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StpA DNA-binding transcriptional repressor

Synonyms: StpA
StpA protein, for "Suppressor of td phenotype A," is a nucleoid-associated multifunctional protein [5, 6]that acts as a transcriptional repressor [7] in chromosomal DNA packaging [] and as a chaperone [8]When StpA binds DNA, it is able to form a rigid filament, and thus the access to DNA is blocked [] This protein is negatively autoregulated [7]and it is involved in the ¿¿-glucoside utilization systems [7]and the homologous recombination and repair of bleomycin damage [] Gueun¿¿ et al.
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Transcription factor      
TF conformation(s):
Name Conformation Type TF-Effector Interaction Type Apo/Holo Conformation Evidence (Confirmed, Strong, Weak) References
StpA Functional   [IE] nd
Evolutionary Family: HNS
Connectivity class: Local Regulator
Gene name: stpA
  Genome position: 2798091-2798495
  Length: 405 bp / 134 aa
Operon name: stpA
TU(s) encoding the TF:
Transcription unit        Promoter

Regulated gene(s) bglB, bglF, bglG, fau, leuO, ssrS, stpA
Multifun term(s) of regulated gene(s) MultiFun Term (List of genes associated to the multifun term)
carbon compounds (3)
Transcription related (2)
activator (2)
operon (2)
posttranslational modification (1)
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Regulated operon(s) bglGFB, leuO, ssrS-fau, stpA
First gene in the operon(s) bglG, bglG, leuO, ssrS, ssrS, ssrS, ssrS, stpA
Simple and complex regulons CRP,Fis,H-NS,LeuO,RcsB-BglJ,StpA
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
  StpA repressor bglGp nd nd 3906567.0 bglG, bglF, bglB nd nd [GEA] [1], [2]
  StpA repressor leuOp2 nd nd -84368.0 leuO nd nd [GEA] [3]
  StpA repressor ssrSp1 Sigma70 nd -3055983.0 ssrS, fau nd nd [BPP], [GEA] [4]
  StpA repressor ssrSp2 Sigma38, Sigma70 nd -3055983.0 ssrS, fau nd nd [BPP], [GEA] [4]
  StpA repressor stpAp1 Sigma70 nd 2798495.0 stpA 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


 [IE] Inferred from experiment

 [GEA] Gene expression analysis

 [BPP] Binding of purified proteins


 [1] Gueune H., Durand MJ., Thouand G., DuBow MS., 2008, The ygaVP genes of Escherichia coli form a tributyltin-inducible operon., Appl Environ Microbiol 74(6):1954-8

 [2] Venkatesh GR., Kembou Koungni FC., Paukner A., Stratmann T., Blissenbach B., Schnetz K., 2010, BglJ-RcsB heterodimers relieve repression of the Escherichia coli bgl operon by H-NS., J Bacteriol 192(24):6456-64

 [3] Stratmann T., Pul U., Wurm R., Wagner R., Schnetz K., 2012, RcsB-BglJ activates the Escherichia coli leuO gene, encoding an H-NS antagonist and pleiotropic regulator of virulence determinants., Mol Microbiol 83(6):1109-23

 [4] Neusser T., Gildehaus N., Wurm R., Wagner R., 2008, Studies on the expression of 6S RNA from E. coli: involvement of regulators important for stress and growth adaptation., Biol Chem 389(3):285-97

 [5] Azam TA., Ishihama A., 1999, Twelve species of the nucleoid-associated protein from Escherichia coli. Sequence recognition specificity and DNA binding affinity., J Biol Chem 274(46):33105-13

 [6] Azam TA., Hiraga S., Ishihama A., 2000, Two types of localization of the DNA-binding proteins within the Escherichia coli nucleoid., Genes Cells 5(8):613-26

 [7] Wolf T., Janzen W., Blum C., Schnetz K., 2006, Differential dependence of StpA on H-NS in autoregulation of stpA and in regulation of bgl., J Bacteriol 188(19):6728-38

 [8] Mayer O., Rajkowitsch L., Lorenz C., Konrat R., Schroeder R., 2007, RNA chaperone activity and RNA-binding properties of the E. coli protein StpA., Nucleic Acids Res 35(4):1257-69

 [9] Shi X., Bennett GN., 1994, Plasmids bearing hfq and the hns-like gene stpA complement hns mutants in modulating arginine decarboxylase gene expression in Escherichia coli., J Bacteriol 176(21):6769-75

 [10] Sonden B., Uhlin BE., 1996, Coordinated and differential expression of histone-like proteins in Escherichia coli: regulation and function of the H-NS analog StpA., EMBO J 15(18):4970-80

 [11] Williams RM., Rimsky S., Buc H., 1996, Probing the structure, function, and interactions of the Escherichia coli H-NS and StpA proteins by using dominant negative derivatives., J Bacteriol 178(15):4335-43

 [12] Paytubi S., Madrid C., Forns N., Nieto JM., Balsalobre C., Uhlin BE., Juarez A., 2004, YdgT, the Hha paralogue in Escherichia coli, forms heteromeric complexes with H-NS and StpA., Mol Microbiol 54(1):251-63

 [13] Delihas N., Forst S., 2001, MicF: an antisense RNA gene involved in response of Escherichia coli to global stress factors., J Mol Biol 313(1):1-12

 [14] Deighan P., Free A., Dorman CJ., 2000, A role for the Escherichia coli H-NS-like protein StpA in OmpF porin expression through modulation of micF RNA stability., Mol Microbiol 38(1):126-39