Single-target regulators form a minor group of transcription factors in Escherichia coli K-12

The identification of regulatory targets of all transcription factors (TFs) is critical for understanding the entire network of genome regulation. A total of approximately 300 TFs exist in the model prokaryote Escherichia coli K-12, but the identification of whole sets of their direct targets is impossible with use of in vivo approaches. For this end, the most direct and quick approach is to identify the TF-binding sites in vitro on the genome. We then developed and utilized the gSELEX screening system in vitro for identification of more than 150 E. coli TF-binding sites along the E. coli genome. Based on the number of predicted regulatory targets, we classified E. coli K-12 TFs into four groups, altogether forming a hierarchy ranging from a single-target TF (ST-TF) to local TFs, global TFs, and nucleoid-associated TFs controlling as many as 1,000 targets. Using the collection of purified TFs and a library of genome DNA segments from a single and the same E. coli K-12, we identified here a total of 11 novel ST-TFs, CsqR, CusR, HprR, NorR, PepA, PutA, QseA, RspR, UvrY, ZraR, and YqhC. The regulation of single-target promoters was analyzed in details for the hitherto uncharacterized QseA and RspR. In most cases, the ST-TF gene and its regulatory target genes are adjacently located on the E. coli K-12 genome, implying their simultaneous transfer in the course of genome evolution. The newly identified 11 ST-TFs and the total of 13 hitherto identified altogether constitute the minority group of TFs in E. coli K-12.

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The functional landscape bound to the transcription factors of Escherichia coli K-12

Computational Biology and Chemistry ◽

10.1016/j.compbiolchem.2015.06.002 ◽

2015 ◽

Vol 58 ◽

pp. 93-103 ◽

Cited By ~ 12

Author(s):

Ernesto Pérez-Rueda ◽

Silvia Tenorio-Salgado ◽

Alejandro Huerta-Saquero ◽

Yalbi I. Balderas-Martínez ◽

Gabriel Moreno-Hagelsieb

Keyword(s):

Escherichia Coli ◽

Transcription Factors ◽

K 12

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Systematic discovery of uncharacterized transcription factors in Escherichia coli K-12 MG1655

Nucleic Acids Research ◽

10.1093/nar/gky752 ◽

2018 ◽

Cited By ~ 11

Author(s):

Ye Gao ◽

James T Yurkovich ◽

Sang Woo Seo ◽

Ilyas Kabimoldayev ◽

Andreas Dräger ◽

...

Keyword(s):

Escherichia Coli ◽

Transcription Factors ◽

K 12

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mcr-9, an Inducible Gene Encoding an Acquired Phosphoethanolamine Transferase in Escherichia coli, and Its Origin

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.00965-19 ◽

2019 ◽

Vol 63 (9) ◽

Cited By ~ 23

Author(s):

Nicolas Kieffer ◽

Guilhem Royer ◽

Jean-Winoc Decousser ◽

Anne-Sophie Bourrel ◽

Mattia Palmieri ◽

...

Keyword(s):

Escherichia Coli ◽

Lipid A ◽

Acquired Resistance ◽

Regulatory System ◽

Amino Acid Identity ◽

Gene Encoding ◽

Content Type ◽

E Coli ◽

K 12 ◽

A Minor

ABSTRACT The plasmid-located mcr-9 gene, encoding a putative phosphoethanolamine transferase, was identified in a colistin-resistant human fecal Escherichia coli strain belonging to a very rare phylogroup, the D-ST69-O15:H6 clone. This MCR-9 protein shares 33% to 65% identity with the other plasmid-encoded MCR-type enzymes identified (MCR-1 to -8) that have been found as sources of acquired resistance to polymyxins in Enterobacteriaceae. Analysis of the lipopolysaccharide of the MCR-9-producing isolate revealed a function similar to that of MCR-1 by adding a phosphoethanolamine group to lipid A and subsequently modifying the structure of the lipopolysaccharide. However, a minor impact on susceptibility to polymyxins was noticed once the mcr-9 gene was cloned and produced in an E. coli K-12-derived strain. Nevertheless, we showed here that subinhibitory concentrations of colistin induced the expression of the mcr-9 gene, leading to increased MIC levels. This inducible expression was mediated by a two-component regulatory system encoded by the qseC and qseB genes located downstream of mcr-9. Genetic analysis showed that the mcr-9 gene was carried by an IncHI2 plasmid. In silico analysis revealed that the plasmid-encoded MCR-9 shared significant amino acid identity (ca. 80%) with the chromosomally encoded MCR-like proteins from Buttiauxella spp. In particular, Buttiauxella gaviniae was found to harbor a gene encoding MCR-BG, sharing 84% identity with MCR-9. That gene was neither expressed nor inducible in its original host, which was fully susceptible to polymyxins. This work showed that mcr genes may circulate silently and remain undetected unless induced by colistin.

