RegulonDB RegulonDB 9.4:Regulon Page

CsiR DNA-binding transcriptional repressor

Synonyms: CsiR
The transcription factor CsiR, for Carbon starvation induced Regulator, is a finely modulated repressor that controls the transcription of genes involved in the degradation and transport of 4-aminobutyrate for utilization as a source of nitrogen [1, 2, 3, 4]. CsiR is expressed upon carbon starvation and has a repressor effect during the stationary phase [1].
Currently, no DNA-binding sites for this regulator have been reported in the literature [1].

Transcription factor      
TF conformation(s):
Name Conformation Type TF-Effector Interaction Type Apo/Holo Conformation Evidence (Confirmed, Strong, Weak) References
CsiR     nd nd
Evolutionary Family: GntR
Connectivity class: Local Regulator
Gene name: csiR
  Genome position: 2795674-2796336
  Length: 663 bp / 220 aa
Operon name: csiR
TU(s) encoding the TF:
Transcription unit        Promoter

Regulated gene(s) csiD, gabD, gabP, gabT, lhgO
Multifun term(s) of regulated gene(s) MultiFun Term (List of genes associated to the multifun term)
aminobutyrate catabolism (2)
putrescine catabolism (2)
carbon compounds (1)
Porters (Uni-, Sym- and Antiporters) (1)
membrane (1)
Regulated operon(s) csiD-lhgO-gabDTP
First gene in the operon(s) csiD
Simple and complex regulons CRP,CsiR,H-NS,Lrp
Simple and complex regulatory phrases Regulatory phrase (List of promoters regulated by the phrase)

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
  CsiR repressor csiDp Sigma38 nd nd csiD, lhgO, gabD, gabT, gabP nd nd [GEA] [1]

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


 [GEA] Gene expression analysis


 [1] Metzner M., Germer J., Hengge R., 2004, Multiple stress signal integration in the regulation of the complex sigma S-dependent csiD-ygaF-gabDTP operon in Escherichia coli., Mol Microbiol. 51(3):799-811

 [2] Schneider BL., Ruback S., Kiupakis AK., Kasbarian H., Pybus C., Reitzer L., 2002, The Escherichia coli gabDTPC operon: specific gamma-aminobutyrate catabolism and nonspecific induction., J Bacteriol. 184(24):6976-86

 [3] Metzer E., Levitz R., Halpern YS., 1979, Isolation and properties of Escherichia coli K-12 mutants impaired in the utilization of gamma-aminobutyrate., J Bacteriol. 137(3):1111-8

 [4] Zaboura M., Halpern YS., 1978, Regulation of gamma-aminobutyric acid degradation in Escherichia coli by nitrogen metabolism enzymes., J Bacteriol. 133(2):447-51