Gene expression profiling of <i>Escherichia coli</i> growth transitions: an expanded stringent response model

Chang, Dong-Eun; Smalley, Darren; Conway, Tyrrell

doi:10.1046/j.1365-2958.2002.03001.x

Cited by 281 publications

(288 citation statements)

References 78 publications

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“…Isolation of total RNA, labeling of samples, and duplicate hybridization to matched Panorama E. coli membrane arrays (Sigma-GenoSys, Woodlands, TX) were described previously (23)(24)(25). Raw data were imported into an Oracle database, normalized by expressing individual spot intensities as a fraction of the sum of all gene-specific spot intensities in each image, and analyzed as described previously (24).…”

Section: Methodsmentioning

confidence: 99%

Carbon nutrition of Escherichia coli in the mouse intestine

Chang

Smalley

Tucker

et al. 2004

Proc. Natl. Acad. Sci. U.S.A.

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467

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Whole-genome expression profiling revealed Escherichia coli MG1655 genes induced by growth on mucus, conditions designed to mimic nutrient availability in the mammalian intestine. Most were nutritional genes corresponding to catabolic pathways for nutrients found in mucus. We knocked out several pathways and tested the relative fitness of the mutants for colonization of the mouse intestine in competition with their wild-type parent. We found that only mutations in sugar pathways affected colonization, not phospholipid and amino acid catabolism, not gluconeogenesis, not the tricarboxylic acid cycle, and not the pentose phosphate pathway. Gluconate appeared to be a major carbon source used by E. coli MG1655 to colonize, having an impact on both the initiation and maintenance stages. N-acetylglucosamine and N-acetylneuraminic acid appeared to be involved in initiation, but not maintenance. Glucuronate, mannose, fucose, and ribose appeared to be involved in maintenance, but not initiation. The in vitro order of preference for these seven sugars paralleled the relative impact of the corresponding metabolic lesions on colonization: gluconate > N-acetylglucosamine > N-acetylneuraminic acid ‫؍‬ glucuronate > mannose > fucose > ribose. The results of this systematic analysis of nutrients used by E. coli MG1655 to colonize the mouse intestine are intriguing in light of the nutrientniche hypothesis, which states that the ecological niches within the intestine are defined by nutrient availability. Because humans are presumably colonized with different commensal strains, differences in nutrient availability may provide an open niche for infecting E. coli pathogens in some individuals and a barrier to infection in others.

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Section: Methodsmentioning

confidence: 99%

Carbon nutrition of Escherichia coli in the mouse intestine

Chang

Smalley

Tucker

et al. 2004

Proc. Natl. Acad. Sci. U.S.A.

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467

452

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“…E. coli MG1655 and isogenic mutants were cultured in a 2-liter Biostat B fermentor (B. Braun Biotech) containing 1 liter of morpholinepropanesulfonic acid (Mops) minimal medium with 0.5 g͞liter glucose and 1.5 g͞liter lactose, as described in ref. 3. The temperature was maintained at 37°C, and pH was kept constant at 7.2 by the addition of 2 M NaOH.…”

Section: Methodsmentioning

confidence: 99%

“…diluted (1:1) in ice-cold RNAlater (Ambion), and purified by using RNeasy columns (Qiagen), as described in ref. 3. RNA was labeled by first-strand cDNA synthesis using reverse transcriptase, random primers, and aminoallyl-dUTP incorporation; Cy-3 and Cy-5 dyes were chemically coupled in vitro to the aminoallylderivatized cDNA.…”

Section: Methodsmentioning

confidence: 99%

“…The genetic basis for biphasic sugar catabolism, elucidated by Jacob and Monod (2), is exemplified by lac operon induction, which is a textbook paradigm for illustrating genetic control. However, transcriptome analysis revealed that diauxie involves much more than induction of the lac operon, and that diauxie is accompanied by a global response to growth arrest that apparently ensures recovery when conditions allow growth to resume (3). The purpose of this study is to dissect the regulatory networks that govern diauxie as a means for understanding how the cell integrates the response to growth arrest.…”

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confidence: 99%

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Guanosine 3′,5′-bispyrophosphate coordinates global gene expression during glucose-lactose diauxie in Escherichia coli

Traxler

Chang

Conway

2006

Proc. Natl. Acad. Sci. U.S.A.

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104

128

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Guanosine 3 ,5 -bispyrophosphate (ppGpp), also known as ''magic spot,'' has been shown to bind prokaryotic RNA polymerase to down-regulate ribosome production and increase transcription of amino acid biosynthesis genes during the stringent response to amino acid starvation. Because many environmental growth perturbations cause ppGpp to accumulate, we hypothesize ppGpp to have an overarching role in regulating the genetic program that coordinates transitions between logarithmic growth (feast) and growth arrest (famine). We used the classic glucose-lactose diauxie as an experimental system to investigate the temporal changes in transcription that accompany growth arrest and recovery in wildtype Escherichia coli and in mutants that lack RelA (ppGpp synthetase) and other global regulators, i.e., RpoS and Crp. In particular, diauxie was delayed in the relA mutant and was accompanied by a 15% decrease in the number of carbon sources used and a 3-fold overall decrease in the induction of RpoS and Crp regulon genes. Thus the data significantly expand the previously known role of ppGpp and support a model wherein the ppGpp-dependent redistribution of RNA polymerase across the genome is the driving force behind control of the stringent response, general stress response, and starvation-induced carbon scavenging. Our conceptual model of diauxie describes these global control circuits as dynamic, interconnected, and dependent upon ppGpp for the efficient temporal coordination of gene expression that programs the cell for transitions between feast and famine.catabolite repression ͉ stringent response ͉ conceptual model T he fitness of free-living organisms depends on their ability to withstand environmental insults and grow as rapidly as possible when conditions allow. Consequently, the coordination of growth control processes constitutes a fundamental level of regulation in prokaryotes. For this reason, the bacterial existence is often thought to be one of ''feast and famine'' (1). In the laboratory, nutritional conditions that cause biphasic growth provide a unique opportunity to investigate this most basic of bacterial behaviors. When cultured on a mixture of glucose and lactose, Escherichia coli grows preferentially on glucose until the glucose is exhausted, resulting in growth arrest while the cells adjust to growth on lactose, i.e., diauxie. The genetic basis for biphasic sugar catabolism, elucidated by Jacob and Monod (2), is exemplified by lac operon induction, which is a textbook paradigm for illustrating genetic control. However, transcriptome analysis revealed that diauxie involves much more than induction of the lac operon, and that diauxie is accompanied by a global response to growth arrest that apparently ensures recovery when conditions allow growth to resume (3). The purpose of this study is to dissect the regulatory networks that govern diauxie as a means for understanding how the cell integrates the response to growth arrest.We showed previously (3) that during steady-state logarithmic growth, gene expressi...

