Transcription start site and induction kinetics of the araC regulatory gene in Escherichia coli K-12

ABSTRACT The InvE protein positively regulates the expression of virulence genes ipaBCD in Shigella sonnei. The InvE has significant homology with ParB of plasmid P1, which is known as a plasmid partitioning factor with DNA binding ability. Although the DNA binding activity of InvE has been predicted, it is not known whether the DNA binding activity is necessary for type III secretion system-associated gene expression. In this study, we determined the transcription start site of the icsB-ipaBCD operon (ipa operon) and constructed a series of deletions of the icsB promoter region in the Escherichia coli K-12 background. The deletion study revealed that an 86-bp region upstream of the icsB transcription start site was essential for expression of the ipa operon, where the ParB binding motif (ParB BoxA-like sequence) was observed. Purified glutathione S-transferase-InvE fusion protein bound directly to the −93 to −54 region (designating the icsB transcription start site as nucleotide +1) containing the ParB BoxA-like sequence. These results indicated that InvE bound directly to the promoter region.

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Transcription Regulation by Tandem-Bound FNR at Escherichia coli Promoters

Journal of Bacteriology ◽

10.1128/jb.185.20.5993-6004.2003 ◽

2003 ◽

Vol 185 (20) ◽

pp. 5993-6004 ◽

Cited By ~ 17

Author(s):

Anne M. L. Barnard ◽

Jeffrey Green ◽

Stephen J. W. Busby

Keyword(s):

Escherichia Coli ◽

Transcription Factor ◽

Binding Site ◽

Transcription Regulation ◽

Transcription Start Site ◽

Promoter Activity ◽

Start Site ◽

Transcription Start ◽

Substitution Mutant

ABSTRACT FNR is an Escherichia coli transcription factor that regulates the transcription of many genes in response to anaerobiosis. We have constructed a series of artificial FNR-dependent promoters, based on the melR promoter, in which a consensus FNR binding site was centered at position −41.5 relative to the transcription start site. A second consensus FNR binding site was introduced at different upstream locations, and promoter activity was assayed in vivo. FNR can activate transcription from these promoters when the upstream FNR binding site is located at many different positions. However, sharp repression is observed when the upstream-bound FNR is located near positions −85 or −95. This repression is relieved by the FNR G74C substitution mutant, previously identified as being defective in transcription repression at the yfiD promoter. A parallel series of artificial FNR-dependent promoters, carrying a consensus FNR binding site at position −61.5 and a second upstream DNA site for FNR, was also constructed. Again, promoter activity was repressed by FNR when the upstream-bound FNR was located at particular positions.

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Lysine Represses Transcription of the Escherichia coli dapB Gene by Preventing Its Activation by the ArgP Activator

Journal of Bacteriology ◽

10.1128/jb.01782-07 ◽

2008 ◽

Vol 190 (15) ◽

pp. 5224-5229 ◽

Cited By ~ 15

Author(s):

Jean Bouvier ◽

Patrick Stragier ◽

Violette Morales ◽

Elisabeth Rémy ◽

Claude Gutierrez

Keyword(s):

Escherichia Coli ◽

Transcription Start Site ◽

Biosynthetic Pathway ◽

Genomic Library ◽

Regulatory Region ◽

Null Mutation ◽

Start Site ◽

Transcription Start ◽

Gene Encoding ◽

Gel Retardation Assay

ABSTRACT The Escherichia coli dapB gene encodes one of the enzymes of the biosynthetic pathway leading to lysine and its immediate precursor, diaminopimelate. Expression of dapB is repressed by lysine, but no trans-acting regulator has been identified so far. Our analysis of the dapB regulatory region shows that sequences located in the −81/−118 interval upstream of the transcription start site are essential for full expression of dapB, as well as for lysine repression. Screening a genomic library for a gene that could alleviate lysine repression when present in multicopy led to the recovery of argP, a gene encoding an activating protein of the LysR-type family, known to use lysine as an effector. An argP null mutation strongly decreases dapB transcription that becomes insensitive to lysine. Purified His6-tagged ArgP protein binds with an apparent K d of 35 nM to the dapB promoter in a gel retardation assay, provided that sequences up to −103 are present. In the presence of l-lysine and l-arginine, the binding of ArgP to dapB is partly relieved. These results fit with a model in which ArgP contributes to enhanced transcription of dapB when lysine becomes limiting.

