Functional Heterogeneity of RpoS in Stress Tolerance of Enterohemorrhagic
            <i>Escherichia coli</i>
            Strains

Bhagwat, Arvind A.; Tan, Jasmine; Sharma, Manan; Kothary, Mahendra H.; Low, Sharon Y.Y.; Tall, Ben D.; Bhagwat, Medha

doi:10.1128/aem.02842-05

Cited by 65 publications

(43 citation statements)

References 56 publications

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“…The rpoS gene is polymorphic in E. coli (6,27), as well as in other gammaproteobacteria (39). Despite the reported high sequence variability of the rpoS gene, we found that the frequency of synonymous mutations in the fliA gene, encoding another nonessential sigma factor, was comparable to that of the rpoS gene.…”

Section: Discussionmentioning

confidence: 99%

Phenotypic Diversity Caused by Differential RpoS Activity among Environmental Escherichia coli Isolates

Chiang

Dong

Edge

et al. 2011

Appl Environ Microbiol

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Enteric bacteria deposited into the environment by animal hosts are subject to diverse selective pressures. These pressures may act on phenotypic differences in bacterial populations and select adaptive mutations for survival in stress. As a model to study phenotypic diversity in environmental bacteria, we examined mutations of the stress response sigma factor, RpoS, in environmental Escherichia coli isolates. A total of 2,040 isolates from urban beaches and nearby fecal pollution sources on Lake Ontario (Canada) were screened for RpoS function by examining growth on succinate and catalase activity, two RpoS-dependent phenotypes. The rpoS sequence was determined for 45 isolates, including all candidate RpoS mutants, and of these, six isolates were confirmed as mutants with the complete loss of RpoS function. Similarly to laboratory strains, the RpoS expression of these environmental isolates was stationary phase dependent. However, the expression of RpoS regulon members KatE and AppA had differing levels of expression in several environmental isolates compared to those in laboratory strains. Furthermore, after plating rpoS ؉ isolates on succinate, RpoS mutants could be readily selected from environmental E. coli. Naturally isolated and succinate-selected RpoS mutants had lower generation times on poor carbon sources and lower stress resistance than their rpoS ؉ isogenic parental strains. These results show that RpoS mutants are present in the environment (with a frequency of 0.003 among isolates) and that, similarly to laboratory and pathogenic strains, growth on poor carbon sources selects for rpoS mutations in environmental E. coli. RpoS selection may be an important determinant of phenotypic diversification and, hence, the survival of E. coli in the environment.

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Section: Discussionmentioning

confidence: 99%

Phenotypic Diversity Caused by Differential RpoS Activity among Environmental Escherichia coli Isolates

Chiang

Dong

Edge

et al. 2011

Appl Environ Microbiol

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“…The genotype-determined phenotypic effects of within-species variation are indeed profound, so one strain of E. coli can have a very different response to the same level of stress than another (24,98) or a very different growth rate or competitive ability in particular environments (157). Genomics efforts have highlighted the relatively small core genome and the relatively large pan-genome within a species such as E. coli (193,348), so it is highly likely that some of the pan-genome differences will affect adaptive responses.…”

Section: Importance Of the Genotype In Determining The Nature Of Adapmentioning

confidence: 99%

Culture History and Population Heterogeneity as Determinants of Bacterial Adaptation: the Adaptomics of a Single Environmental Transition

