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131.
Oligoribonuclease is the only RNase in Escherichia coli that is able to degrade RNA oligonucleotides five residues and shorter in length. Firmicutes including Bacillus subtilis do not have an Oligoribonuclease (Orn) homologous protein and it is not yet understood which proteins accomplish the equivalent function in these organisms. We had previously identified oligoribonucleases Orn from E. coli and its human homolog Sfn in a screen for proteins that are regulated by 3′-phosphoadenosine 5′-phosphate (pAp). Here, we identify YtqI as a potential functional analog of Orn through its interaction with pAp. YtqI degrades RNA oligonucleotides in vitro with preference for 3-mers. In addition, YtqI has pAp-phosphatase activity in vitro. In agreement with these data, YtqI is able to complement both orn and cysQ mutants in E. coli. An ytqI mutant in B. subtilis shows impairment of growth in the absence of cysteine, a phenotype resembling that of a cysQ mutant in E. coli. Phylogenetic distribution of YtqI, Orn and CysQ supports bifunctionality of YtqI. 相似文献
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133.
Coutard B Danchin EG Oubelaid R Canard B Bignon C 《Protein expression and purification》2012,82(2):352-359
We previously reported the set up of an automated test for screening the refolding of recombinant proteins expressed as inclusion bodies in Escherichia coli[1]. The screen used 96 refolding buffers and was validated with 24 proteins, 70% of which remained soluble in at least one buffer. In the present paper, we have analyzed in more detail these experimental data to see if the refolding process can be driven by general rules. Notably, we found that proteins with an acidic isoelectric point (pI) refolded in buffers the average pH of which was alkaline and conversely. In addition, the number of refolding buffers wherein a protein remained soluble increased with the difference between its pI and the average pH of the buffers in which it refolded. A trend analysis of the other variables (ionic strength, detergents, etc.) was also performed. On the basis of this analysis, we devised and validated a new refolding screen made of a single buffer for acidic proteins and a single buffer for alkaline proteins. 相似文献
134.
Ashida H Saito Y Nakano T Tandeau de Marsac N Sekowska A Danchin A Yokota A 《Journal of experimental botany》2008,59(7):1543-1554
Ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO) is the key enzyme in the fixation of CO(2) in the Calvin cycle of plants. Many genome projects have revealed that bacteria, including Bacillus subtilis, possess genes for proteins that are similar to the large subunit of RuBisCO. These RuBisCO homologues are called RuBisCO-like proteins (RLPs) because they are not able to catalyse the carboxylase or the oxygenase reactions that are catalysed by photosynthetic RuBisCO. It has been demonstrated that B. subtilis RLP catalyses the 2,3-diketo-5-methylthiopentyl-1-phosphate (DK-MTP-1-P) enolase reaction in the methionine salvage pathway. The structure of DK-MTP-1-P is very similar to that of ribulose-1,5-bisphosphate (RuBP) and the enolase reaction is a part of the reaction catalysed by photosynthetic RuBisCO. In this review, functional and evolutionary relationships between B. subtilis RLP of the methionine salvage pathway, other RLPs, and photosynthetic RuBisCO are discussed. In addition, the fundamental question, 'How has RuBisCO evolved?' is also considered, and evidence is presented that RuBisCOs evolved from RLPs. 相似文献
135.
Hervé Mulard Etienne Danchin Sandra L Talbot Andrew M Ramey Scott A Hatch Joël F White Fabrice Helfenstein Richard H Wagner 《BMC evolutionary biology》2009,9(1):147-12
Background
Evidence of multiple genetic criteria of mate choice is accumulating in numerous taxa. In many species, females have been shown to pair with genetically dissimilar mates or with extra-pair partners that are more genetically compatible than their social mates, thereby increasing their offsprings' heterozygosity which often correlates with offspring fitness. While most studies have focused on genetically promiscuous species, few studies have addressed genetically monogamous species, in which mate choice tends to be mutual. 相似文献136.
Jennifer J Hill Tammy-Lynn Tremblay Christiane Cantin Maureen O'Connor-McCourt John F Kelly Anne EG Lenferink 《Proteome science》2009,7(1):2-17
Background
TGF-β acts as an antiproliferative factor in normal epithelial cells and at early stages of oncogenesis. However, later in tumor development TGF-β can become tumor promoting through mechanisms including the induction of epithelial-to-mesenchymal transition (EMT), a process that is thought to contribute to tumor progression, invasion and metastasis. To identify EMT-related breast cancer therapeutic targets and biomarkers, we have used two proteomic approaches to find proteins that change in abundance upon the induction of EMT by TGF-β in two mouse mammary epithelial cell lines, NMuMG and BRI-JM01. 相似文献137.
