1 Nature Reviews Microbiology 2004 Vol: 2(5):391-400. DOI: 10.1038/nrmicro883

H-NS: a universal regulator for a dynamic genome

The effect of the bacterial heat-stable nucleoid-structuring (H-NS) protein on gene expression is overwhelmingly negative and extends throughout the genome, pointing to an almost universal role for this nucleoid-associated protein as a transcriptional repressor. Its ability to exert widespread effects on gene expression probably reflects the fact that it binds to curved DNA, which is commonly found at promoters. H-NS and related proteins can engage in both homologous and heterologous protein–protein interactions. Recent data show that the genes that encode H-NS-like proteins can be carried on mobile genetic elements. This raises the possibility that horizontal gene transfer expands the repertoire of protein–protein interactions that nucleoid-associated proteins can engage in, with potentially profound consequences for the global gene-expression profile of the cell.

Mentions
Figures
Figure 1: Protein-dependent constraint of DNA supercoiling.If part of a supercoiled DNA molecule is wrapped around a protein, one strand of the protein-free DNA can be nicked and re-ligated without affecting the integrity of the supercoil. However, in the absence of a DNA-binding protein, nicking one DNA strand results in loss of the unconstrained supercoil when the protein-free DNA swivels around its intact strand. Figure 2: H-NS-mediated repression of the virF virulence-gene promoter in Shigella flexneri.a | At the S. flexneri virF promoter, there are two binding sites for the heat-stable nucleoid-structuring (H-NS) protein centred at -1 and -250 with respect to the transcriptional start site, which is shown as an angled arrow. Formation of the repression complex at low temperatures requires looping of the intervening DNA. The formation of a DNA topology that is conducive to repression is antagonized by increased temperature. The resulting loss of contact between the bound H-NS proteins is thought to result in the instability of the nucleoprotein complex at the virF promoter, leading to derepression of transcription64. b | The Fis protein binds to four sites at the virF promoter, which are located at positions +55, -1, -130 and -200 (Ref. 47). Fis binding to the -1 site can hinder H-NS binding, contributing to the destabilization of the repression complex. The binding of Fis to the sites that are centred at -130 and -200 causes an adjustment to the geometry of the DNA that hinders the H-NS–H-NS interaction. This destabilizes the repression complex, contributing to derepression. The ternary structure undergoes a number of stages of development that depend on the temperature. For example, at 32 °C, the threshold temperature for relief of repression, H-NS and Fis can occupy the promoter simultaneously. A combination of protein–protein and protein–DNA interactions and DNA geometrical adjustments, all of which are modulated by changes in temperature, determine whether or not the virF promoter is transcriptionally active. A further variable is the temperature-dependent movement of the bend centre towards the virF open reading frame as the temperature rises, accompanied by an abrupt opening of the Fis binding site107. Figure 3: H-NS-mediated trapping of RNA polymerase and antagonism by Fis.The rrnB ribosomal RNA gene promoter is flanked by binding sites for the heat-stable nucleoid-structuring (H-NS) protein. Wrapping of DNA around RNA polymerase encourages interactions between sequences that are upstream and downstream of the promoter. In agreement with genetic data108, analysis by scanning-force microscopy indicates that H-NS 'zips up' the DNA flanking the promoter, producing an H-NS–polymerase–DNA ternary complex that prevents the escape of RNA polymerase into the elongation phase of transcription44. The Fis protein binds to three sites that are centred at -70, -100 and -140 with respect to the rrnB transcriptional start site at position +1. Fis binding antagonizes H-NS-mediated repression, presumably by disrupting the repression complex and releasing the trapped RNA polymerase77, 109. Figure 4: Structure of the H-NS protein.The main features of the 137-amino-acid heat-stable nucleoid-structuring (H-NS) protein from Escherichia coli are indicated. The numbering scheme designates the amino-terminal methionine as residue 1. Alterations to key residues that have provided important insights into the division of functions within the protein are summarized. The dimerization domain is composed of three -helices, consisting of residues 1–8, 12–19 and 23–47. The flexible linkers that connect these helices allow helices 1 and 2 to fold back and contribute to interactions between the dimerizing protomers, at least in the E. coli protein69 (see ). Figure 5: Two views of H-NS-mediated DNA bridging.a | The heat-stable nucleoid-structuring (H-NS) dimer interacts simultaneously with two DNA duplexes or different parts of the same duplex through its carboxy-terminal domains. This is based on the model proposed by Esposito et al. (Ref. 70) for the Salmonella protein. Here, -helices 1 (residues 1–8) and 2 (residues 12–19) of the amino terminus lie in an antiparallel orientation with -helix 3 (residues 23–47) of the dimerization domain. b | Two H-NS dimers, each bound to a separate DNA duplex (or to separate parts of the same duplex), interact with each other through their extended linker regions. It is proposed that extension of the unstructured linker may be brought about by simultaneous involvement of the amino- and carboxy-terminal domains in DNA binding56. The first -helices of each dimer are in contact with each other and -helix 2 of each protomer contacts -helix 3 of the other. This model is based on NMR analysis of the E. coli protein56 and is reviewed in Ref. 110. The protomers within the dimers are shown in dark green and light green. See  for further details of the H-NS structure. C, carboxyl terminus; N, amino terminus. Figure 6: Single-molecule experiments to examine the effect of H-NS binding on DNA structure.Identical linear DNA molecules, with magnetic beads attached at one end and anchored to a solid support at the other, are placed under tension in a magnetic field in the presence (a) or absence (b) of the heat-stable nucleoid-structuring (H-NS) protein. The open or closed nature of the complex is a reflection of the effect of H-NS binding on the effective persistence length of the DNA55. Surprisingly, H-NS causes the DNA to form a more extended structure, in contrast to its described role as a condensing agent in the nucleoid80. Further work is required to reconcile these contrasting views of the effects of H-NS on DNA structure.
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References
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    • . . . Although at least 12 polypeptides in E. coli have been described as being nucleoid-associated1, most research has focused on the heat-stable nucleoid-structuring (H-NS) protein, its PARALOGUE StpA, the factor for inversion stimulation (Fis), the heat-unstable (HU) protein and its near relative, integration host factor (IHF) . . .
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    • . . . The oligomeric H-NS protein is expressed at a relatively constant level throughout growth, with some reports of a small increase in early stationary phase6, 7, 8, 9, 10 . . .
    • . . . The H-NS and StpA proteins negatively autoregulate the transcription of their own genes and each represses the gene that encodes the other protein in trans6, 10, 11, 12, 13, 14, 15. . . .
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    • . . . The oligomeric H-NS protein is expressed at a relatively constant level throughout growth, with some reports of a small increase in early stationary phase6, 7, 8, 9, 10 . . .
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    • . . . The oligomeric H-NS protein is expressed at a relatively constant level throughout growth, with some reports of a small increase in early stationary phase6, 7, 8, 9, 10 . . .
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    • . . . The oligomeric H-NS protein is expressed at a relatively constant level throughout growth, with some reports of a small increase in early stationary phase6, 7, 8, 9, 10 . . .