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The UP Element Is Necessary but Not Sufficient for Growth Rate-Dependent Control of the Escherichia coli guaB Promoter

Journal of Bacteriology ◽

10.1128/jb.01732-07 ◽

2008 ◽

Vol 190 (7) ◽

pp. 2450-2457 ◽

Cited By ~ 9

Author(s):

Seyyed I. Husnain ◽

Mark S. Thomas

Keyword(s):

Escherichia Coli ◽

Growth Rate ◽

Transcription Start Site ◽

De Novo ◽

Start Site ◽

Transcription Start ◽

Lower Growth ◽

Α Subunit ◽

Rate Dependent ◽

Up Elements

ABSTRACT The Escherichia coli guaB promoter (P guaB ) regulates the transcription of two genes, guaB and guaA, that are required for de novo synthesis of GMP, a precursor for the synthesis of guanine nucleoside triphosphates. The activity of P guaB is subject to growth rate-dependent control (GRDC). Here we show that the A+T-rich sequence located between positions −59 and −38 relative to the guaB transcription start site stimulates transcription from P guaB ∼8- to 10-fold and, in common with other UP elements, requires the C-terminal domain of the RNA polymerase α subunit for activity. Like the rrnB P1 UP element, the P guaB UP element contains two independently acting subsites located at positions −59 to −47 and −46 to −38 and can stimulate transcription when placed upstream of the lacP1 promoter. We reveal a novel role for the P guaB UP element by demonstrating that it is required for GRDC. The involvement of the UP element in GRDC also requires the participation of sequences located at least 100 bp upstream of the guaB transcription start site. These sequences are required for down-regulation of P guaB activity at lower growth rates.

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Genetic Features of MCR-1-Producing Colistin-Resistant Escherichia coli Isolates in South Africa

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.00444-16 ◽

2016 ◽

Vol 60 (7) ◽

pp. 4394-4397 ◽

Cited By ~ 89

Author(s):

Laurent Poirel ◽

Nicolas Kieffer ◽

Adrian Brink ◽

Jennifer Coetze ◽

Aurélie Jayol ◽

...

Keyword(s):

Escherichia Coli ◽

South Africa ◽

Transcription Start Site ◽

Dna Sequences ◽

Start Site ◽

Transcription Start ◽

Content Type ◽

Promoter Sequences ◽

Genetic Features ◽

Community Patients

ABSTRACTA series of colistin-resistantEscherichia coliclinical isolates was recovered from hospitalized and community patients in South Africa. Seven clonally unrelated isolates harbored themcr-1gene located on different plasmid backbones. Two distinct plasmids were fully sequenced, and identical 2,600-bp-long DNA sequences defining amcr-1cassette were identified. Promoter sequences responsible for the expression ofmcr-1, deduced from the precise identification of the +1 transcription start site formcr-1, were characterized.

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Regulation of Expression of the Region 3 Promoter of the Escherichia coli K5 Capsule Gene Cluster Involves H-NS, SlyA, and a Large 5′ Untranslated Region

Journal of Bacteriology ◽

10.1128/jb.01388-08 ◽

2008 ◽

Vol 191 (6) ◽

pp. 1838-1846 ◽

Cited By ~ 17

Author(s):

Peng Xue ◽

David Corbett ◽

Marie Goldrick ◽

Clare Naylor ◽

Ian S. Roberts

Keyword(s):

