@article{15179, abstract = {The fungal bioluminescence pathway can be reconstituted in other organisms allowing luminescence imaging without exogenously supplied substrate. The pathway starts from hispidin biosynthesis—a step catalyzed by a large fungal polyketide synthase that requires a posttranslational modification for activity. Here, we report identification of alternative compact hispidin synthases encoded by a phylogenetically diverse group of plants. A hybrid bioluminescence pathway that combines plant and fungal genes is more compact, not dependent on availability of machinery for posttranslational modifications, and confers autonomous bioluminescence in yeast, mammalian, and plant hosts. The compact size of plant hispidin synthases enables additional modes of delivery of autoluminescence, such as delivery with viral vectors.}, author = {Palkina, Kseniia A. and Karataeva, Tatiana A. and Perfilov, Maxim M. and Fakhranurova, Liliia I. and Markina, Nadezhda M. and Gonzalez Somermeyer, Louisa and Garcia-Perez, Elena and Vazquez-Vilar, Marta and Rodriguez-Rodriguez, Marta and Vazquez-Vilriales, Victor and Shakhova, Ekaterina S. and Mitiouchkina, Tatiana and Belozerova, Olga A. and Kovalchuk, Sergey I. and Alekberova, Anna and Malyshevskaia, Alena K. and Bugaeva, Evgenia N. and Guglya, Elena B. and Balakireva, Anastasia and Sytov, Nikita and Bezlikhotnova, Anastasia and Boldyreva, Daria I. and Babenko, Vladislav V. and Kondrashov, Fyodor and Choob, Vladimir V. and Orzaez, Diego and Yampolsky, Ilia V. and Mishin, Alexander S. and Sarkisyan, Karen S.}, issn = {2375-2548}, journal = {Science Advances}, number = {10}, publisher = {American Association for the Advancement of Science}, title = {{A hybrid pathway for self-sustained luminescence}}, doi = {10.1126/sciadv.adk1992}, volume = {10}, year = {2024}, } @article{12334, abstract = {Regulation of the Arp2/3 complex is required for productive nucleation of branched actin networks. An emerging aspect of regulation is the incorporation of subunit isoforms into the Arp2/3 complex. Specifically, both ArpC5 subunit isoforms, ArpC5 and ArpC5L, have been reported to fine-tune nucleation activity and branch junction stability. We have combined reverse genetics and cellular structural biology to describe how ArpC5 and ArpC5L differentially affect cell migration. Both define the structural stability of ArpC1 in branch junctions and, in turn, by determining protrusion characteristics, affect protein dynamics and actin network ultrastructure. ArpC5 isoforms also affect the positioning of members of the Ena/Vasodilator-stimulated phosphoprotein (VASP) family of actin filament elongators, which mediate ArpC5 isoform–specific effects on the actin assembly level. Our results suggest that ArpC5 and Ena/VASP proteins are part of a signaling pathway enhancing cell migration.}, author = {Fäßler, Florian and Javoor, Manjunath and Datler, Julia and Döring, Hermann and Hofer, Florian and Dimchev, Georgi A and Hodirnau, Victor-Valentin and Faix, Jan and Rottner, Klemens and Schur, Florian KM}, issn = {2375-2548}, journal = {Science Advances}, keywords = {Multidisciplinary}, number = {3}, publisher = {American Association for the Advancement of Science}, title = {{ArpC5 isoforms regulate Arp2/3 complex–dependent protrusion through differential Ena/VASP positioning}}, doi = {10.1126/sciadv.add6495}, volume = {9}, year = {2023}, } @article{14784, abstract = {The next steps of deep space exploration are manned missions to Moon and Mars. For safe space missions for crew members, it is important to understand the impact of space flight on the immune system. We studied the effects of 21 days dry immersion (DI) exposure on the transcriptomes of T cells isolated from blood samples of eight healthy volunteers. Samples were collected 7 days before DI, at day 7, 14, and 21 during DI, and 7 days after DI. RNA sequencing of CD3+T cells revealed transcriptional alterations across all time points, with most changes occurring 14 days after DI exposure. At day 21, T cells showed evidence of adaptation with a transcriptional profile resembling that of 7 days before DI. At 7 days after DI, T cells again changed their transcriptional profile. These data suggest that T cells adapt by rewiring their transcriptomes in response to simulated weightlessness and that remodeling cues persist when reexposed to normal gravity.