The φ29 transcriptional regulator contacts the nucleoid protein p6 to organize a repression complex

EMBO Journal

Volumn 21, Issue 22, 2002, Pages 6185-6194

  Calles, Belén ^a,b   Salas, Margarita ^a   Rojo, Fernando ^a  

^a UNIVERSIDAD AUTÓNOMA DE MADRID   (Spain)

^b Ciudad Politécnica de la Innovación   (Spain)

Author keywords

Bacterial promoters; Nucleoid proteins; Phage 29; Protein protein interactions; Transcription regulation

Indexed keywords

BACTERIAL PROTEIN; NUCLEOID PROTEIN P6; NUCLEOPROTEIN; UNCLASSIFIED DRUG; VIRUS DNA; DNA DIRECTED RNA POLYMERASE; P4 PROTEIN, BACTERIOPHAGE PHI 29; PHAGE PHI29 PROTEIN P6; REPRESSOR PROTEIN; RNA POLYMERASE SIGMA A; SIGMA FACTOR; TRANSCRIPTION FACTOR; VIRUS PROTEIN;

AMINO ACID SEQUENCE; ARTICLE; BACILLUS SUBTILIS; BACTERIOPHAGE; COMPLEX FORMATION; CONTROLLED STUDY; DNA BINDING; DNA REPLICATION; GENE REPRESSION; NONHUMAN; PRIORITY JOURNAL; PROMOTER REGION; PROTEIN ASSEMBLY; PROTEIN BINDING; PROTEIN MODIFICATION; PROTEIN POLYMERIZATION; PROTEIN PROTEIN INTERACTION; TRANSCRIPTION INITIATION; TRANSCRIPTION REGULATION; BACILLUS PHAGE; CHEMISTRY; GENETIC TRANSCRIPTION; GENETICS; MACROMOLECULE; METABOLISM; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; PHYSIOLOGY; PROTEIN ANALYSIS; STRUCTURE ACTIVITY RELATION; VIROLOGY;

BACILLUS SUBTILIS; BACTERIA (MICROORGANISMS); POSIBACTERIA; UNIDENTIFIED BACTERIOPHAGE;

BACILLUS PHAGES; BACILLUS SUBTILIS; BACTERIAL PROTEINS; BASE SEQUENCE; DNA REPLICATION; DNA, VIRAL; DNA-DIRECTED RNA POLYMERASES; MACROMOLECULAR SUBSTANCES; MOLECULAR SEQUENCE DATA; PROMOTER REGIONS (GENETICS); PROTEIN BINDING; PROTEIN INTERACTION MAPPING; REPRESSOR PROTEINS; SIGMA FACTOR; STRUCTURE-ACTIVITY RELATIONSHIP; TRANSCRIPTION FACTORS; TRANSCRIPTION, GENETIC; VIRAL PROTEINS;

EID: 0037112903     PISSN: 02614189     EISSN: None     Source Type: Journal    
DOI: 10.1093/emboj/cdf623     Document Type: Article

References (43)