    • . . . The H-NS and StpA proteins negatively autoregulate the transcription of their own genes and each represses the gene that encodes the other protein in trans6, 10, 11, 12, 13, 14, 15. . . .
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    • . . . The StpA protein (which is also oligomeric) is expressed at low levels in wild-type bacteria growing in rich media, but the levels increase during growth in minimal media and in bacteria that are undergoing stress11, 12 . . .
    • . . . The H-NS and StpA proteins negatively autoregulate the transcription of their own genes and each represses the gene that encodes the other protein in trans6, 10, 11, 12, 13, 14, 15. . . .
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    • . . . The StpA protein (which is also oligomeric) is expressed at low levels in wild-type bacteria growing in rich media, but the levels increase during growth in minimal media and in bacteria that are undergoing stress11, 12 . . .
    • . . . The H-NS and StpA proteins negatively autoregulate the transcription of their own genes and each represses the gene that encodes the other protein in trans6, 10, 11, 12, 13, 14, 15. . . .
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    • . . . The H-NS and StpA proteins negatively autoregulate the transcription of their own genes and each represses the gene that encodes the other protein in trans6, 10, 11, 12, 13, 14, 15. . . .
  14. Falconi, M., Higgins, N. P., Spurio, R., Pon, C. L. & Gualerzi, C. O. Expression of the gene encoding the major bacterial nucleoid protein H-NS is subject to transcriptional auto-repression. Mol. Microbiol. 10, 273-282 , (1993) .
    • . . . The H-NS and StpA proteins negatively autoregulate the transcription of their own genes and each represses the gene that encodes the other protein in trans6, 10, 11, 12, 13, 14, 15. . . .
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    • . . . The H-NS and StpA proteins negatively autoregulate the transcription of their own genes and each represses the gene that encodes the other protein in trans6, 10, 11, 12, 13, 14, 15. . . .
    • . . . Both proteins bind preferentially to curved DNA and have the ability to constrain supercoils in vitro (Fig. 1)15, 19 . . .
    • . . . They also both have significant RNA-binding activity, in addition to an ability to bind to DNA15, 20 . . .
    • . . . In fact, StpA functions as an RNA CHAPERONE in bacterial and bacteriophage gene regulation15, 21, 22 . . .
  16. Dorman, C. J., Hinton, J. C. D. & Free, A. Domain organization and oligomerization among H-NS-like nucleoid-associated proteins in bacteria. Trends Microbiol. 7, 124-128 , (1999) .
    • . . . H-NS is an abundant protein of approximately 15 kDa that is present at about 20,000 copies per genome equivalent16, 17, 18; StpA has a similar molecular mass but is much less abundant . . .
    • . . . The overwhelming impression that is formed from reading the literature on H-NS is that it is a protein that exists to turn things off16, 17, 18 . . .
    • . . . The H-NS protein is 137 amino acids in length and has three structural components (in this discussion, the amino-terminal methionine of H-NS is referred to as position 1): an N-terminal domain extending up to residue 65 that contains oligomerization activity; a carboxy-terminal domain beginning at residue 90 that has nucleic-acid-binding activity; and a flexible linker that connects the two16, 56, 69, 70 (Fig. 4) . . .
    • . . . These data point to a key role for this region of the protein in binding to intrinsically curved DNA, and a core DNA-binding motif, TWTGXGRXP (where 'X' is any amino acid) — which lies between residues 108 and 116 — is highly conserved throughout the H-NS protein family16 . . .
    • . . . An analogy can be drawn between the relationship of H-NS with StpA and the relationship between the subunits of the E. coli nucleoid-associated protein HU16, 41 . . .
    • . . . For example, H. influenzae has just one gene that encodes a member of the H-NS family, and Gram-positive bacteria have none16, 92 . . .
    • . . . Several other proteins have been identified that contain the H-NS C terminus fused to an unrelated N terminus16, 71, so this might be a relatively common mechanism for attenuating the effects of H-NS. . . .
  17. Schröder, O. & Wagner, R. The bacterial regulatory protein H-NS - a versatile modulator of nucleic acid structures. Biol. Chem. 383, 945-960 , (2002) .
    • . . . H-NS is an abundant protein of approximately 15 kDa that is present at about 20,000 copies per genome equivalent16, 17, 18; StpA has a similar molecular mass but is much less abundant . . .
    • . . . The overwhelming impression that is formed from reading the literature on H-NS is that it is a protein that exists to turn things off16, 17, 18 . . .
  18. Tendeng, C. & Bertin, P. H-NS in Gram-negative bacteria: a family of multifaceted proteins. Trends Microbiol. 11, 511-518 , (2003) .
    • . . . H-NS is an abundant protein of approximately 15 kDa that is present at about 20,000 copies per genome equivalent16, 17, 18; StpA has a similar molecular mass but is much less abundant . . .
    • . . . The overwhelming impression that is formed from reading the literature on H-NS is that it is a protein that exists to turn things off16, 17, 18 . . .
  19. Tupper, A. E. et al. The chromatin associated protein H-NS alters DNA topology in vitro. EMBO J. 13, 258-268 , (1994) .
    • . . . Both proteins bind preferentially to curved DNA and have the ability to constrain supercoils in vitro (Fig. 1)15, 19 . . .
  20. Sonnenfield, J. M., Burns, C. M., Higgins, C. F. & Hinton, J. C. D. 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, 1-7 , (2001) .
    • . . . They also both have significant RNA-binding activity, in addition to an ability to bind to DNA15, 20 . . .
  21. Deighan, P., Free, A. & Dorman, C. J. A role for the Escherichia coli H-NS-like protein StpA in OmpF porin expression through modulation of micF RNA stability. Mol. Microbiol. 38, 126-139 , (2000) .
    • . . . In fact, StpA functions as an RNA CHAPERONE in bacterial and bacteriophage gene regulation15, 21, 22 . . .
    • . . . The results of transcriptomic and proteomic studies attest to the global effects of this protein within the genome21, 23 . . .
  22. Zhang, A., Derbyshire, V., Salvo, J. L. & Belfort, M. Escherichia coli protein StpA stimulates self-splicing by promoting RNA assembly in vitro. RNA 1, 783-793 , (1995) .
    • . . . In fact, StpA functions as an RNA CHAPERONE in bacterial and bacteriophage gene regulation15, 21, 22 . . .
  23. Hommais, F. et al. Large-scale monitoring of pleiotropic regulation of gene expression by the prokaryotic nucleoid-associated protein, H-NS. Mol. Microbiol. 40, 20-36 , (2001) .
    • . . . The results of transcriptomic and proteomic studies attest to the global effects of this protein within the genome21, 23 . . .
  24. Kawula, T. H. & Orndorff, P. E. Rapid site-specific DNA inversion in Escherichia coli mutants lacking the histonelike protein H-NS. J. Bacteriol. 173, 4116-4123 , (1991) .
    • . . . Furthermore, the negative influence of H-NS is not confined to transcription — it can also inhibit recombination24, 25. . . .
  25. O'Gara, J. P. & Dorman, C. J. Effects of local transcription and H-NS on inversion of the fim switch of Escherichia coli. Mol. Microbiol. 36, 457-466 , (2000) .
