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YfeC DNA-binding transcriptional dual regulator

Synonyms: YfeC
Summary:
YfeC was initially identified as a putative transcription factor using a homology-based algorithm [1]. DNA binding was probed by chromatin immunoprecipitation assays (ChIP-exo) [1]. Gene expression profile analysis of the wild-type strain and a yfeC knockout strain using RNA-seq showed differential expression of a set of genes also identified by ChIP-exo (between others), indicating they are the direct regulatory targets [1]. Some of these direct regulatory targets were upregulated and others were downregulated, indicating that YfeC is a dual regulator [1]. Consensus binding motif analysis showed that the TFBSs of YfeC have TTC-rich inverted repeats separated by 6 nt [1]. Based on SWISS-MODEL, YfeC was predicted to form homodimers [1]. The yfeCD locus was predicted to encode a toxin/antitoxin pair [2].
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Transcription factor      
TF conformation(s):
Name Conformation Type TF-Effector Interaction Type Apo/Holo Conformation Evidence Confidence level (C: Confirmed, S: Strong, W: Weak) References
YfeC Functional   nd nd nd
TFBs symmetry: inverted-repeat
Connectivity class: Local Regulator
Gene name: yfeC
  Genome position: 2518467-2518811
  Length: 345 bp / 114 aa
Operon name: yfeCD
TU(s) encoding the TF:
Transcription unit        Promoter
yfeCD
yfeCp


Regulon       
Regulated gene(s)
Regulated operon(s)
First gene in the operon(s)
Simple and complex regulatory phrases Regulatory phrase (List of promoters regulated by the phrase)


Transcription factor regulation    


Transcription factor binding sites (TFBSs) arrangements
      

  Functional conformation Function Promoter Sigma factor Central Rel-Pos Distance to first Gene Genes Sequence LeftPos RightPos Evidence Confidence level (C: Confirmed, S: Strong, W: Weak) References



High-throughput Transcription factor binding sites (TFBSs)
      

  Functional conformation Function Object name Object type Distance to first Gene Sequence LeftPos RightPos Center Position Growth Condition Evidence Confidence level (C: Confirmed, S: Strong, W: Weak) References
  YfeC activator yfeC Gene nd
ttgcagcgagGGTTGGAAATTTGGTGGAGCTAAGCGGGATCGAACcgctgacctc
2518030 2518064 2518046.5 nd [EXP-IEP-RNA-SEQ], [EXP-CHIP-EXO-MANUAL] W [1]
  YfeC repressor rpmH Gene nd
cggcggatatCCAATAAAGCCATTGAATTTATTCAAGTTTAGGTAGAaatcgccatg
3884292 3884328 3884309.5 nd [EXP-IEP-RNA-SEQ], [EXP-CHIP-EXO-MANUAL] W [1]
  YfeC repressor hybE Gene nd
tggcttccacGCCAGATTCACGCAGCGCAGCCAGAACCTGCTCAAGCGCaggttcaatc
3140828 3140866 3140846.5 nd [EXP-IEP-RNA-SEQ], [EXP-CHIP-EXO-MANUAL] W [1]
  YfeC repressor rpmB Gene nd
tggcgcctcgTCAGGCTTTACAGCCCGGTCATCGCAGTTCTATGTgaactctcga
3811731 3811765 3811747.5 nd [EXP-IEP-RNA-SEQ], [EXP-CHIP-EXO-MANUAL] W [1]
  YfeC repressor rpsU Gene nd
tgaaataagcTGGCGTTGATGCCAGCGGCAAACCGAATTAATCAAAggtgagaggc
3210733 3210768 3210750.0 nd [EXP-IEP-RNA-SEQ], [EXP-CHIP-EXO-MANUAL] W [1]
  YfeC repressor ygdR Gene nd
ttttaccctcACAGTTTAAGATTTTCCTGCTTTCAAGATATATAACGTcggtttataa
2971183 2971220 2971201.0 nd [EXP-IEP-RNA-SEQ], [EXP-CHIP-EXO-MANUAL] W [1]


Evolutionary conservation of regulatory elements    
     Note: Evolutionary conservation of regulatory interactions and promoters is limited to gammaproteobacteria.
Promoter-target gene evolutionary conservation


Evidence    


Reference(s)    

 [1] Gao Y., Lim HG., Verkler H., Szubin R., Quach D., Rodionova I., Chen K., Yurkovich JT., Cho BK., Palsson BO., 2021, Unraveling the functions of uncharacterized transcription factors in Escherichia coli using ChIP-exo., Nucleic Acids Res 49(17):9696-9710

 [2] Sevin EW, Barloy-Hubler F, 2007, RASTA-Bacteria: a web-based tool for identifying toxin-antitoxin loci in prokaryotes., Genome Biol, 8(8):R155 10.1186/gb-2007-8-8-r155

 [3] Christensen-Dalsgaard M., Jorgensen MG., Gerdes K., 2010, Three new RelE-homologous mRNA interferases of Escherichia coli differentially induced by environmental stresses., Mol Microbiol 75(2):333-48

 [4] Sanchez-Torres V, Maeda T, Wood TK, 2010, Global regulator H-NS and lipoprotein NlpI influence production of extracellular DNA in Escherichia coli., Biochem Biophys Res Commun, 401(2):197 10.1016/j.bbrc.2010.09.026


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