Global Impact of
            <i>sdiA</i>
            Amplification Revealed by Comprehensive Gene Expression Profiling of
            <i>Escherichia coli</i>

Yan, Wei; Lee, Jian-Ming; Smulski, Dana R.; LaRossa, Robert A.

doi:10.1128/jb.183.7.2265-2272.2001

Cited by 107 publications

(108 citation statements)

References 23 publications

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“…However, these acrAB induction rates are low (about twofold increase), probably because of the semi-constitutive expression of acrAB caused by the leakiness of AcrR control. SdiA overexpression also increases the transcriptional level of acrA in addition to that of acrD (Wei et al, 2001). Furthermore, it has been reported that carbonyl cyanide m-chlorophenylhydrazone (CCCP), 2,4-dinitrophenol, tetrachlorosalicylanilide (TCS) and nalidixic acid upregulate the expression of emrAB, via the action of the EmrR repressor protein (Lomovskaya et al, 1995).…”

Section: Discussionmentioning

confidence: 99%

Indole induces the expression of multidrug exporter genes in Escherichia coli

Hirakawa

Inazumi

Tomita

et al. 2005

Molecular Microbiology

277

265

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SummaryOur comprehensive expression cloning studies previously revealed that 20 intrinsic xenobiotic exporter systems are encoded in the Escherichia coli chromosome, but most of them are not expressed under normal conditions. In this study, we investigated the compounds that induce the expression of these xenobiotic exporter genes, and found that indole induces a variety of xenobiotic exporter genes including acrD , acrE , cusB , emrK , mdtA , mdtE and yceL . Indole treatment of E. coli cells confers rhodamine 6G and SDS resistance through the induction of mdtEF and acrD gene expression respectively. The induction of mdtE by indole is independent of the EvgSA twocomponent signal transduction system that regulates the mdtE gene, but mediated by GadX. On the other hand, the induction of acrD and mdtA was mediated by BaeSR and CpxAR, two-component systems. Interestingly, CpxAR system-mediated induction required intrinsic baeSR genes, whereas BaeSR-mediated induction was observed in the cpxAR gene-deletion mutant. BaeR and CpxR directly bound to different sequences of the acrD and mdtA promoter regions. These observations indicate that BaeR is a primary regulator, and CpxR enhances the effect of BaeR.

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Section: Discussionmentioning

confidence: 99%

Indole induces the expression of multidrug exporter genes in Escherichia coli

Hirakawa

Inazumi

Tomita

et al. 2005

Molecular Microbiology

277

265

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“…Interestingly, one of the SOS promoters, uvrY, is found to have a large error (Ϸ45%). This operon has been recently found to participate in a twocomponent signaling system related to stationary-phase response (27,28), and there is evidence that it is regulated by transcription factors other than LexA (29). The relatively large 30% error of polB may hint that it also has slight, as of yet uncharacterized, additional regulation.…”

Section: Detection Of Promoters With Additional Regulationmentioning

confidence: 99%

Assigning numbers to the arrows: Parameterizing a gene regulation network by using accurate expression kinetics

