Transcription Factor
| Accessions: | ECK120004926 (RegulonDB 7.5) |
| Names: | H-NS DNA-binding transcriptional dual regulator, HNS |
| Organisms: | ECK12 |
| Libraries: | RegulonDB 7.5 1 1 Salgado H, Peralta-Gil M, Gama-Castro S, Santos-Zavaleta A, Muniz-Rascado L, Garcia-Sotelo JS, Weiss V, Solano-Lira H, Martinez-Flores I, Medina-Rivera A, Salgado-Osorio G, Alquicira-Hernandez S, Alquicira-Hernandez K, Lopez-Fuentes A, Porron-Sotelo L, Huerta AM, Bonavides-Martinez C, Balderas-Martinez YI, Pannier L, Olvera M, Labastida A, Jimenez-Jacinto V, Vega-Alvarado L, Del Moral-Chavez V, Hernandez-Alvarez A, Morett E, Collado-Vides J. RegulonDB v8.0: omics data sets, evolutionary conservation, regulatory phrases, cross-validated gold standards and more. Nucleic Acids Res. 2013 Jan 1;41(D1):D203-D213. [Pubmed] |
| Notes: | The H-NS protein, for Histone-like nucleoid structuring protein, is a nucleoid-associated multifunctional protein that is capable of condensing Dame RT,2000and supercoiling DNA Zimmerman SB.,2006; Dame RT.,2005; McLeod SM,2001; Tupper AE,1994 It is a global transcriptional silencer of genes with high AT content Dorman CJ.,2004; Fang FC,2008 regulates 5% of all Escherichia coli genes Hommais F,2001 and plays a key role in global chromosome organization in bacteria Wang W,2011 This protein acts as a pleiotropic transcriptional factor with a strong preference for horizontally acquired genes among the 250 loci to which it binds Yamada H,1990; Oshima T,2006 H-NS functions almost exclusively as a transcriptional repressor, although there is no clear evidence that this regulator is an activator; Currently, no inducer for this regulator has been reported in the literature, although Reush et al; proposed that this regulator can form a complex with a short chain of polyhydroxybutyrate Reusch RN,2002 Additional genes might be identified by high-throughput analysis Uyar E,2009H-NS plays an important role in the regulation of many genes in response to environmental changes and adaptation to stress; therefore, it is capable of controlling its own synthesis Falconi M,1993; Falconi M,1996 It also regulates transcription of many other genes that participate in a variety of cellular functions, including genes involved in the following processes or responses: biogenesis of flagella Bertin P,1994; Soutourina O,1999; Landini P,2002 transcription control of the type I fimbria structural genes Donato GM,1999; Donato GM,1997; Olsen PB,1998; Olsen PB,1994; Schembri MA,1998 acid resistance Shin M,2005 the functional glutamic acid-dependent system De Biase D,1999 osmotically inducible genes Bouvier J,1998 the glutamate decarboxylase-dependent acid resistance system Giangrossi M,2005; Ma Z,2002; Tramonti A,2002; Hommais F,2001 osmotic control Lucht JM,1994; Rajkumari K,2001 the type II secretion pathway Francetic O,2000 carbon sources Rimsky S,1990 genes involved in the RNA component of the small subunit (30S subunit) Afflerbach H,1998; Gralla JD.,2005 and proteases Forns N,2005 among others.H-NS is capable of inducing severe bends in the DNA, interacting with a large number of DNA regions that contain a planar curvature Yamada H,1990; Yamada H,1991; Jauregui R,2003 It has been suggested that H-NS binds strongly to sites carrying a 10-bp AT-rich consensus sequence, which functions as a nucleation site for the formation of a repressive higher-order nucleoprotein complex Lang B,2007; Sette M,2009 H-NS binds to intergenic regions as well as regions within genes, but not all genes that bind H-NS are affected by this protein, a fact that is in agreement with the primary role assigned to HN-S in maintenance of nucleoid structure; Currently, there are different models for the formation of DNA-H-NS-DNA bridges which show that this protein binds in tandem to sequences in the genome, forming multimers Dame RT.,2005; Dorman CJ.,2007; Luijsterburg MS,2006As expected for a gene involved in the modulation of many cellular processes, the expression of hns is regulated by several systems and at different