    • . . . Furthermore, the negative influence of H-NS is not confined to transcription — it can also inhibit recombination24, 25. . . .
  26. Starcic-Erjavec, M. et al. H-NS and Lrp serve as positive modulators of traJ expression from the Escherichia coli plasmid pRK100. Mol. Gen. Genomics 270, 94-102 , (2003) .
    • . . . However, H-NS binds to this promoter in vitro only at very high concentrations of the protein and no details of the mechanism of direct activation are available26 . . .
  27. Nasser, W. & Reverchon, S. H-NS-dependent activation of pectate lyases synthesis in the phytopathogenic bacterium Erwinia chrysanthemi is mediated by the PecT repressor. Mol. Microbiol. 43, 733-748 , (2002) .
    • . . . An apparent role for H-NS as a positive regulator of pectate-lyase synthesis in the plant pathogen Erwinia chrysanthemi has been explained by the discovery that H-NS is in fact a repressor of the pecT repressor gene27 . . .
  28. Bertin, P. et al. The H-NS protein is involved in the biogenesis of flagella in Escherichia coli. J. Bacteriol. 176, 5537-5540 , (1994) .
    • . . . H-NS has been shown to positively influence bacterial motility28; however, this does not necessarily reflect a direct role for this protein as a transcriptional activator . . .
  29. Ko, M. & Park, C. H-NS-dependent regulation of flagellar synthesis is mediated by a LysR-like family protein. J. Bacteriol. 182, 4670-4672 , (2000) .
    • . . . First, H-NS is a repressor of hdfR, a gene that codes for a LysR-like protein that negatively regulates the promoter of the flagellar master-regulator operon, flhDC29 . . .
  30. Soutourina, O. et al. 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, 7500-7508 , (1999) .
    • . . . Interestingly, the flhDC promoter is also subject to direct repression by H-NS30 . . .
  31. Donato, G. M. & Kawula, T. H. Enhanced binding of altered H-NS protein to flagellar rotor protein FliG causes increased flagellar rotational speed and hypermotility in Escherichia coli. J. Biol. Chem. 273, 24030-24036 , (1998) .
    • . . . Second, H-NS seems to be able to interact directly with the FliG flagellar motor protein, enhancing its operation31 . . .
    • . . . The interaction of H-NS with the FliG flagellar motor protein31 has been referred to already . . .
  32. Yamada, H., Muramatsu, S. & Mizuno, T. An Escherichia coli protein that preferentially binds to sharply curved DNA. J. Biochem. 108, 420-425 , (1990) .
    • . . . This structure is curved DNA32, 33, which is commonly associated with promoters34, 35 . . .
  33. 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, 332-336 , (1991) .
    • . . . This structure is curved DNA32, 33, which is commonly associated with promoters34, 35 . . .
  34. Bracco, L., Kotlarz, D., Kolb, A., Diekmann, S. & Buc, H. Synthetic curved DNA sequences can act as transcriptional activators in Escherichia coli. EMBO J. 8, 4289-4296 , (1989) .
    • . . . This structure is curved DNA32, 33, which is commonly associated with promoters34, 35 . . .
  35. 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, 6770-6777 , (2003) .
    • . . . This structure is curved DNA32, 33, which is commonly associated with promoters34, 35 . . .
  36. Barbic, A., Zimmer, D. P. & Crothers, D. M. Structural origins of adenine-tract bending. Proc. Natl Acad. Sci. USA 100, 2369-2373 , (2003) .
    • . . . Furthermore, intrinsic DNA curvature can be specified by a variety of DNA sequences4, 36, affording proteins that bind to curved regions extraordinary latitude in their ability to interact with DNA. . . .
  37. La Teana, A. et al. Identification of a cold shock transcriptional enhancer of the Escherichia coli gene encoding nucleoid protein H-NS. Proc. Natl Acad. Sci. USA 88, 10907-10911 , (1991) .
    • . . . In addition to regulation by H-NS, StpA and Fis, the hns promoter is stimulated by cold shock through the CspA protein37 . . .
  38. Lease, R. A. & Belfort, M. Riboregulation by DsrA RNA: trans-actions for global economy. Mol. Microbiol. 38, 667-672 , (2000) .
    • . . . There is also a post-transcriptional negative regulatory mechanism, which involves an ANTISENSE RNA called DsrA and an RNA-binding protein called Hfq38, 39 . . .
  39. Brescia, C. C., Mikulecky, P. J., Feig, A. L. & Sledjeski, D. D. Identification of the Hfq-binding site on DsrA RNA: Hfq binds without altering DsrA secondary structure. RNA 9, 33-43 , (2003) .
    • . . . There is also a post-transcriptional negative regulatory mechanism, which involves an ANTISENSE RNA called DsrA and an RNA-binding protein called Hfq38, 39 . . .
  40. Welch, T. J., Farewell, A., Neidhardt, F. C. & Bartlett, D. H. Stress response of Escherichia coli to elevated hydrostatic pressure. J. Bacteriol. 175, 7170-7177 , (1993) .
    • . . . The expression of H-NS is also increased by an unknown mechanism during growth at elevated hydrostatic pressure40 . . .
  41. Johansson, J. & Uhlin, B. E. 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. USA 96, 10776-10781 , (1999) .
    • . . . Unlike its paralogue StpA, it is not subject to protease-mediated degradation41 . . .
    • . . . Genetic and protein crosslinking studies have shown that H-NS and StpA can form oligomers41, 83, 84, 85, 86 . . .
    • . . . The formation of a heteromeric partnership with H-NS protects StpA from LON-MEDIATED PROTEOLYSIS41 . . .
    • . . . A key difference in amino-acid sequence at position 21 of the proteins contributes to the Lon sensitivity of StpA — StpA has a phenylalanine residue at this position, whereas H-NS has a cysteine41 (Fig. 4) . . .
    • . . . An analogy can be drawn between the relationship of H-NS with StpA and the relationship between the subunits of the E. coli nucleoid-associated protein HU16, 41 . . .
  42. Reusch, R. N. et al. Posttranslational modification of E. coli histone-like protein H-NS and bovine histones by short-chain poly-(R)-3-hydroxybutyrate (cPHB). FEBS Lett. 527, 319-322.Tackles the neglected topic of small-molecule interactions with H-NS , (2002) .
    • . . . Although it has been found to form a complex with short-chain POLY-(R)-3-HYDROXYBUTYRATE42, the physiological significance of these complexes is still under investigation . . .
  43. Schneider, D. A., Ross, W. & Gourse, R. L. Control of rRNA expression in Escherichia coli. Curr. Opin. Microbiol. 6, 151-156 , (2003) .
    • . . . For example, the rRNA-encoding rrn operons of E. coli are repressed by H-NS43 . . .
    • . . . For example, the translational machinery of the cell is under the dynamic control of both Fis and H-NS43 . . .
  44. Dame, R. T., Wyman, C., Wurm, R., Wagner, R. & Goosen, N. Structural basis for H-NS mediated trapping of RNA polymerase in the open initiation complex at the rrnB P1. J. Biol. Chem. 277, 2146-2150.Uses scanning-force microscopy to analyse the H-NS-mediated DNA bridging that prevents the elongation phase of rrnB transcription , (2002) .