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A Systems Approach Discovers the Role and Characteristics of Seven LysR Type Transcription Factors in Escherichia Coli

10.21203/rs.3.rs-1083621/v1 ◽

2021 ◽

Author(s):

Irina Rodionova ◽

Bernhard Palsson ◽

Ye Gao ◽

Nicholas Wong ◽

Richard Szubin ◽

...

Keyword(s):

Escherichia Coli ◽

Transcription Factors ◽

Bacterial Growth ◽

Target Genes ◽

Systems Approach ◽

Gene Clustering ◽

Phosphotransferase System ◽

E Coli ◽

Semialdehyde Dehydrogenase ◽

K 12

Abstract Although Escherichia coli K-12 strains represent perhaps the best known model bacteria, we do not know the identity or functions of all of their transcription factors (TFs). It is now possible to systematically discover the physiological function of TFs in E. coli BW25113 using a set of synergistic methods; including ChIP-exo, growth phenotyping, conserved gene clustering, and transcriptome analysis. Among 47 LysR-type TFs (LTFs) found on the E. coli K-12 genome, many regulate nitrogen source utilization or amino acid metabolism. However, 19 LTFs remain unknown. In this study, we elucidated the regulation of seven of these 19 LTFs: YbdO, YbeF, YgfI, YiaU, YneJ, YcaN, YbhD. We show that: 1) YbdO regulation has an effect on bacterial growth at low pH with citrate supplementation. YbdO is a repressor of the ybdNM operon and is implicated in the regulation of citrate lyase genes (citCDEFG); 2) YgfI activates the dhaKLM operon that encodes the phosphotransferase system involved in glycerol and dihydroxyacetone utilization; 3) YiaU regulates the yiaT gene encoding an outer membrane protein, and waaPSBOJYZU operon is also important in determining cell density at the stationary phase; 4) YneJ, re-named here as PtrR, directly regulates the expression of the succinate-semialdehyde dehydrogenase, Sad (also known as YneI), and is a predicted regulator of fnrS (a small RNA molecule). PtrR is important for bacterial growth in the presence of L-glutamate and putrescine as nitrogen sources; and 5) YbhD and YcaN regulate adjacent y-genes on the genome and YbeF is involved in flagella gene regulation. We have thus established the functions for four LTFs and identified the target genes for three LTFs.

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Repression of YdaS Toxin Is Mediated by Transcriptional Repressor RacR in the Cryptic rac Prophage of Escherichia coli K-12

mSphere ◽

10.1128/msphere.00392-17 ◽

2017 ◽

Vol 2 (6) ◽

Cited By ~ 5

Author(s):

Revathy Krishnamurthi ◽

Swagatha Ghosh ◽

Supriya Khedkar ◽

Aswin Sai Narain Seshasayee

Keyword(s):

Escherichia Coli ◽

Transcription Factor ◽

Transcriptional Regulation ◽

Transcription Factors ◽

Transcriptional Repressor ◽

Type Ii ◽

Content Type ◽

E Coli ◽

Putative Transcription Factor ◽

K 12

ABSTRACT Transcription factors in the bacterium E. coli are rarely essential, and when they are essential, they are largely toxin-antitoxin systems. While studying transcription factors encoded in horizontally acquired regions in E. coli, we realized that the protein RacR, a putative transcription factor encoded by a gene on the rac prophage, is an essential protein. Here, using genetics, biochemistry, and bioinformatics, we show that its essentiality derives from its role as a transcriptional repressor of the ydaS and ydaT genes, whose products are toxic to the cell. Unlike type II toxin-antitoxin systems in which transcriptional regulation involves complexes of the toxin and antitoxin, repression by RacR is sufficient to keep ydaS transcriptionally silent. Horizontal gene transfer is a major driving force behind the genomic diversity seen in prokaryotes. The cryptic rac prophage in Escherichia coli K-12 carries the gene for a putative transcription factor RacR, whose deletion is lethal. We have shown that the essentiality of racR in E. coli K-12 is attributed to its role in transcriptionally repressing toxin gene(s) called ydaS and ydaT, which are adjacent to and coded divergently to racR. IMPORTANCE Transcription factors in the bacterium E. coli are rarely essential, and when they are essential, they are largely toxin-antitoxin systems. While studying transcription factors encoded in horizontally acquired regions in E. coli, we realized that the protein RacR, a putative transcription factor encoded by a gene on the rac prophage, is an essential protein. Here, using genetics, biochemistry, and bioinformatics, we show that its essentiality derives from its role as a transcriptional repressor of the ydaS and ydaT genes, whose products are toxic to the cell. Unlike type II toxin-antitoxin systems in which transcriptional regulation involves complexes of the toxin and antitoxin, repression by RacR is sufficient to keep ydaS transcriptionally silent.

