A precise DNA bend angle is essential for the function of the phage φ 29 transcriptional regulator

Nucleic Acids Research

Volumn 33, Issue 1, 2005, Pages 126-134

  Pérez Lago, Laura ^a   Salas, Margarita ^a   Camacho, Ana ^a  

^a UNIVERSIDAD AUTÓNOMA DE MADRID   (Spain)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL DNA; PROTEIN P4; REGULATOR PROTEIN; UNCLASSIFIED DRUG; DNA BINDING PROTEIN; P4 PROTEIN, BACTERIOPHAGE PHI 29; TRANSCRIPTION FACTOR; VIRUS DNA; VIRUS PROTEIN;

ARTICLE; BACTERIOPHAGE; BINDING AFFINITY; BINDING SITE; CALCULATION; CONTROLLED STUDY; GENE LOCATION; INVERTED REPEAT; MOLECULAR RECOGNITION; NONHUMAN; PRIORITY JOURNAL; PROMOTER REGION; PROTEIN BINDING; PROTEIN DNA BINDING; PROTEIN DNA INTERACTION; PROTEIN FUNCTION; SEQUENCE ANALYSIS; STRUCTURE ANALYSIS; TRANSCRIPTION REGULATION; BACILLUS PHAGE; CHEMISTRY; CONFORMATION; GENETICS; METABOLISM; MOLECULAR GENETICS; NUCLEOTIDE REPEAT; NUCLEOTIDE SEQUENCE;

BACILLUS PHAGES; BASE SEQUENCE; BINDING SITES; DNA, VIRAL; DNA-BINDING PROTEINS; MOLECULAR SEQUENCE DATA; NUCLEIC ACID CONFORMATION; REPETITIVE SEQUENCES, NUCLEIC ACID; TRANSCRIPTION FACTORS; VIRAL PROTEINS;

EID: 13744261995     PISSN: 03051048     EISSN: None     Source Type: Journal    
DOI: 10.1093/nar/gki146     Document Type: Article

References (33)