    • . . . Interaction between the two 'patches' of bound H-NS creates a repressive nucleoprotein complex that traps RNA polymerase at the promoter, preventing transcript elongation44 . . .
    • . . . In agreement with genetic data108, analysis by scanning-force microscopy indicates that H-NS 'zips up' the DNA flanking the promoter, producing an H-NS–polymerase–DNA ternary complex that prevents the escape of RNA polymerase into the elongation phase of transcription44 . . .
  45. Beloin, C. & Dorman, C. J. An extended role for the nucleoid structuring protein H-NS in the virulence gene regulatory cascade of Shigella flexneri. Mol. Microbiol. 47, 825-838 , (2003) .
    • . . . In cases for which this has been examined, these activators have been found to antagonize the repressive activity of H-NS — that is, they act as anti-repressors45, 46, 47, 48, 49, 50, 51, 52 (Fig. 2; Fig. 3). . . .
    • . . . H-NS has been found to be a repressor of the promoter of every regulatory and structural gene in this regulon for which its influence has been investigated45 . . .
  46. Caramel, A. & Schnetz, K. Lac and lambda repressors relieve silencing of the Escherichia coli bgl promoter. Activation by alteration of a repressing nucleoprotein complex. J. Mol. Biol. 284, 875-883 , (1998) .
    • . . . In cases for which this has been examined, these activators have been found to antagonize the repressive activity of H-NS — that is, they act as anti-repressors45, 46, 47, 48, 49, 50, 51, 52 (Fig. 2; Fig. 3). . . .
  47. Falconi, M., Prosseda, G., Giangrossi, M., Beghetto, E. & Colonna, B. Involvement of Fis in the H-NS-mediated regulation of virF gene of Shigella and enteroinvasive Escherichia coli. Mol. Microbiol. 42, 439-452.Provides a molecular explanation of the subtleties of Fis-H-NS antagonism at the virF promoter that may have implications for other genes that are subject to conflicting regulatory influences , (2001) .
    • . . . In cases for which this has been examined, these activators have been found to antagonize the repressive activity of H-NS — that is, they act as anti-repressors45, 46, 47, 48, 49, 50, 51, 52 (Fig. 2; Fig. 3). . . .
    • . . . The resulting loss of contact between the bound H-NS proteins is thought to result in the instability of the nucleoprotein complex at the virF promoter, leading to derepression of transcription64. b | The Fis protein binds to four sites at the virF promoter, which are located at positions +55, -1, -130 and -200 (Ref. 47) . . .
    • . . . These findings are significant, given the well-documented contribution of H-NS to the osmotic and thermal regulation of transcription47, 57, 58, 59, 60, 61, 62, 63, 64 . . .
  48. Haack, K. R., Robinson, C. L., Miller, K. J., Fowlkes, J. W. & Mellies, J. L. Interaction of Ler at the LEE5 (tir) operon of enteropathogenic Escherichia coli. Infect. Immun. 71, 384-392.Describes a model for Ler-H-NS antagonism at promoters within the LEE pathogenicity island. Should be read in conjunction with reference 105 , (2003) .
    • . . . In cases for which this has been examined, these activators have been found to antagonize the repressive activity of H-NS — that is, they act as anti-repressors45, 46, 47, 48, 49, 50, 51, 52 (Fig. 2; Fig. 3). . . .
    • . . . Interestingly, this island — which is thought to have been acquired horizontally — encodes Ler, a protein antagonist of H-NS that shares the same nucleic-acid-binding domain but lacks a homologue of the H-NS oligomerization domain48, 105 . . .
  49. Jordi, B. J. A. M. et al. The positive regulator CfaD overcomes the repression mediated by the histone-like protein H-NS (H1) in the CFA/I fimbrial operon of Escherichia coli. EMBO J. 11, 2627-2632 , (1992) .
    • . . . In cases for which this has been examined, these activators have been found to antagonize the repressive activity of H-NS — that is, they act as anti-repressors45, 46, 47, 48, 49, 50, 51, 52 (Fig. 2; Fig. 3). . . .
  50. Tobe, T., Yoshikawa, M., Mizuno, T. & Sasakawa, C. Transcriptional control of the invasion regulatory gene virB of Shigella flexneri: activation by VirF and repression by H-NS. J. Bacteriol. 175, 6142-6149 , (1993) .
    • . . . In cases for which this has been examined, these activators have been found to antagonize the repressive activity of H-NS — that is, they act as anti-repressors45, 46, 47, 48, 49, 50, 51, 52 (Fig. 2; Fig. 3). . . .
  51. Westermark, M., Oscarsson, J., Mizunoe, Y., Urbonaviciene, J. & Uhlin, B. E. Silencing and activation of ClyA cytotoxin expression in Escherichia coli. J. Bacteriol. 182, 6347-6357 , (2000) .
    • . . . In cases for which this has been examined, these activators have been found to antagonize the repressive activity of H-NS — that is, they act as anti-repressors45, 46, 47, 48, 49, 50, 51, 52 (Fig. 2; Fig. 3). . . .
  52. Yu, R. R. & DiRita, V. Regulation of gene expression in Vibrio cholerae by ToxT involves both antirepression and RNA polymerase stimulation. Mol. Microbiol. 43, 119-134 , (2002) .
    • . . . In cases for which this has been examined, these activators have been found to antagonize the repressive activity of H-NS — that is, they act as anti-repressors45, 46, 47, 48, 49, 50, 51, 52 (Fig. 2; Fig. 3). . . .
    • . . . Similarly, the virulence regulon in V. cholerae, which is a veritable mosaic of ancestral and horizontally acquired genes, uses H-NS as a transcriptional repressor of imported genes52, 103, 104 . . .
  53. Schnetz, K. & Wang, J. C. Silencing of the Escherichia coli bgl promoter: effects of template supercoiling and cell extracts on promoter activity in vitro. Nucleic Acids Res. 24, 2422-2428 , (1996) .
    • . . . For example, H-NS-mediated silencing of the E. coli bgl operon can be relieved by changes in local DNA topology53, 54 . . .
  54. Mukerji, M. & Mahadevan, S. Characterization of the negative elements involved in silencing the bgl operon of Escherichia coli: possible roles for DNA gyrase, H-NS, and CRP-cAMP in regulation. Mol. Microbiol. 24, 617-627 , (1997) .
    • . . . For example, H-NS-mediated silencing of the E. coli bgl operon can be relieved by changes in local DNA topology53, 54 . . .
  55. Amit, R., Oppenheim, A. B. & Stavans, J. Increased bending rigidity of single DNA molecules by H-NS, a temperature and osmolarity sensor. Biophys. J. 84, 2467-2473.Excellent single-molecule study that examines the formation of H-NS polymers on DNA , (2003) .
    • . . . Increases in temperature or the addition of osmolytes, such as NaCl or KCl, inhibit the interaction of H-NS with purified bacteriophage DNA55, and increased temperature inhibits the in vitro interaction between H-NS and a curved DNA sequence from the proU promoter56 . . .
