RegulonDB RegulonDB 10.7:Regulon Page

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 [8] and as a chaperone [9, 10]When StpA binds DNA, it is able to form a rigid filament, and thus the access to DNA is blocked [8] This protein is negatively autoregulated [7]and it is involved in the ss-glucoside utilization systems [7, 11, 12]and the homologous recombination and repair of bleomycin damage [13] Gueune et al.
Read more >

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)
Read more >
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 nd bglG, bglF, bglB nd nd [GEA] [1], [2]
  StpA repressor leuOp2 nd nd nd leuO nd nd [GEA] [3]
  StpA repressor ssrSp1 Sigma70 nd nd ssrS, fau nd nd [BPP], [GEA] [4]
  StpA repressor ssrSp2 Sigma38, Sigma70 nd nd ssrS, fau nd nd [BPP], [GEA] [4]
  StpA repressor stpAp1 Sigma70 nd nd 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, 1999 Nov 12

 [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] Lim CJ, Whang YR, Kenney LJ, Yan J, 2012, Gene silencing H-NS paralogue StpA forms a rigid protein filament along DNA that blocks DNA accessibility., Nucleic Acids Res, 2012 Apr

 [9] 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, 2007

 [10] Grossberger R, Mayer O, Waldsich C, Semrad K, Urschitz S, Schroeder R, 2005, Influence of RNA structural stability on the RNA chaperone activity of the Escherichia coli protein StpA., Nucleic Acids Res, 2005

 [11] Free A, Porter ME, Deighan P, Dorman CJ, 2001, Requirement for the molecular adapter function of StpA at the Escherichia coli bgl promoter depends upon the level of truncated H-NS protein., Mol Microbiol, 2001 Nov

 [12] Free A, Williams RM, Dorman CJ, 1998, The StpA protein functions as a molecular adapter to mediate repression of the bgl operon by truncated H-NS in Escherichia coli., J Bacteriol, 1998 Feb

 [13] Shiraishi K, Ogata Y, Hanada K, Kano Y, Ikeda H, 2007, Roles of the DNA binding proteins H-NS and StpA in homologous recombination and repair of bleomycin-induced damage in Escherichia coli., Genes Genet Syst, 2007 Oct

 [14] Uyar E, Kurokawa K, Yoshimura M, Ishikawa S, Ogasawara N, Oshima T, 2009, Differential binding profiles of StpA in wild-type and h-ns mutant cells: a comparative analysis of cooperative partners by chromatin immunoprecipitation-microarray analysis., J Bacteriol, 2009 Apr

 [15] 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, 1994 Nov

 [16] Zhang A, Belfort M, 1992, Nucleotide sequence of a newly-identified Escherichia coli gene, stpA, encoding an H-NS-like protein., Nucleic Acids Res, 1992 Dec 25

 [17] Ali Azam T, Iwata A, Nishimura A, Ueda S, Ishihama A, 1999, Growth phase-dependent variation in protein composition of the Escherichia coli nucleoid., J Bacteriol, 1999 Oct

 [18] Sonnenfield JM, Burns CM, Higgins CF, Hinton JC, 2001, The nucleoid-associated protein StpA binds curved DNA, has a greater DNA-binding affinity than H-NS and is present in significant levels in hns mutants., Biochimie, 2001 Feb

 [19] 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

 [20] Zhang A, Rimsky S, Reaban ME, Buc H, Belfort M, 1996, Escherichia coli protein analogs StpA and H-NS: regulatory loops, similar and disparate effects on nucleic acid dynamics., EMBO J, 1996 Mar 15

 [21] Johansson J, Eriksson S, Sondén B, Wai SN, Uhlin BE, 2001, Heteromeric interactions among nucleoid-associated bacterial proteins: localization of StpA-stabilizing regions in H-NS of Escherichia coli., J Bacteriol, 2001 Apr

 [22] 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, 1996 Aug

 [23] Dorman CJ, Hinton JC, Free A, 1999, Domain organization and oligomerization among H-NS-like nucleoid-associated proteins in bacteria., Trends Microbiol, 1999 Mar

 [24] Johansson J, Uhlin BE, 1999, Differential protease-mediated turnover of H-NS and StpA revealed by a mutation altering protein stability and stationary-phase survival of Escherichia coli., Proc Natl Acad Sci U S A, 1999 Sep 14

 [25] 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

 [26] Cusick ME, Belfort M, 1998, Domain structure and RNA annealing activity of the Escherichia coli regulatory protein StpA., Mol Microbiol, 1998 May

 [27] Rajkowitsch L, Schroeder R, 2007, Dissecting RNA chaperone activity., RNA, 2007 Dec

 [28] Zhang A, Derbyshire V, Salvo JL, Belfort M, 1995, Escherichia coli protein StpA stimulates self-splicing by promoting RNA assembly in vitro., RNA, 1995 Oct

 [29] Clodi E, Semrad K, Schroeder R, 1999, Assaying RNA chaperone activity in vivo using a novel RNA folding trap., EMBO J, 1999 Jul 1

 [30] Waldsich C, Grossberger R, Schroeder R, 2002, RNA chaperone StpA loosens interactions of the tertiary structure in the td group I intron in vivo., Genes Dev, 2002 Sep 1

 [31] Mayer O, Waldsich C, Grossberger R, Schroeder R, 2002, Folding of the td pre-RNA with the help of the RNA chaperone StpA., Biochem Soc Trans, 2002 Nov

 [32] 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

 [33] 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