1. Abril, A.M., Salas, M., Andreu, J.M., Hermoso, J.M. and Rivas, G. (1997) Phage φ29 protein p6 is in a monomer-dimer equilibrium that shifts to higher association states at the millimolar concentrations found in vivo. Biochemistry, 36, 11901-11908.
2. Adhya, S., Geanacopoulos, M., Lewis, D.E., Roy, S. and Aki, T. (1998) Transcription regulation by repressosome and by RNA polymerase contact. Cold Spring Harbor Symp. Quant. Biol., 63, 1-9.
3. Aki, T. and Adhya, S. (1997) Repressor induced site-specific binding of HU for transcriptional regulation. EMBO J., 16, 3666-3674.
4. Azam, T.A., Iwata, A., Nishimura, A., Ueda, S. and Ishihama, A. (1999) Growth phase-dependent variation in protein composition of the Escherichia coli nucleoid. J. Bacteriol., 181, 6361-6370.
5. Barthelemy, I. and Salas, M. (1989) Characterization of a new prokaryotic transcriptional activator and its DNA recognition site. J. Mol. Biol., 208, 225-232.
6. Barthelemy, I., Mellado, R.P. and Salas, M. (1989) In vitro transcription of bacteriophage φ29 DNA: Inhibition of early promoters by the viral replication protein p6. J. Virol., 63, 460-462.
7. Bianchi, M.E. (1994) Prokaryotic HU and eukaryotic HMG1: A kinked relationship. Mol. Microbiol., 14, 1-5.
8. Browning, D.F., Beatty, C.M., Wolfe, A.J., Cole, J.A. and Busby, S.J. (2002) Independent regulation of the divergent Escherichia coli nrfA and acsP1 promoters by a nucleoprotein assembly at a shared regulatory region. Mol. Microbiol., 43, 687-701.
9. Calles, B. (2002) Transcription Regulation of the A2c and A3 Promoters from the Bacillus Subtilis Phage φ29: Role of the p4 and p6 Proteins. PhD thesis, Department of Molecular Biology, Universidad Autónoma de Madrid, Madrid, Spain.
10. Camacho, A. and Salas, M. (2000) Pleiotropic effect of protein p6 on the viral cycle of bacteriophage φ29. J. Bacteriol., 182, 6927-6932.
11. Camacho, A. and Salas, M. (2001a) Repression of bacteriophage φ29 early promoter C2 by viral protein p6 is due to impairment of closed complex. J. Biol. Chem., 276, 28927-28932.
12. Camacho, A. and Salas, M. (2001b) Mechanism for the switch of φ29 DNA early to late transcription by regulatory protein p4 and histone-like protein p6. EMBO J., 20, 6060-6070.
13. Castaing, B., Zelwer, C., Laval, J. and Boiteux, S. (1995) HU protein of Escherichia coli binds specifically to DNA that contains single-strand breaks or gaps. J. Biol. Chem., 270, 10291-10296.
14. Elías-Arnanz, M. and Salas, M. (1999) Functional interactions between a phage histone-like protein and a transcriptional factor in regulation of φ29 early-late transcriptional switch. Genes Dev., 13, 2502-2513.
15. Goodrich, J.A., Schwartz, M.L. and McClure, W.R. (1990) Searching for and predicting the activity of sites for DNA binding proteins: Compilation and analysis of the binding sites for Escherichia coli integration host factor (IHF). Nucleic Acids Res., 18, 4993-5000.
16. Hengen, P.N., Bartram, S.L., Stewart, L.E. and Schneider, T.D. (1997) Information analysis of Fis binding sites. Nucleic Acids Res., 25, 4994-5002.
17. Jordi, B.J. and Higgins, C.F. (2000) The downstream regulatory element of the proU operon of Salmonella typhimurium inhibits open complex formation by RNA polymerase at a distance. J. Biol. Chem., 275, 12123-12128.
18. Kar, S. and Adhya, S. (2001) Recruitment of HU by piggyback: A special role of GalR in repressosome assembly. Genes Dev., 15, 2273-2281.
19. Kobryn, K., Lavoie, B.D. and Chaconas, G. (1999) Supercoiling-dependent site-specific binding of HU to naked Mu DNA. J. Mol. Biol., 289, 777-784.
20. McLeod, S.M. and Johnson, R.C. (2001) Control of transcription by nucleoid proteins. Curr. Opin. Microbiol., 4, 152-159.
21. Mencía, M., Salas, M. and Rojo, F. (1993) Residues of the Bacillus subtilis phage φ29 transcriptional activator required both to interact with RNA polymerase and to activate transcription. J. Mol. Biol., 233, 695-704.
22. Mencía, M., Monsalve, M., Rojo, F. and Salas, M. (1996a) Transcription activation by phage φ29 protein p4 is mediated by interaction with the α subunit of Bacillus subtilis RNA polymerase. Proc. Natl Acad. Sci. USA, 93, 6616-6620.