    • . . . Other studies have shown that H-NS binds to DNA at a region of curvature and nucleates along the polymer55 . . .
    • . . . A single-molecule study that examined the effect of H-NS binding on the extension of individual DNA molecules (Fig. 6) showed that, rather than condensing the DNA, H-NS binding extended its effective PERSISTENCE LENGTH55 . . .
    • . . . The open or closed nature of the complex is a reflection of the effect of H-NS binding on the effective persistence length of the DNA55 . . .
  56. Badaut, C. et al. The degree of oligomerization of the H-NS nucleoid structuring protein is related to specific binding to DNA. J. Biol. Chem. 277, 41657-41666 , (2002) .
    • . . . Increases in temperature or the addition of osmolytes, such as NaCl or KCl, inhibit the interaction of H-NS with purified bacteriophage DNA55, and increased temperature inhibits the in vitro interaction between H-NS and a curved DNA sequence from the proU promoter56 . . .
    • . . . The H-NS protein is 137 amino acids in length and has three structural components (in this discussion, the amino-terminal methionine of H-NS is referred to as position 1): an N-terminal domain extending up to residue 65 that contains oligomerization activity; a carboxy-terminal domain beginning at residue 90 that has nucleic-acid-binding activity; and a flexible linker that connects the two16, 56, 69, 70 (Fig. 4) . . .
    • . . . It is proposed that extension of the unstructured linker may be brought about by simultaneous involvement of the amino- and carboxy-terminal domains in DNA binding56 . . .
    • . . . This model is based on NMR analysis of the E. coli protein56 and is reviewed in Ref. 110 . . .
    • . . . Truncated proteins that consist of the first 64 amino acids of the N-terminal domain are capable of forming dimers, but not higher-order oligomers56 . . .
    • . . . Moreover, changing the proline at position 116 to alanine abolishes the ability of H-NS to distinguish curved from non-curved DNA, while retaining non-specific DNA-binding activity78, and changing this residue to serine has a similar effect56 . . .
  57. Barth, M., Marschall, C., Muffler, A., Fischer, D. & Hengge-Aronis, R. Role of the histone-like protein H-NS in growth phase-dependent and osmotic regulation of s and many s-dependent genes in Escherichia coli. J. Bacteriol. 177, 3455-3464 , (1995) .
    • . . . These findings are significant, given the well-documented contribution of H-NS to the osmotic and thermal regulation of transcription47, 57, 58, 59, 60, 61, 62, 63, 64 . . .
  58. Fletcher, S. A. & Csonka, L. N. Fine-structure deletion analysis of the transcriptional silencer of the proU operon of Salmonella typhimurium. J. Bacteriol. 177, 4508-4513 , (1995) .
    • . . . These findings are significant, given the well-documented contribution of H-NS to the osmotic and thermal regulation of transcription47, 57, 58, 59, 60, 61, 62, 63, 64 . . .
  59. Nieto, J. M. et al. Expression of the haemolysin operon in Escherichia coli is modulated by a nucleoid-protein complex that includes the proteins Hha and H-NS. Mol. Gen. Genet. 263, 349-358 , (2000) .
    • . . . These findings are significant, given the well-documented contribution of H-NS to the osmotic and thermal regulation of transcription47, 57, 58, 59, 60, 61, 62, 63, 64 . . .
    • . . . Another protein that forms a complex with H-NS is Hha, an 8.5-kDa DNA-binding polypeptide that is also referred to as being nucleoid-associated59, 60, 96 . . .
    • . . . The interaction of the Hha–H-NS complex with DNA differs from those of the individual proteins59 and it has been proposed that the heteromeric complex is the active form that is required for haemolysin gene regulation in response to thermal and osmotic signals60. . . .
  60. Nieto, J. M. et al. Evidence for direct protein-protein interaction between members of the Enterobacterial Hha/YmoA and H-NS families of proteins. J. Bacteriol. 184, 629-635.Shows that Hha shows homology throughout its length to the oligomerization domain of H-NS , (2002) .
    • . . . These findings are significant, given the well-documented contribution of H-NS to the osmotic and thermal regulation of transcription47, 57, 58, 59, 60, 61, 62, 63, 64 . . .
    • . . . Another protein that forms a complex with H-NS is Hha, an 8.5-kDa DNA-binding polypeptide that is also referred to as being nucleoid-associated59, 60, 96 . . .
    • . . . Originally identified as a thermoregulator and osmotic regulator of -HAEMOLYSIN TOXIN expression in E. coli, Hha has been shown to form a complex with H-NS60 . . .
    • . . . The interaction of the Hha–H-NS complex with DNA differs from those of the individual proteins59 and it has been proposed that the heteromeric complex is the active form that is required for haemolysin gene regulation in response to thermal and osmotic signals60. . . .
    • . . . Sequence alignments have shown that Hha and H-NS share significant amino-acid homology in their N-terminal regions, corresponding to the site of the H-NS oligomerization domain60 . . .
    • . . . This case is also interesting because the IncHI plasmid in strain 2457T, like its counterparts in Salmonella, also encodes a homologue of Hha106, a protein that is known to interact with H-NS60 . . .
  61. Porter, M. E. & Dorman, C. J. A role for H-NS in the thermo-osmotic regulation of virulence-gene expression in Shigella flexneri. J. Bacteriol. 176, 4187-4191 , (1994) .
    • . . . These findings are significant, given the well-documented contribution of H-NS to the osmotic and thermal regulation of transcription47, 57, 58, 59, 60, 61, 62, 63, 64 . . .
  62. Rajkumari, K., Kusano, S., Ishihama, A., Mizuno, T. & Gowrishankar, J. Effects of H-NS and potassium glutamate on S- and 70-directed transcription in vitro from osmotically regulated P1 and P2 promoters of proU in Escherichia coli. J. Bacteriol. 178, 4176-4181 , (1996) .
    • . . . These findings are significant, given the well-documented contribution of H-NS to the osmotic and thermal regulation of transcription47, 57, 58, 59, 60, 61, 62, 63, 64 . . .
  63. Gowrishankar, J. & Manna, D. How is osmotic regulation of transcription of the Escherichia coli proU operon achieved? A review and a model. Genetica 97, 363-378 , .
    • . . . These findings are significant, given the well-documented contribution of H-NS to the osmotic and thermal regulation of transcription47, 57, 58, 59, 60, 61, 62, 63, 64 . . .
  64. Falconi, M., Colonna, B., Prosseda, G., Micheli, G. & Gualerzi, C. O. Thermoregulation of Shigella and Escherichia coli EIEC pathogenicity. A temperature-dependent structural transition of DNA modulates accessibility of virF promoter to transcriptional repressor H-NS. EMBO J. 17, 7033-7043 , (1998) .
    • . . . The resulting loss of contact between the bound H-NS proteins is thought to result in the instability of the nucleoprotein complex at the virF promoter, leading to derepression of transcription64. b | The Fis protein binds to four sites at the virF promoter, which are located at positions +55, -1, -130 and -200 (Ref. 47) . . .
