW - General Physics and Astronomy
KW - General Chemistry
SN - 2041-1723
TI - Cysteine oxidation and disulfide formation in the ribosomal exit tunnel
VL - 11
ER -
TY - JOUR
AB - Resources are rarely distributed uniformly within a population. Heterogeneity in the concentration of a drug, the quality of breeding sites, or wealth can all affect evolutionary dynamics. In this study, we represent a collection of properties affecting the fitness at a given location using a color. A green node is rich in resources while a red node is poorer. More colors can represent a broader spectrum of resource qualities. For a population evolving according to the birth-death Moran model, the first question we address is which structures, identified by graph connectivity and graph coloring, are evolutionarily equivalent. We prove that all properly two-colored, undirected, regular graphs are evolutionarily equivalent (where “properly colored” means that no two neighbors have the same color). We then compare the effects of background heterogeneity on properly two-colored graphs to those with alternative schemes in which the colors are permuted. Finally, we discuss dynamic coloring as a model for spatiotemporal resource fluctuations, and we illustrate that random dynamic colorings often diminish the effects of background heterogeneity relative to a proper two-coloring.
AU - Kaveh, Kamran
AU - McAvoy, Alex
AU - Chatterjee, Krishnendu
AU - Nowak, Martin A.
ID - 8767
IS - 11
JF - PLOS Computational Biology
KW - Ecology
KW - Modelling and Simulation
KW - Computational Theory and Mathematics
KW - Genetics
KW - Ecology
KW - Evolution
KW - Behavior and Systematics
KW - Molecular Biology
KW - Cellular and Molecular Neuroscience
SN - 1553-734X
TI - The Moran process on 2-chromatic graphs
VL - 16
ER -
TY - JOUR
AB - The actin-related protein (Arp)2/3 complex nucleates branched actin filament networks pivotal for cell migration, endocytosis and pathogen infection. Its activation is tightly regulated and involves complex structural rearrangements and actin filament binding, which are yet to be understood. Here, we report a 9.0 Å resolution structure of the actin filament Arp2/3 complex branch junction in cells using cryo-electron tomography and subtomogram averaging. This allows us to generate an accurate model of the active Arp2/3 complex in the branch junction and its interaction with actin filaments. Notably, our model reveals a previously undescribed set of interactions of the Arp2/3 complex with the mother filament, significantly different to the previous branch junction model. Our structure also indicates a central role for the ArpC3 subunit in stabilizing the active conformation.
AU - Fäßler, Florian
AU - Dimchev, Georgi A
AU - Hodirnau, Victor-Valentin
AU - Wan, William
AU - Schur, Florian KM
ID - 8971
JF - Nature Communications
KW - General Biochemistry
KW - Genetics and Molecular Biology
KW - General Physics and Astronomy
KW - General Chemistry
SN - 2041-1723
TI - Cryo-electron tomography structure of Arp2/3 complex in cells reveals new insights into the branch junction
VL - 11
ER -
TY - JOUR
AB - Motivation: Recent technological advances have led to an increase in the production and availability of single-cell data. The ability to integrate a set of multi-technology measurements would allow the identification of biologically or clinically meaningful observations through the unification of the perspectives afforded by each technology. In most cases, however, profiling technologies consume the used cells and thus pairwise correspondences between datasets are lost. Due to the sheer size single-cell datasets can acquire, scalable algorithms that are able to universally match single-cell measurements carried out in one cell to its corresponding sibling in another technology are needed.
Results: We propose Single-Cell data Integration via Matching (SCIM), a scalable approach to recover such correspondences in two or more technologies. SCIM assumes that cells share a common (low-dimensional) underlying structure and that the underlying cell distribution is approximately constant across technologies. It constructs a technology-invariant latent space using an autoencoder framework with an adversarial objective. Multi-modal datasets are integrated by pairing cells across technologies using a bipartite matching scheme that operates on the low-dimensional latent representations. We evaluate SCIM on a simulated cellular branching process and show that the cell-to-cell matches derived by SCIM reflect the same pseudotime on the simulated dataset. Moreover, we apply our method to two real-world scenarios, a melanoma tumor sample and a human bone marrow sample, where we pair cells from a scRNA dataset to their sibling cells in a CyTOF dataset achieving 90% and 78% cell-matching accuracy for each one of the samples, respectively.
