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Nicolas Fossat Tania Radziewic Vanessa Jones Karin Tourle Patrick P. L. Tam 《Genesis (New York, N.Y. : 2000)》2016,54(3):115-122
Rbm47 encodes a RNA binding protein that is necessary for Cytidine to Uridine RNA editing. Rbm47gt/gt mutant mice that harbor inactivated Rbm47 display poor viability. Here it was determined that the loss of Rbm47gt/gt offspring is due to embryonic lethality at mid‐gestation. It was further showed that growth of the surviving Rbm47gt/gt mutants is impaired. Rbm47 is expressed in both the visceral endoderm and the definitive endoderm. Using the utility of the switchable FlEx gene‐trap cassette and the activity of Cre and FLP recombinases to generate mice that conditionally inactivate and restore Rbm47 function in tissue‐specific manner, it was demonstrated that Rbm47 function is required in the embryo proper, and not the visceral endoderm, for viability and growth. genesis 54:115–122, 2016. © 2016 Wiley Periodicals, Inc. 相似文献
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Mónica Serrano Nicolas Kint Fátima C. Pereira Laure Saujet Pierre Boudry Bruno Dupuy Adriano O. Henriques Isabelle Martin-Verstraete 《PLoS genetics》2016,12(9)
The strict anaerobe Clostridium difficile is the most common cause of nosocomial diarrhea, and the oxygen-resistant spores that it forms have a central role in the infectious cycle. The late stages of sporulation require the mother cell regulatory protein σK. In Bacillus subtilis, the onset of σK activity requires both excision of a prophage-like element (skinBs) inserted in the sigK gene and proteolytical removal of an inhibitory pro-sequence. Importantly, the rearrangement is restricted to the mother cell because the skinBs recombinase is produced specifically in this cell. In C. difficile, σK lacks a pro-sequence but a skinCd element is present. The product of the skinCd gene CD1231 shares similarity with large serine recombinases. We show that CD1231 is necessary for sporulation and skinCd excision. However, contrary to B. subtilis, expression of CD1231 is observed in vegetative cells and in both sporangial compartments. Nevertheless, we show that skinCd excision is under the control of mother cell regulatory proteins σE and SpoIIID. We then demonstrate that σE and SpoIIID control the expression of the skinCd gene CD1234, and that this gene is required for sporulation and skinCd excision. CD1231 and CD1234 appear to interact and both proteins are required for skinCd excision while only CD1231 is necessary for skinCd integration. Thus, CD1234 is a recombination directionality factor that delays and restricts skinCd excision to the terminal mother cell. Finally, while the skinCd element is not essential for sporulation, deletion of skinCd results in premature activity of σK and in spores with altered surface layers. Thus, skinCd excision is a key element controlling the onset of σK activity and the fidelity of spore development. 相似文献
245.
The prediction of protein side chain conformations from backbone coordinates is an important task in structural biology, with applications in structure prediction and protein design. It is a difficult problem due to its combinatorial nature. We study the performance of an “MMGBSA” energy function, implemented in our protein design program Proteus, which combines molecular mechanics terms, a Generalized Born and Surface Area (GBSA) solvent model, with approximations that make the model pairwise additive. Proteus is not a competitor to specialized side chain prediction programs due to its cost, but it allows protein design applications, where side chain prediction is an important step and MMGBSA an effective energy model. We predict the side chain conformations for 18 proteins. The side chains are first predicted individually, with the rest of the protein in its crystallographic conformation. Next, all side chains are predicted together. The contributions of individual energy terms are evaluated and various parameterizations are compared. We find that the GB and SA terms, with an appropriate choice of the dielectric constant and surface energy coefficients, are beneficial for single side chain predictions. For the prediction of all side chains, however, errors due to the pairwise additive approximation overcome the improvement brought by these terms. We also show the crucial contribution of side chain minimization to alleviate the rigid rotamer approximation. Even without GB and SA terms, we obtain accuracies comparable to SCWRL4, a specialized side chain prediction program. In particular, we obtain a better RMSD than SCWRL4 for core residues (at a higher cost), despite our simpler rotamer library. Proteins 2016; 84:803–819. © 2016 Wiley Periodicals, Inc. 相似文献
246.
Timothée Poisot Benjamin Baiser Jennifer A. Dunne Sonia Kéfi François Massol Nicolas Mouquet Tamara N. Romanuk Daniel B. Stouffer Spencer A. Wood Dominique Gravel 《Ecography》2016,39(4):384-390
The study of ecological networks is severely limited by 1) the difficulty to access data, 2) the lack of a standardized way to link meta‐data with interactions, and 3) the disparity of formats in which ecological networks themselves are stored and represented. To overcome these limitations, we have designed a data specification for ecological networks. We implemented a database respecting this standard, and released an R package (rmangal) allowing users to programmatically access, curate, and deposit data on ecological interactions. In this article, we show how these tools, in conjunction with other frameworks for the programmatic manipulation of open ecological data, streamlines the analysis process and improves replicability and reproducibility of ecological network studies. 相似文献
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248.