levels; At the transcription level, hns is autoregulated, and it is controlled by different transcription factors; hns is induced by high hydrostatic pressure Welch TJ,1993 and DNA synthesis Free A,1995 At the posttranscriptional level, it is subject to regulation by the sRNAs Hfq and DsrA Lease RA,2000; Brescia CC,2003; Majdalani N,2005; Brescia CC,2004; Repoila F,2003It is a DNA-binding protein with similarity to StpA Shi X,1994; Zhang A,1992and these two proteins can have similar functions Ali Azam T,1999; Azam TA,2000 It has an approximately fivefold-lower affinity for DNA than StpA and has a major preference for curved DNA Sonnenfield JM,2001 Expression of stpA from a plasmid can complement an hns mutant phenotype and StpA is able to repress and activate a subset of H-NS-regulated genes, but the specific mechanisms remain to be determined Shi X,1994; Sonnenfield JM,2001; Sonden B,1996; Zhang A,1996; Uyar E,2009; Sonden B,1996 A dominant negative form of StpA can disrupt H-NS activity and vice versa, and H-NS can interact with StpA at two distinct domains to form heterodimers in vitro; also, there is evidence that these proteins can form homodimers Johansson J,2001; Williams RM,1996; Dorman CJ,1999; Williams RM,1996 For this reason, in the absence of H-NS the StpA protein is rapidly degraded in a Lon protease-dependent manner Johansson J,2001; Johansson J,1999 protection from proteolytic degradation appears to be mediated by a direct interaction between StpA and H-NS Johansson J,2001 On the other hand H-NS also may form heterotrimeric complexes with Hha and YdgT Madrid C,2007; Paytubi S,2004H-NS is a small protein and it is an abundant nucleic acid protein in the genome, with about 20,000 copies per cell; This regulator belongs to the histone-like family of transcriptional regulators and the structure of the protein consists of two structured domains which are separated by a flexible linker Dorman CJ.,2004 The N-terminal domain is required for oligomerization and it is involved in protein-protein interactions, while the purified C-terminal domain is involved in DNA binding Dorman CJ.,2004; Rimsky S.,2004; Sette M,2009 H-NS forms two compact clusters associated with each copy of the chromosome; These clusters are located near the one-quarter and three-quarter positions along the long axis of the cell Wang W,2011 In cells with three clusters, the additional cluster tends to appear in the middle Wang W,2011 The two cluster formations are induced by the N-terminal domain-driven oligomerization of the protein Wang W,2011 H-NS sequesters the regulated genes and operons into these clusters and juxtaposed numerous DNA segments broadly distributed throughout the chromosome Wang W,2011 Wang et al; (2011) reported that H-NS clusters could thus serve as anchoring points for numerous DNA loci distributed throughout the genome, creating DNA loops connecting the anchored loci Wang W,2011 Reviews: Luijsterburg MS,2006; Williams RM,1997; Dorman CJ.,2004; Repoila F,2003; repressor; activator; Transcription related; nucleoproteins, basic proteins; cytoplasm; bent DNA binding; membrane; intracellular; DNA binding; transcription activator activity; transcription repressor activity; regulation of transcription, DNA-dependent; transcription, DNA-dependent |
| Length: | 138 |
| Pfam Domains: | 25-127 H-NS histone family |
| Sequence: (in bold interface residues) | 1 MSEALKILNNIRTLRAQARECTLETLEEMLEKLEVVVNERREEESAAAAEVEERTRKLQQ 60 61 YREMLIADGIDPNELLNSLAAVKSGTKAKRAQRPAKYSYVDENGETKTWTGQGRTPAVIK 120 121 KAMDEQGKSLDDFLIKQ* |
| Interface Residues: | 47, 48, 49, 50, 52, 114 |
| 3D-footprint Homologues: | 2e1c_A, 2lev_A |
| Binding Motifs: | HNS dAAwwwawysarw |
