---
_id: '826'
abstract:
- lang: eng
text: Plants exhibit a unique developmental flexibility to ever-changing environmental
conditions. To achieve their profound adaptability, plants are able to maintain
permanent stem cell populations and form new organs during the entire plant life
cycle. Signaling substances, called plant hormones, such as auxin, cytokinin,
abscisic acid, brassinosteroid, ethylene, gibberellin, jasmonic acid, and strigolactone,
govern and coordinate these developmental processes. Physiological and genetic
studies have dissected the molecular components of signal perception and transduction
of the individual hormonal pathways. However, over recent years it has become
evident that hormones do not act only in a linear pathway. Hormonal pathways are
interconnected by a complex network of interactions and feedback circuits that
determines the final outcome of the individual hormone actions. This raises questions
about the molecular mechanisms underlying hormonal cross talk and about how these
hormonal networks are established, maintained, and modulated throughout plant
development.
acknowledgement: We would like to thank Annick Bleys for help in preparing the manuscript.
This work was supported by the European Research Council with a Starting Independent
Research grant (ERC-2007-Stg-207362-HCPO) and the project CZ.1.07/2.3.00/20.0043
(to the Central European Institute of Technology, CEITEC) to E.B. M.V. is a postdoctoral
fellow of the Research Foundation Flanders. We apologize that, because of space
restrictions, the scientific contributions of only a limited number of original
articles could be cited and discussed.
author:
- first_name: Marleen
full_name: Vanstraelen, Marleen
last_name: Vanstraelen
- first_name: Eva
full_name: Eva Benková
id: 38F4F166-F248-11E8-B48F-1D18A9856A87
last_name: Benková
orcid: 0000-0002-8510-9739
citation:
ama: Vanstraelen M, Benková E. Hormonal interactions in the regulation of plant
development. Annual Review of Cell and Developmental Biology. 2012;28:463-487.
doi:10.1146/annurev-cellbio-101011-155741
apa: Vanstraelen, M., & Benková, E. (2012). Hormonal interactions in the regulation
of plant development. Annual Review of Cell and Developmental Biology.
Annual Reviews. https://doi.org/10.1146/annurev-cellbio-101011-155741
chicago: Vanstraelen, Marleen, and Eva Benková. “Hormonal Interactions in the Regulation
of Plant Development.” Annual Review of Cell and Developmental Biology.
Annual Reviews, 2012. https://doi.org/10.1146/annurev-cellbio-101011-155741.
ieee: M. Vanstraelen and E. Benková, “Hormonal interactions in the regulation of
plant development,” Annual Review of Cell and Developmental Biology, vol.
28. Annual Reviews, pp. 463–487, 2012.
ista: Vanstraelen M, Benková E. 2012. Hormonal interactions in the regulation of
plant development. Annual Review of Cell and Developmental Biology. 28, 463–487.
mla: Vanstraelen, Marleen, and Eva Benková. “Hormonal Interactions in the Regulation
of Plant Development.” Annual Review of Cell and Developmental Biology,
vol. 28, Annual Reviews, 2012, pp. 463–87, doi:10.1146/annurev-cellbio-101011-155741.
short: M. Vanstraelen, E. Benková, Annual Review of Cell and Developmental Biology
28 (2012) 463–487.
date_created: 2018-12-11T11:48:43Z
date_published: 2012-11-01T00:00:00Z
date_updated: 2021-01-12T08:17:46Z
day: '01'
doi: 10.1146/annurev-cellbio-101011-155741
extern: 1
intvolume: ' 28'
month: '11'
page: 463 - 487
publication: Annual Review of Cell and Developmental Biology
publication_status: published
publisher: Annual Reviews
publist_id: '6822'
quality_controlled: 0
status: public
title: Hormonal interactions in the regulation of plant development
type: journal_article
volume: 28
year: '2012'
...
