The crystal structure of the <i>E. coli</i> stress protein YciF

Hindupur, Aditya; Liu, Deqian; Zhao, Yong-Qi; Bellamy, Henry D.; White, Mark A.; Fox, Robert O.

doi:10.1110/ps.062307706

Cited by 24 publications

(20 citation statements)

References 46 publications

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“…An additional RpoE2-dependent gene encodes another ECF sigma factor (rpoE5). In addition to katC, some other genes share homologies with genes that are controlled by the master regulator of the general stress response, RpoS, in other gram-negative bacteria: smc00371, whose product is 40% identical to the E. coli YciF protein of unknown function (30), as well as the glgA2 and glgX2 genes, possibly involved in glycogen synthesis. However, the functions of these proteins in stress response are not known.…”

Section: Discussionmentioning

confidence: 99%

An Extracytoplasmic Function Sigma Factor Acts as a General Stress Response Regulator inSinorhizobium meliloti

et al. 2007

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Sinorhizobium meliloti genes transcriptionally up-regulated after heat stress, as well as upon entry into stationary phase, were identified by microarray analyses. Sixty stress response genes were thus found to be up-regulated under both conditions. One of them, rpoE2 (smc01506), encodes a putative extracytoplasmic function (ECF) sigma factor. We showed that this sigma factor controls its own transcription and is activated by various stress conditions, including heat and salt, as well as entry into stationary phase after either carbon or nitrogen starvation. We also present evidence that the product of the gene cotranscribed with rpoE2 negatively regulates RpoE2 activity, and we therefore propose that it plays the function of anti-sigma factor. By combining transcriptomic, bioinformatic, and quantitative reverse transcription-PCR analyses, we identified 44 RpoE2-controlled genes and predicted the number of RpoE2 targets to be higher. Strikingly, more than one-third of the 60 stress response genes identified in this study are RpoE2 targets. Interestingly, two genes encoding proteins with known functions in stress responses, namely, katC and rpoH2, as well as a second ECF-encoding gene, rpoE5, were found to be RpoE2 regulated. Altogether, these data suggest that RpoE2 is a major global regulator of the general stress response in S. meliloti. Despite these observations, and although this sigma factor is well conserved among alphaproteobacteria, no in vitro nor in planta phenotypic difference from the wild-type strain could be detected for rpoE2 mutants. This therefore suggests that other important actors in the general stress response have still to be identified in S. meliloti.To survive the many stress conditions that they encounter in nature, bacteria have evolved rapid responses that result in the prevention or repair of cellular damages caused by stresses. In addition to these usually stress-specific responses, more general stress responses take place in reaction to a variety of insults as different as high osmolarity, heat or cold shock, pH variation, and nutrient starvation (which results in stationary phase). One well-known consequence of these general stress responses is the ability of bacteria to resist stress better in stationary phase than in exponential phase. This phenomenon, observed in most bacterial species studied so far, is considered a universal way for these microorganisms to survive not only the stress that they currently experience, but also stress conditions that they could potentially face in the future, and is therefore of primary importance in nature, where bacteria often are nutrient or oxygen limited and where environmental conditions constantly change (28).Much of our knowledge regarding the mechanisms of induction of general stress responses derives from studies of the model bacterium Escherichia coli and its close relatives. In these bacteria, entry into stationary phase, as well as a number of different stress conditions, leads to the activation of alternative sigma factors, which re...

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Section: Discussionmentioning

confidence: 99%

An Extracytoplasmic Function Sigma Factor Acts as a General Stress Response Regulator inSinorhizobium meliloti

et al. 2007

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“…The physiological role of the yciGFE(katN) locus is unknown, and the significance, in the fitness of E. coli and Salmonella, of the differential regulation of these genes requires further investigation. Structural comparisons suggest a role for YciF in iron storage and/or protection against oxidative damage (53). KatN belongs to the family of manganese catalases but it does not play a major role in hydrogen peroxide resistance of Salmonella under standard growth conditions or in virulence in mice (12,54).…”

Section: Discussionmentioning

confidence: 99%

A Proteomic Analysis Reveals Differential Regulation of the σS-Dependent yciGFE(katN) Locus by YncC and H-NS in Salmonella and Escherichia coli K-12

