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YciT DNA-binding transcriptional dual regulator

Synonyms: YciT
Summary:
YciT was predicted to be a DeoR-type transcription factor using the Hidden Markov Model [1]. DNA binding was probed by chromatin immunoprecipitation assays (ChIP-exo) [1]. Consensus binding motif of YciT was found to be palindromic and approximately 16 nt: NTTTCANNTNAAANNN [1]. Gene expression profile analysis of the wild-type strain and a yciT 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 of this transcription factor [1]. RNA-seq studies and mutant phenotype analysis showed that YciT is involved in the control of osmolarity in E. coli [1]. The deletion of the yciT gene did not affect significantly the growth in glucose, fructose, or sorbitol; however, in glucose and fructose the stationary phase was reached at an OD600 slightly lower than that for the wild-type strain [1]. ciT belongs to the DeoR family of transcriptional regulators.
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Transcription factor      
TF conformation(s):
Name Conformation Type TF-Effector Interaction Type Apo/Holo Conformation Evidence (Confirmed, Strong, Weak) References
YciT Functional   nd nd
TFBs symmetry: inverted-repeat
Connectivity class: Local Regulator
Gene name: yciT
  Genome position: 1343597-1344346
  Length: 750 bp / 249 aa
Operon name: yciZT
TU(s) encoding the TF:
Transcription unit        Promoter
yciT
yciTp
yciZT
yciZp


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 (Confirmed, Strong, 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 (Confirmed, Strong, Weak) References
  YciT activator ybiY Gene nd
ttatggaactGTATCTGGATACTTCAGACGTTGTTGCGGtgaaggcgct
863650 863678 863663.5 nd [RSE], [CEEUMA] [1]
  YciT activator bsmA Gene nd
attgttacctGGTACGCGATTTTCGAATGAAAACGTGACGAaagcgtaacc
4416824 4416854 4416838.5 nd [RSE], [CEEUMA] [1]
  YciT repressor cusF Gene nd
acttatgtaaGCTCCTGGGGATTCACTCGCTTGTCGCcttcctgcaa
597050 597076 597062.5 nd [RSE], [CEEUMA] [1]
  YciT repressor rdcA Gene nd
tgattttagaCGACGATCGTTTTCATTTGAAAGGAAACGCAAaaagaaaata
4326850 4326881 4326865.0 nd [RSE], [CEEUMA] [1]


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


Evidence    




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