    • . . . These findings are significant, given the well-documented contribution of H-NS to the osmotic and thermal regulation of transcription47, 57, 58, 59, 60, 61, 62, 63, 64 . . .
  65. Rohde, J. R., Luan, X. S., Rohde, H., Fox, J. M. & Minnich, S. A. The Yersinia enterocolitica pYV virulence plasmid contains multiple intrinsic DNA bends which melt at 37 °C. J. Bacteriol. 181, 4198-4204 , (1999) .
    • . . . For example, DNA curvature is attenuated by increases in temperature65, 66 and the addition of NaCl up to 300 mM is also known to reduce or remove DNA curvature67 . . .
  66. Ussery, D. W., Higgins, C. F. & Bolshoy, A. Environmental influences on DNA curvature. J. Biomol. Struct. Dyn. 16, 811-823 , (1999) .
    • . . . For example, DNA curvature is attenuated by increases in temperature65, 66 and the addition of NaCl up to 300 mM is also known to reduce or remove DNA curvature67 . . .
  67. Sinden, R. R., Pearson, C. E., Potaman, V. N. & Ussery, D. W. DNA: structure and function. Adv. Gen. Biol. 5A, 1-141 , (1998) .
    • . . . For example, DNA curvature is attenuated by increases in temperature65, 66 and the addition of NaCl up to 300 mM is also known to reduce or remove DNA curvature67 . . .
  68. Ceschini, S. et al. Multimeric self-assembly equilibria involving the histone-like protein H-NS. A thermodynamic study. J. Biol. Chem. 275, 729-734 , (2000) .
    • . . . Of course, the possibility that the structure of H-NS is itself altered by changes in temperature or osmolarity remains open68. . . .
  69. Bloch, V. et al. The H-NS dimerization domain defines a new fold contributing to DNA recognition. Nature Struct. Biol. 10, 212-218.Defines the core dimerization motif of E. coli H-NS using NMR analysis and suggests a role for the linker region in protein-protein interactions , (2003) .
    • . . . The flexible linkers that connect these helices allow helices 1 and 2 to fold back and contribute to interactions between the dimerizing protomers, at least in the E. coli protein69 (see Fig. 5). . . .
    • . . . The H-NS protein is 137 amino acids in length and has three structural components (in this discussion, the amino-terminal methionine of H-NS is referred to as position 1): an N-terminal domain extending up to residue 65 that contains oligomerization activity; a carboxy-terminal domain beginning at residue 90 that has nucleic-acid-binding activity; and a flexible linker that connects the two16, 56, 69, 70 (Fig. 4) . . .
    • . . . A 46-residue segment of the N-terminal domain of the E. coli protein has been identified as the minimal dimerization domain69 . . .
    • . . . It has been argued that these mutations do not alter the folding of the protein or its dimerization activity but instead impair its ability to recognize curved DNA, with a concomitant weakening of its affinity for all DNA69 . . .
    • . . . Based on work with regions of the H-NS protein, it has been suggested that higher-order oligomerization is a function of the central region of the protein (residues 46–90)69, which includes the flexible linker domain . . .
  70. Esposito, D. et al. H-NS oligomerization domain structure reveals the mechanism for high order self-association of the intact protein. J. Mol. Biol. 324, 841-850.Presents evidence for a head-to-tail mechanism for the assembly of H-NS polymers based on interactions between the oligomerization domains of dimers , (2002) .
    • . . . The H-NS protein is 137 amino acids in length and has three structural components (in this discussion, the amino-terminal methionine of H-NS is referred to as position 1): an N-terminal domain extending up to residue 65 that contains oligomerization activity; a carboxy-terminal domain beginning at residue 90 that has nucleic-acid-binding activity; and a flexible linker that connects the two16, 56, 69, 70 (Fig. 4) . . .
    • . . . This is based on the model proposed by Esposito et al. (Ref. 70) for the Salmonella protein . . .
    • . . . Another model, based on data from the S. typhimurium H-NS protein, suggests a role for the dimeric N terminus in forming head-to-tail oligomers70 . . .
  71. Cusick, M. E. & Belfort, M. E. Domain structure and RNA annealing activity of the Escherichia coli regulatory protein StpA. Mol. Microbiol. 28, 847-857 , (1998) .
    • . . . A similar domain structure has been proposed for StpA, with its RNA-annealing activity being located within the C terminus71. . . .
    • . . . Several other proteins have been identified that contain the H-NS C terminus fused to an unrelated N terminus16, 71, so this might be a relatively common mechanism for attenuating the effects of H-NS. . . .
  72. Ueguchi, C., Seto, C., Suzuki, T. & Mizuno, T. Clarification of the dimerization domain and its functional significance for the Escherichia coli nucleoid protein H-NS. J. Mol. Biol. 274, 145-151 , (1997) .
    • . . . Substitution of proline for leucine at position 30 produces a protein that has lost the ability to dimerize and bind to DNA72 . . .
  73. Ueguchi, C., Suzuki, T., Yoshida, T., Tanaka, K. & Mizuno, T. Systematic mutational analysis revealing the functional domain organization of Escherichia coli nucleoid protein H-NS. J. Mol. Biol. 263, 149-162 , (1996) .
    • . . . Studies using deletion derivatives of H-NS have assigned the DNA-binding domain to the C terminus73 . . .
  74. Shindo, H. et al. Solution structure of the DNA binding domain of a nucleoid-associated protein, H-NS, from Escherichia coli. FEBS Lett. 360, 125-131 , (1995) .
    • . . . The isolated C-terminal domain (resides 90–137) is unable to form dimers or higher-order oligomers74, 75, whereas truncated proteins that lack this domain retain oligomerization activity76 . . .
  75. Shindo, H. et al. Identification of the DNA binding surface of H-NS protein from Escherichia coli by heteronuclear NMR spectroscopy. FEBS Lett. 455, 63-69 , (1999) .
    • . . . The isolated C-terminal domain (resides 90–137) is unable to form dimers or higher-order oligomers74, 75, whereas truncated proteins that lack this domain retain oligomerization activity76 . . .
  76. Smyth, C. P. et al. Oligomerization of the chromatin-structuring protein HNS. Mol. Microbiol. 36, 962-972 , (2000) .
    • . . . The isolated C-terminal domain (resides 90–137) is unable to form dimers or higher-order oligomers74, 75, whereas truncated proteins that lack this domain retain oligomerization activity76 . . .
  77. Tippner, D. & Wagner, R. Fluorescence analysis of the Escherichia coli transcription regulator H-NS reveals two distinguishable complexes dependent on binding to specific or non-specific DNA sites. J. Biol. Chem. 270, 22243-22247 , (1995) .
    • . . . Fis binding antagonizes H-NS-mediated repression, presumably by disrupting the repression complex and releasing the trapped RNA polymerase77, 109. . . .
    • . . . Biochemical analysis shows that the fluorescence of the tryptophan at position 109 (which is used to monitor protein conformation) is enhanced when the protein interacts with curved DNA, but is decreased on interaction with non-specific competitor DNA77 . . .
