RegulonDB RegulonDB 11.2:Regulon Page

StpA DNA-binding transcriptional dual regulator

Synonyms: StpA
StpA protein, for "Suppressor of td phenotype A," is a nucleoid-associated multifunctional protein [9, 10] that acts as a transcriptional repressor [11], in chromosomal DNA packaging [12], and as a chaperone [13, 14]. When StpA binds DNA, it is able to form a rigid filament, and thus the access to DNA is blocked [12]. This protein is negatively autoregulated [11] and it is involved in the ss-glucoside utilization systems [11, 15, 16] and the homologous recombination and repair of bleomycin damage [17].
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Transcription factor      
TF conformation(s):
Name Conformation Type TF-Effector Interaction Type Apo/Holo Conformation Evidence Confidence level (C: Confirmed, S: Strong, W: Weak) References
StpA Functional   nd nd nd
Evolutionary Family: HNS
TFBs length: 15
TFBs symmetry: inverted-repeat
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, cas1, cas2, casA, casB, casC, casD, casE, fau, leuO, malE, malF, malG, malH, ssrS, stpA
Multifun term(s) of regulated gene(s) MultiFun Term (List of genes associated to the multifun term)
defense/survival (7)
carbon compounds (5)
membrane (3)
Transcription related (2)
activator (2)
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Regulated operon(s) bglGFB, casABCDE12, leuO, malEFGH, ssrS-fau, stpA
First gene in the operon(s) bglG, casA, leuO, malE, ssrS, stpA
Simple and complex regulons CRP,CreB,Fis,H-NS,MalT,StpA
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Simple and complex regulatory phrases Regulatory phrase (List of promoters regulated by the phrase)

Transcription factor regulation    

Transcription factor binding sites (TFBSs) arrangements

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


 [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] Sun D., Mao X., Fei M., Chen Z., Zhu T., Qiu J., 2020, Histone-like Nucleoid-Structuring Protein (H-NS) Paralogue StpA Activates the Type I-E CRISPR-Cas System against Natural Transformation in Escherichia coli., Appl Environ Microbiol 86(14)

 [3] 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

 [4] Pul U., Wurm R., Arslan Z., Geissen R., Hofmann N., Wagner R., 2010, Identification and characterization of E. coli CRISPR-cas promoters and their silencing by H-NS., Mol Microbiol 75(6):1495-512

 [5] Baumgart LA, Lee JE, Salamov A, Dilworth DJ, Na H, Mingay M, Blow MJ, Zhang Y, Yoshinaga Y, Daum CG, O'Malley RC, 2021, Persistence and plasticity in bacterial gene regulation., Nat Methods, 18(12):1499 10.1038/s41592-021-01312-2

 [6] Decker KT, Gao Y, Rychel K, Al Bulushi T, Chauhan SM, Kim D, Cho BK, Palsson BO, 2022, proChIPdb: a chromatin immunoprecipitation database for prokaryotic organisms., Nucleic Acids Res, 50(D1):D1077 10.1093/nar/gkab1043

 [7] 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

 [8] 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

 [9] 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 10.1074/jbc.274.46.33105

 [10] 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

 [11] 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

 [12] 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 10.1093/nar/gkr1247

 [13] 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 10.1093/nar/gkl1143

 [14] 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 10.1093/nar/gki515

 [15] 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 10.1046/j.1365-2958.2001.02678.x

 [16] 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 10.1128/JB.180.4.994-997.1998

 [17] 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 10.1266/ggs.82.433

 [18] 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 10.1128/JB.01594-08

 [19] 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 10.1128/jb.176.21.6769-6775.1994

 [20] 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 10.1093/nar/20.24.6735

 [21] 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 10.1128/JB.181.20.6361-6370.1999

 [22] 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 10.1016/s0300-9084(01)01232-9

 [23] 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

 [24] 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 None

 [25] 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, 183(7):2343 10.1128/JB.183.7.2343-2347.2001

 [26] 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 10.1128/jb.178.15.4335-4343.1996

 [27] 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 10.1016/s0966-842x(99)01455-9

 [28] 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 10.1073/pnas.96.19.10776

 [29] 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

 [30] Boudreau BA, Hron DR, Qin L, van der Valk RA, Kotlajich MV, Dame RT, Landick R, 2018, StpA and Hha stimulate pausing by RNA polymerase by promoting DNA-DNA bridging of H-NS filaments., Nucleic Acids Res, 46(11):5525 10.1093/nar/gky265

 [31] Cusick ME, Belfort M, 1998, Domain structure and RNA annealing activity of the Escherichia coli regulatory protein StpA., Mol Microbiol, 28(4):847 10.1046/j.1365-2958.1998.00848.x

 [32] Rajkowitsch L, Schroeder R, 2007, Dissecting RNA chaperone activity., RNA, 13(12):2053 10.1261/rna.671807

 [33] 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 None

 [34] Clodi E, Semrad K, Schroeder R, 1999, Assaying RNA chaperone activity in vivo using a novel RNA folding trap., EMBO J, 18(13):3776 10.1093/emboj/18.13.3776

 [35] 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 10.1101/gad.231302

 [36] 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 10.1042/bst0301175

 [37] 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

 [38] 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