| Publications: | Repoila F., Majdalani N., Gottesman S. Small non-coding RNAs, co-ordinators of adaptation processes in Escherichia coli: the RpoS paradigm. Mol Microbiol. 48(4):855-61 (2003). [Pubmed] Soutourina O., Kolb A., Krin E., Laurent-Winter C., Rimsky S., Danchin A., Bertin P. Multiple control of flagellum biosynthesis in Escherichia coli: role of H-NS protein and the cyclic AMP-catabolite activator protein complex in transcription of the flhDC master operon. J Bacteriol. 181(24):7500-8 (1999). [Pubmed] Bertin P., Terao E., Lee EH., Lejeune P., Colson C., Danchin A., Collatz E. The H-NS protein is involved in the biogenesis of flagella in Escherichia coli. J Bacteriol. 176(17):5537-40 (1994). [Pubmed] Ali Azam T., Iwata A., Nishimura A., Ueda S., Ishihama A. Growth phase-dependent variation in protein composition of the Escherichia coli nucleoid. J Bacteriol. 181(20):6361-70 (1999). [Pubmed] Brescia CC., Kaw MK., Sledjeski DD. The DNA binding protein H-NS binds to and alters the stability of RNA in vitro and in vivo. J Mol Biol. 339(3):505-14 (2004). [Pubmed] Majdalani N., Vanderpool CK., Gottesman S. Bacterial small RNA regulators. Crit Rev Biochem Mol Biol. 40(2):93-113 (2005). [Pubmed] Shi X., Bennett GN. 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 (1994). [Pubmed] Zhang A., Belfort M. Nucleotide sequence of a newly-identified Escherichia coli gene, stpA, encoding an H-NS-like protein. Nucleic Acids Res. 20(24):6735 (1992). [Pubmed] Azam TA., Hiraga S., Ishihama A. Two types of localization of the DNA-binding proteins within the Escherichia coli nucleoid. Genes Cells. 5(8):613-26 (2000). [Pubmed] Sonnenfield JM., Burns CM., Higgins CF., Hinton JC. 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 (2001). [Pubmed] Sonden B., Uhlin BE. 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 (1996). [Pubmed] Zhang A., Rimsky S., Reaban ME., Buc H., Belfort M. Escherichia coli protein analogs StpA and H-NS: regulatory loops, similar and disparate effects on nucleic acid dynamics. EMBO J. 15(6):1340-9 (1996). [Pubmed] Johansson J., Eriksson S., Sonden B., Wai SN., Uhlin BE. Heteromeric interactions among nucleoid-associated bacterial proteins: localization of StpA-stabilizing regions in H-NS of Escherichia coli. J Bacteriol. 183(7):2343-7 (2001). [Pubmed] Williams RM., Rimsky S., Buc H. 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 (1996). [Pubmed] Dorman CJ., Hinton JC., Free A. Domain organization and oligomerization among H-NS-like nucleoid-associated proteins in bacteria. Trends Microbiol. 7(3):124-8 (1999). [Pubmed] Johansson J., Uhlin BE. 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 (1999). [Pubmed] Madrid C., Balsalobre C., Garcia J., Juarez A. The novel Hha/YmoA family of nucleoid-associated proteins: use of structural mimicry to modulate the activity of the H-NS family of proteins. Mol Microbiol. 63(1):7-14 (2007). [Pubmed] Paytubi S., Madrid C., Forns N., Nieto JM., Balsalobre C., Uhlin BE., Juarez A. YdgT, the Hha paralogue in Escherichia coli, forms heteromeric complexes with H-NS and StpA. Mol Microbiol. 54(1):251-63 (2004). [Pubmed] Rimsky S. Structure of the histone-like protein H-NS and its role in regulation and genome superstructure. Curr Opin Microbiol. 7(2):109-14 (2004). [Pubmed] Williams RM., Rimsky S. Molecular aspects of the E. coli nucleoid protein, H-NS: a central controller of gene regulatory networks. FEMS Microbiol Lett. 156(2):175-85 (1997). [Pubmed] Dame RT., Wyman C., Goosen N. H-NS mediated compaction of DNA visualised by atomic force microscopy. Nucleic Acids Res. 28(18):3504-10 (2000). [Pubmed] Zimmerman SB. Cooperative transitions of isolated Escherichia coli nucleoids: implications for the nucleoid as a cellular phase. J Struct Biol. 153(2):160-75 (2006). [Pubmed] Dame RT. The role of nucleoid-associated proteins in the organization and compaction of bacterial chromatin. Mol Microbiol. 56(4):858-70 (2005). [Pubmed] McLeod SM., Johnson RC. Control of transcription by nucleoid proteins. Curr Opin Microbiol. 4(2):152-9 (2001). [Pubmed] Tupper AE., Owen-Hughes TA., Ussery DW., Santos DS., Ferguson DJ., Sidebotham JM., Hinton JC., Higgins CF. The chromatin-associated protein H-NS alters DNA topology in vitro. EMBO J. 13(1):258-68 (1994). [Pubmed] Dorman CJ. H-NS: a universal regulator for a dynamic genome. Nat Rev Microbiol. 