---
_id: '829'
abstract:
- lang: eng
text: The architecture of a plant's root system, established postembryonically,
results from both coordinated root growth and lateral root branching. The plant
hormones auxin and cytokinin are central endogenous signaling molecules that regulate
lateral root organogenesis positively and negatively, respectively. Tight control
and mutual balance of their antagonistic activities are particularly important
during the early phases of lateral root organogenesis to ensure continuous lateral
root initiation (LRI) and proper development of lateral root primordia (LRP).
Here, we show that the early phases of lateral root organogenesis, including priming
and initiation, take place in root zones with a repressed cytokinin response.
Accordingly, ectopic overproduction of cytokinin in the root basal meristem most
efficiently inhibits LRI. Enhanced cytokinin responses in pericycle cells between
existing LRP might restrict LRI near existing LRP and, when compromised, ectopic
LRI occurs. Furthermore, our results demonstrate that young LRP are more sensitive
to perturbations in the cytokinin activity than are developmentally more advanced
primordia. We hypothesize that the effect of cytokinin on the development of primordia
possibly depends on the robustness and stability of the auxin gradient.
acknowledgement: We thank Jen Sheen, Dolf Weijers, Tatsuo Kakimoto, Stephen Depuydt,
and Laurent Laplaze for sharing published material, Jiri Friml for discussions,
and Martine De Cock and Annick Bleys for help in preparing the manuscript. This
work was supported by a Starting Independent Research grant from the European Research
Council (ERC-2007-Stg-207362-HCPO) and the project CZ.1.07/2.3.00/20.0043 to the
Central European Institute of Technology to E.B. and grants from the Ministry of
Education, Youth, and Sports of the Czech Republic (MSM 6198959216) and the Centre
of the Region Haná for Biotechnological and Agricultural Research (ED0007/01/01)
to P.T.
author:
- first_name: Agnieszka
full_name: Bielach, Agnieszka
last_name: Bielach
- first_name: Katerina
full_name: Podlesakova, Katerina
last_name: Podlesakova
- first_name: Peter
full_name: Peter Marhavy
id: 3F45B078-F248-11E8-B48F-1D18A9856A87
last_name: Marhavy
orcid: 0000-0001-5227-5741
- first_name: Jérôme
full_name: Duclercq, Jérôme
last_name: Duclercq
- first_name: Candela
full_name: Candela Cuesta
id: 33A3C818-F248-11E8-B48F-1D18A9856A87
last_name: Cuesta
orcid: 0000-0003-1923-2410
- first_name: Bruno
full_name: Muller, Bruno
last_name: Muller
- first_name: Wim
full_name: Grunewald, Wim
last_name: Grunewald
- first_name: Petr
full_name: Tarkowski, Petr
last_name: Tarkowski
- first_name: Eva
full_name: Eva Benková
id: 38F4F166-F248-11E8-B48F-1D18A9856A87
last_name: Benková
orcid: 0000-0002-8510-9739
citation:
ama: Bielach A, Podlesakova K, Marhavý P, et al. Spatiotemporal regulation of lateral
root organogenesis in Arabidopsis by cytokinin. The Plant Cell. 2012;24(10):3967-3981.
doi:10.1105/tpc.112.103044
apa: Bielach, A., Podlesakova, K., Marhavý, P., Duclercq, J., Cuesta, C., Muller,
B., … Benková, E. (2012). Spatiotemporal regulation of lateral root organogenesis
in Arabidopsis by cytokinin. The Plant Cell. American Society of Plant
Biologists. https://doi.org/10.1105/tpc.112.103044
chicago: Bielach, Agnieszka, Katerina Podlesakova, Peter Marhavý, Jérôme Duclercq,
Candela Cuesta, Bruno Muller, Wim Grunewald, Petr Tarkowski, and Eva Benková.
“Spatiotemporal Regulation of Lateral Root Organogenesis in Arabidopsis by Cytokinin.”
