Screening of promoter-specific transcription factors: multiple regulators for the sdiA gene involved in cell division control and quorum sensing

Shimada, Kaori; Ogasawara, Hiroshi; Yamada, Kayoko; Shimura, Miki; Kori, Ayako; Shimada, Tomohiro; Yamanaka, Yuko; Ishihama, Akira

doi:10.1099/mic.0.067538-0

Cited by 27 publications

(34 citation statements)

References 77 publications

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“…Wild-type E. coli K-12 W3110 type A was grown in LB medium under aeration with constant shaking at 140 rpm. The cell culture was carried out at five different temperatures (22,27,32,37, and 42°C) and for various times from exponential growth to stationary phase. Cell growth was monitored by measuring the culture turbidity at 600 nm.…”

Section: Methodsmentioning

confidence: 99%

“…Using this Genomic SELEX screening system, we also succeeded in identifying the set of constitutive promoters recognized in vitro by the RpoD holoenzyme alone in the absence of supporting TFs (21). In parallel, we have developed the promoterspecific transcription factor (PS-TF) screening system for identification of the set of promoter-specific TFs working on one specific promoter (22). Concomitant with the advance in Genomic SELEX and PS-TF screening systems, the concept of transcription regulation has changed remarkably in two aspects: (i) a single TF is generally involved in regulation of a number of genes and (ii) one promoter is often regulated by a number of TFs (2).…”

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confidence: 99%

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Intracellular Concentrations of 65 Species of Transcription Factors with Known Regulatory Functions in Escherichia coli

et al. 2014

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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.

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Section: Methodsmentioning

confidence: 99%

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Intracellular Concentrations of 65 Species of Transcription Factors with Known Regulatory Functions in Escherichia coli

et al. 2014

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“…97) Together with Genomic SELEX screening, it turned clear that most E. coli promoters are under the direct control of multiple transcription factors. 6,7) For instance, most of the genes under the control of MntR are also repressed by Fe 2+ -sensing global regulator Fur (Fig.…”

Section: Promoters Under the Control Of Multiple Metalresponse Regulamentioning

confidence: 99%

The hierarchic network of metal-response transcription factors in Escherichia coli

Yamamoto

2014

Bioscience, Biotechnology, and Biochemistry

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“…For the identification of direct targets by each TF, we have developed two in vitro screening systems: an improved method of the Genomic SELEX screening system (Shimada et al, 2005); and the promoter-specific TF screening system (Shimada et al, 2013). Results so far obtained using these two lines of research indicate that: (1) a single TF is generally involved in the regulation of several genes and (2) one promoter is often regulated by several TFs.…”

Section: Introductionmentioning

confidence: 99%

“…For instance, the csgD gene encoding the master regulator of biofilm formation is regulated by as many as 30 TFs (Ogasawara et al, 2010;Ishihama, 2012). More than 15 TFs are involved in regulation of the sdiA gene encoding the regulator for cell division and differentiation (Shimada et al, 2013). On these multifactor-regulated promoters, the positive and negative TFs compete with each other for effective binding to a narrow region of a single and the same promoter, but in addition, collaborative interplay takes place between positive TFs and between negative TFs (Ogasawara et al, 2010;Ishihama, 2012).…”

Section: Introductionmentioning

confidence: 99%

Expression levels of transcription factors in Escherichia coli: growth phase- and growth condition-dependent variation of 90 regulators from six families

Watanabe

Ishihama

2014

Microbiology

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The expression pattern of the genome in Escherichia coli is controlled by regulating the utilization of a limited number of RNA polymerases between a total of 4600 genes on its genome. The distribution pattern of RNA polymerase on the genome changes after two steps of protein-protein interaction with seven sigma subunits and about 300 transcription factors (TFs). Based on a systematic search for the regulation target promoters recognized by each TF, we propose two novel concepts: each TF regulates a number of target promoters; and each promoter is regulated by many TFs. In parallel, attempts have been made to determine the intracellular concentrations of all TFs using two systems: quantitative immunoblot analysis using TF-specific antibodies; and reporter assay of TF promoter activities. The direct measurement of TF protein level has so far been published for a set of 60 regulators with known functions. This study describes the determination of growth phase-dependent expression levels of 90 TFs using the reporter assay system. The translational fusion vector was constructed from the TF promoter sequence including an N-terminal proximal TF segment and the reporter GFP. At the beginning of cell growth, highlevel expression was observed only for a small number of TFs. In the exponential phase, approximately 80 % TFs are expressed, but the expressed TF species change upon transfer to the stationary phase. Significant changes in the pattern of TF expression were observed between aerobic and anaerobic conditions. The list of intracellular levels of TFs provides further understanding to the transcription regulation of the E. coli genome under various stressful conditions. INTRODUCTIONSingle-cell bacteria are directly exposed to frequently changing environments in nature and thus carry sophisticated genetic systems for adaptation to environmental changes (Ishihama, 2010(Ishihama, , 2012Yamamoto, 2014). On the basis of the complete genome sequence of several model Escherichia coli strains, the whole set of about 4600 genes has been predicted to exist in E. coli K-12 (Hayashi et al., 2006;Riley et al., 2006). In growing E. coli cells under laboratory culture conditions, only one-quarter to one-third of the genes on its genome are expressed, the others remaining silent. The majority of these uncharacterized silent genes must be expressed and utilized for adaptation and survival of E. coli under stressful conditions. Thus, even for this well-characterized model organism, the gene functions remain unidentified or unpredicted for approximately one-quarter because expression conditions of these silent genes have not yet been established.As the total number of RNA polymerases (RNAPs) in E. coli K-12 is less than the total number of genes on its genome (Ishihama, 2000), we proposed a model in which the change in genome transcription pattern takes place mainly through controlling the utilization of this limited number of transcription apparatuses between 4600 genes on the genome (Ishihama, 2010(Ishihama, , 2012. Two groups of reg...

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Screening of promoter-specific transcription factors: multiple regulators for the sdiA gene involved in cell division control and quorum sensing

Cited by 27 publications

References 77 publications

Intracellular Concentrations of 65 Species of Transcription Factors with Known Regulatory Functions in Escherichia coli

Intracellular Concentrations of 65 Species of Transcription Factors with Known Regulatory Functions in Escherichia coli

The hierarchic network of metal-response transcription factors in Escherichia coli

Expression levels of transcription factors in Escherichia coli: growth phase- and growth condition-dependent variation of 90 regulators from six families

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