2(5):391-400 (2004). [Pubmed] Fang FC., Rimsky S. New insights into transcriptional regulation by H-NS. Curr Opin Microbiol. 11(2):113-20 (2008). [Pubmed] Hommais F., Krin E., Laurent-Winter C., Soutourina O., Malpertuy A., Le Caer JP., Danchin A., Bertin P. Large-scale monitoring of pleiotropic regulation of gene expression by the prokaryotic nucleoid-associated protein, H-NS. Mol Microbiol. 40(1):20-36 (2001). [Pubmed] Wang W., Li GW., Chen C., Xie XS., Zhuang X. Chromosome organization by a nucleoid-associated protein in live bacteria. Science. 333(6048):1445-9 (2011). [Pubmed] Yamada H., Muramatsu S., Mizuno T. An Escherichia coli protein that preferentially binds to sharply curved DNA. J Biochem (Tokyo). 108(3):420-5 (1990). [Pubmed] Oshima T., Ishikawa S., Kurokawa K., Aiba H., Ogasawara N. Escherichia coli histone-like protein H-NS preferentially binds to horizontally acquired DNA in association with RNA polymerase. DNA Res. 13(4):141-53 (2006). [Pubmed] Reusch RN., Shabalin O., Crumbaugh A., Wagner R., Schroder O., Wurm R. Posttranslational modification of E. coli histone-like protein H-NS and bovine histones by short-chain poly-(R)-3-hydroxybutyrate (cPHB). FEBS Lett. 527(1-3):319-22 (2002). [Pubmed] Uyar E., Kurokawa K., Yoshimura M., Ishikawa S., Ogasawara N., Oshima T. 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 (2009). [Pubmed] Falconi M., Higgins NP., Spurio R., Pon CL., Gualerzi CO. Expression of the gene encoding the major bacterial nucleotide protein H-NS is subject to transcriptional auto-repression. Mol Microbiol. 10(2):273-82 (1993). [Pubmed] Falconi M., Brandi A., La Teana A., Gualerzi CO., Pon CL. Antagonistic involvement of FIS and H-NS proteins in the transcriptional control of hns expression. Mol Microbiol. 19(5):965-75 (1996). [Pubmed] Landini P., Zehnder AJ. The global regulatory hns gene negatively affects adhesion to solid surfaces by anaerobically grown Escherichia coli by modulating expression of flagellar genes and lipopolysaccharide production. J Bacteriol. 184(6):1522-9 (2002). [Pubmed] Donato GM., Kawula TH. Phenotypic analysis of random hns mutations differentiate DNA-binding activity from properties of fimA promoter inversion modulation and bacterial motility. J Bacteriol. 181(3):941-8 (1999). [Pubmed] Donato GM., Lelivelt MJ., Kawula TH. Promoter-specific repression of fimB expression by the Escherichia coli nucleoid-associated protein H-NS. J Bacteriol. 179(21):6618-25 (1997). [Pubmed] Olsen PB., Schembri MA., Gally DL., Klemm P. Differential temperature modulation by H-NS of the fimB and fimE recombinase genes which control the orientation of the type 1 fimbrial phase switch. FEMS Microbiol Lett. 162(1):17-23 (1998). [Pubmed] Olsen PB., Klemm P. Localization of promoters in the fim gene cluster and the effect of H-NS on the transcription of fimB and fimE. FEMS Microbiol Lett. 116(1):95-100 (1994). [Pubmed] Schembri MA., Olsen PB., Klemm P. Orientation-dependent enhancement by H-NS of the activity of the type 1 fimbrial phase switch promoter in Escherichia coli. Mol Gen Genet. 259(3):336-44 (1998). [Pubmed] Shin M., Song M., Rhee JH., Hong Y., Kim YJ., Seok YJ., Ha KS., Jung SH., Choy HE. DNA looping-mediated repression by histone-like protein H-NS: specific requirement of Esigma70 as a cofactor for looping. Genes Dev. 19(19):2388-98 (2005). [Pubmed] De Biase D., Tramonti A., Bossa F., Visca P. The response to stationary-phase stress conditions in Escherichia coli: role and regulation of the glutamic acid decarboxylase system. Mol Microbiol. 32(6):1198-211 (1999). [Pubmed] Bouvier J., Gordia S., Kampmann G., Lange R., Hengge-Aronis R., Gutierrez C. Interplay between global regulators of Escherichia coli: effect of RpoS, Lrp and H-NS on transcription of the gene osmC. Mol Microbiol. 28(5):971-80 (1998). [Pubmed] Giangrossi M., Zattoni S., Tramonti A., De Biase D., Falconi M. Antagonistic role of H-NS and GadX in the regulation of the glutamate decarboxylase-dependent acid resistance system in Escherichia coli. J Biol Chem. 280(22):21498-505 (2005). [Pubmed] Ma Z., Richard H., Tucker DL., Conway T., Foster JW. Collaborative regulation of Escherichia coli glutamate-dependent acid resistance by two AraC-like regulators, GadX and GadW (YhiW). J Bacteriol. 