The extracytoplasmic function (ECF) sigma factors

Helmann, John D.

doi:10.1016/s0065-2911(02)46002-x

Cited by 645 publications

(800 citation statements)

References 150 publications

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“…Our analysis identified 31 gene families in the core genome which have putative sigma factor activity (GO:0005525). Notably, 20 of these families encode the ECF (extracytoplasmic function) sigma factors [39,40], which regulate gene expression in response to environmental challenges. In addition to the ECF sigma factors, streptomycetes harbor powerful two-component transcriptional regulator systems which can globally activate or repress gene transcription in response to extracellular stimulus.…”

Section: Resultsmentioning

confidence: 99%

Genome plasticity and systems evolution in Streptomyces

Zhou

et al. 2012

BMC Bioinformatics

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BackgroundStreptomycetes are filamentous soil-dwelling bacteria. They are best known as the producers of a great variety of natural products such as antibiotics, antifungals, antiparasitics, and anticancer agents and the decomposers of organic substances for carbon recycling. They are also model organisms for the studies of gene regulatory networks, morphological differentiation, and stress response. The availability of sets of genomes from closely related Streptomyces strains makes it possible to assess the mechanisms underlying genome plasticity and systems adaptation.ResultsWe present the results of a comprehensive analysis of the genomes of five Streptomyces species with distinct phenotypes. These streptomycetes have a pan-genome comprised of 17,362 orthologous families which includes 3,096 components in the core genome, 5,066 components in the dispensable genome, and 9,200 components that are uniquely present in only one species. The core genome makes up about 33%-45% of each genome repertoire. It contains important genes for Streptomyces biology including those involved in gene regulation, secretion, secondary metabolism and morphological differentiation. Abundant duplicate genes have been identified, with 4%-11% of the whole genomes composed of lineage-specific expansions (LSEs), suggesting that frequent gene duplication or lateral gene transfer events play a role in shaping the genome diversification within this genus. Two patterns of expansion, single gene expansion and chromosome block expansion are observed, representing different scales of duplication.ConclusionsOur results provide a catalog of genome components and their potential functional roles in gene regulatory networks and metabolic networks. The core genome components reveal the minimum requirement for streptomycetes to sustain a successful lifecycle in the soil environment, reflecting the effects of both genome evolution and environmental stress acting upon the expressed phenotypes. A better understanding of the LSE gene families will, on the other hand, bring a wealth of new insights into the mechanisms underlying strain-specific phenotypes, such as the production of novel antibiotics, pathogenesis, and adaptive response to environmental challenges.

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Section: Resultsmentioning

confidence: 99%

Genome plasticity and systems evolution in Streptomyces

Zhou

et al. 2012

BMC Bioinformatics

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“…A sequencepredicted helix-turn-helix motif was shown to be irrelevant, as it is periplasmic (12,13). NosR exhibits no winged helix-turnhelix domain like that of the membrane-bound transcription factor ToxR (11) and is not recognized as part of a twocomponent regulatory system, either of the classical type or of the extracytoplasmic function sigma factors (19), since the cognate components for interaction with the putative sensor, NosR, are missing. The only currently known factor which can be hypothesized to interact with NosR is the denitrification regulator DnrD.…”

Section: Discussionmentioning

confidence: 99%

Functional Domains of NosR, a Novel Transmembrane Iron-Sulfur Flavoprotein Necessary for Nitrous Oxide Respiration

Wunsch

Zumft

2005

J Bacteriol

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Bacterial nitrous oxide (N 2 O) respiration depends on the polytopic membrane protein NosR for the expression of N 2 O reductase from the nosZ gene. We constructed His-tagged NosR and purified it from detergentsolubilized membranes of Pseudomonas stutzeri ATCC 14405. NosR is an iron-sulfur flavoprotein with redox centers positioned at opposite sides of the cytoplasmic membrane. The flavin cofactor is presumably bound covalently to an invariant threonine residue of the periplasmic domain. NosR also features conserved CX 3 CP motifs, located C-terminally of the transmembrane helices TM4 and TM6. We genetically manipulated nosR with respect to these different domains and putative functional centers and expressed recombinant derivatives in a nosR null mutant, MK418nosR::Tn5. NosR's function was studied by its effects on N 2 O respiration, NosZ synthesis, and the properties of purified NosZ proteins. Although all recombinant NosR proteins allowed the synthesis of NosZ, a loss of N 2 O respiration was observed upon deletion of most of the periplasmic domain or of the C-terminal parts beyond TM2 or upon modification of the cysteine residues in a highly conserved motif, CGWLCP, following TM4. Nonetheless, NosZ purified from the recombinant NosR background exhibited in vitro catalytic activity. Certain NosR derivatives caused an increase in NosZ of the spectral contribution from a modified catalytic Cu site. In addition to its role in nosZ expression, NosR supports in vivo N 2 O respiration. We also discuss its putative functions in electron donation and redox activation.

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“…Since HS can dissolve in the cell membrane and is thought to affect membrane integrity, we expected to see a membraneremodeling response or an adaptation of the cell envelope to limit HS entry. Functions associated with the cell surface or transport are controlled by extracytoplasmic function sigma factors, like SigM, SigW, and SigX (32). Indeed, the gene groups regulated by extracytoplasmic function sigma factors SigW and SigX showed altered expression upon sorbic acid treatment (Fig.…”

Section: Vol 190 2008 B Subtilis Sorbic Acid Stress Response 1755mentioning

confidence: 97%

Transcriptome Analysis of Sorbic Acid-Stressed Bacillus subtilis Reveals a Nutrient Limitation Response and Indicates Plasma Membrane Remodeling

et al. 2008

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The weak organic acid sorbic acid is a commonly used food preservative, as it inhibits the growth of bacteria, yeasts, and molds. We have used genome-wide transcriptional profiling of Bacillus subtilis cells during mild sorbic acid stress to reveal the growth-inhibitory activity of this preservative and to identify potential resistance mechanisms. Our analysis demonstrated that sorbic acid-stressed cells induce responses normally seen upon nutrient limitation. This is indicated by the strong derepression of the CcpA, CodY, and Fur regulon and the induction of tricarboxylic acid cycle genes, SigL-and SigH-mediated genes, and the stringent response. Intriguingly, these conditions did not lead to the activation of sporulation, competence, or the general stress response. The fatty acid biosynthesis (fab) genes and BkdR-regulated genes are upregulated, which may indicate plasma membrane remodeling. This was further supported by the reduced sensitivity toward the fab inhibitor cerulenin upon sorbic acid stress. We are the first to present a comprehensive analysis of the transcriptional response of B. subtilis to sorbic acid stress.

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The extracytoplasmic function (ECF) sigma factors

Cited by 645 publications

References 150 publications

Genome plasticity and systems evolution in Streptomyces

Genome plasticity and systems evolution in Streptomyces

Functional Domains of NosR, a Novel Transmembrane Iron-Sulfur Flavoprotein Necessary for Nitrous Oxide Respiration

Transcriptome Analysis of Sorbic Acid-Stressed Bacillus subtilis Reveals a Nutrient Limitation Response and Indicates Plasma Membrane Remodeling

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