}, author = {Gallardo-Dodd, Carlos J. and Oertlin, Christian and Record, Julien and Galvani, Rômulo G. and Sommerauer, Christian and Kuznetsov, Nikolai V. and Doukoumopoulos, Evangelos and Ali, Liaqat and Oliveira, Mariana M. S. and Seitz, Christina and Percipalle, Mathias and Nikić, Tijana and Sadova, Anastasia A. and Shulgina, Sofia M. and Shmarov, Vjacheslav A. and Kutko, Olga V. and Vlasova, Daria D. and Orlova, Kseniya D. and Rykova, Marina P. and Andersson, John and Percipalle, Piergiorgio and Kutter, Claudia and Ponomarev, Sergey A. and Westerberg, Lisa S.}, issn = {2375-2548}, journal = {Science Advances}, keywords = {Multidisciplinary}, number = {34}, publisher = {American Association for the Advancement of Science}, title = {{Exposure of volunteers to microgravity by dry immersion bed over 21 days results in gene expression changes and adaptation of T cells}}, doi = {10.1126/sciadv.adg1610}, volume = {9}, year = {2023}, } @article{11336, abstract = {The generation of a correctly-sized cerebral cortex with all-embracing neuronal and glial cell-type diversity critically depends on faithful radial glial progenitor (RGP) cell proliferation/differentiation programs. Temporal RGP lineage progression is regulated by Polycomb Repressive Complex 2 (PRC2) and loss of PRC2 activity results in severe neurogenesis defects and microcephaly. How PRC2-dependent gene expression instructs RGP lineage progression is unknown. Here we utilize Mosaic Analysis with Double Markers (MADM)-based single cell technology and demonstrate that PRC2 is not cell-autonomously required in neurogenic RGPs but rather acts at the global tissue-wide level. Conversely, cortical astrocyte production and maturation is cell-autonomously controlled by PRC2-dependent transcriptional regulation. We thus reveal highly distinct and sequential PRC2 functions in RGP lineage progression that are dependent on complex interplays between intrinsic and tissue-wide properties. In a broader context our results imply a critical role for the genetic and cellular niche environment in neural stem cell behavior.}, author = {Amberg, Nicole and Pauler, Florian and Streicher, Carmen and Hippenmeyer, Simon}, issn = {2375-2548}, journal = {Science Advances}, number = {44}, publisher = {American Association for the Advancement of Science}, title = {{Tissue-wide genetic and cellular landscape shapes the execution of sequential PRC2 functions in neural stem cell lineage progression}}, doi = {10.1126/sciadv.abq1263}, volume = {8}, year = {2022}, } @article{12253, abstract = {The sculpting of germ layers during gastrulation relies on the coordinated migration of progenitor cells, yet the cues controlling these long-range directed movements remain largely unknown. While directional migration often relies on a chemokine gradient generated from a localized source, we find that zebrafish ventrolateral mesoderm is guided by a self-generated gradient of the initially uniformly expressed and secreted protein Toddler/ELABELA/Apela. We show that the Apelin receptor, which is specifically expressed in mesodermal cells, has a dual role during gastrulation, acting as a scavenger receptor to generate a Toddler gradient, and as a chemokine receptor to sense this guidance cue. Thus, we uncover a single receptor–based self-generated gradient as the enigmatic guidance cue that can robustly steer the directional migration of mesoderm through the complex and continuously changing environment of the gastrulating embryo.}, author = {Stock, Jessica and Kazmar, Tomas and Schlumm, Friederike and Hannezo, Edouard B and Pauli, Andrea}, issn = {2375-2548}, journal = {Science Advances}, number = {37}, publisher = {American Association for the Advancement of Science}, title = {{A self-generated Toddler gradient guides mesodermal cell migration}}, doi = {10.1126/sciadv.add2488}, volume = {8}, year = {2022}, } @article{9262, abstract = {Sequence-specific oligomers with predictable folding patterns, i.e., foldamers, provide new opportunities to mimic α-helical peptides and design inhibitors of protein-protein interactions. One major hurdle of this strategy is to retain the correct orientation of key side chains involved in protein surface recognition. Here, we show that the structural plasticity of a foldamer backbone may notably contribute to the required spatial adjustment for optimal interaction with the protein surface. By using oligoureas as α helix mimics, we designed a foldamer/peptide hybrid inhibitor of histone chaperone ASF1, a key regulator of chromatin dynamics. The crystal structure of its complex with ASF1 reveals a notable plasticity of the urea backbone, which adapts to the ASF1 surface to maintain the same binding interface. One additional benefit of generating ASF1 ligands with nonpeptide oligourea segments is the resistance to proteolysis in human plasma, which was highly improved compared to the cognate α-helical peptide.