The Plant Cell. American Society of Plant Biologists, 2012. https://doi.org/10.1105/tpc.112.103044.
ieee: A. Bielach et al., “Spatiotemporal regulation of lateral root organogenesis
in Arabidopsis by cytokinin,” The Plant Cell, vol. 24, no. 10. American
Society of Plant Biologists, pp. 3967–3981, 2012.
ista: Bielach A, Podlesakova K, Marhavý P, Duclercq J, Cuesta C, Muller B, Grunewald
W, Tarkowski P, Benková E. 2012. Spatiotemporal regulation of lateral root organogenesis
in Arabidopsis by cytokinin. The Plant Cell. 24(10), 3967–3981.
mla: Bielach, Agnieszka, et al. “Spatiotemporal Regulation of Lateral Root Organogenesis
in Arabidopsis by Cytokinin.” The Plant Cell, vol. 24, no. 10, American
Society of Plant Biologists, 2012, pp. 3967–81, doi:10.1105/tpc.112.103044.
short: A. Bielach, K. Podlesakova, P. Marhavý, J. Duclercq, C. Cuesta, B. Muller,
W. Grunewald, P. Tarkowski, E. Benková, The Plant Cell 24 (2012) 3967–3981.
date_created: 2018-12-11T11:48:43Z
date_published: 2012-10-01T00:00:00Z
date_updated: 2021-01-12T08:17:55Z
day: '01'
doi: 10.1105/tpc.112.103044
extern: 1
intvolume: ' 24'
issue: '10'
month: '10'
page: 3967 - 3981
publication: The Plant Cell
publication_status: published
publisher: American Society of Plant Biologists
publist_id: '6819'
quality_controlled: 0
status: public
title: Spatiotemporal regulation of lateral root organogenesis in Arabidopsis by cytokinin
type: journal_article
volume: 24
year: '2012'
...
---
_id: '846'
abstract:
- lang: eng
text: Whether or not evolutionary change is inherently irreversible remains a controversial
topic. Some examples of evolutionary irreversibility are known; however, this
question has not been comprehensively addressed at the molecular level. Here,
we use data from 221 human genes with known pathogenic mutations to estimate the
rate of irreversibility in protein evolution. For these genes, we reconstruct
ancestral amino acid sequences along the mammalian phylogeny and identify ancestral
amino acid states that match known pathogenic mutations. Such cases represent
inherent evolutionary irreversibility because, at the present moment, reversals
to these ancestral amino acid states are impossible for the human lineage. We
estimate that approximately 10% of all amino acid substitutions along the mammalian
phylogeny are irreversible, such that a return to the ancestral amino acid state
would lead to a pathogenic phenotype. For a subset of 51 genes with high rates
of irreversibility, as much as 40% of all amino acid evolution was estimated to
be irreversible. Because pathogenic phenotypes do not resemble ancestral phenotypes,
the molecular nature of the high rate of irreversibility in proteins is best explained
by evolution with a high prevalence of compensatory, epistatic interactions between
amino acid sites. Under such mode of protein evolution, once an amino acid substitution
is fixed, the probability of its reversal declines as the protein sequence accumulates
changes that affect the phenotypic manifestation of the ancestral state. The prevalence
of epistasis in evolution indicates that the observed high rate of irreversibility
in protein evolution is an inherent property of protein structure and function.
acknowledgement: This work was supported by Plan Nacional grant BFU2009-09271 from
the Spanish Ministry of Science and Innovation and by FPU (Formación del Profesorado
Universitario) program grant AP2008-01888 from the Spanish Ministry of Education
to O.S. F.A.K. is a European Molecular Biology Organization Young Investigator and
Howard Hughes Medical Institute International Early Career Scientist.
