RegulonDB RegulonDB 10.0: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, 5]. 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 Functional   [IMP] [1], [2]
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 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
  CsiR repressor csiDp Sigma38 nd -2788985.0 csiD, lhgO, gabD, gabT, gabP nd nd [GEA] [1]

High-throughput Transcription factor binding sites (TFBSs)

  Functional conformation Function Object name Object type Distance to first Gene Sequence LeftPos RightPos Evidence (Confirmed, Strong, Weak) References
  CsiR repressor aroP gene -353.0 121904 121919 nd nd
  CsiR repressor pdxA gene -123.0 53539 53554 nd nd
  CsiR repressor yeaE gene -86.0 1865715 1865726 nd nd
  CsiR activator yigG gene -81.0 4003274 4003289 nd nd
  CsiR repressor ttdA gene -48.0 3206511 3206526 nd nd
  CsiR repressor tam gene -22.0 1607368 1607383 nd nd
  CsiR activator yehS gene 17.0 2212179 2212194 nd nd
  CsiR repressor ydcK gene 18.0 1500431 1500446 nd nd
  CsiR repressor nlpA gene 27.0 3839966 3839981 nd nd
  CsiR activator kdsA gene 35.0 1268130 1268145 nd nd
  CsiR repressor baeS gene 35.0 2162841 2162856 nd nd
  CsiR repressor cysS gene 55.0 554556 554571 nd nd
  CsiR activator yfbO gene 75.0 2388560 2388575 nd nd
  CsiR repressor csiD gene 78.0 2788907 2788922 nd [3]
  CsiR activator rfbB gene 98.0 2112963 2112978 nd nd
  CsiR repressor yjfY gene 101.0 4424690 4424705 nd nd
  CsiR activator smg gene 125.0 3432339 3432354 nd nd
  CsiR repressor tehA gene 142.0 1500431 1500446 nd nd
  CsiR repressor ppx gene 154.0 2624961 2624976 nd nd
  CsiR repressor yfjD gene 161.0 2748613 2748628 nd nd
  CsiR activator cadC gene 167.0 4361767 4361782 nd nd
  CsiR activator pdhR gene 188.0 121904 121919 nd nd
  CsiR activator ydeO gene 189.0 1583498 1583513 nd nd
  CsiR repressor yjjQ gene 224.0 4603253 4603268 nd nd
  CsiR activator gltF gene 242.0 3360934 3360949 nd nd
  CsiR repressor yfcO gene 281.0 2449768 2449783 nd nd
  CsiR repressor dinQ gene 286.0 3647502 3647517 nd nd
  CsiR repressor mrdA gene 290.0 667927 667942 nd nd
  CsiR activator bdcA gene 293.0 4473760 4473775 nd nd
  CsiR repressor apt gene 358.0 491054 491069 nd [4]
  CsiR repressor bdcR gene 364.0 4473760 4473775 nd nd
  CsiR repressor yehE gene 386.0 2192410 2192425 nd nd
  CsiR activator pliG gene 389.0 1227083 1227098 nd nd
  CsiR repressor yjdP gene 394.0 4313474 4313489 nd nd
  CsiR activator ydfK gene 397.0 1632675 1632690 nd nd
  CsiR activator rpsF gene 428.0 4424690 4424705 nd nd
  CsiR activator safA gene 461.0 1583498 1583513 nd nd

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


 [IMP] Inferred from mutant phenotype

 [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] Marschall C., Labrousse V., Kreimer M., Weichart D., Kolb A., Hengge-Aronis R., 1998, Molecular analysis of the regulation of csiD, a carbon starvation-inducible gene in Escherichia coli that is exclusively dependent on sigma s and requires activation by cAMP-CRP., J Mol Biol 276(2):339-53

 [4] Hershey HV., Taylor MW., 1986, Nucleotide sequence and deduced amino acid sequence of Escherichia coli adenine phosphoribosyltransferase and comparison with other analogous enzymes., Gene 43(3):287-93

 [5] 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