Escherichia Coli ◽

Transcription Start Site ◽

Untranslated Region ◽

Regulatory Element ◽

Gene Clusters ◽

Regulation Of Transcription ◽

Start Site ◽

Transcription Start ◽

Regulation Of Expression ◽

Group 2

ABSTRACT Escherichia coli group 2 capsule gene clusters are temperature regulated, being expressed at 37°C but not at 20°C. Expression is regulated at the level of transcription by two convergent promoters, PR1 and PR3. In this paper, we show that regulation of transcription from PR3 involves a number of novel features including H-NS, SlyA, and a large 741-bp 5′ untranslated region (UTR). H-NS represses transcription from PR3 at 20°C and binds both 5′ and 3′ of the transcription start site. The 3′ downstream regulatory element (DRE) was essential for temperature-dependent H-NS repression. At 37°C, SlyA activates transcription independent of H-NS but maximal transcription requires H-NS. The UTR is present between the transcription start site and the first gene in the operon, kpsM. We demonstrate that the UTR, as well as containing the H-NS DRE, functions to moderate the extent of transcription that reaches kpsM and allows the binding of antitermination factor RfaH.

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DNA binding properties of the Escherichia coli nitric oxide sensor NorR: towards an understanding of the regulation of flavorubredoxin expression

Biochemical Society Transactions ◽

10.1042/bst0330181 ◽

2005 ◽

Vol 33 (1) ◽

pp. 181-183 ◽

Cited By ~ 10

Author(s):

N. Tucker ◽

B. D'Autréaux ◽

S. Spiro ◽

R. Dixon

Keyword(s):

Nitric Oxide ◽

Escherichia Coli ◽

Rna Polymerase ◽

Transcription Start Site ◽

Binding Sites ◽

Regulatory Protein ◽

Enteric Bacteria ◽

Integration Host Factor ◽

Start Site ◽

Transcription Start

Nitric oxide is an intermediate of denitrification, and is one of the radical species deployed by macrophages against invading pathogens, therefore bacterial responses to NO are of considerable importance. The Escherichia coli flavorubredoxin and its associated oxidoreductase reduce NO to nitrous oxide under anaerobic conditions, and are encoded by the norVW transcription unit. Expression of norVW requires the NO sensing regulatory protein NorR and is dependent on RNA polymerase containing the alternative sigma factor, σ54. We have purified NorR and shown that it binds to three sites in the norVW promoter region, located 75–140 bp upstream of the experimentally verified transcription start site. We have also identified two binding sites for the integration host factor, one between the NorR sites and the σ54-RNA polymerase binding site, and a second downstream of the norVW transcription start site. Comparison of the norVW promoters of enteric bacteria along with known and putative NorR-regulated promoters from Vibrio, Ralstonia and Pseudomonas species suggests that NorR binding sites contain an invariant GT(N7)AC motif flanking an AT-rich central region. The identification of a consensus for NorR binding sites will help to elucidate additional members of the NorR regulon.

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T7 phage protein Gp2 inhibits the Escherichia coli RNA polymerase by antagonizing stable DNA strand separation near the transcription start site

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.0907908107 ◽

2010 ◽

Vol 107 (5) ◽

pp. 2247-2252 ◽

Cited By ~ 51

Author(s):

Beatriz Cámara ◽

Minhao Liu ◽

Jonathan Reynolds ◽

Andrey Shadrin ◽

Bing Liu ◽

...

Keyword(s):

Escherichia Coli ◽

Rna Polymerase ◽

Transcription Start Site ◽

Structural Model ◽

Start Site ◽

Transcription Start ◽

Strand Separation ◽

Arginine Residues ◽

Dna Strand ◽

T7 Phage

Infection of Escherichia coli by the T7 phage leads to rapid and selective inhibition of the host RNA polymerase (RNAP)—a multi-subunit enzyme responsible for gene transcription—by a small (∼7 kDa) phage-encoded protein called Gp2. Gp2 is also a potent inhibitor of E. coli RNAP in vitro. Here we describe the first atomic resolution structure of Gp2, which reveals a distinct run of surface-exposed negatively charged amino acid residues on one side of the molecule. Our comprehensive mutagenesis data reveal that two conserved arginine residues located on the opposite side of Gp2 are important for binding to and inhibition of RNAP. Based on a structural model of the Gp2-RNAP complex, we propose that inhibition of transcription by Gp2 involves prevention of RNAP-promoter DNA interactions required for stable DNA strand separation and maintenance of the “transcription bubble” near the transcription start site, an obligatory step in the formation of a transcriptionally competent promoter complex.

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