}, author = {Mbianda, Johanne and Bakail, May M and André, Christophe and Moal, Gwenaëlle and Perrin, Marie E. and Pinna, Guillaume and Guerois, Raphaël and Becher, Francois and Legrand, Pierre and Traoré, Seydou and Douat, Céline and Guichard, Gilles and Ochsenbein, Françoise}, issn = {2375-2548}, journal = {Science Advances}, number = {12}, publisher = {American Association for the Advancement of Science}, title = {{Optimal anchoring of a foldamer inhibitor of ASF1 histone chaperone through backbone plasticity}}, doi = {10.1126/sciadv.abd9153}, volume = {7}, year = {2021}, } @article{10342, abstract = {The blood-brain barrier is made of polarized brain endothelial cells (BECs) phenotypically conditioned by the central nervous system (CNS). Although transport across BECs is of paramount importance for nutrient uptake as well as ridding the brain of waste products, the intracellular sorting mechanisms that regulate successful receptor-mediated transcytosis in BECs remain to be elucidated. Here, we used a synthetic multivalent system with tunable avidity to the low-density lipoprotein receptor–related protein 1 (LRP1) to investigate the mechanisms of transport across BECs. We used a combination of conventional and super-resolution microscopy, both in vivo and in vitro, accompanied with biophysical modeling of transport kinetics and membrane-bound interactions to elucidate the role of membrane-sculpting protein syndapin-2 on fast transport via tubule formation. We show that high-avidity cargo biases the LRP1 toward internalization associated with fast degradation, while mid-avidity augments the formation of syndapin-2 tubular carriers promoting a fast shuttling across.}, author = {Tian, Xiaohe and Leite, Diana M. and Scarpa, Edoardo and Nyberg, Sophie and Fullstone, Gavin and Forth, Joe and Matias, Diana and Apriceno, Azzurra and Poma, Alessandro and Duro-Castano, Aroa and Vuyyuru, Manish and Harker-Kirschneck, Lena and Šarić, Anđela and Zhang, Zhongping and Xiang, Pan and Fang, Bin and Tian, Yupeng and Luo, Lei and Rizzello, Loris and Battaglia, Giuseppe}, issn = {2375-2548}, journal = {Science Advances}, keywords = {multidisciplinary}, number = {48}, publisher = {American Association for the Advancement of Science}, title = {{On the shuttling across the blood-brain barrier via tubule formation: Mechanism and cargo avidity bias}}, doi = {10.1126/sciadv.abc4397}, volume = {6}, year = {2020}, } @article{8406, abstract = {Coordinated conformational transitions in oligomeric enzymatic complexes modulate function in response to substrates and play a crucial role in enzyme inhibition and activation. Caseinolytic protease (ClpP) is a tetradecameric complex, which has emerged as a drug target against multiple pathogenic bacteria. Activation of different ClpPs by inhibitors has been independently reported from drug development efforts, but no rationale for inhibitor-induced activation has been hitherto proposed. Using an integrated approach that includes x-ray crystallography, solid- and solution-state nuclear magnetic resonance, molecular dynamics simulations, and isothermal titration calorimetry, we show that the proteasome inhibitor bortezomib binds to the ClpP active-site serine, mimicking a peptide substrate, and induces a concerted allosteric activation of the complex. The bortezomib-activated conformation also exhibits a higher affinity for its cognate unfoldase ClpX. We propose a universal allosteric mechanism, where substrate binding to a single subunit locks ClpP into an active conformation optimized for chaperone association and protein processive degradation.}, author = {Felix, Jan and Weinhäupl, Katharina and Chipot, Christophe and Dehez, François and Hessel, Audrey and Gauto, Diego F. and Morlot, Cecile and Abian, Olga and Gutsche, Irina and Velazquez-Campoy, Adrian and Schanda, Paul and Fraga, Hugo}, issn = {2375-2548}, journal = {Science Advances}, number = {9}, publisher = {American Association for the Advancement of Science}, title = {{Mechanism of the allosteric activation of the ClpP protease machinery by substrates and active-site inhibitors}}, doi = {10.1126/sciadv.aaw3818}, volume = {5}, year = {2019}, } @article{7393, abstract = {The study of parallel ecological divergence provides important clues to the operation of natural selection. Parallel divergence often occurs in heterogeneous environments with different kinds of environmental gradients in different locations, but the genomic basis underlying this process is unknown. We investigated the genomics of rapid parallel adaptation in the marine snail Littorina saxatilis