An intrastrand three-DNA-base interaction is a key specificity determinant of F transfer initiation and of F TraI relaxase DNA recognition and cleavage

Nucleic Acids Research

Volumn 36, Issue 14, 2008, Pages 4565-4572

  Hekman, Katherine ^a   Guja, Kip ^a   Larkin, Chris ^a   Schildbach, Joel F ^a  

^a JOHNS HOPKINS UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DEOXYRIBONUCLEASE; F TRAI RELAXASE; OLIGONUCLEOTIDE; SINGLE STRANDED DNA;

ARTICLE; BACTERIAL STRAIN; BACTERIUM CONJUGATION; BASE PAIRING; BINDING AFFINITY; BINDING SITE; CELL MOTION; CONTROLLED STUDY; DNA BINDING; DNA CLEAVAGE; DNA SEQUENCE; ESCHERICHIA COLI; GENE TRANSFER; INTERACTIONS WITH DNA; MOLECULAR RECOGNITION; NONHUMAN; NUCLEIC ACID BASE SUBSTITUTION; PLASMID; PRIORITY JOURNAL; PROTEIN VARIANT; SEQUENCE ANALYSIS;

BASE PAIRING; CONJUGATION, GENETIC; DNA CLEAVAGE; DNA HELICASES; DNA NUCLEOTIDYLTRANSFERASES; DNA, BACTERIAL; DNA, SINGLE-STRANDED; ENDODEOXYRIBONUCLEASES; ESCHERICHIA COLI PROTEINS; F FACTOR; MODELS, MOLECULAR; PROTEIN BINDING;

BACTERIA (MICROORGANISMS); PROKARYOTA;

EID: 49249094306     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkn422     Document Type: Article

References (25)

