Transposition into Replicating DNA Occurs through Interaction with the Processivity Factor

Cell

Volumn 138, Issue 4, 2009, Pages 685-695

  Parks, Adam R ^a   Li, Zaoping ^a   Shi, Qiaojuan ^a   Owens, Roisin M ^b   Jin, Moonsoo M ^b   Peters, Joseph E ^a  

^a Department of Molecular Biology and Genetics   (United States)

^b School of Chemical and Molecular Engineering   (United States)

Author keywords

DNA; MICROBIO; PROTEINS

Indexed keywords

DNA; TRANSPOSASE; TRANSPOSASE E; UNCLASSIFIED DRUG;

ARTICLE; CONTROLLED STUDY; DNA REPLICATION; DNA STRUCTURE; DNA TRANSPOSITION; GENE ORDER; GENE TARGETING; IN VITRO STUDY; IN VIVO STUDY; NONHUMAN; PRIORITY JOURNAL; PROTEIN DNA INTERACTION; PROTEIN FUNCTION; PROTEIN PURIFICATION; PROTEIN STRUCTURE; TRANSPOSON;

BACTERIA (MICROORGANISMS);

EID: 68849118539     PISSN: 00928674     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.cell.2009.06.011     Document Type: Article

References (62)

1. Amberg, D.C., Burke, D.J., and Strathern, J.N. (2006). Assay of {beta}-galactosidase in yeast: permeabilized cell assay. Cold Spring Harbor Protocols. 10.1101/pdb.prot4158.
2. Bainton R.J., Kubo K.M., Feng J.-N., and Craig N.L. Tn7 transposition: target DNA recognition is mediated by multiple Tn7-encoded proteins in a purified in vitro system. Cell 72 (1993) 931-943
3. Beuning P.J., Sawicka D., Barsky D., and Walker G.C. Two processivity clamp interactions differentially alter the dual activities of UmuC. Mol. Microbiol. 59 (2006) 460-474
4. Biacore I. BIAevaluation Software Handbook, version 3.0 (1997), Biacore, Inc, Uppsala, Sweden
5. Biery M.C., Steward F., Stellwagen A.E., Raleigh E.A., and Craig N.L. A simple in vitro Tn7-based transposition system with low target site selectivity for genome and gene analysis. Nucleic Acids Res. 28 (2000) 1067-1077
6. Bordi C., Butcher B.G., Shi Q., Hachmann A.B., Peters J.E., and Helmann J.D. In vitro mutagenesis of Bacillus subtilis by using a modified Tn7 transposon with an outward-facing inducible promoter. Appl. Environ. Microbiol. 74 (2008) 3419-3425
7. Bunting K.A., Roe S.M., and Pearl L.H. Structural basis for recruitment of translesion DNA polymerase Pol IV/DinB to the beta-clamp. EMBO J. 22 (2003) 5883-5892
8. Chen J., Greenblatt I.M., and Dellaporta S.L. Molecular analysis of Ac transposition and DNA replication. Genetics 130 (1992) 665-676
9. Clamp M., Cuff J., Searle S.M., and Barton G.J. The Jalview Java alignment editor. Bioinformatics 20 (2004) 426-427
10. Craig N.L. Tn7. In: Craig Nancy L., Craigie R., Gellert M., and Lambowitz-Alan M. (Eds). Mobile DNA II (2002), ASM Press, Washington, DC 423-456
11. Craig N., Craigie R., Gellert M., and Lambowitz A. Mobile DNA II (2002), ASM Press, Washington, D.C.
12. Dallmann H.G., and McHenry C.S. DnaX complex of Escherichia coli DNA polymerase III holoenzyme. Physical characterization of the DnaX subunits and complexes. J. Biol. Chem. 270 (1995) 29563-29569
13. Dalrymple B.P., Kongsuwan K., Wijffels G., Dixon N.E., and Jennings P.A. A universal protein-protein interaction motif in the eubacterial DNA replication and repair systems. Proc. Natl. Acad. Sci. USA 98 (2001) 11627-11632
14. Einarson, M.B., Pugacheva, E.N., and Orlinick, J.R. (2007). Far western: probing membranes. Cold Spring Harbor Protocols. 10.1101/pdb.prot4759.
15. Fields S., and Song O. A novel genetic system to detect protein-protein interactions. Nature 340 (1989) 245-246
16. Flores M.J., Sanchez N., and Michel B. A fork-clearing role for UvrD. Mol. Microbiol. 57 (2005) 1664-1675
17. Garsin D.A., Urbach J., Huguet-Tapia J.C., Peters J.E., and Ausubel F.M. Construction of a Enterococcus faecalis Tn917-mediated-gene-disruption library offers insight into Tn917 insertion patterns. J. Bacteriol. 186 (2004) 7280-7289