  78. Spurio, R., Falconi, M., Brandi, A., Pon, C. L. & Gualerzi, C. O. The oligomeric structure of nucleoid protein H-NS is necessary for recognition of intrinsically curved DNA and for DNA bending. EMBO J. 16, 1795-1805 , (1995) .
    • . . . Moreover, changing the proline at position 116 to alanine abolishes the ability of H-NS to distinguish curved from non-curved DNA, while retaining non-specific DNA-binding activity78, and changing this residue to serine has a similar effect56 . . .
    • . . . The proline-to-alanine substitution at position 116 has also been reported to disrupt the oligomerization of H-NS in vitro and that of a fusion protein in which H-NS replaces the missing oligomerization domain of a truncated bacteriophage cI repressor in vivo78 . . .
  79. Dame, R. T., Wyman, C. & Goosen, N. H-NS mediated compaction of DNA visualized by atomic force microscopy. Nucleic Acids Res. 28, 3504-3510 , (2000) .
    • . . . Atomic-force microscopic analysis of covalently closed circular plasmid DNA bound by H-NS supports the proposal that H-NS can crosslink DNA in this way79 . . .
  80. Spurio, R. et al. Lethal overproduction of the Escherichia coli nucleoid protein H-NS: ultramicroscopic and molecular autopsy. Mol. Gen. Genet. 231, 201-211 , (1992) .
    • . . . This property would allow the protein to contribute to the condensation of the nucleoid, in agreement with data from studies in which H-NS has been overexpressed80 . . .
    • . . . Surprisingly, H-NS causes the DNA to form a more extended structure, in contrast to its described role as a condensing agent in the nucleoid80 . . .
  81. Rimsky, S., Zuber, F., Buckle, M. & Buc, H. A molecular mechanism for the repression of transcription by the H-NS protein. Mol. Microbiol. 42, 1311-1323 , (2001) .
    • . . . These data are consistent with models of transcriptional silencing in which the curved DNA sequence to which H-NS initially binds is located upstream or downstream of the promoter that is to be repressed81 . . .
  82. Dame, R. T. & Goosen, N. HU: promoting or counteracting DNA compaction? FEBS Lett. 529, 151-156 , (2002) .
    • . . . For example, HU has been described as antagonizing the formation of H-NS–DNA structures, leading to a dynamic equilibrium throughout the nucleoid82 . . .
  83. Free, A., Williams, R. M. & Dorman, C. J. 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, 994-997 , (1998) .
    • . . . Genetic and protein crosslinking studies have shown that H-NS and StpA can form oligomers41, 83, 84, 85, 86 . . .
  84. Free, A., Porter, M. E., Deighan, P. & Dorman, C. J. 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, 903-918 , (2001) .
    • . . . Genetic and protein crosslinking studies have shown that H-NS and StpA can form oligomers41, 83, 84, 85, 86 . . .
  85. Johansson, J., Eriksson, S., Sondén, B., Wai, S. N. & Uhlin, B. E. Heteromeric interactions among nucleoid-associated bacterial proteins: localization of StpA-stabilizing regions in H-NS of Escherichia coli. J. Bacteriol. 183, 2343-2347 , (2001) .
    • . . . Genetic and protein crosslinking studies have shown that H-NS and StpA can form oligomers41, 83, 84, 85, 86 . . .
  86. Williams, R. M., Rimsky, S. & Buc, H. Probing the structure, function, and interactions of the Escherichia coli H-NS and StpA proteins using dominant negative derivatives. J. Bacteriol. 178, 4335-4343 , (1996) .
    • . . . Genetic and protein crosslinking studies have shown that H-NS and StpA can form oligomers41, 83, 84, 85, 86 . . .
  87. Claret, L. & Rouvière-Yaniv, J. Variation in HU composition during growth of Escherichia coli: the heterodimer is required for long term survival. J. Mol. Biol. 273, 93-104 , (1997) .
    • . . . The - and -subunits of the HU protein show approximately 70% amino-acid-sequence similarity and HU can exist as an -homodimer, a -homodimer or an -heterodimer87 . . .
    • . . . Like the hns and stpA genes, the genes that encode the HU subunits, hupA (-subunit) and hupB (-subunit), are subject to differential regulation87, 88 . . .
    • . . . The -homodimer differs from the heterodimers and the -homodimer in being unable to constrain DNA supercoils87, 89 (Fig. 1) . . .
  88. Claret, L. & Rouvière-Yaniv, J. Regulation of HU and HU by CRP and FIS in Escherichia coli. J. Mol. Biol. 263, 126-139 , (1996) .
    • . . . Like the hns and stpA genes, the genes that encode the HU subunits, hupA (-subunit) and hupB (-subunit), are subject to differential regulation87, 88 . . .
  89. Tanaka, H. et al. Role of HU proteins in forming and constraining supercoils of chromosomal DNA in Escherichia coli. Mol. Gen. Genet. 248, 518-526 , (1995) .
    • . . . The -homodimer differs from the heterodimers and the -homodimer in being unable to constrain DNA supercoils87, 89 (Fig. 1) . . .
  90. Oberto, J. & Rouvière-Yaniv, J. Serratia marcescens contains a heterodimeric HU protein like Escherichia coli and Salmonella typhimurium. J. Bacteriol. 178, 293-297 , (1996) .
    • . . . For example, Bacillus subtilis and Haemophilus influenzae each have just one hup gene, so their HU proteins are homodimeric90 . . .
  91. Cases, I. & de Lorenzo, V. The genomes of Pseudomonas encode a third HU protein. Microbiol. 148, 1243-1245 , (2002) .
    • . . . By contrast, bioinformatics data indicate that Pseudomonas spp. can have up to three HU proteins, which is consistent with their ability to adapt to a wide range of environmental niches91. . . .
  92. Fleischmann, R. D. et al. Whole-genome random sequencing of Haemophilus influenzae Rd. Science 269, 496-512 , (1995) .
    • . . . For example, H. influenzae has just one gene that encodes a member of the H-NS family, and Gram-positive bacteria have none16, 92 . . .
  93. Kajitani, M. & Ishihama, A. Identification and sequence determination of the host factor gene for bacteriophage QB. Nucleic Acids Res. 19, 1063-1066 , (1991) .
    • . . . H-NS also interacts with Hfq (or HF-1)93, a protein that binds to RNA and modulates the translation of rpoS mRNA, although the details of this interaction are unknown94, 95 . . .
  94. Muffler, A., Fischer, D., Altuvia, S., Storz, G. & Hengge-Aronis, R. The RNA binding protein HF-1, known as a host factor for phage QB RNA replication, is essential for rpoS translation in Escherichia coli. Genes Dev. 10, 1143-1151 , (1996) .
    • . . . H-NS also interacts with Hfq (or HF-1)93, a protein that binds to RNA and modulates the translation of rpoS mRNA, although the details of this interaction are unknown94, 95 . . .
  95. Nogueira, T. & Springer, M. Post-transcriptional control by global regulators of gene expression in bacteria. Curr. Opin. Microbiol. 3, 154-158 , (2000) .
    • . . . H-NS also interacts with Hfq (or HF-1)93, a protein that binds to RNA and modulates the translation of rpoS mRNA, although the details of this interaction are unknown94, 95 . . .