Ryall

Eydallin

Ferenci

2012

Microbiol Mol Biol Rev

133

109

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SUMMARY Diversity in adaptive responses is common within species and populations, especially when the heterogeneity of the frequently large populations found in environments is considered. By focusing on events in a single clonal population undergoing a single transition, we discuss how environmental cues and changes in growth rate initiate a multiplicity of adaptive pathways. Adaptation is a comprehensive process, and stochastic, regulatory, epigenetic, and mutational changes can contribute to fitness and overlap in timing and frequency. We identify culture history as a major determinant of both regulatory adaptations and microevolutionary change. Population history before a transition determines heterogeneities due to errors in translation, stochastic differences in regulation, the presence of aged, damaged, cheating, or dormant cells, and variations in intracellular metabolite or regulator concentrations. It matters whether bacteria come from dense, slow-growing, stressed, or structured states. Genotypic adaptations are history dependent due to variations in mutation supply, contingency gene changes, phase variation, lateral gene transfer, and genome amplifications. Phenotypic adaptations underpin genotypic changes in situations such as stress-induced mutagenesis or prophage induction or in biofilms to give a continuum of adaptive possibilities. Evolutionary selection additionally provides diverse adaptive outcomes in a single transition and generally does not result in single fitter types. The totality of heterogeneities in an adapting population increases the chance that at least some individuals meet immediate or future challenges. However, heterogeneity complicates the adaptomics of single transitions, and we propose that subpopulations will need to be integrated into future population biology and systems biology predictions of bacterial behavior.

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“…For example, naturally occurring strains can differ in the amount of RpoS they produce during exponential phase (12) or stationary phase (13). All studies that have measured RpoS levels in naturally occurring strains of E. coli have detected variations (13)(14)(15)(16)(17), though the extent and cause of the variations in RpoS between strains is still a matter of some controversy (16,17).…”

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confidence: 99%

Genome-Wide Transcriptional Response to Varying RpoS Levels in Escherichia coli K-12

et al. 2017

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The alternative sigma factor RpoS is a central regulator of many stress responses in Escherichia coli. The level of functional RpoS differs depending on the stress. The effect of these differing concentrations of RpoS on global transcriptional responses remains unclear. We investigated the effect of RpoS concentration on the transcriptome during stationary phase in rich media. We found that 23% of genes in the E. coli genome are regulated by RpoS, and we identified many RpoS-transcribed genes and promoters. We observed three distinct classes of response to RpoS by genes in the regulon: genes whose expression changes linearly with increasing RpoS level, genes whose expression changes dramatically with the production of only a little RpoS ("sensitive" genes), and genes whose expression changes very little with the production of a little RpoS ("insensitive"). We show that sequences outside the core promoter region determine whether an RpoS-regulated gene is sensitive or insensitive. Moreover, we show that sensitive and insensitive genes are enriched for specific functional classes and that the sensitivity of a gene to RpoS corresponds to the timing of induction as cells enter stationary phase. Thus, promoter sensitivity to RpoS is a mechanism to coordinate specific cellular processes with growth phase and may also contribute to the diversity of stress responses directed by RpoS. IMPORTANCEThe sigma factor RpoS is a global regulator that controls the response to many stresses in Escherichia coli. Different stresses result in different levels of RpoS production, but the consequences of this variation are unknown. We describe how changing the level of RpoS does not influence all RpoS-regulated genes equally. The cause of this variation is likely the action of transcription factors that bind the promoters of the genes. We show that the sensitivity of a gene to RpoS levels explains the timing of expression as cells enter stationary phase and that genes with different RpoS sensitivities are enriched for specific functional groups. Thus, promoter sensitivity to RpoS is a mechanism that coordinates specific cellular processes in response to stresses. KEYWORDS RpoS, promoters, S , stress response, transcriptional regulation, transcriptome G enome-wide measurements of RNA levels have revolutionized our understanding of how cells organize their patterns of transcription. These studies have given us snapshots of how patterns of gene expression change in response to changes in the external environment. They have also allowed us to define the regulons controlled by specific transcription factors (TFs). A major weakness of the vast majority of these

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Functional Heterogeneity of RpoS in Stress Tolerance of Enterohemorrhagic Escherichia coli Strains

Cited by 65 publications

References 56 publications

Phenotypic Diversity Caused by Differential RpoS Activity among Environmental Escherichia coli Isolates

Phenotypic Diversity Caused by Differential RpoS Activity among Environmental Escherichia coli Isolates

Culture History and Population Heterogeneity as Determinants of Bacterial Adaptation: the Adaptomics of a Single Environmental Transition

Genome-Wide Transcriptional Response to Varying RpoS Levels in Escherichia coli K-12

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