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Analysis of lambda insertions in the fucose utilization region of Escherichia coli K-12: use of lambda fuc and lambda argA transducing bacteriophages to partially order the fucose utilization genes

Journal of Bacteriology ◽

10.1128/jb.152.1.120-125.1982 ◽

1982 ◽

Vol 152 (1) ◽

pp. 120-125 ◽

Cited By ~ 1

Author(s):

A C Skjold ◽

D H Ezekiel

Keyword(s):

Escherichia Coli ◽

Integration Site ◽

Burst Size ◽

Low Frequency ◽

The Other ◽

Partially Order ◽

K 12 ◽

A Minor ◽

A Site ◽

Aldolase A

Escherichia coli K-12 strains have deletions for the normal lambda integration site were lysogenized with bacteriophage lambda at a site within the L-fucose utilization system (fuc). The frequency of lambda integration at this site is approximately 2 X 10(-8) to 5 X 10(-7). Studies of the lytic properties of these strains indicated very infrequent cell lysis with a relatively low phage burst size. Transductional ability of the phage lysates was found to be normal, comparable to that found in conventional low-frequency transducing lysates. Two major classes of transducing phage were found. One carried the markers argA and fucA (a fucose utilization gene of unknown function previously referred to as fuc-1) and the gene for D-arabinose utilization (dar+). The other carried only fucC, the gene specifying L-fuculose-1-phosphate aldolase. A minor class of phage was found that carried fucA, but not argA or dar+. Upon consideration of the transductional nature of these phage classes, we are proposing that the gene order for the L-fucose utilization system is dar, fucA, (lambda), fucC.

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Unraveling the functions of uncharacterized transcription factors in Escherichia coli using ChIP-exo

10.1101/2021.06.10.447994 ◽

2021 ◽

Author(s):

Ye Gao ◽

Hyun Gyu Lim ◽

Hans Verkler ◽

Richard Szubin ◽

Daniel Quach ◽

...

Keyword(s):

Escherichia Coli ◽

Transcription Factors ◽

Dna Binding ◽

Binding Sites ◽

Regulatory Networks ◽

Transcriptional Regulatory Networks ◽

Cellular Processes ◽

Transcriptional Regulatory ◽

Mutant Phenotypes ◽

K 12

Bacteria regulate gene expression to adapt to changing environments through transcriptional regulatory networks (TRNs). Although extensively studied, no TRN is fully characterized since the identity and activity of all the transcriptional regulators that comprise a TRN are not known. Here, we experimentally evaluate 40 uncharacterized proteins in Escherichia coli K-12 MG1655, which were computationally predicted to be transcription factors (TFs). First, we used a multiplexed ChIP-exo assay to characterize genome-wide binding sites for these candidate TFs; 34 of them were found to be DNA-binding protein. We then compared the relative location between binding sites and RNA polymerase (RNAP). We found 48% (283/588) overlap between the TFs and RNAP. Finally, we used these data to infer potential functions for 10 of the 34 TFs with validated DNA binding sites and consensus binding motifs. These TFs were found to have various roles in regulating primary cellular processes in E. coli. Taken together, this study: (1) significantly expands the number of confirmed TFs, close to the estimated total of about 280 TFs; (2) predicts the putative functions of the newly discovered TFs, and (3) confirms the functions of representative TFs through mutant phenotypes.

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Functional Prediction of Hypothetical Transcription Factors of Escherichia coli K-12 Based on Expression Data

Computational and Structural Biotechnology Journal ◽

10.1016/j.csbj.2018.03.003 ◽

2018 ◽

Vol 16 ◽

pp. 157-166 ◽

Cited By ~ 2

Author(s):

Emanuel Flores-Bautista ◽

Carenne Ludeña Cronick ◽

Anny Rodriguez Fersaca ◽

Mario Alberto Martinez-Nuñez ◽

Ernesto Perez-Rueda

Keyword(s):

Escherichia Coli ◽

Transcription Factors ◽

Expression Data ◽

Functional Prediction ◽

K 12

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Activation and Repression at the Escherichia coli ynfEFGHI Operon Promoter

Journal of Bacteriology ◽

10.1128/jb.00040-09 ◽

2009 ◽

Vol 191 (9) ◽

pp. 3172-3176 ◽

Cited By ~ 8

Author(s):

Meng Xu ◽

Stephen J. W. Busby ◽

Douglas F. Browning

Keyword(s):

Escherichia Coli ◽

Transcription Factor ◽

Rna Polymerase ◽

Class Ii ◽

Nitrate Ions ◽

Single Target ◽

Promoter Complex ◽

Polymerase Binding ◽

K 12 ◽

Rna Polymerase Promoter

ABSTRACT Induction of the Escherichia coli K-12 ynfEFGHI operon in response to anaerobiosis is repressed by nitrate ions. In this study, we show that the global transcription factor FNR is a class II activator at the ynfEFGHI promoter and that NarL represses activation by binding to a single target that overlaps the promoter −10 element. Electromobility shift assays show that NarL does not prevent RNA polymerase binding and suggest that repression may involve a quaternary NarL-FNR-RNA polymerase-promoter complex.

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