Recombineering using recTE from pseudomonas syringae

Applied and Environmental Microbiology

Volumn 76, Issue 15, 2010, Pages 4960-4968

  Swingle, Bryan ^a   Bao, Zhongmeng ^a   Markel, Eric ^a   Chambers, Alan ^a   Cartinhour, Samuel ^a  

^a AGRICULTURAL RESEARCH SERVICE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DOUBLE STRANDED DNA; ELECTROPORATION; ENCODED PROTEINS; GENE DISRUPTIONS; GENES ENCODING; PSEUDOMONAS CELLS; PSEUDOMONAS SYRINGAE; QUANTITATIVE ASSAY; RECOMBINATION FREQUENCIES; RECOMBINEERING; SINGLE-STRANDED DNA;

BACTERIOPHAGES; DNA; ESCHERICHIA COLI; OLIGONUCLEOTIDES; PROTEINS;

GENES;

BACTERIAL DNA; DNA; DNA BINDING PROTEIN; SINGLE STRANDED DNA;

BACTERIOPHAGE; BACTERIUM; CHROMOSOME; DICOTYLEDON; GENE EXPRESSION; GENOME; MITOCHONDRIAL DNA; PROTEIN; RECOMBINATION;

ARTICLE; BACTERIOPHAGE LAMBDA; CHEMISTRY; DNA SEQUENCE; ENZYMOLOGY; GENETIC RECOMBINATION; GENETICS; METABOLISM; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; PSEUDOMONAS SYRINGAE; SEQUENCE HOMOLOGY; ENTEROBACTERIA PHAGE LAMBDA;

BACTERIOPHAGE LAMBDA; DNA; DNA, BACTERIAL; DNA, SINGLE-STRANDED; DNA-BINDING PROTEINS; MOLECULAR SEQUENCE DATA; PSEUDOMONAS SYRINGAE; RECOMBINATION, GENETIC; SEQUENCE ANALYSIS, DNA; SEQUENCE HOMOLOGY;

ESCHERICHIA COLI; LYCOPERSICON ESCULENTUM; PSEUDOMONAS; PSEUDOMONAS SYRINGAE; PSEUDOMONAS SYRINGAE PV. SYRINGAE; PSEUDOMONAS SYRINGAE PV. TOMATO;

EID: 77955561819     PISSN: 00992240     EISSN: 10985336     Source Type: Journal    
DOI: 10.1128/AEM.00911-10     Document Type: Article

References (43)

