The functional landscape bound to the transcription factors of Escherichia coli 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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Single-Target Regulators Constitute the Minority Group of Transcription Factors in Escherichia coli K-12

Frontiers in Microbiology ◽

10.3389/fmicb.2021.697803 ◽

2021 ◽

Vol 12 ◽

Author(s):

Tomohiro Shimada ◽

Hiroshi Ogasawara ◽

Ikki Kobayashi ◽

Naoki Kobayashi ◽

Akira Ishihama

Keyword(s):

Escherichia Coli ◽

Transcription Factors ◽

Binding Sites ◽

Target Genes ◽

Minority Group ◽

E Coli ◽

Single Target ◽

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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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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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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Mutations That StimulateflhDCExpression in Escherichia coli K-12

Journal of Bacteriology ◽

10.1128/jb.00455-15 ◽

2015 ◽

Vol 197 (19) ◽

pp. 3087-3096 ◽

Cited By ~ 20

Author(s):

Karen A. Fahrner ◽

Howard C. Berg

Keyword(s):

Escherichia Coli ◽

Transcription Factors ◽

Insertion Sequence ◽

Receptor Protein ◽

Upstream Region ◽

Single Nucleotide ◽

Content Type ◽

Sequence Elements ◽

Camp Receptor ◽

K 12

ABSTRACTMotility is a beneficial attribute that enables cells to access and explore new environments and to escape detrimental ones. The organelle of motility inEscherichia coliis the flagellum, and its production is initiated by the activating transcription factors FlhD and FlhC. The expression of these factors by theflhDCoperon is highly regulated and influenced by environmental conditions. TheflhDCpromoter is recognized by σ70and is dependent on the transcriptional activator cyclic AMP (cAMP)-cAMP receptor protein complex (cAMP-CRP). A number of K-12 strains exhibit limited motility due to low expression levels offlhDC. We report here a large number of mutations that stimulateflhDCexpression in such strains. They include single nucleotide changes in the −10 element of the promoter, in the promoter spacer, and in the cAMP-CRP binding region. In addition, we show that insertion sequence (IS) elements or a kanamycin gene located hundreds of base pairs upstream of the promoter can effectively enhance transcription, suggesting that the topology of a large upstream region plays a significant role in the regulation offlhDCexpression. None of the mutations eliminated the requirement for cAMP-CRP for activation. However, several mutations allowed expression in the absence of the nucleoid organizing protein, H-NS, which is normally required forflhDCexpression.IMPORTANCETheflhDCoperon ofEscherichia coliencodes transcription factors that initiate flagellar synthesis, an energetically costly process that is highly regulated. Few deregulating mutations have been reported thus far. This paper describes new single nucleotide mutations that stimulateflhDCexpression, including a number that map to the promoter spacer region. In addition, this work shows that insertion sequence elements or a kanamycin gene located far upstream from the promoter or repressor binding sites also stimulate transcription, indicating a role of regional topology in the regulation offlhDCexpression.

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Identification of σ32-like factors and ftsX-rpoH gene arrangements in enteric bacteria

Canadian Journal of Microbiology ◽

10.1139/w98-041 ◽

1998 ◽

Vol 44 (6) ◽

pp. 565-568

Author(s):

Jesús Ramírez-Santos ◽

M Carmen Gómez-Eichelmann

Keyword(s):

Escherichia Coli ◽

Transcription Factors ◽

Heat Shock ◽

Western Blot ◽

Southern Blot ◽

Enteric Bacteria ◽

Dna Probes ◽

Bacterial Strains ◽

K 12

Western blot analyses using anti-Escherichia coli K-12 σ32 antibodies and Southern blot analyses using rpoH and ftsX DNA probes were performed using different enteric bacteria. Results show that the bacterial strains analysed have σ32-like transcription factors and ftsX and rpoH homologs in a similar map position. Although the presence of σ32-like factors seems to be extended to all Proteobacteria, rpoH and ftsX homologs seem to be present as neighbors in the genome only in the enteric bacteria.Key words: enteric bacteria, heat shock, σ32, ftsX-rpoH.

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

10.1101/343913 ◽

2018 ◽

Cited By ~ 1

Author(s):

Ye Gao ◽

James T. Yurkovich ◽

Sang Woo Seo ◽

Ilyas Kabimoldayev ◽

Andreas Dräger ◽

...

Keyword(s):

Escherichia Coli ◽

Transcription Factors ◽

Iron Homeostasis ◽

Environmental Changes ◽

Transcriptional Regulatory Network ◽

Computational Prediction ◽

Acetate Metabolism ◽

Transcriptional Regulatory ◽

K 12 ◽

Regulatory Functions

ABSTRACTTranscriptional regulation enables cells to respond to environmental changes. Yet, among the estimated 304 candidate transcription factors (TFs) in Escherichia coli K-12 MG1655, 185 have been experimentally identified and only a few tens of them have been fully characterized by ChIP methods. Understanding the remaining TFs is key to improving our knowledge of the E. coli transcriptional regulatory network (TRN). Here, we developed an integrated workflow for the computational prediction and comprehensive experimental validation of TFs using a suite of genome-wide experiments. We applied this workflow to: 1) identify 16 candidate TFs from over a hundred candidate uncharacterized genes; 2) capture a total of 255 DNA binding peaks for 10 candidate TFs resulting in six high-confidence binding motifs; 3) reconstruct the regulons of these 10 TFs by determining gene expression changes upon deletion of each TF; and 4) determine the regulatory roles of three TFs (YiaJ, YdcI, and YeiE) as regulators of L-ascorbate utilization, proton transfer and acetate metabolism, and iron homeostasis under iron limited condition, respectively. Together, these results demonstrate how this workflow can be used to discover, characterize, and elucidate regulatory functions of uncharacterized TFs in parallel.

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