Regulation of gene expression by histone-like proteins in bacteria

Current Opinion in Genetics and Development

Volumn 13, Issue 2, 2003, Pages 179-184

  Dorman, Charles J ^a   Deighan, Padraig ^a  

^a TRINITY COLLEGE DUBLIN   (Ireland)

Author keywords

[No Author keywords available]

Indexed keywords

DNA TOPOISOMERASE; HISTONE; INTEGRATION HOST FACTOR;

DNA RECOMBINATION; DNA REPLICATION; ESCHERICHIA COLI; GENE CONTROL; GENE EXPRESSION; GENE EXPRESSION REGULATION; GENOME; NONHUMAN; OPERON; PRIORITY JOURNAL; PROMOTER REGION; REVIEW;

BACTERIA (MICROORGANISMS); ESCHERICHIA COLI;

EID: 0037381650     PISSN: 0959437X     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0959-437X(03)00025-X     Document Type: Review

References (43)

1. Bahloul A., Boubrik F., Rouvière-Yaniv J. Roles of Escherichia coli histone-like protein HU in DNA replication: HU-beta suppresses the thermosensitivity of dnaA46ts. Biochimie. 83:2001;219-229.
2. Kar S., Adhya S. Recruitment of HU by piggyback: a special role of GalR in repressosome assembly. Genes Dev. 15:2001;2273-2281 The authors demonstrate for the first time that protein:protein interaction occurs between HU and another protein (GalR). This significant finding shows that HU interacts not only with DNA but also with other (protein) components of a nucleoprotein complex and this may apply in cases other than the transcription regulator, GalR.
3. Oberto J., Rouvière-Yaniv J. Does the parallel evolution pattern between the replication-segregation proteins and HU have a biological significance? Biochimie. 83:2001;61-66.
4. Ussery D., Larsen T.S., Wilkes K.T., Friis C., Worning P., Krogh A., Brunak S. Genome organization and chromatin structure in Escherichia coli. Biochimie. 83:2001;201-212.
5. Ali B.M., Amit R., Braslavsky I., Oppenheim A.B., Gileadi O., Stavans J. Compaction of single DNA molecules induced by binding of integration host factor (IHF). Proc. Natl. Acad. Sci. U.S.A. 98:2001;10658-10663.
6. Wagner R: Lessons from a manifold regulated system. In Transcription Regulation in Prokaryotes. Oxford: Oxford University Press; 2000:309-330.
7. Grove A., Saavedra T.C. The role of surface-exposed lysines in wrapping DNA about the bacterial histone-like protein HU. Biochemistry. 41:2002;7597-7603.
8. Krylov A., Zasedateleva O.A., Prokopenko D.V., Rouvière-Yaniv J., Mirzabekov A.D. Massive parallel analysis of the binding specificity of histone-like protein HU to single- and double-stranded DNA with generic oligodeoxyribonucleotide microchips. Nucleic Acids Res. 29:2001;2654-2660.
9. Schröder O., Wagner R. The bacterial regulatory protein H-NS - a versatile modulator of nucleic acid structures. Biol. Chem. 383:2002;945-960.
10. Dame R.T., Wyman C., Goosen N. Structural basis for preferential binding of H-NS to curved DNA. Biochimie. 83:2001;231-234.
11. Rimsky S., Zuber F., Buckle M., Buc H. A molecular mechanism for the repression of transcription by the H-NS protein. Mol. Microbiol. 42:2001;1311-1323.
12. Brunetti R., Prosseda G., Beghetto E., Colonna B., Micheli G. The looped domain organization of the nucleoid in histone-like protein defective Escherichia coli strains. Biochimie. 83:2001;873-882 Challenges the long-standing assumption that the bacterial histone-like proteins must in some way contribute to the looped domain structure of the nucleoid by demonstrating that this structure is preserved even in mutants genetically unable to express these.
13. Azam A.T., Iwata A., Nishimura A., Ueda S., Ishihama A. Growth phase-dependent variation in protein composition of the Escherichia coli nucleoid. J. Bacteriol. 181:1999;6361-6370.
14. Free A., Dorman C.J. Coupling of Escherichia coli hns mRNA levels to DNA synthesis by autoregulation: implications for growth phase control. Mol. Microbiol. 18:1995;101-113.
15. Balandina A., Claret L., Hengge-Aronis R., Rouvière-Yaniv J. The Escherichia coli histone-like protein HU regulates rpoS translation. Mol. Microbiol. 39:2001;1069-1079.
16. Semsey S., Geanacopoulos M., Lewis D.E., Adhya S. Operator-bound GalR dimers close DNA loops by direct interaction: tetramerization and inducer binding. EMBO J. 21:2002;4349-4356.
17. Dame R.T., Goosen N. HU: promoting or counteracting DNA compaction? FEBS Lett. 529:2002;151-156 The authors challenge very effectively the long-standing assumption that HU acts to compact the bacterial nucleoid, by analogy with eukaryotic histones. They use atomic force microscopy data to show clearly that this is not the case.
18. Morales P., Rouvière-Yaniv J., Dreyfus M. The histone-like protein HU does not obstruct movement of T7 RNA polymerase in Escherichia coli cells but stimulates its activity. J. Bacteriol. 184:2002;1565-1570.
19. Hommais F., Krin E., Laurent-Winter C., Soutourina O., Malpertuy A., Le Caer J.P., Danchin A., Bertin P. Large-scale monitoring of pleiotropic regulation of gene expression by the prokaryotic nucleoid-associated protein, H-NS. Mol. Microbiol. 40:2001;20-36 Uses transcriptomic and proteomic methods to establish the membership of the H-NS regulon in E. coli. This was a first for this nucleoid structuring protein and at least 5% of the genes in the cell were found to respond to its presence or absence.