1. Wirth,T., Falush,D., Lan,R., Colles,F., Mensa,P., Wieler,L.H., Karch,H., Reeves,P.R., Maiden,M.C. et al. (2006) Sex and virulence in Escherichia coli: An evolutionary perspective. Mol. Microbiol., 60, 1136-1151.
2. Hill,V.T., Townsend,S.M., Arias,R.S., Jenabi,J.M., Gomez-Gonzalez,I., Shimada,H. and Badger,J.L. (2004) TraJ-dependent Escherichia coli K1 interactions with professional phagocytes are important for early systemic dissemination of infectibn in the neonatal rat. Infect. Immun., 72, 478-488.
3. Zechner,E.L., de la Cruz,F., Eisenbrandt,R., Grahn,A.M., Koraimann,G., Lanka,E., Muth,G., Pansegrau,W., Thomas,C.M. et al. (2000) Conjugative-DNA transfer processes. In Thomas,C.M. (ed), The Horizontal Gene Pool, Harwood Academic Publishers, Amsterdam, pp. 87-174.
4. Waters, V.L., Hirata,K.H., Pansegrau,W., Lanka,E. and Guiney,D.G. (1991) Sequence identity in the nick regions of IncP plasmid transfer origins and T-DNA borders of Agrobacterium Ti plasmids [published erratum appears in Proc Natl Acad Sci USA 1991 Jul 15;88(14):6388]. Proc. Natl Acad. Sci. USA, 88, 1456-1460.
5. Willetts,N. and Maule,J. (1979) Investigations of the F conjugation gene traI:tRaI mutants and lambdatral transducig phages. Mol. Gen. Genet. 169, 325-336.
6. Fekete,R.A. and Frost,L.S. (2000) Mobilization of chimeric oriT plasmids by F and R100-1: Role of relaxosome formation in defining plasmid specificity. J. Bacteriol., 182, 4022-4027.
7. Willetts,N. and Maule,J. (1986) Specificities of IncF plasmid conjugation genes. Genet. Res., 47, 1-11.
8. Stern,J.C. and Schildbach,J.F. (2001) DNA recognition by F Factor TraI36: Highly sequence-specific binding of single-stranded DNA. Biochemistry, 40, 11586-11595.
9. Matson,S.W., Nelson,W.C. and Morton,B.S. (1993) Characterization of the reaction product of the oriT micking reaction catalyzed by Escherichia coli DNA helicase I. J. Bacteriol., 175, 2599-2606.
10. Pansegrau,W., Ziegelin,G. and Lanka,E. (1990) Covalent association of the traI gene product of plasmid RP4 with the 5-terminal nucleotide at the relaxation nick site. J. Biol. Chem., 265, 10637-10644.
11. Draper,O., Cesar,C.E.. Machon,C., de la Cruz,F. and Llosa,M. (2005) Site-specific recombinase and integrase activities of a conjugative relaxase in recipient cells. Proc. Natl Acad. Sci. USA, 102, 16385-16390.
12. Larkin,C., Datta,S., Harley,M.J., Andersen,B.J., Ebic,A., Hargreaves,V. and Schildbach,J.F. (2005) Inter- and intramolecular determinants of the specificity of single-stranded DNA binding and cleavage by the F factor relaxase. Structure (Camb), 13, 1533-1544.
13. Frost,L.S., Ippen-Ihler,K. and Skurray,R.A. (1994) Analysis of the sequence and gene products of the transfer region of the F sex factor. Microbiol. Rev., 58, 162-210.
14. Boer,R., Russi,S., Guasch,A., Lucas,M., Blanco,A.G.. Perez-Luque,R., Coll,M. and de la Cruz,F. (2000) Unveiling the molecular mechanism of a conjugative relaxase: The structure of TrwC complexed with a 27-mer DNA comprising the recognition hairpin and the cleavage site. J. Mol. Biol., 358, 857-869.
15. Williams,S.L. and Schildbach,J.F. (2006) Examination of an inverted repeat within the F factor origin of transfer: Context dependence of F TraI relaxase DNA specificity. Nucleic Acids Res., 34, 426-435.
16. Street,L.M., Harley,M.J., Stern,J.C., Larkin,C., Williams,S.L., Miller,D.L., Dohm,J.A., Rodgers,M.E. and Schildbach,J.F. (2003) Subdomain organization and catalytic residues of the F factor TraI relaxase domain. Biochim. Biophys. Acta, 1646, 86-99.
17. Wang,Z.X. (1995) An exact mathematical expression for describing competitive binding of two different ligands to a protein molecule. FEBS Lett., 360, 111-114.
18. Harley,M.J. and Schildbach,J.F. (2003) Swapping single-stranded DNA sequence specificities of relaxases from conjugative plasmids F and R100. Proc. Natl Acad. Sci. USA, 100, 11243-11248.
19. Harley,M.J.. Toptygin,D., Troxler,T. and Schildbach,J.F. (2002) R150A mutant of F TraI relaxase domain: Reduced affinity and specificity for single-stranded DNA and altered fluorescence anisotropy of a bound labeled oligonucleotide. Biochemistry, 41, 6460-6468.
20. Stern,J.C., Anderson,B.J., Owens.T.J. and Schildhach,J.F. (2004) Energetics of the sequence-spccific binding of single-stranded DNA by the F factor relaxase domain. J. Biol. Chem., 279, 29155-29159.
21. Larkin.C., Haft,R.J., Harley,M.J., Traxler,B. and Schildbach,J.F. (2007) Roles of active site residues and the HUH motif of the F plasmid TraI relaxase. J. Biol. Chem., 282, 33707-33713.
22. Theobald,D.L. and Schultz,S.C. (2003) Nucleotide shuffling and ssDNA recognition in Oxytricha nova telomere end-binding protein complexes. EMBO J., 22, 4314-4324.
23. Guasch,A., Lucas,M., Moncalian,G., Cabezas,M., Perez-Luquc,R., Gomis-Ruth, F.X., de la Cruz,F. and Coll,M. (2003) Recognition and processing of the origin of transfer DNA by conjugative relaxase TrwC. Nat. Struct. Biol., 10, 1002-1010.
24. Monzingo,A.F., Ozburn,A., Xia,S., Meyer,R.J. and Robertus,J.D. (2007) The structure of the minimal relaxase domain of MobA at 2.1 A resolution. J. Mol. Biol., 366, 165-178.
25. Lei,M., Podell,E.R., Baumann,P. and Cech,T.R. (2003) DNA self-recognition in the structure of Potl bound to telomeric single-stranded DNA. Nature, 426, 198-203.