18. Georgescu R.E., Kim S.S., Yurieva O., Kuriyan J., Kong X.P., and O'Donnell M. Structure of a sliding clamp on DNA. Cell 132 (2008) 43-54
19. Golemis E. Protein-Protein Interactions (2002), Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY
20. Jeruzalmi D., O'Donnell M., and Kuriyan J. Crystal structure of the processivity clamp loader gamma (gamma) complex of E. coli DNA polymerase III. Cell 106 (2001) 429-441
21. Jeruzalmi D., Yurieva O., Zhao Y., Young M., Stewart J., Hingorani M., O'Donnell M., and Kuriyan J. Mechanism of processivity clamp opening by the delta subunit wrench of the clamp loader complex of E. coli DNA polymerase III. Cell 106 (2001) 417-428
22. Jiricny J. The multifaceted mismatch-repair system. Nat. Rev. Mol. Cell Biol. 7 (2006) 335-346
23. Johnson A., and O'Donnell M. Cellular DNA replicases: components and dynamics at the replication fork. Annu. Rev. Biochem. 74 (2005) 283-315
24. Kelman Z., Naktinis V., and O'Donnell M. Radiolabeling of proteins for biochemical studies. Methods Enzymol. 262 (1995) 430-442
25. Kelman Z., Yao N., and O'Donnell M. Escherichia coli expression vectors containing a protein kinase recognition motif, His6-tag and hemagglutinin epitope. Gene 166 (1995) 177-178
26. Kuduvalli P.N., Rao J.E., and Craig N.L. Target DNA structure plays a critical role in Tn7 transposition. EMBO J. 20 (2001) 924-932
27. Kuzminov A. Instability of inhibited replication forks in E. coli. Bioessays 17 (1995) 733-741
28. Laurence T.A., Kwon Y., Johnson A., Hollars C.W., O'Donnell M., Camarero J.A., and Barsky D. Motion of a DNA sliding clamp observed by single molecule fluorescence spectroscopy. J. Biol. Chem. 283 (2008) 22895-22906
29. Leu F.P., and O'Donnell M. Interplay of clamp loader subunits in opening the beta sliding clamp of Escherichia coli DNA polymerase III holoenzyme. J. Biol. Chem. 276 (2001) 47185-47194
30. Leu F.P., Hingorani M.M., Turner J., and O'Donnell M. The delta subunit of DNA polymerase III holoenzyme serves as a sliding clamp unloader in Escherichia coli. J. Biol. Chem. 275 (2000) 34609-34618
31. Liachko I., and Tye B.K. Mcm10 is required for the maintenance of transcriptional silencing in Saccharomyces cerevisiae. Genetics 171 (2005) 503-515
32. Lopez de Saro F.J., and O'Donnell M. Interaction of the beta sliding clamp with MutS, ligase, and DNA polymerase I. Proc. Natl. Acad. Sci. USA 98 (2001) 8376-8380
33. Lopez de Saro F., Georgescu R.E., Leu F., and O'Donnell M. Protein trafficking on sliding clamps. Philos. Trans. R. Soc. Lond. B Biol. Sci. 359 (2004) 25-30
34. Lopez de Saro F.J., Marinus M.G., Modrich P., and O'Donnell M. The beta sliding clamp binds to multiple sites within MutL and MutS. J. Biol. Chem. 281 (2006) 14340-14349
35. Maul R.W., Ponticelli S.K., Duzen J.M., and Sutton M.D. Differential binding of Escherichia coli DNA polymerases to the beta-sliding clamp. Mol. Microbiol. 65 (2007) 811-827
36. McKown R.L., Orle K.A., Chen T., and Craig N.L. Sequence requirements of Escherichia coli attTn7, a specific site of transposon Tn7 insertion. J. Bacteriol. 170 (1988) 352-358
37. Miller J.H. A Short Course in Bacterial Genetics (1992), Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY
38. Parks A.R., and Peters J.E. Transposon Tn7 is widespread in diverse bacteria and forms genomic islands. J. Bacteriol. 189 (2007) 2170-2173
39. Parks A.R., and Peters J.E. Tn7 elements: engendering diversity from chromosomes to episomes. Plasmid 61 (2009) 1-14
40. Peters J.E. Gene transfer - gram-negative bacteria, Chapter 31. In: Reddy C.A., Beveridge T.J., Breznak J.A., Marzluf G.A., Schmidt T.M., and Snyder L.R. (Eds). Methods for General and Molecular Microbiology (2007), ASM Press, Washington, DC 735-755