Ronen

Rosenberg

Shraiman

et al. 2002

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

478

445

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A basic challenge in systems biology is to understand the dynamical behavior of gene regulation networks. Current approaches aim at determining the network structure based on genomic-scale data. However, the network connectivity alone is not sufficient to define its dynamics; one needs to also specify the kinetic parameters for the regulation reactions. Here, we ask whether effective kinetic parameters can be assigned to a transcriptional network based on expression data. We present a combined experimental and theoretical approach based on accurate high temporal-resolution measurement of promoter activities from living cells by using green fluorescent protein (GFP) reporter plasmids. We present algorithms that use these data to assign effective kinetic parameters within a mathematical model of the network. To demonstrate this, we employ a well defined network, the SOS DNA repair system of Escherichia coli. We find a strikingly detailed temporal program of expression that correlates with the functional role of the SOS genes and is driven by a hierarchy of effective kinetic parameter strengths for the various promoters. The calculated parameters can be used to determine the kinetics of all SOS genes given the expression profile of just one representative, allowing a significant reduction in complexity. The concentration profile of the master SOS transcriptional repressor can be calculated, demonstrating that relative protein levels may be determined from purely transcriptional data. This finding opens the possibility of assigning kinetic parameters to transcriptional networks on a genomic scale.T here is much interest in understanding the design principles underlying the structure and dynamics of gene regulation networks (1)(2)(3)(4)(5)(6)(7)(8)(9)(10)36). Determining the dynamic behavior of these systems requires specifying not only the network connectivity, but also the kinetic parameters for the various regulation reactions. Standard biochemical methods of measuring these kinetic parameters are usually done outside of the cellular context and cannot be easily scaled up to a genomic level. It would therefore be valuable to develop methods to assign effective kinetic parameters to transcriptional networks based on in vivo measurements. Here we present an approach for determining the effective kinetic parameters of a transcriptional network based on accurate promoter activity measurements and analysis algorithms (Fig. 1).We developed a system for real-time monitoring of the transcriptional activity of operons by means of low-copy reporter plasmids (10) in which a promoter controls green fluorescent protein (GFP) (11). In each plasmid a different promoter controls the transcription rate of the same reporter gene, gfp, and thus rate of transcript production from the promoter is proportional to the rate of GFP accumulation. By continuous measurements from living cells grown in a multiwell plate fluorimeter, high-resolution time courses of the promoter strength and cell density are obtained. With this method, temporal...

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“…Quantitative real-time reverse transcription-PCR (qRT-PCR) was performed with the Applied Biosystems 7500 real-time PCR system (Applied Biosystems) with cDNA samples from bacteria. Transcription rates of the stxA 2e gene in bacteria were compared to those of the icdA housekeeping gene (51). Primers and TaqMan MGB probes were developed with ABI Prism Primer software (Applied Biosystems) and produced by Applied Biosystems (Applera Deutschland, Darmstadt, Germany).…”

Section: Bacteriamentioning

confidence: 99%

Evaluation of Major Types of Shiga Toxin 2e-Producing Escherichia coli Bacteria Present in Food, Pigs, and the Environment as Potential Pathogens for Humans

Beutin¹,

Krüger²,

Krause³

et al. 2008

Appl Environ Microbiol

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Shiga toxin 2e (Stx2e)-producing strains from food (n ‫؍‬ 36), slaughtered pigs (n ‫؍‬ 25), the environment (n ‫؍‬ 21), diseased pigs (n ‫؍‬ 19), and humans (n ‫؍‬ 9) were investigated for production of Stx2e by enzymelinked immunosorbent assay, for virulence markers by PCR, and for their serotypes to evaluate their role as potential human pathogens. Stx2e production was low in 64% of all 110 strains. Stx2e production was inducible by mitomycin C but differed considerably between strains. Analysis by nucleotide sequencing and transcription of stx 2e genes in high-and low-Stx2e-producing strains showed that toxin production correlated with transcription rates of stx 2e genes. DNA sequences specific for the int, Q, dam, and S genes of the stx 2e bacteriophage P27 were found in 109 strains, indicating cryptic P27-like prophages, although 102 of these were not complete for all genes tested. Genes encoding intimin (eae), enterohemorrhagic Escherichia coli hemolysin (ehx), or other stx 1 or stx 2 variants were not found, whereas genes for heat-stable enterotoxins STI, STII, or EAST1 were present in 54.5% of the strains. Seven major serotypes that were associated with diseased pigs (O138:H14, O139:H1, and O141:H4) or with slaughter pigs, food, and the environment (O8:H4, O8:H9, O100:H30, and O101:H9) accounted for 60% of all Stx2e strains. The human Stx2e isolates did not belong to these major serotypes of Stx2e strains, and high production of Stx2e in human strains was not related to diarrheal disease. The results from this study and other studies do not point to Stx2e as a pathogenicity factor for diarrhea and hemolytic uremic syndrome in humans.

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Global Impact of sdiA Amplification Revealed by Comprehensive Gene Expression Profiling of Escherichia coli

Cited by 107 publications

References 23 publications

Indole induces the expression of multidrug exporter genes in Escherichia coli

Indole induces the expression of multidrug exporter genes in Escherichia coli

Assigning numbers to the arrows: Parameterizing a gene regulation network by using accurate expression kinetics

Evaluation of Major Types of Shiga Toxin 2e-Producing Escherichia coli Bacteria Present in Food, Pigs, and the Environment as Potential Pathogens for Humans

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