in response to two independent environmental axes (crab-predation versus wave-action and low-shore versus high-shore). Using pooled whole-genome resequencing, we show that sharing of genomic regions of high differentiation between environments is generally low but increases at smaller spatial scales. We identify different shared genomic regions of divergence for each environmental axis and show that most of these regions overlap with candidate chromosomal inversions. Several inversion regions are divergent and polymorphic across many localities. We argue that chromosomal inversions could store shared variation that fuels rapid parallel adaptation to heterogeneous environments, possibly as balanced polymorphism shared by adaptive gene flow.}, author = {Morales, Hernán E. and Faria, Rui and Johannesson, Kerstin and Larsson, Tomas and Panova, Marina and Westram, Anja M and Butlin, Roger K.}, issn = {2375-2548}, journal = {Science Advances}, number = {12}, publisher = {AAAS}, title = {{Genomic architecture of parallel ecological divergence: Beyond a single environmental contrast}}, doi = {10.1126/sciadv.aav9963}, volume = {5}, year = {2019}, } @article{8437, abstract = {Chaperonins are ubiquitous protein assemblies present in bacteria, eukaryota, and archaea, facilitating the folding of proteins, preventing protein aggregation, and thus participating in maintaining protein homeostasis in the cell. During their functional cycle, they bind unfolded client proteins inside their double ring structure and promote protein folding by closing the ring chamber in an adenosine 5′-triphosphate (ATP)–dependent manner. Although the static structures of fully open and closed forms of chaperonins were solved by x-ray crystallography or electron microscopy, elucidating the mechanisms of such ATP-driven molecular events requires studying the proteins at the structural level under working conditions. We introduce an approach that combines site-specific nuclear magnetic resonance observation of very large proteins, enabled by advanced isotope labeling methods, with an in situ ATP regeneration system. Using this method, we provide functional insight into the 1-MDa large hsp60 chaperonin while processing client proteins and reveal how nucleotide binding, hydrolysis, and release control switching between closed and open states. While the open conformation stabilizes the unfolded state of client proteins, the internalization of the client protein inside the chaperonin cavity speeds up its functional cycle. This approach opens new perspectives to study structures and mechanisms of various ATP-driven biological machineries in the heat of action.}, author = {Mas, Guillaume and Guan, Jia-Ying and Crublet, Elodie and Debled, Elisa Colas and Moriscot, Christine and Gans, Pierre and Schoehn, Guy and Macek, Pavel and Schanda, Paul and Boisbouvier, Jerome}, issn = {2375-2548}, journal = {Science Advances}, number = {9}, publisher = {American Association for the Advancement of Science}, title = {{Structural investigation of a chaperonin in action reveals how nucleotide binding regulates the functional cycle}}, doi = {10.1126/sciadv.aau4196}, volume = {4}, year = {2018}, } @article{9057, abstract = {Motility is a basic feature of living microorganisms, and how it works is often determined by environmental cues. Recent efforts have focused on developing artificial systems that can mimic microorganisms, in particular their self-propulsion. We report on the design and characterization of synthetic self-propelled particles that migrate upstream, known as positive rheotaxis. This phenomenon results from a purely physical mechanism involving the interplay between the polarity of the particles and their alignment by a viscous torque. We show quantitative agreement between experimental data and a simple model of an overdamped Brownian pendulum. The model notably predicts the existence of a stagnation point in a diverging flow. We take advantage of this property to demonstrate that our active particles can sense and predictably organize in an imposed flow. Our colloidal system represents an important step toward the realization of biomimetic microsystems with the ability to sense and respond to environmental changes.}, author = {Palacci, Jérémie A and Sacanna, Stefano and Abramian, Anaïs and Barral, Jérémie and Hanson, Kasey and Grosberg, Alexander Y. and Pine, David J. and Chaikin, Paul M.}, issn = {2375-2548}, journal = {Science Advances}, number = {4}, publisher = {American Association for the Advancement of Science }, title = {{Artificial rheotaxis}}, doi = {10.1126/sciadv.1400214}, volume = {1}, year = {2015}, }