author:
- first_name: Onuralp
full_name: Soylemez, Onuralp
last_name: Soylemez
- first_name: Fyodor
full_name: Fyodor Kondrashov
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
citation:
ama: Soylemez O, Kondrashov F. Estimating the rate of irreversibility in protein
evolution. Genome Biology and Evolution. 2012;4(12):1213-1222. doi:10.1093/gbe/evs096
apa: Soylemez, O., & Kondrashov, F. (2012). Estimating the rate of irreversibility
in protein evolution. Genome Biology and Evolution. Oxford University Press.
https://doi.org/10.1093/gbe/evs096
chicago: Soylemez, Onuralp, and Fyodor Kondrashov. “Estimating the Rate of Irreversibility
in Protein Evolution.” Genome Biology and Evolution. Oxford University
Press, 2012. https://doi.org/10.1093/gbe/evs096.
ieee: O. Soylemez and F. Kondrashov, “Estimating the rate of irreversibility in
protein evolution,” Genome Biology and Evolution, vol. 4, no. 12. Oxford
University Press, pp. 1213–1222, 2012.
ista: Soylemez O, Kondrashov F. 2012. Estimating the rate of irreversibility in
protein evolution. Genome Biology and Evolution. 4(12), 1213–1222.
mla: Soylemez, Onuralp, and Fyodor Kondrashov. “Estimating the Rate of Irreversibility
in Protein Evolution.” Genome Biology and Evolution, vol. 4, no. 12, Oxford
University Press, 2012, pp. 1213–22, doi:10.1093/gbe/evs096.
short: O. Soylemez, F. Kondrashov, Genome Biology and Evolution 4 (2012) 1213–1222.
date_created: 2018-12-11T11:48:49Z
date_published: 2012-01-01T00:00:00Z
date_updated: 2021-01-12T08:19:25Z
day: '01'
doi: 10.1093/gbe/evs096
extern: 1
intvolume: ' 4'
issue: '12'
license: https://creativecommons.org/licenses/by-nc/4.0/
month: '01'
page: 1213 - 1222
publication: Genome Biology and Evolution
publication_status: published
publisher: Oxford University Press
publist_id: '6802'
quality_controlled: 0
status: public
title: Estimating the rate of irreversibility in protein evolution
tmp:
image: /images/cc_by_nc.png
legal_code_url: https://creativecommons.org/licenses/by-nc/4.0/legalcode
name: Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)
short: CC BY-NC (4.0)
type: journal_article
volume: 4
year: '2012'
...
---
_id: '8463'
abstract:
- lang: eng
text: The 1H dipolar network, which is the major obstacle for applying proton detection
in the solid-state, can be reduced by deuteration, employing the RAP (Reduced
Adjoining Protonation) labeling scheme, which yields random protonation at non-exchangeable
sites. We present here a systematic study on the optimal degree of random sidechain
protonation in RAP samples as a function of the MAS (magic angle spinning) frequency.
In particular, we compare 1H sensitivity and linewidth of a microcrystalline protein,
the SH3 domain of chicken α-spectrin, for samples, prepared with 5–25 % H2O in
the E. coli growth medium, in the MAS frequency range of 20–60 kHz. At an external
field of 19.96 T (850 MHz), we find that using a proton concentration between
15 and 25 % in the M9 medium yields the best compromise in terms of sensitivity
and resolution, with an achievable average 1H linewidth on the order of 40–50
Hz. Comparing sensitivities at a MAS frequency of 60 versus 20 kHz, a gain in
sensitivity by a factor of 4–4.5 is observed in INEPT-based 1H detected 1D 1H,13C
correlation experiments. In total, we find that spectra recorded with a 1.3 mm
rotor at 60 kHz have almost the same sensitivity as spectra recorded with a fully
packed 3.2 mm rotor at 20 kHz, even though ~20× less material is employed. The
improved sensitivity is attributed to 1H line narrowing due to fast MAS and to
the increased efficiency of the 1.3 mm coil.
