Single-Target Regulators Constitute the Minority 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 imp...
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Published in | Frontiers in microbiology Vol. 12; p. 697803 |
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Main Authors | , , , , |
Format | Journal Article |
Language | English |
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18.06.2021
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Abstract | 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. |
---|---|
AbstractList | 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. 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. |
Author | Shimada, Tomohiro Ogasawara, Hiroshi Kobayashi, Naoki Kobayashi, Ikki Ishihama, Akira |
AuthorAffiliation | 5 Micro-Nano Technology Research Center, Hosei University , Koganei , Japan 1 School of Agriculture, Meiji University , Kawasaki , Japan 2 Research Center for Supports to Advanced Science, Division of Gene Research, Shinshu University , Nagano , Japan 3 Research Center for Fungal and Microbial Dynamism, Shinshu University , Nagano , Japan 4 Department of Frontier Science, Hosei University , Koganei , Japan |
AuthorAffiliation_xml | – name: 2 Research Center for Supports to Advanced Science, Division of Gene Research, Shinshu University , Nagano , Japan – name: 3 Research Center for Fungal and Microbial Dynamism, Shinshu University , Nagano , Japan – name: 4 Department of Frontier Science, Hosei University , Koganei , Japan – name: 5 Micro-Nano Technology Research Center, Hosei University , Koganei , Japan – name: 1 School of Agriculture, Meiji University , Kawasaki , Japan |
Author_xml | – sequence: 1 givenname: Tomohiro surname: Shimada fullname: Shimada, Tomohiro – sequence: 2 givenname: Hiroshi surname: Ogasawara fullname: Ogasawara, Hiroshi – sequence: 3 givenname: Ikki surname: Kobayashi fullname: Kobayashi, Ikki – sequence: 4 givenname: Naoki surname: Kobayashi fullname: Kobayashi, Naoki – sequence: 5 givenname: Akira surname: Ishihama fullname: Ishihama, Akira |
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Copyright | Copyright © 2021 Shimada, Ogasawara, Kobayashi, Kobayashi and Ishihama. 2021 Shimada, Ogasawara, Kobayashi, Kobayashi and Ishihama |
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Notes | ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 23 Reviewed by: Andrew Travers, Medical Research Council, Laboratory of Molecular Biology, United Kingdom; Bernhard O. Palsson, University of California, San Diego, United States; Daniel Charlier, Vrije University Brussel, Belgium Edited by: Frank T. Robb, University of Maryland, Baltimore, United States This article was submitted to Evolutionary and Genomic Microbiology, a section of the journal Frontiers in Microbiology |
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Title | Single-Target Regulators Constitute the Minority Group of Transcription Factors in Escherichia coli K-12 |
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