Beraud

Kolb

Monteil

et al. 2010

Molecular & Cellular Proteomics

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The stationary phase sigma factor S (RpoS) controls a regulon required for general stress resistance of the closely related enterobacteria Salmonella and Escherichia coli. In eubacteria, transcription depends on a multisubunit RNA polymerase (RNAP) consisting of a catalytically active core enzyme (E) with a subunit structure ␣ 2 ␤␤', that associates with any one of several factors to form different holoenzyme (E) species. The subunit is required for specific promoter binding, and different factors direct RNAP to different classes of promoters, thereby modulating gene expression patterns (1). The RNA polymerase holoenzyme containing the 70 subunit is responsible for the transcription of most genes during exponential growth (1). When cells enter stationary phase or are under specific stress conditions during exponential growth, S , encoded by the rpoS gene, becomes more abundant, associates with the core enzyme, and directs the transcription of genes essential for the general stress response (1-3). In the closely related Enterobacteria Salmonella and Escherichia coli, S is required for stationary phase survival, stress resistance, and biofilm formation. It is also involved in the virulence of Salmonella enterica serovar Typhimurium (S. Typhimurium) (4). Transcriptome analyses in S. Typhimurium and E. coli K-12 have shown that rpoS controls more than 300 genes, 40% of which are of unknown function (3,5,6). A large fraction of S -controlled genes encode putative regulators and signal transducing factors, suggesting that S controls a complex network with regulatory cascades and signal input at levels downstream of S itself. We previously used a bank of S.Typhimurium mutants to identify S -regulated genes (7). One of these genes, the yncC gene (7), encoded a putative DNA binding protein of the GntR/FadR family of bacterial regulators (8 -10). To further investigate the function of the yncC gene, we decided to characterize the proteome of the Salmonella yncC mutant by the surface-enhanced laser desorption/ionization-time of flight (SELDI-TOF 1 ) ProteinChip technology.The SELDI-TOF method is based on the selective protein retention on a solid-phase chromatographic chip surface and successive analysis by simple laser desorption/ionization mass spectrometry (11). Because of its high-throughput nature and experimental simplicity, this technology has been widely used for protein profiling of tissues and biomarker discovery (11) and unpublished work from our laboratory reFrom the §Institut Pasteur, Unité de Gé né tique molé culaire, Dé partement de Microbiologie

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“…On the other hand, in S. enterica and E. coli, the csbD-like homolog is stress induced (1) and regulated by rpoS (55,56). Furthermore, in E. coli the CH00268 homolog, encoding the YciF protein of unknown function, is rpoS dependent (29,30). These results, along with the gene expression data, suggest that rpoE4 plays an important role in R. etli during the stationary growth phase.…”

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confidence: 87%

Role of the Extracytoplasmic Function Sigma Factor RpoE4 in Oxidative and Osmotic Stress Responses in Rhizobium etli

et al. 2009

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The aims of this study were to functionally characterize and analyze the transcriptional regulation and transcriptome of the Rhizobium etli rpoE4 gene. An R. etli rpoE4 mutant was sensitive to oxidative, saline, and osmotic stresses. Using transcriptional fusions, we determined that RpoE4 controls its own transcription and that it is negatively regulated by rseF (regulator of sigma rpoE4; CH03274), which is cotranscribed with rpoE4. rpoE4 expression was induced not only after oxidative, saline, and osmotic shocks, but also under microaerobic and stationary-phase growth conditions. The transcriptome analyses of an rpoE4 mutant and an rpoE4-overexpressing strain revealed that the RpoE4 extracytoplasmic function sigma factor regulates about 98 genes; 50 of them have the rpoE4 promoter motifs in the upstream regulatory regions. Interestingly, 16 of 38 genes upregulated in the rpoE4-overexpressing strain encode unknown putative cell envelope proteins. Other genes controlled by RpoE4 include rpoH2, CH00462, CH02434, CH03474, and xthA1, which encode proteins involved in the stress response (a heat shock sigma factor, a putative Mn-catalase, an alkylation DNA repair protein, pyridoxine phosphate oxidase, and exonuclease III, respectively), as well as several genes, such as CH01253, CH03555, and PF00247, encoding putative proteins involved in cell envelope biogenesis (a putative peptidoglycan binding protein, a cell wall degradation protein, and phospholipase D, respectively). These results suggest that rpoE4 has a relevant function in cell envelope biogenesis and that it plays a role as a general regulator in the responses to several kinds of stress.In eubacteria, gene expression is controlled at the transcriptional level by the combined actions of sigma factors, activators, and repressors. Sigma factors bind to core RNA polymerase (␣ 2 ␤␤Ј) and recognize specific promoters. The replacement of one sigma factor with another allows the controlled transcription of different genes. Gene expression in exponentially growing bacterial cells depends on a single sigma factor (the 70 factor) aimed at transcribing housekeeping genes (8,23). A variable number of alternative sigma factors coordinate the expression of genes required for defined growth conditions and/or responses to specific stimuli (23). Therefore, alternative sigma factors play relevant roles in responding and adapting to different kinds of stresses and environments.Based on sequence similarities and conserved regions, sigma factors are grouped into two families: 54 and 70 . In general, bacterial cells have several members from the 70 family and usually only one or two members from the 54 family. Members of the diverse 70 family have four conserved regions; the 2.4 and 4.2 subregions are significantly conserved and recognize the Ϫ10 and Ϫ35 promoter elements, respectively (8,23,32). Moreover, the 70 family is divided into four phylogenetic groups (23, 26, 32): group 1, the primary sigma factors ( 70 -related factors); group 2, nonessential proteins highly similar to...

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The crystal structure of the E. coli stress protein YciF

Cited by 24 publications

References 46 publications

An Extracytoplasmic Function Sigma Factor Acts as a General Stress Response Regulator inSinorhizobium meliloti

An Extracytoplasmic Function Sigma Factor Acts as a General Stress Response Regulator inSinorhizobium meliloti

A Proteomic Analysis Reveals Differential Regulation of the σS-Dependent yciGFE(katN) Locus by YncC and H-NS in Salmonella and Escherichia coli K-12

Role of the Extracytoplasmic Function Sigma Factor RpoE4 in Oxidative and Osmotic Stress Responses in Rhizobium etli

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