IntDOT Interactions with Core Sites during Integrative Recombination

Journal of Bacteriology

Volumn 195, Issue 9, 2013, Pages 1883-1891

  Laprise, Jennifer ^a   Yoneji, Sumiko ^a   Gardner, Jeffrey F ^a  

^a UNIVERSITY OF ILLINOIS AT URBANA CHAMPAIGN   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DNA; ERYTHROMYCIN; OLIGONUCLEOTIDE; PROTEIN INTDOT; RECOMBINASE; TETRACYCLINE; UNCLASSIFIED DRUG;

ARTICLE; BACTERIUM ADHERENCE; BACTEROIDES; BASE PAIRING; BINDING AFFINITY; BINDING SITE; CRYSTAL STRUCTURE; GENE MUTATION; GENE SEQUENCE; NONHUMAN; PRIORITY JOURNAL; PROTEIN BINDING; PROTEIN DNA INTERACTION; TRANSPOSON;

BACTERIAL PROTEINS; BACTEROIDES; BASE SEQUENCE; CONJUGATION, GENETIC; INTEGRASES; MOLECULAR SEQUENCE DATA; RECOMBINATION, GENETIC;

BACTERIA (MICROORGANISMS); BACTEROIDES SP.;

EID: 84876198817     PISSN: 00219193     EISSN: 10985530     Source Type: Journal    
DOI: 10.1128/JB.01540-12     Document Type: Article

References (28)

1. Costello EK, Lauber CL, Hamady M, Fierer N, Gordon JI, Knight R. 2009. Bacterial community variation in human body habitats across space and time. Science 326:1694 -1697.
2. Falagas ME, Siakavellas E. 2000. Bacteroides, Prevotella, and Porphyromonas species: a review of antibiotic resistance and therapeutic options. Int. J. Antimicrob. Agents 15:1-9.
3. Senecoff JF, Bruckner RC, Cox MM. 1985. The FLP recombinase of the yeast 2-micron plasmid: characterization of its recombination site. Proc. Natl. Acad. Sci. U. S. A. 82:7270 -7274.
4. Shoemaker NB, Vlamakis H, Hayes K, Salyers AA. 2001. Evidence for extensive resistance gene transfer among Bacteroides spp. and among Bacteroides and other genera in the human colon. Appl. Environ. Microbiol. 67:561-568.
5. Salyers AA, Shoemaker NB, Stevens AM, Li LY. 1995. Conjugative transposons: an unusual and diverse set of integrated gene transfer elements. Microbiol. Rev. 59:579 -590.
6. Abremski K, Hoess R. 1984. Bacteriophage P1 site-specific recombination. Purification and properties of the Cre recombinase protein. J. Biol. Chem. 259:1509 -1514.
7. Sternberg N, Hamilton D. 1981. Bacteriophage P1 site-specific recombination. I. Recombination between loxP sites. J. Mol. Biol. 150:467- 486.
8. Dichiara JM, Mattis AN, Gardner JF. 2007. IntDOT interactions with core- and arm-type sites of the conjugative transposon CTnDOT. J. Bacteriol. 189:2692-2701.
9. Ross W, Landy A. 1982. Bacteriophage lambda int protein recognizes two classes of sequence in the phage att site: characterization of arm-type sites. Proc. Natl. Acad. Sci. U. S. A. 79:7724 -7728.
10. Tirumalai RS, Kwon HJ, Cardente EH, Ellenberger T, Landy A. 1998. Recognition of core-type DNA sites by lambda integrase. J. Mol. Biol. 279:513-527.
11. Wojciak JM, Sarkar D, Landy A, Clubb RT. 2002. Arm-site binding by lambda-integrase: solution structure and functional characterization of its amino-terminal domain. Proc. Natl. Acad. Sci. U. S. A. 99:3434 -3439.
12. Wood MM, Dichiara JM, Yoneji S, Gardner JF. 2010. CTnDOT integrase interactions with attachment site DNA and control of directionality of the recombination reaction. J. Bacteriol. 192:3934 -3943.
13. Cheng Q, Paszkiet BJ, Shoemaker NB, Gardner JF, Salyers AA. 2000. Integration and excision of a Bacteroides conjugative transposon, CTnDOT. J. Bacteriol. 182:4035- 4043.
14. Laprise J, Yoneji S, Gardner JF. 2010. Homology-dependent interactions determine the order of strand exchange by IntDOT recombinase. Nucleic Acids Res. 38:958 -969.
15. Nash HA. 1983. Purification and properties of the bacteriophage lambda Int protein. Methods Enzymol. 100:210 -216.
16. Malanowska K, Salyers AA, Gardner JF. 2006. Characterization of a conjugative transposon integrase, IntDOT. Mol. Microbiol. 60:1228- 1240.
17. Malanowska K, Yoneji S, Salyers AA, Gardner JF. 2007. CTnDOT integrase performs ordered homology-dependent and homologyindependent strand exchanges. Nucleic Acids Res. 35:5861-5873.
18. Luscombe NM, Laskowski RA, Thornton JM. 2001. Amino acid-base interactions: a three-dimensional analysis of protein-DNA interactions at an atomic level. Nucleic Acids Res. 29:2860 -2874.
19. Moitoso de Vargas L, Pargellis CA, Hasan NM, Bushman EW, Landy A. 1988. Autonomous DNA binding domains of lambda integrase recognize two different sequence families. Cell 54:923-929.
20. Ross W, Landy A. 1983. Patterns of lambda Int recognition in the regions of strand exchange. Cell 33:261-272.
21. Ross W, Landy A, Kikuchi Y, Nash H. 1979. Interaction of Int protein with specific sites on lambda att DNA. Cell 18:297-307.
22. Nunes-Duby SE, Azaro MA, Landy A. 1995. Swapping DNA strands and sensing homology without branch migration in lambda site-specific recombination. Curr. Biol. 5:139 -148.
23. Lee J, Jayaram M. 1995. Role of partner homology in DNA recombi-nation. Complementary base pairing orients the 5=-hydroxyl for strand joining during Flp site-specific recombination. J. Biol. Chem. 270: 4042- 4052.
24. Chen Y, Narendra U, Iype LE, Cox MM, Rice PA. 2000. Crystal structure of a Flp recombinase-Holliday junction complex: assembly of an active oligomer by helix swapping. Mol. Cell 6:885- 897.
25. Senecoff JF, Rossmeissl PJ, Cox MM. 1988. DNA recognition by the FLP recombinase of the yeast 2 mu plasmid. A mutational analysis of the FLP binding site. J. Mol. Biol. 201:405- 421.
26. Guo F, Gopaul DN, Van Duyne GD. 1999. Asymmetric DNA bending in the Cre-loxP site-specific recombination synapse. Proc. Natl. Acad. Sci. U. S. A. 96:7143-7148.
27. Guo F, Gopaul DN, van Duyne GD. 1997. Structure of Cre recombinase complexed with DNA in a site-specific recombination synapse. Nature 389:40-46.
28. Aihara H, Kwon HJ, Nunes-Duby SE, Landy A, Ellenberger T. 2003. A conformational switch controls the DNA cleavage activity of lambda integrase. Mol. Cell 12:187-198.