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“…The effector molecule (called bacterial alarmone) of the stringent control is a hyperphosphorylated guanosine nucleotide, ppGpp, which binds to the ␤ and ␤Ј subunits of core RNAP. Alarmone takes part in the global control of gene expression in bacteria (32,33). In E. coli, it was shown that certain Rif r mutants behave like "stringent" RNAPs even in the absence of the stringent response (7).…”

Section: Ntd Functions As An Autoinducer For Itsmentioning

confidence: 99%

RNA Polymerase Mutation Activates the Production of a Dormant Antibiotic 3,3′-Neotrehalosadiamine via an Autoinduction Mechanism in Bacillus subtilis

Inaoka

Takahashi

Yada

et al. 2004

Journal of Biological Chemistry

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Bacillus and Streptomyces species possess the ability to produce a variety of commercially important metabolites and extracellular enzymes. We previously demonstrated that antibiotic production in Streptomyces coelicolor A3(2) and Streptomyces lividans can be enhanced by RNA polymerase (RNAP) mutations selected for the rifampicin-resistant (Rif r ) phenotype. Here, we have shown that the introduction of a certain Rif r rpoB mutation into a B. subtilis strain resulted in cells that overproduce an aminosugar antibiotic 3,3 -neotrehalosadiamine (NTD), the production of which is dormant in the wild-type strain. Mutational and recombinant gene expression analyses have revealed a polycistronic gene ntdABC (formally yhjLKJ) and a monocistronic gene ntdR (formally yhjM) as the NTD biosynthesis operon and a positive regulator for ntdABC, respectively. Analysis of transcriptional fusions to a lacZ reporter revealed that NTD acts as an autoinducer for its own biosynthesis genes via NtdR protein. Our results also showed that the Rif r rpoB mutation causes an increase in the activity of A -dependent promoters including ntdABC promoter. Therefore, we propose that unlike the wild-type RNAP, the mutant RNAP efficiently recognized the A -dependent promoters, resulting in the dramatic activation of the NTD biosynthesis pathway by an autoinduction mechanism.The ability of bacteria to survive in a wide range of adverse environmental conditions depends on diverse molecular mechanisms that adjust gene expression pattern in response to changing environment. DNA-dependent RNA polymerase (RNAP), 1 which is composed of an essential catalytic core enzyme (␣ 2 ␤␤Ј ) and one of the sigma ( ) factors, is the central enzyme for expression of genomic information in all organisms.Rifampicin (Rif) inhibits transcription initiation by blocking the ␤ subunit of bacterial RNAP (1, 2). Many Rif-resistant (Rif r ) mutants have been isolated and characterized in various bacteria, notably Escherichia coli. To our knowledge, most Rif r mutations are found within the rpoB gene that encodes the ␤ subunit of RNAP (3-6). E. coli Rif r rpoB mutations that suppress the auxotrophy due to lack of stringent response were demonstrated to affect the transcription of stringently controlled genes by destabilizing the RNAP-stable RNA promoter complex (7). Recently, we successfully activated the secondary metabolism (antibiotic production) by introducing certain Rif r rpoB mutations in Streptomyces coelicolor A3(2) and Streptomyces lividans (8 -11). On the basis of those findings, we proposed that improvement of RNAP by introduction of a Rif r mutation can be useful to elicit bacterial ability by altering the gene expression in a variety of microorganisms.The members of the genus Bacillus produce several antibiotics to inhibit growth of the competing organisms in nature. Neotrehalosadiamine (3,3Ј-diamino-3,3Ј-dideoxy-␣,␤-trehalose; NTD), which is an aminosugar antibiotic produced by Bacillus pumilus (12) and Bacillus circulans (13), inhibits growth of Staphylococcus a...

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Gene expression profiling of Escherichia coli growth transitions: an expanded stringent response model

Abstract: Fig. 2. Culture reproducibility of whole-genome expression profiles. The normalized, averaged data for the first time-point of the diauxic culture (culture 1) and the H 2 O 2 -treated culture (culture 2) are compared. The correlation coefficient is 0.992.

Cited by 281 publications

References 78 publications

Carbon nutrition of Escherichia coli in the mouse intestine

Carbon nutrition of Escherichia coli in the mouse intestine

Guanosine 3′,5′-bispyrophosphate coordinates global gene expression during glucose-lactose diauxie in Escherichia coli

RNA Polymerase Mutation Activates the Production of a Dormant Antibiotic 3,3′-Neotrehalosadiamine via an Autoinduction Mechanism in Bacillus subtilis

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