184(24):7001-12 (2002). [Pubmed] Tramonti A., Visca P., De Canio M., Falconi M., De Biase D. Functional characterization and regulation of gadX, a gene encoding an AraC/XylS-like transcriptional activator of the Escherichia coli glutamic acid decarboxylase system. J Bacteriol. 184(10):2603-13 (2002). [Pubmed] Lucht JM., Dersch P., Kempf B., Bremer E. Interactions of the nucleoid-associated DNA-binding protein H-NS with the regulatory region of the osmotically controlled proU operon of Escherichia coli. J Biol Chem. 269(9):6578-8 (1994). [Pubmed] Rajkumari K., Gowrishankar J. In vivo expression from the RpoS-dependent P1 promoter of the osmotically regulated proU operon in Escherichia coli and Salmonella enterica serovar Typhimurium: activation by rho and hns mutations and by cold stress. J Bacteriol. 183(22):6543-50 (2001). [Pubmed] Francetic O., Belin D., Badaut C., Pugsley AP. Expression of the endogenous type II secretion pathway in Escherichia coli leads to chitinase secretion. EMBO J. 19(24):6697-703 (2000). [Pubmed] Rimsky S., Spassky A. Sequence determinants for H1 binding on Escherichia coli lac and gal promoters. Biochemistry. 29(15):3765-71 (1990). [Pubmed] Afflerbach H., Schroder O., Wagner R. Effects of the Escherichia coli DNA-binding protein H-NS on rRNA synthesis in vivo. Mol Microbiol. 28(3):641-53 (1998). [Pubmed] Gralla JD. Escherichia coli ribosomal RNA transcription: regulatory roles for ppGpp, NTPs, architectural proteins and a polymerase-binding protein. Mol Microbiol. 55(4):973-7 (2005). [Pubmed] Forns N., Juarez A., Madrid C. Osmoregulation of the HtrA (DegP) protease of Escherichia coli: an Hha-H-NS complex represses HtrA expression at low osmolarity. FEMS Microbiol Lett. 251(1):75-80 (2005). [Pubmed] Yamada H., Yoshida T., Tanaka K., Sasakawa C., Mizuno T. Molecular analysis of the Escherichia coli hns gene encoding a DNA-binding protein, which preferentially recognizes curved DNA sequences. Mol Gen Genet. 230(1-2):332-6 (1991). [Pubmed] Jauregui R., Abreu-Goodger C., Moreno-Hagelsieb G., Collado-Vides J., Merino E. Conservation of DNA curvature signals in regulatory regions of prokaryotic genes. Nucleic Acids Res. 31(23):6770-7 (2003). [Pubmed] Lang B., Blot N., Bouffartigues E., Buckle M., Geertz M., Gualerzi CO., Mavathur R., Muskhelishvili G., Pon CL., Rimsky S., Stella S., Babu MM., Travers A. High-affinity DNA binding sites for H-NS provide a molecular basis for selective silencing within proteobacterial genomes. Nucleic Acids Res. 35(18):6330-7 (2007). [Pubmed] Sette M., Spurio R., Trotta E., Brandizi C., Brandi A., Pon CL., Barbato G., Boelens R., Gualerzi CO. Sequence-specific recognition of DNA by the C-terminal domain of nucleoid-associated protein H-NS. J Biol Chem. 284(44):30453-62 (2009). [Pubmed] Dorman CJ. H-NS, the genome sentinel. Nat Rev Microbiol. 5(2):157-61 (2007). [Pubmed] Luijsterburg MS., Noom MC., Wuite GJ., Dame RT. The architectural role of nucleoid-associated proteins in the organization of bacterial chromatin: a molecular perspective. J Struct Biol. 156(2):262-72 (2006). [Pubmed] Welch TJ., Farewell A., Neidhardt FC., Bartlett DH. Stress response of Escherichia coli to elevated hydrostatic pressure. J Bacteriol. 175(22):7170-7 (1993). [Pubmed] Free A., Dorman CJ. Coupling of Escherichia coli hns mRNA levels to DNA synthesis by autoregulation: implications for growth phase control. Mol Microbiol. 18(1):101-13 (1995). [Pubmed] Lease RA., Belfort M. Riboregulation by DsrA RNA: trans-actions for global economy. Mol Microbiol. 38(4):667-72 (2000). [Pubmed] Brescia CC., Mikulecky PJ., Feig AL., Sledjeski DD. Identification of the Hfq-binding site on DsrA RNA: Hfq binds without altering DsrA secondary structure. RNA. 9(1):33-43 (2003). [Pubmed] |
| Related annotations: | PaperBLAST |
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