There are few existing indications that strain variation in prokaryotic gene regulation is common or has evolutionary advantage. In this study, we report on isolates of Escherichia coli with distinct ratios of sigma factors (RpoD, D , or 70 and RpoS or S ) that affect transcription initiated by RNA polymerase. Both laboratory E. coli K-12 lineages and nondomesticated isolates exhibit strain-specific endogenous levels of RpoS protein. We demonstrate that variation in genome usage underpins intraspecific variability in transcription patterns, resistance to external stresses, and the choice of beneficial mutations under nutrient limitation. Most unexpectedly, RpoS also controlled strain variation with respect to the metabolic capability of bacteria with more than a dozen carbon sources. Strains with higher S levels were more resistant to external stress but metabolized fewer substrates and poorly competed for low concentrations of nutrients. On the other hand, strains with lower S levels had broader nutritional capabilities and better competitive ability with low nutrient concentrations but low resistance to external stress. In other words, RpoS influenced both r and K strategist functions of bacteria simultaneously. The evolutionary principle driving strain variation is proposed to be a conceptually novel trade-off that we term SPANC (for "self-preservation and nutritional competence"). The availability of multiple SPANC settings potentially broadens the niche occupied by a species consisting of individuals with narrow specialization and reveals an evolutionary advantage offered by polymorphic regulation. Regulatory diversity is likely to be a significant contributor to complexity in a bacterial world in which multiple sigma factors are a universal feature.The major source of variation in prokaryotes is thought to be the loss or gain of functional genes or elements, such as pathogenicity islands (14, 33). Members of a bacterial species such as Escherichia coli have common properties and similar chromosomal organizations, but the species is phenotypically diverse (44). Isolates of E. coli exhibit many distinct properties, including distinct growth rates (28) and stress sensitivities (1, 43). Some of the differences are undoubtedly due to loss or gain of genes, but is there also a difference in gene usage or expression between strains? The gene regulatory consistency of bacteria is relatively poorly studied, but it needs to be understood if the full range of bacterial variation is to be established. In this study, we investigated whether strain-specific gene usage is a source of bacterial variation in E. coli.Our starting point for examining this question arose from recent studies of the polymorphism of the RpoS sigma factor in isolates of E. coli and Salmonella (11, 31). If a central regulator of stress resistance genes (RpoS or S [24,40]) is not conserved, then how constant is gene usage on a global scale? It is evident from both laboratory studies and the occurrence of rpoS mutations in natural populations that ...
Under stressful conditions in nature, Escherichia coli forms biofilms for long-term survival. Curli fimbriae are an essential architecture for cell-cell contacts within biofilms. Structural components and assembly factors of curli are encoded by two operons, csgBA and csgDEFG. The csgD gene product controls transcription of both operons. Reflecting the response of csgD expression to external stresses, a number of transcription factors participate in the regulation of the csgD promoter. Analysis of the csgD mRNA obtained from E. coli mutants in different transcription factors indicated that CpxR and H-NS act as repressors while OmpR, RstA and IHF act as activators. An acid-stress response regulator, RstA, activates csgD only under acidic conditions. These five factors bind within a narrow region of about 200 bp upstream of the csgD promoter. After pair-wise promoter-binding assays, the increase in csgD transcription in the stationary phase was suggested to be due, at least in part, to the increase in IHF level cancelling the silencing effect of H-NS. In addition, we propose a novel regulation model of this complex csgD promoter through cooperation between the two positive factors (OmpR-IHF and RstA-IHF) and also between the two negative factors (CpxR-H-NS). INTRODUCTIONBacteria can switch from a single-cell planktonic growth mode to a multicellular community (biofilm) mode. During such a growth transition state, cell morphology, physiology and metabolism are markedly altered (PrigentCombaret et al., 2001;Schembri et al., 2003;Beloin et al., 2004;Ren et al., 2004). In single-cell growth mode, cell motility using flagella is critical for adaptation to environments. The master regulator FlhCD complex plays a key role in controlling transcription of a set of genes for flagella formation (Claret & Huges, 2000). When Escherichia coli cells switch their life mode from single planktonic cell growth to multicellular community (biofilm) mode, the genetic system for flagella formation is turned off and the genes involved in cell-cell adhesion are activated. The biofilm matrix is a complex architecture of cell aggregates that are attached on the surface of inorganic solid materials in nature or on eukaryotic tissues in host animals. After a comprehensive analysis of a set of E. coli mutants, each lacking one of 3985 non-essential genes, a total of 110 genes were indicated to be involved in biofilm formation (Niba et al., 2007).During biofilm development, curli fimbriae, the major biofilm component, play a key role in both initial adhesion to solid surfaces and subsequent cell-cell interactions (Vidal et al., 1998;Chapman et al., 2002;Prigent-Combaret et al., 2000). Curli fimbriae also mediate bacterial adhesion to host cells and invasion, and activation of both the proinflammatory response and the immune system (Bian et al., 2000;Zogaj et al., 2001). Accordingly, curli participate in virulence phenotypes (Hammar et al., 1995; Vidal et al., 1998;Bian et al., 2000; Gophna et al., 2001;Cookson et al., 2002). A set of polysacch...