article_processing_charge: No
article_type: original
author:
- first_name: Sam
full_name: Asami, Sam
last_name: Asami
- first_name: Kathrin
full_name: Szekely, Kathrin
last_name: Szekely
- first_name: Paul
full_name: Schanda, Paul
id: 7B541462-FAF6-11E9-A490-E8DFE5697425
last_name: Schanda
orcid: 0000-0002-9350-7606
- first_name: Beat H.
full_name: Meier, Beat H.
last_name: Meier
- first_name: Bernd
full_name: Reif, Bernd
last_name: Reif
citation:
ama: Asami S, Szekely K, Schanda P, Meier BH, Reif B. Optimal degree of protonation
for 1H detection of aliphatic sites in randomly deuterated proteins as a function
of the MAS frequency. Journal of Biomolecular NMR. 2012;54(2):155-168.
doi:10.1007/s10858-012-9659-9
apa: Asami, S., Szekely, K., Schanda, P., Meier, B. H., & Reif, B. (2012). Optimal
degree of protonation for 1H detection of aliphatic sites in randomly deuterated
proteins as a function of the MAS frequency. Journal of Biomolecular NMR.
Springer Nature. https://doi.org/10.1007/s10858-012-9659-9
chicago: Asami, Sam, Kathrin Szekely, Paul Schanda, Beat H. Meier, and Bernd Reif.
“Optimal Degree of Protonation for 1H Detection of Aliphatic Sites in Randomly
Deuterated Proteins as a Function of the MAS Frequency.” Journal of Biomolecular
NMR. Springer Nature, 2012. https://doi.org/10.1007/s10858-012-9659-9.
ieee: S. Asami, K. Szekely, P. Schanda, B. H. Meier, and B. Reif, “Optimal degree
of protonation for 1H detection of aliphatic sites in randomly deuterated proteins
as a function of the MAS frequency,” Journal of Biomolecular NMR, vol.
54, no. 2. Springer Nature, pp. 155–168, 2012.
ista: Asami S, Szekely K, Schanda P, Meier BH, Reif B. 2012. Optimal degree of protonation
for 1H detection of aliphatic sites in randomly deuterated proteins as a function
of the MAS frequency. Journal of Biomolecular NMR. 54(2), 155–168.
mla: Asami, Sam, et al. “Optimal Degree of Protonation for 1H Detection of Aliphatic
Sites in Randomly Deuterated Proteins as a Function of the MAS Frequency.” Journal
of Biomolecular NMR, vol. 54, no. 2, Springer Nature, 2012, pp. 155–68, doi:10.1007/s10858-012-9659-9.
short: S. Asami, K. Szekely, P. Schanda, B.H. Meier, B. Reif, Journal of Biomolecular
NMR 54 (2012) 155–168.
date_created: 2020-09-18T10:09:18Z
date_published: 2012-08-23T00:00:00Z
date_updated: 2021-01-12T08:19:27Z
day: '23'
doi: 10.1007/s10858-012-9659-9
extern: '1'
intvolume: ' 54'
issue: '2'
language:
- iso: eng
month: '08'
oa_version: None
page: 155-168
publication: Journal of Biomolecular NMR
publication_identifier:
issn:
- 0925-2738
- 1573-5001
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
status: public
title: Optimal degree of protonation for 1H detection of aliphatic sites in randomly
deuterated proteins as a function of the MAS frequency
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 54
year: '2012'
...
---
_id: '8465'
abstract:
- lang: eng
text: We demonstrate that conformational exchange processes in proteins on microsecond-to-millisecond
time scales can be detected and quantified by solid-state NMR spectroscopy. We
show two independent approaches that measure the effect of conformational exchange
on transverse relaxation parameters, namely Carr–Purcell–Meiboom–Gill relaxation-dispersion
experiments and measurement of differential multiple-quantum coherence decay.
Long coherence lifetimes, as required for these experiments, are achieved by the
use of highly deuterated samples and fast magic-angle spinning. The usefulness
of the approaches is demonstrated by application to microcrystalline ubiquitin.
