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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 [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 %Beta;-glucoside utilization systems [7, 11, 12]and the homologous recombination and repair of bleomycin damage [13] Gueun%e'; 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     nd 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 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 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


 [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 ¿¿., 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] 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. 40(8):3316-3328

 [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. 35(4):1257-69

 [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. 33(7):2280-9

 [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. 42(4):903-17

 [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. 180(4):994-7

 [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. 82(5):433-9

 [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. 191(7):2388-91

 [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. 176(21):6769-75

 [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. 20(24):6735

 [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. 181(20):6361-70

 [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. 83(2):243-9

 [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. 15(6):1340-9

 [21] Johansson J., Eriksson S., Sonden 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. 183(7):2343-7

 [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. 178(15):4335-43

 [23] Dorman CJ., Hinton JC., Free A., 1999, Domain organization and oligomerization among H-NS-like nucleoid-associated proteins in bacteria., Trends Microbiol. 7(3):124-8

 [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. 96(19):10776-81

 [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. 28(4):847-57

 [27] Rajkowitsch L., Schroeder R., 2007, Dissecting RNA chaperone activity., RNA. 13(12):2053-60

 [28] Zhang A., Derbyshire V., Salvo JL., Belfort M., 1995, Escherichia coli protein StpA stimulates self-splicing by promoting RNA assembly in vitro., RNA. 1(8):783-93

 [29] Clodi E., Semrad K., Schroeder R., 1999, Assaying RNA chaperone activity in vivo using a novel RNA folding trap., EMBO J. 18(13):3776-82

 [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. 16(17):2300-12

 [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. 30(Pt 6):1175-80

 [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