AU - Stark, Stefan G
AU - Ficek, Joanna
AU - Locatello, Francesco
AU - Bonilla, Ximena
AU - Chevrier, Stéphane
AU - Singer, Franziska
AU - Aebersold, Rudolf
AU - Al-Quaddoomi, Faisal S
AU - Albinus, Jonas
AU - Alborelli, Ilaria
AU - Andani, Sonali
AU - Attinger, Per-Olof
AU - Bacac, Marina
AU - Baumhoer, Daniel
AU - Beck-Schimmer, Beatrice
AU - Beerenwinkel, Niko
AU - Beisel, Christian
AU - Bernasconi, Lara
AU - Bertolini, Anne
AU - Bodenmiller, Bernd
AU - Bonilla, Ximena
AU - Casanova, Ruben
AU - Chevrier, Stéphane
AU - Chicherova, Natalia
AU - D'Costa, Maya
AU - Danenberg, Esther
AU - Davidson, Natalie
AU - gan, Monica-Andreea Dră
AU - Dummer, Reinhard
AU - Engler, Stefanie
AU - Erkens, Martin
AU - Eschbach, Katja
AU - Esposito, Cinzia
AU - Fedier, André
AU - Ferreira, Pedro
AU - Ficek, Joanna
AU - Frei, Anja L
AU - Frey, Bruno
AU - Goetze, Sandra
AU - Grob, Linda
AU - Gut, Gabriele
AU - Günther, Detlef
AU - Haberecker, Martina
AU - Haeuptle, Pirmin
AU - Heinzelmann-Schwarz, Viola
AU - Herter, Sylvia
AU - Holtackers, Rene
AU - Huesser, Tamara
AU - Irmisch, Anja
AU - Jacob, Francis
AU - Jacobs, Andrea
AU - Jaeger, Tim M
AU - Jahn, Katharina
AU - James, Alva R
AU - Jermann, Philip M
AU - Kahles, André
AU - Kahraman, Abdullah
AU - Koelzer, Viktor H
AU - Kuebler, Werner
AU - Kuipers, Jack
AU - Kunze, Christian P
AU - Kurzeder, Christian
AU - Lehmann, Kjong-Van
AU - Levesque, Mitchell
AU - Lugert, Sebastian
AU - Maass, Gerd
AU - Manz, Markus
AU - Markolin, Philipp
AU - Mena, Julien
AU - Menzel, Ulrike
AU - Metzler, Julian M
AU - Miglino, Nicola
AU - Milani, Emanuela S
AU - Moch, Holger
AU - Muenst, Simone
AU - Murri, Riccardo
AU - Ng, Charlotte KY
AU - Nicolet, Stefan
AU - Nowak, Marta
AU - Pedrioli, Patrick GA
AU - Pelkmans, Lucas
AU - Piscuoglio, Salvatore
AU - Prummer, Michael
AU - Ritter, Mathilde
AU - Rommel, Christian
AU - Rosano-González, María L
AU - Rätsch, Gunnar
AU - Santacroce, Natascha
AU - Castillo, Jacobo Sarabia del
AU - Schlenker, Ramona
AU - Schwalie, Petra C
AU - Schwan, Severin
AU - Schär, Tobias
AU - Senti, Gabriela
AU - Singer, Franziska
AU - Sivapatham, Sujana
AU - Snijder, Berend
AU - Sobottka, Bettina
AU - Sreedharan, Vipin T
AU - Stark, Stefan
AU - Stekhoven, Daniel J
AU - Theocharides, Alexandre PA
AU - Thomas, Tinu M
AU - Tolnay, Markus
AU - Tosevski, Vinko
AU - Toussaint, Nora C
AU - Tuncel, Mustafa A
AU - Tusup, Marina
AU - Drogen, Audrey Van
AU - Vetter, Marcus
AU - Vlajnic, Tatjana
AU - Weber, Sandra
AU - Weber, Walter P
AU - Wegmann, Rebekka
AU - Weller, Michael
AU - Wendt, Fabian
AU - Wey, Norbert
AU - Wicki, Andreas
AU - Wollscheid, Bernd
AU - Yu, Shuqing
AU - Ziegler, Johanna
AU - Zimmermann, Marc
AU - Zoche, Martin
AU - Zuend, Gregor
AU - Rätsch, Gunnar
AU - Lehmann, Kjong-Van
ID - 14125
IS - Supplement_2
JF - Bioinformatics
KW - Computational Mathematics
KW - Computational Theory and Mathematics
KW - Computer Science Applications
KW - Molecular Biology
KW - Biochemistry
KW - Statistics and Probability
TI - SCIM: Universal single-cell matching with unpaired feature sets
VL - 36
ER -