SummaryUsing the genomic SELEX, a total of six Escherichia coli DNA fragments have been identified, which formed complexes with transcription factor RutR. The RutR regulon was found to include a large number of genes encoding components for not only degradation of pyrimidines but also transport of glutamate, synthesis of glutamine, synthesis of pyrimidine nucleotides and arginine, and degradation of purines. DNase I footprinting indicated that RutR recognizes a palindromic sequence of TTGACCAnnTGGTCAA. The RutR box in P1 promoter of carAB encoding carbamoyl phosphate synthetase, a key enzyme of pyrimidine synthesis, overlaps with the PepA (CarP) repressor binding site, implying competition between RutR and PepA. Adding either uracil or thymine abolished RutR binding in vitro to the carAB P1 promoter. Accordingly, in the rutR-deletion mutant or in the presence of uracil, the activation in vivo of carAB P1 promoter was markedly reduced. Northern blot analysis of the RutR target genes indicated that RutR represses the Gad system genes involved in glutamate-dependent acid resistance and allantoin degradation. Altogether we propose that RutR is the pyrimidine sensor and the master regulator for a large set of the genes involved in the synthesis and degradation of pyrimidines.
The expression pattern of the Escherichia coli genome is controlled in part by regulating the utilization of a limited number of RNA polymerases among a total of its approximately 4,600 genes. The distribution pattern of RNA polymerase changes from modulation of two types of protein-protein interactions: the interaction of core RNA polymerase with seven species of the sigma subunit for differential promoter recognition and the interaction of RNA polymerase holoenzyme with about 300 different species of transcription factors (TFs) with regulatory functions. We have been involved in the systematic search for the target promoters recognized by each sigma factor and each TF using the newly developed Genomic SELEX system. In parallel, we developed the promoter-specific (PS)-TF screening system for identification of the whole set of TFs involved in regulation of each promoter. Understanding the regulation of genome transcription also requires knowing the intracellular concentrations of the sigma subunits and TFs under various growth conditions. This report describes the intracellular levels of 65 species of TF with known function in E. coli K-12 W3110 at various phases of cell growth and at various temperatures. The list of intracellular concentrations of the sigma factors and TFs provides a community resource for understanding the transcription regulation of E. coli under various stressful conditions in nature.
scite is a Brooklyn-based organization that helps researchers better discover and understand research articles through Smart Citations–citations that display the context of the citation and describe whether the article provides supporting or contrasting evidence. scite is used by students and researchers from around the world and is funded in part by the National Science Foundation and the National Institute on Drug Abuse of the National Institutes of Health.
hi@scite.ai
10624 S. Eastern Ave., Ste. A-614
Henderson, NV 89052, USA
Copyright © 2024 scite LLC. All rights reserved.
Made with 💙 for researchers
Part of the Research Solutions Family.