23. Mencía, M., Monsalve, M., Salas, M. and Rojo, F. (1996b) Transcriptional activator of phage φ29 late promoter: Mapping of residues involved in interaction with RNA polymerase and in DNA bending. Mol. Microbiol., 20, 273-282.
24. Monsalve, M., Mencía, M., Rojo, F. and Salas, M. (1995) Transcription regulation in Bacillus subtilis phage φ29: Expression of the viral promoters throughout the infection cycle. Virology, 207, 23-31.
25. Monsalve, M., Mencía, M., Rojo, F. and Salas, M. (1996a) Activation and repression of transcription at two different phage φ29 promoters are mediated by interaction of the same residues of regulatory protein p4 with RNA polymerase. EMBO J., 15, 383-391.
26. Monsalve, M., Mencía, M., Salas, M. and Rojo, F. (1996b) Protein p4 represses phage φ29 A2c promoter by interacting with the α subunit of Bacillus subtilis RNA polymerase. Proc. Natl Acad. Sci. USA, 93, 8913-8918.
27. Monsalve, M., Calles, B., Mencía, M., Salas, M. and Rojo, F. (1997) Transcription activation or repression by phage φ29 protein p4 depends on the strength of the RNA polymerase-promoter interactions. Mol. Cell, 1, 99-107.
28. Monsalve, M., Calles, B., Mencía, M., Rojo, F. and Salas, M. (1998) Binding of phage φ29 protein p4 to the early A2c promoter: Recruitment of a repressor by the RNA polymerase. J. Mol. Biol., 283, 559-569.
29. Nuez, B. and Salas, M. (1993) Bacteriophage Nf DNA region controlling late transcription: Structural and functional homology with bacteriophage φ29. Nucleic Acids Res., 21, 2861-2865.
30. Nuez, B., Rojo, F. and Salas, M. (1992) Phage φ29 regulatory protein p4 stabilizes the binding of the RNA polymerase to the late promoter in a process involving direct protein-protein contacts. Proc. Natl Acad. Sci. USA, 89, 11401-11405.
31. Pastrana, R., Lázaro, J.M., Blanco, L., García, J.A., Méndez, E. and Salas, M. (1985) Overproduction and purification of protein p6 of Bacillus subtilis phage φ29: Role in the initiation of DNA replication. Nucleic Acids Res., 13, 3083-3100.
32. Pinson, V., Takahashi, M. and Rouviere-Yaniv, J. (1999) Differential binding of the Escherichia coli HU, homodimeric forms and heterodimeric form to linear, gapped and cruciform DNA. J. Mol. Biol., 287, 485-497.
33. Richet, E. and Sogaard-Andersen, L. (1994) CRP induces the repositioning of MalT at the Escherichia coli malKp promoter primarily through DNA bending. EMBO J., 13, 4558-4567.
34. Richet, E., Vidal-Ingigliardi, D. and Raibaud, O. (1991) A new mechanism for coactivation of transcription initiation: Repositioning of an activator triggered by the binding of a second activator. Cell, 66, 1185-1195.
35. Rodionov, O., Lobocka, M. and Yarmolinsky, M. (1999) Silencing of genes flanking the P1 plasmid centromere. Science, 238, 546-549.
36. Rojo, F. and Salas, M. (1991) A DNA curvature can substitute phage φ29 regulatory protein p4 when acting as a transcriptional repressor. EMBO J., 10, 3429-3438.
37. Rojo, F., Zaballos, A. and Salas, M. (1990) Bend induced by the phage φ29 transcriptional activator in the viral late promoter is required for activation. J. Mol. Biol., 211, 713-25.
38. Rojo, F., Mencía, M., Monsalve, M. and Salas, M. (1998) Transcription activation and repression by interaction of a regulator with the α subunit of RNA polymerase: The model of phage φ29 protein p4. Prog. Nucleic Acid Res. Mol. Biol., 60, 29-46.
39. Salas, M. and Rojo, F. (1993) Replication and transcription of bacteriophage φ29 DNA. In Hoch, J.A. and Losick, R. (eds), Bacillus Subtilis and Other Gram-positive Bacteria: Biochemistry, Physiology and Molecular Genetics. American Society for Microbiology, Washington, DC, pp. 843-857.
40. Serrano, M., Gutiérrez, J., Prieto, I., Hermoso, J.M. and Salas, M. (1989) Signals at the bacteriophage φ29 DNA replication origins required for protein p6 binding and activity. EMBO J., 8, 1879-1885.
41. Serrano, M., Salas, M. and Hermoso, J.M. (1990) A novel nucleoprotein complex at a replication origin. Science, 248, 1012-1016.
42. Sogo, J.M., Inciarte, M.R., Corral, J., Viñuela, E. and Salas, M. (1979) RNA polymerase binding sites and transcription of the DNA of Bacillus subtilis phage φ29. J. Mol. Biol., 127, 411-436.
43. Whiteley, H.R., Ramey, W.D., Spiegelman, G.B. and Holder, R.D. (1986) Modulation of in vivo and in vitro transcription of bacteriophage φ29 early genes. Virology, 155, 392-401.