Alan Walton Elisabeth Stes Nicolas Cybulski Michiel Van Bel Sabrina I?igo Astrid Nagels Durand Evy Timmerman Jefri Heyman Laurens Pauwels Lieven De Veylder Alain Goossens Ive De Smet Frederik Coppens Sofie Goormachtig Kris Gevaert 《The Plant cell》2016,28(1):6-16
Ubiquitination, the covalent binding of the small protein modifier ubiquitin to a target protein, is an important and frequently studied posttranslational protein modification. Multiple reports provide useful insights into the plant ubiquitinome, but mostly at the protein level without comprehensive site identification. Here, we implemented ubiquitin combined fractional diagonal chromatography (COFRADIC) for proteome-wide ubiquitination site mapping on Arabidopsis thaliana cell cultures. We identified 3009 sites on 1607 proteins, thereby greatly increasing the number of known ubiquitination sites in this model plant. Finally, The Ubiquitination Site tool (http://bioinformatics.psb.ugent.be/webtools/ubiquitin_viewer/) gives access to the obtained ubiquitination sites, not only to consult the ubiquitination status of a given protein, but also to conduct intricate experiments aiming to study the roles of specific ubiquitination events. Together with the antibodies recognizing the ubiquitin remnant motif, ubiquitin COFRADIC represents a powerful tool to resolve the ubiquitination maps of numerous cellular processes in plants. 相似文献
249.
Chrystelle Aillaud Christophe Bosc Yasmina Saoudi Eric Denarier Leticia Peris Laila Sago Nicolas Taulet Adeline Cieren Olivia Tort Maria M. Magiera Carsten Janke Virginie Redeker Annie Andrieux Marie-Jo Moutin 《Molecular biology of the cell》2016,27(4):640-653
Cellular α-tubulin can bear various carboxy-terminal sequences: full-length tubulin arising from gene neosynthesis is tyrosinated, and two truncated variants, corresponding to detyrosinated and Δ2 α‑tubulin, result from the sequential cleavage of one or two C-terminal residues, respectively. Here, by using a novel antibody named 3EG that is highly specific to the –EEEG C-terminal sequence, we demonstrate the occurrence in neuronal tissues of a new αΔ3‑tubulin variant corresponding to α1A/B‑tubulin deleted of its last three residues (EEY). αΔ3‑tubulin has a specific distribution pattern: its quantity in the brain is similar to that of αΔ2-tubulin around birth but is much lower in adult tissue. This truncated α1A/B-tubulin variant can be generated from αΔ2-tubulin by the deglutamylases CCP1, CCP4, CCP5, and CCP6 but not by CCP2 and CCP3. Moreover, using 3EG antibody, we identify a C‑terminally truncated β-tubulin form with the same –EEEG C-terminal sequence. Using mass spectrometry, we demonstrate that β2A/B-tubulin is modified by truncation of the four C-terminal residues (EDEA). We show that this newly identified βΔ4-tubulin is ubiquitously present in cells and tissues and that its level is constant throughout the cell cycle. These new C-terminally truncated α- and β-tubulin variants, both ending with –EEEG sequence, are expected to regulate microtubule physiology. Of interest, the αΔ3-tubulin seems to be related to dynamic microtubules, resembling tyrosinated-tubulin rather than the other truncated variants, and may have critical function(s) in neuronal development. 相似文献
250.
Nicolas Larranaga Michel Baguette Olivier Calvez Delphine Legrand 《Insect Science》2019,26(4):743-752
When, how often and for how long organisms mate can have strong consequences for individual fitness and are crucial aspects of evolutionary ecology. Such determinants are likely to be of even greater importance in monandrous species and species with short adult life stages. Previous work suggests that mobility, a key dispersal? related trait, may affect the dynamics of copulations, but few studies have investigated the impact of individual mobility on mating latency, copulation duration and oviposition latency simultaneously. In this paper, we monitored the copulation dynamics of 40 males and 40 females, as well as the oviposition dynamics of the females of the Large White butterfly Pieris brassicae, a facultative long-distance disperser butterfly. Individuals from a breeding were selected to create a uniform distribution of mobility and we recorded the timing, number and duration of all copulations in a semiexperimental system. We showed that mobility, measured as the time spent in flight under stressful conditions (a proxy of dispersal tendency), correlates with all aspects of copulation dynamics: mobile males and females mated earlier and for shorter periods than less mobile individuals. In turn, late mating females increased the time between copulation and oviposition. These results feed the previously described mobility syndrome of R brassicae, involving morphological and physiological characters, with life-history traits. We suggest that the reduction of mating latency and copulation duration has an adaptive value in dispersing individuals, as their life expectancy might be shorter than that of sedentary individuals. 相似文献