We detect a conformational exchange process in a region of the protein for which
dynamics have also been observed in solution. Interestingly, quantitative analysis
of the data reveals that the exchange process is more than 1 order of magnitude
slower than in solution, and this points to the impact of the crystalline environment
on free energy barriers.
article_processing_charge: No
article_type: original
author:
- first_name: Martin
full_name: Tollinger, Martin
last_name: Tollinger
- first_name: Astrid C.
full_name: Sivertsen, Astrid C.
last_name: Sivertsen
- first_name: Beat H.
full_name: Meier, Beat H.
last_name: Meier
- first_name: Matthias
full_name: Ernst, Matthias
last_name: Ernst
- first_name: Paul
full_name: Schanda, Paul
id: 7B541462-FAF6-11E9-A490-E8DFE5697425
last_name: Schanda
orcid: 0000-0002-9350-7606
citation:
ama: Tollinger M, Sivertsen AC, Meier BH, Ernst M, Schanda P. Site-resolved measurement
of microsecond-to-millisecond conformational-exchange processes in proteins by
solid-state NMR spectroscopy. Journal of the American Chemical Society.
2012;134(36):14800-14807. doi:10.1021/ja303591y
apa: Tollinger, M., Sivertsen, A. C., Meier, B. H., Ernst, M., & Schanda, P.
(2012). Site-resolved measurement of microsecond-to-millisecond conformational-exchange
processes in proteins by solid-state NMR spectroscopy. Journal of the American
Chemical Society. American Chemical Society. https://doi.org/10.1021/ja303591y
chicago: Tollinger, Martin, Astrid C. Sivertsen, Beat H. Meier, Matthias Ernst,
and Paul Schanda. “Site-Resolved Measurement of Microsecond-to-Millisecond Conformational-Exchange
Processes in Proteins by Solid-State NMR Spectroscopy.” Journal of the American
Chemical Society. American Chemical Society, 2012. https://doi.org/10.1021/ja303591y.
ieee: M. Tollinger, A. C. Sivertsen, B. H. Meier, M. Ernst, and P. Schanda, “Site-resolved
measurement of microsecond-to-millisecond conformational-exchange processes in
proteins by solid-state NMR spectroscopy,” Journal of the American Chemical
Society, vol. 134, no. 36. American Chemical Society, pp. 14800–14807, 2012.
ista: Tollinger M, Sivertsen AC, Meier BH, Ernst M, Schanda P. 2012. Site-resolved
measurement of microsecond-to-millisecond conformational-exchange processes in
proteins by solid-state NMR spectroscopy. Journal of the American Chemical Society.
134(36), 14800–14807.
mla: Tollinger, Martin, et al. “Site-Resolved Measurement of Microsecond-to-Millisecond
Conformational-Exchange Processes in Proteins by Solid-State NMR Spectroscopy.”
Journal of the American Chemical Society, vol. 134, no. 36, American Chemical
Society, 2012, pp. 14800–07, doi:10.1021/ja303591y.
short: M. Tollinger, A.C. Sivertsen, B.H. Meier, M. Ernst, P. Schanda, Journal of
the American Chemical Society 134 (2012) 14800–14807.
date_created: 2020-09-18T10:10:20Z
date_published: 2012-08-21T00:00:00Z
date_updated: 2021-01-12T08:19:27Z
day: '21'
doi: 10.1021/ja303591y
extern: '1'
intvolume: ' 134'
issue: '36'
language:
- iso: eng
month: '08'
oa_version: None
page: 14800-14807
publication: Journal of the American Chemical Society
publication_identifier:
issn:
- 0002-7863
- 1520-5126
publication_status: published
publisher: American Chemical Society
quality_controlled: '1'
status: public
title: Site-resolved measurement of microsecond-to-millisecond conformational-exchange
processes in proteins by solid-state NMR spectroscopy
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 134
year: '2012'
...