1. Pérez-Martin,J. and de Lorenzo,V. (1997) Clues and consequences of DNA bending in transcription. Annu. Rev. Microbiol. 51, 593-628.
2. Grosschedl,R. (1995) Higher-order nucleoprotein complexes in transcription: analogies with site-specific recombination. Curr. Opin. Cell Biol., 7, 362-370.
3. Kahn,J.D. and Crothers,D.M. (1998) Measurement of the DNA bend angle induced by the catabolite activator protein using Monte Carlo simulation of cyclization kinetics. J. Mol. Biol., 276, 287-309.
4. Lewis,D.E., Lee,H.J., Liu,M. and Adhya,S. (2003) Effect of varying the supercoiling of DNA on transcription and its regulation. Biochemistry, 42, 10718-10725.
5. Kim,S.I., Jourlin-Caselli,C., Wellington,S.R. and Sonenshein,A.L. (2003) Mechanism of repression by Bacillus subtilis CcpC, a LysR family regulator. J. Mol. Biol., 334, 609-624.
6. Ross,E.D., Keating,A.M. and Maher,L.J. (2000) DNA constraints on transcription activation in vitro. J. Mol. Biol., 297, 321-334.
7. Bourgerie,S.J., Michan,C.M., Thomas,M.S., Busby,S.J. and Hyde,E.I. (1997) DNA binding and DNA bending by the MelR transcription activator protein from Escherichia coli. Nucleic Acids Res., 25 1685-1693.
8. Lim,F.L., Hayes,A., West,A.G., Pic-Taylor,A., Darieva,Z., Morgan,B.A., Oliver,S.G. and Sharrocks,A.D. (2003) Mcm1p-induced DNA bending regulates the formation of ternary transcription factor complex. Mol. Cell. Biol., 23, 450-461.
9. Scaffidi,P. and Bianchi,M.E. (2001) Spatially precise DNA bending is an essential activity of the Sox2 transcription factor. J. Biol. Chem., 276, 47296-47302.
10. Serrano,M., Salas,M. and Hermoso,J.M. (1990) A novel nucleoprotein complex at a replication origin. Science, 248, 1012-1016.
11. 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.
12. Camacho,A. and Salas,M. (2001) 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. Calles,B., Salas,M. and Rojo,F. (2002) The φ29 transcriptional regulator contacts the nucleoid protein p6 to organize a repression complex. EMBO J., 21, 6185-6194.
14. Camacho,A. and Salas,M. (2004) Molecular interplay between RNA polymerase and two transcriptional regulators in promoter switch. J. Mol. Biol., 336, 357-368.
15. Barthelemy,I. and Salas,M. (1989) Characterization of a new prokaryotic transcriptional activator and its DNA recognition site. J. Mol. Biol., 208, 225-232.
16. 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.
17. Sambrook,J., Fritsch,E.F. and Maniatis,T. (1989) Molecular cloning: A laboratory Manual. 2nd edn. Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 13.78-13.95.
18. Kim,J., Zwieb,C., Wu,C. and Adhya,S. (1989) Bending of DNA by gene-regulatory proteins: construction and use of a DNA bending vector. Gene, 85, 15-23.
19. Thompson,J.F. and Landy,A. (1988) Empirical estimation of the protein-induced DNA bend to lambda site-specific recombination complexes. Nucleic Acids Res., 16, 9687-9705.
20. 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, 713-725.
21. Dieckman,S. (1989) The migration anomaly of DNA fragments in polyacrylamide gels allows the detection of small sequence-specific DNA structure variations. Electrophoresis, 10, 354-359.
22. Kahn,J.D. (1999) Methods for analyzing DNA bending. Methods Mol. Biol., 94, 109-124.
23. Crothers,D.M. and Drak,J. (1992) Global features of DNA structure by comparative gel electrophoresis. Methods Enzymol., 212, 46-57.
24. Nuez,B., Rojo,F. and Salas,M. (1991) Identification of the sequences recognized by phage φ29 transcriptional activator: possible interaction between the activator and the RNA polymerase. Nucleic Acids Res., 19, 2337-2342.
25. Nuez,B., Rojo,F. and Salas,M. (1994) Requirement for an A-tract structure at the binding site of phage φ29 transcriptional activator. J. Mol. Biol., 237, 175-181.
26. Hagerman,P.J.Jr,II (1996) From sequence to structure to function. Curr. Opin. Struct. Biol., 6, 277-280.
27. van der Vliet,P.C. and Verrijzer,C.P. (1993) Bending of DNA by transcription factors. BioEssays, 15, 24-32.
28. Starr,D.B., Hoopes,B.C. and Hawley,D.K. (1995) DNA bending is an important component of site-specific recognition by the TATA binding protein. J. Mol. Biol., 250, 434-446.
29. Nagaich,A.K., Appella,E. and Harrington,R.E. (1997) DNA bending is essential for the site-specific recognition of DNA response elements by DNA binding domain of the tumour suppressor protein p53. J. Biol. Chem., 272, 14842-14849.
30. Ross,W., Ernst,R. and Gourse,L. (2001) Fine structure of E.coli RNA polymerase-promoter interactions: alpha subunit binding to the UP element minor groove. Genes Dev., 15, 491-506.
31. Murakami,K.S., Masuda,S., Capbell,E.A., Muzzin,O. and Darst,S.T. (2002) Structural basis of transcription initiation: an RNA polymerase holoenzyme-DNA complex. Science, 296, 1285-1290.
32. Mencía,M., Monsalve,M., Rojo,F. and Salas,M. (1996) 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.
33. Serrano,M., Barthelemy,I. and Salas,M. (1991) Transcription activation at a distance by phage φ29 protein p4. Effect of bent and non-bent intervening DNA sequences. J. Mol. Biol., 219, 403-414.