Most bird species endure a high mortality at fledging, and selection should favour parental behaviour diminishing these costs. Post-fledging parental care varies greatly among species and is often linked to parent–offspring recognition. In the Black-legged Kittiwake (Rissa tridactyla), fledglings need to return to the natal nest to be fed by their parents until independence. Rejections of fledglings by non-parent adults may be fairly violent, and parents are expected to recognize and help their chicks at the time of first return. However, previous cross-fostering experiments pointed out that parents are not able to recognize their chicks up to 15 days before fledging. In this paper, we study the behaviour of both parents and juveniles at fledging. We found that parents answered significantly more to their fledgling's calls than to those of others. Compared to silent juveniles, juveniles that called before landing were more likely to be accepted by their parents. No such pattern was observed with foreign juveniles, indicating that fledglings’ voice may carry individual identity. Furthermore, fledglings found their way back to the natal nest faster when parents attended the natal nest and reacted to their offspring's calls than when they were absent or inactive. Such interactions may therefore diminish juvenile mortality at fledging. 相似文献
138.
139.
Genome sequencing and analysis of the biomass-degrading fungus Trichoderma reesei (syn. Hypocrea jecorina) 总被引:1,自引:0,他引:1
Martinez D Berka RM Henrissat B Saloheimo M Arvas M Baker SE Chapman J Chertkov O Coutinho PM Cullen D Danchin EG Grigoriev IV Harris P Jackson M Kubicek CP Han CS Ho I Larrondo LF de Leon AL Magnuson JK Merino S Misra M Nelson B Putnam N Robbertse B Salamov AA Schmoll M Terry A Thayer N Westerholm-Parvinen A Schoch CL Yao J Barabote R Barbote R Nelson MA Detter C Bruce D Kuske CR Xie G Richardson P Rokhsar DS Lucas SM Rubin EM Dunn-Coleman N Ward M Brettin TS 《Nature biotechnology》2008,26(5):553-560
Trichoderma reesei is the main industrial source of cellulases and hemicellulases used to depolymerize biomass to simple sugars that are converted to chemical intermediates and biofuels, such as ethanol. We assembled 89 scaffolds (sets of ordered and oriented contigs) to generate 34 Mbp of nearly contiguous T. reesei genome sequence comprising 9,129 predicted gene models. Unexpectedly, considering the industrial utility and effectiveness of the carbohydrate-active enzymes of T. reesei, its genome encodes fewer cellulases and hemicellulases than any other sequenced fungus able to hydrolyze plant cell wall polysaccharides. Many T. reesei genes encoding carbohydrate-active enzymes are distributed nonrandomly in clusters that lie between regions of synteny with other Sordariomycetes. Numerous genes encoding biosynthetic pathways for secondary metabolites may promote survival of T. reesei in its competitive soil habitat, but genome analysis provided little mechanistic insight into its extraordinary capacity for protein secretion. Our analysis, coupled with the genome sequence data, provides a roadmap for constructing enhanced T. reesei strains for industrial applications such as biofuel production. 相似文献
140.
Abad P Gouzy J Aury JM Castagnone-Sereno P Danchin EG Deleury E Perfus-Barbeoch L Anthouard V Artiguenave F Blok VC Caillaud MC Coutinho PM Dasilva C De Luca F Deau F Esquibet M Flutre T Goldstone JV Hamamouch N Hewezi T Jaillon O Jubin C Leonetti P Magliano M Maier TR Markov GV McVeigh P Pesole G Poulain J Robinson-Rechavi M Sallet E Ségurens B Steinbach D Tytgat T Ugarte E van Ghelder C Veronico P Baum TJ Blaxter M Bleve-Zacheo T Davis EL Ewbank JJ Favery B Grenier E Henrissat B Jones JT 《Nature biotechnology》2008,26(8):909-915
Plant-parasitic nematodes are major agricultural pests worldwide and novel approaches to control them are sorely needed. We report the draft genome sequence of the root-knot nematode Meloidogyne incognita, a biotrophic parasite of many crops, including tomato, cotton and coffee. Most of the assembled sequence of this asexually reproducing nematode, totaling 86 Mb, exists in pairs of homologous but divergent segments. This suggests that ancient allelic regions in M. incognita are evolving toward effective haploidy, permitting new mechanisms of adaptation. The number and diversity of plant cell wall-degrading enzymes in M. incognita is unprecedented in any animal for which a genome sequence is available, and may derive from multiple horizontal gene transfers from bacterial sources. Our results provide insights into the adaptations required by metazoans to successfully parasitize immunocompetent plants, and open the way for discovering new antiparasitic strategies. 相似文献