20. Schröder O., Wagner R. The bacterial DNA-binding protein H-NS represses ribosomal RNA transcription by trapping RNA polymerase in the initiation complex. J. Mol. Biol. 298:2000;737-748.
21. 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. 277:2002;2146-2150 Provides one of the clearest explanations of how H-NS impedes the function of RNA polymerase during transcription initiation. It shows how two patches of H-NS-bound DNA form a loop to trap the polymerase at the ribosomal RNA gene promoter.
22. 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. 42:2001;439-452 Two regions of the virF promoter region bound by the H-NS protein form a repression loop in DNA but this complex is disrupted by the intervention of a second histone-like protein, Fis. This paper provides important molecular detail on how antagonistic relationships between such proteins might set the transcriptional profile of the cell.
23. Dorman C.J., Hinton J.C.D., Free A. Domain organization and oligomerization among H-NS-like nucleoid-associated proteins in bacteria. Trends Microbiol. 7:1999;124-128.
24. Badaut C., Williams R., Arluison V., Bouffartigues E., Robert B., Buc H., Rimsky S. The degree of oligomerization of the H-NS nucleoid structuring protein is related to specific binding to DNA. J. Biol. Chem. 277:2002;41657-41666.
25. Yu R.R., DiRita V.J. Regulation of gene expression in Vibrio cholerae by ToxT involves both antirepression and RNA polymerase stimulation. Mol. Microbiol. 43:2002;119-134.
26. Dorman CJ: DNA topology and regulation of bacterial gene expression. In Signals, Switches, Regulons and Cascades: Control of Bacterial Gene Expression. Edited by Hodgson DA, Thomas CM. Cambridge: Cambridge University Press; 2002:41-56.
27. Dorman C.J., McKenna S., Beloin C. Regulation of virulence gene expression in Shigella flexneri, a facultative intracellular pathogen. Int. J. Med. Microbiol. 291:2001;89-96.
28. 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. 38:2000;126-139.
29. 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 on the level of truncated H-NS protein. Mol. Microbiol. 42:2001;903-918.
30. Waldsich C., Grossberger R., Schroeder R. RNA chaperone StpA loosens interactions of the tertiary structure in the td group I intron in vivo. Genes Dev. 16:2002;2300-2312.
31. Walker K.A., Atkins C.L., Osuna R. Functional determinants of the Escherichia coli fis promoter: roles of -35, -10, and transcription initiation regions in the response to stringent control and growth phase-dependent regulation. J. Bacteriol. 181:1999;1269-1280.
32. Schneider R., Travers A., Kutateladze T., Muskhelishvili G. A DNA architectural protein couples cellular physiology and DNA topology in Escherichia coli. Mol. Microbiol. 34:1999;953-964.
33. Weinstein-Fischer D., Elgrably-Weiss M., Altuvia S. Escherichia coli response to hydrogen peroxide: a role for DNA supercoiling, topoisomerase I and Fis. Mol. Microbiol. 35:2000;1413-1420.
34. Hirvonen C.A., Ross W., Wozniak C.E., Marasco E., Anthony J.R., Aiyar S.E., Newburn V.H., Gourse R.L. Contributions of UP elements and the transcription factor FIS to expression from the seven rrn P1 promoters in Escherichia coli. J. Bacteriol. 183:2001;6305-6314.
35. Muskhelishvili G., Travers A. Transcription factor as a topological homeostat. Front Biosci. 8:2003;D279-D285.
36. Wilson R.L., Libby S.J., Freet A.M., Boddicker J.D., Fahlen T.F., Jones B.D. Fis, a DNA nucleoid-associated protein, is involved in Salmonella typhimurium SPI-1 invasion gene expression. Mol. Microbiol. 39:2001;79-88 The Fis protein is shown to be a transcriptional regulator of genes within the SPI-1 pathogenicity island of Salmonella typhimurium. These genes are required for invasion of host epithelial cells by this bacterium and it is significant that they are found to be members of the Fis regulon and hence co-regulated with genes coding for house-keeping functions such as stable RNA and the translational machinery of the cell.
37. Goldberg M.D., Johnson M., Hinton J.C.D., Williams P.H. Role of the nucleoid-associated protein Fis in the regulation of virulence properties of enteropathogenic Escherichia coli. Mol. Microbiol. 41:2001;549-559.
38. Sheikh J., Hicks S., Dall'Agnol M., Philips A.D., Nataro J.P. Roles for Fis and YafK in biofilm formation by enteroaggregative Escherichia coli. Mol. Microbiol. 41:2001;983-997.
39. Appleman J.A., Ross W., Salomon J., Gourse R.L. Activation of Escherichia coli rRNA transcription by FIS during a growth cycle. J. Bacteriol. 180:1998;1525-1532.
40. Pemberton I.K., Muskhelishvili G., Travers A.A., Buckle M. FIS modulates the kinetics of successive interactions of RNA polymerase with the core and upstream regions of the tyrT promoter. J. Mol. Biol. 318:2002;651-663.
41. Schneider R., Travers A., Muskhelishvili G. FIS modulates growth phase-dependent topological transitions of DNA in Escherichia coli. Mol. Microbiol. 26:1997;519-530.
42. Schneider R., Travers A., Muskhelishvili G. The expression of the Escherichia coli fis gene is strongly dependent on the superhelical density of DNA. Mol. Microbiol. 38:2000;167-175.
43. Schneider R., Lurz R., Lüder R., Tolksdorf C., Travers A., Muskhelishvili G. An architectural role for the Escherichia coli chromatin protein FIS in organizing DNA. Nucleic Acids Res. 29:2001;5107-5114.