41. Peters J.E., and Craig N.L. Tn7 transposes proximal to DNA double-strand breaks and into regions where chromosomal DNA replication terminates. Mol. Cell 6 (2000) 573-582
42. Peters J.E., and Craig N.L. Tn7 recognizes target structures associated with DNA replication using the DNA binding protein TnsE. Genes Dev. 15 (2001) 737-747
43. Peters J.E., and Craig N.L. Tn7: smarter than we thought. Nat. Rev. Mol. Cell Biol. 2 (2001) 806-814
44. Rao J.E., and Craig N.L. Selective recognition of pyrimidine motif triplexes by a protein encoded by the bacterial transposon Tn7. J. Mol. Biol. 307 (2001) 1161-1170
45. Rao J.E., Miller P.S., and Craig N.L. Recognition of triple-helical DNA structures by transposon Tn7. Proc. Natl. Acad. Sci. USA 97 (2000) 3936-3941
46. Sambrook J., Fritsch E.F., and Maniatis T. Molecular Cloning: A Laboratory Manual. Second Edition (1989), Cold Spring Harbor Press, Cold Spring Harbor, NY
47. Seringhaus M., Kumar A., Hartigan J., Snyder M., and Gerstein M. Genomic analysis of insertion behavior and target specificity of mini-Tn7 and Tn3 transposons in Saccharomyces cerevisiae. Nucleic Acids Res. 34 (2006) e57
48. Shafferman A., Kolter R., Stalker D., and Helinski D.R. Plasmid R6K DNA replication. III. Regulatory properties of the pi initiation protein. J. Mol. Biol. 161 (1982) 57-76
49. Sharpe P.L., and Craig N.L. Host proteins can stimulate Tn7 transposition: a novel role for the ribosomal protein L29 and the acyl carrier protein. EMBO J. 17 (1998) 5822-5831
50. Shi Q., Parks A.R., Potter B.D., Safir I.J., Luo Y., Forster B.M., and Peters J.E. DNA damage differentially activates regional chromosomal loci for Tn7 transposition in Escherichia coli. Genetics 179 (2008) 1237-1250
51. Simmons L.A., Davies B.W., Grossman A.D., and Walker G.C. Beta clamp directs localization of mismatch repair in Bacillus subtilis. Mol. Cell 29 (2008) 291-301
52. Stellwagen A.E., and Craig N.L. Gain-of-function mutations in TnsC, an ATP-dependent transposition protein which activates the bacterial transposon Tn7. Genetics 145 (1997) 573-585
53. Stellwagen A.E., and Craig N.L. Mobile DNA elements: controlling transposition with ATP-dependent molecular switches. Trends Biochem. Sci. 23 (1998) 486-490
54. Stellwagen A.E., and Craig N.L. Analysis of gain of function mutants of an ATP-dependent regulator of Tn7 transposition. J. Mol. Biol. 305 (2001) 633-642
55. Sutton M.D. The Escherichia coli dnaN159 mutant displays altered DNA polymerase usage and chronic SOS induction. J. Bacteriol. 186 (2004) 6738-6748
56. Thompson J.D., Higgins D.G., and Gibson T.J. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22 (1994) 4673-4680
57. Wang H., and Hays J.B. Simple and rapid preparation of gapped plasmid DNA for incorporation of oligomers containing specific DNA lesions. Mol. Biotechnol. 19 (2001) 133-140
58. Warbrick E. The puzzle of PCNA's many partners. Bioessays 22 (2000) 997-1006
59. Warbrick E., Heatherington W., Lane D.P., and Glover D.M. PCNA binding proteins in Drosophila melanogaster: the analysis of a conserved PCNA binding domain. Nucleic Acids Res. 26 (1998) 3925-3932
60. Wijffels G., Dalrymple B.P., Prosselkov P., Kongsuwan K., Epa V.C., Lilley P.E., Jergic S., Buchardt J., Brown S.E., Alewood P.F., et al. Inhibition of protein interactions with the beta 2 sliding clamp of Escherichia coli DNA polymerase III by peptides from beta 2-binding proteins. Biochemistry 43 (2004) 5661-5671
61. Wilkins B., and Lanka E. DNA processing and replication during plasmid transfer between gram-negative bacteria. In: Clewell D.B. (Ed). Bacterial Conjugation (1993), Plenum Press, New York 105-136
62. Wolkow C.A., DeBoy R.T., and Craig N.L. Conjugating plasmids are preferred targets for Tn7. Genes Dev. 10 (1996) 2145-2157