  96. Nieto, J. M. et al. The hha gene modulates haemolysin expression in Escherichia coli. Mol. Microbiol. 5, 1285-1293 , (1991) .
    • . . . Another protein that forms a complex with H-NS is Hha, an 8.5-kDa DNA-binding polypeptide that is also referred to as being nucleoid-associated59, 60, 96 . . .
  97. Robertson, C. A. & Nash, H. A. Bending of the bacteriophage attachment site by Escherichia coli integration host factor. J. Biol. Chem. 263, 3554-3557 , (1988) .
    • . . . For example, IHF got its name from the role that it plays in bacteriophage integration and excision97 . . .
  98. Ball, C. A. & Johnson, R. C. Multiple effects of Fis on integration and the control of lysogeny in phage . J. Bacteriol. 173, 4032-4038 , (1991) .
    • . . . Moreover, the Fis protein makes a contribution to the integration and excision of the same virus into or from the E. coli chromosome98 . . .
  99. Liu, Q. & Richardson, C. C. Gene 5.5 protein of bacteriophage T7 inhibits the nucleoid protein H-NS of Escherichia coli. Proc. Natl Acad. Sci. USA 90, 1761-1765 , (1993) .
    • . . . For example, the protein that is encoded by gene 5.5 of bacteriophage T7 inactivates H-NS, resulting in derepression of both host and viral promoters99 . . .
  100. Buchrieser, C. et al. The virulence plasmid pWR100 and the repertoire of proteins secreted by the type III secretion apparatus of Shigella flexneri. Mol. Microbiol. 38, 760-771 , (2000) .
    • . . . For example, the 230-kb virulence plasmid of Shigella and enteroinvasive E. coli carries a complex regulon of genes that encodes a type III secretion system and effector proteins that are required for invasion and spreading in human epithelial cells100 . . .
  101. Wilson, R. L. et al. Fis, a DNA nucleoid-associated protein, is involved in Salmonella typhimurium SPI-1 invasion gene expression. Mol. Microbiol. 39, 79-88 , (2001) .
    • . . . In Salmonella, the genes within the SPI-1 PATHOGENICITY ISLAND, a genetic element that is thought to have originated outside the enteric bacteria, is positively regulated by Fis101, and there is ample evidence of regulatory roles for other nucleoid-associated proteins in this genus, including H-NS102 . . .
  102. Schechter, L. M., Jain, S., Akbar, S. & Lee, C. A. The small nucleoid-binding proteins H-NS, HU, and Fis affect hilA expression in Salmonella enterica serovar Typhimurium. Infect. Immun. 71, 5432-5435 , (2003) .
    • . . . In Salmonella, the genes within the SPI-1 PATHOGENICITY ISLAND, a genetic element that is thought to have originated outside the enteric bacteria, is positively regulated by Fis101, and there is ample evidence of regulatory roles for other nucleoid-associated proteins in this genus, including H-NS102 . . .
  103. Nye, M. B. & Taylor, R. K. Vibrio cholerae H-NS domain structure and function with respect to transcriptional repression of ToxR regulon genes reveals differences among H-NS family members. Mol. Microbiol. 50, 427-444.Discusses evidence that the H-NS protein of the pathogen Vibrio cholerae has an additional oligomerization motif in the extreme amino terminus of the protein , (2003) .
    • . . . Similarly, the virulence regulon in V. cholerae, which is a veritable mosaic of ancestral and horizontally acquired genes, uses H-NS as a transcriptional repressor of imported genes52, 103, 104 . . .
  104. Cerdan, R. et al. Crystal structure of the N-terminal dimerization domain of VicH, the H-NS-like protein of Vibrio cholerae. J. Mol. Biol. 334, 179-185.Shows that the amino-terminal domain of the Vibrio cholerae H-NS protein folds in a similar way to the Escherichia coli protein , (2003) .
    • . . . Similarly, the virulence regulon in V. cholerae, which is a veritable mosaic of ancestral and horizontally acquired genes, uses H-NS as a transcriptional repressor of imported genes52, 103, 104 . . .
  105. Bustamante, V. H., Santana, F. J., Calva, E. & Puente, J. L. Transcriptional regulation of type III secretion genes in enteropathogenic Escherichia coli: Ler antagonizes H-NS-dependent repression. Mol. Microbiol. 39, 664-678.Describes the antagonism of H-NS-mediated transcriptional repression by Ler, a protein that shares the DNA-binding domain of H-NS but not its oligomerization region. See also reference 48 , (2001) .
    • . . . Interestingly, this island — which is thought to have been acquired horizontally — encodes Ler, a protein antagonist of H-NS that shares the same nucleic-acid-binding domain but lacks a homologue of the H-NS oligomerization domain48, 105 . . .
  106. Beloin, C., Deighan, P., Doyle, M. & Dorman, C. J. Shigella flexneri 2a strain 2457T expresses three members of the H-NS-like protein family: characterization of the Sfh protein. Mol. Gen. Genomics 270, 66-77 , (2003) .
    • . . . The case of Sfh in S. flexneri 2a strain 2457T (Box 1) shows that plasmid-borne nucleoid-associated proteins can function beyond the replicon that encodes them106 . . .
    • . . . This case is also interesting because the IncHI plasmid in strain 2457T, like its counterparts in Salmonella, also encodes a homologue of Hha106, a protein that is known to interact with H-NS60 . . .
  107. Prosseda, G. et al. The virF promoter in Shigella: more than just a curved DNA stretch. Mol. Microbiol. 51, 523-537 , (2004) .
    • . . . A further variable is the temperature-dependent movement of the bend centre towards the virF open reading frame as the temperature rises, accompanied by an abrupt opening of the Fis binding site107. . . .
  108. Afflerbach, H., Schröder, O. & Wagner, R. Conformational changes of the upstream DNA mediated by H-NS and Fis regulate E. coli rrnB promoter activity. J. Mol. Biol. 286, 339-353 , (1999) .
    • . . . In agreement with genetic data108, analysis by scanning-force microscopy indicates that H-NS 'zips up' the DNA flanking the promoter, producing an H-NS–polymerase–DNA ternary complex that prevents the escape of RNA polymerase into the elongation phase of transcription44 . . .
  109. Afflerbach, H., Schröder, O. & Wagner, R. Effects of the Escherichia coli DNA-binding protein H-NS on rRNA synthesis in vivo. Mol. Microbiol. 28, 641-653.Provides a vivid account of the dynamic interplay between DNA topology, nucleoid-associated proteins and temperature in promoter activation , (1998) .
    • . . . Fis binding antagonizes H-NS-mediated repression, presumably by disrupting the repression complex and releasing the trapped RNA polymerase77, 109. . . .
  110. Rimsky, S. Structure of the histone-like protein H-NS and its role in regulation and genome superstructure. Curr. Opin. Microbiol. 7, 1-6.Provides a useful summary of the most recent structural data available for H-NS , (2004) .
    • . . . This model is based on NMR analysis of the E. coli protein56 and is reviewed in Ref. 110 . . .
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