1. Altschul, S. F., T. L. Madden, A. A. Schaffer, J. Zhang, Z. Zhang, W. Miller, and D. J. Lipman. 1997. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25:3389-3402.
2. Bolivar, F., R. L. Rodriguez, P. J. Greene, M. C. Betlach, H. L. Heyneker, H. W. Boyer, J. H. Crosa, and S. Falkow. 1977. Construction and characterization of new cloning vehicles. II. A multipurpose cloning system. Gene 2:95-113.
3. Buell, C. R., V. Joardar, M. Lindeberg, J. Selengut, I. T. Paulsen, M. L. Gwinn, R. J. Dodson, R. T. Deboy, A. S. Durkin, J. F. Kolonay, R. Madupu, S. Daugherty, L. Brinkac, M. J. Beanan, D. H. Haft, W. C. Nelson, T. Davidsen, N. Zafar, L. W. Zhou, J. Liu, Q. P. Yuan, H. Khouri, N. Fedorova, B. Tran, D. Russell, K. Berry, T. Utterback, S. E. Van Aken, T. V. Feldblyum, M. D'Ascenzo, W. L. Deng, A. R. Ramos, J. R. Alfano, S. Cartinhour, A. K.Chatterjee, T. P. Delaney, S. G. Lazarowitz, G. B. Martin, D. J. Schneider, X. Y. Tang, C. L. Bender, O. White, C. M. Fraser, and A. Collmer. 2003. The complete genome sequence of the Arabidopsis and tomato pathogen Pseudomonas syringae pv. tomato DC3000. Proc. Natl. Acad. Sci. U. S. A. 100:10181-10186.
4. Cassuto, E., and C. M. Radding. 1971. Mechanism for the action of lambda exonuclease in genetic recombination. Nat. New Biol. 229:13-16.
5. Choi, K. H., A. Kumar, and H. P. Schweizer. 2006. A 10-min method for preparation of highly electrocompetent Pseudomonas aeruginosa cells: application for DNA fragment transfer between chromosomes and plasmid transformation. J. Microbiol. Methods 64:391-397.
6. Clark, A. J., V. Sharma, S. Brenowitz, C. C. Chu, S. Sandler, L. Satin, A. Templin, I. Berger, and A. Cohen. 1993. Genetic and molecular analyses of the C-terminal region of the recE gene from the Rac prophage of Escherichia coli K-12 reveal the recT gene. J. Bacteriol. 175:7673-7682.
7. Costantino, N., and D. L. Court. 2003. Enhanced levels of lambda Redmediated recombinants in mismatch repair mutants. Proc. Natl. Acad. Sci. U. S. A. 100:15748-15753.
8. Court, D. L., J. A. Sawitzke, and L. C. Thomason. 2002. Genetic engineering using homologous recombination. Annu. Rev. Genet. 36:361-388.
9. Datta, S., N. Costantino, X. Zhou, and D. L. Court. 2008. Identification and analysis of recombineering functions from Gram-negative and Gram-positive bacteria and their phages. Proc. Natl. Acad. Sci. U. S. A. 105:1626-1631.
10. Dutra, B. E., V. A. Sutera, Jr., and S. T. Lovett. 2007. RecA-independent recombination is efficient but limited by exonucleases. Proc. Natl. Acad. Sci. U. S. A. 104:216-221.
11. Ellis, H. M., D. Yu, T. DiTizio, and D. L. Court. 2001. High efficiency mutagenesis, repair, and engineering of chromosomal DNA using singlestranded oligonucleotides. Proc. Natl. Acad. Sci. U. S. A. 98:6742-6746.
12. Feil, H., W. S. Feil, P. Chain, F. Larimer, G. DiBartolo, A. Copeland, A. Lykidis, S. Trong, M. Nolan, E. Goltsman, J. Thiel, S. Malfatti, J. E. Loper, A. Lapidus, J. C. Detter, M. Land, P. M. Richardson, N. C. Kyrpides, N. Ivanova, and S. E. Lindow. 2005. Comparison of the complete genome sequences of Pseudomonas syringae pv. syringae B728a and pv. tomato DC3000. Proc. Natl. Acad. Sci. U. S. A. 102:11064-11069.
13. Funatsu, G., and H. G. Wittmann. 1972. Ribosomal proteins. 33. Location of amino-acid replacements in protein S12 isolated from Escherichia coli mutants resistant to streptomycin. J. Mol. Biol. 68:547-550.
14. Gallagher, L. A., S. L. McKnight, M. S. Kuznetsova, E. C. Pesci, and C. Manoll. 2002. Functions required for extracellular quinolone signaling by Pseudomonas aeruginosa. J. Bacteriol. 184:6472-6480.
15. Hall, S. D., and R. D. Kolodner. 1994. Homologous pairing and strand exchange promoted by the Escherichia coli RecT protein. Proc. Natl. Acad. Sci. U. S. A. 91:3205-3209.
16. Iyer, L. M., E. V. Koonin, and L. Aravind. 2002. Classification and evolutionary history of the single-strand annealing proteins, RecT, Redbeta, ERF and RAD52. BMC Genomics 3:8.
17. Karakousis, G., N. Ye, Z. Li, S. K. Chiu, G. Reddy, and C. M. Radding. 1998. The beta protein of phage lambda binds preferentially to an intermediate in DNA renaturation. J. Mol. Biol. 276:721-731.
18. King, E. O., M. K. Ward, and D. E. Raney. 1954. Two simple media for the demonstration of pyocyanin and fluorescin. J. Lab. Clin. Med. 44:301-307.
19. Kmiec, E., and W. K. Holloman. 1981. Beta protein of bacteriophage lambda promotes renaturation of DNA. J. Biol. Chem. 256:12636-12639.
20. Kowalczykowski, S. C., D. A. Dixon, A. K. Eggleston, S. D. Lauder, and W. M. Rehrauer. 1994. Biochemistry of homologous recombination in Escherichia coli. Microbiol. Rev. 58:401-465.
21. Kuzminov, A. 1999. Recombinational repair of DNA damage in Escherichia coli and bacteriophage lambda. Microbiol. Mol. Biol. Rev. 63:751-813.
22. Kvitko, B. H., D. H. Park, A. C. Velasquez, C. F. Wei, A. B. Russell, G. B. Martin, D. J. Schneider, and A. Collmer. 2009. Deletions in the repertoire of Pseudomonas syringae pv. tomato DC3000 type III secretion effector genes reveal functional overlap among effectors. PLoS Pathog. 5:e1000388.
23. Lesic, B., and L. G. Rahme. 2008. Use of the lambda Red recombinase system to rapidly generate mutants in Pseudomonas aeruginosa. BMC Mol. Biol. 9:20.
24. Little, J. W. 1967. An exonuclease induced by bacteriophage lambda. II. Nature of the enzymatic reaction. J. Biol. Chem. 242:679-686.
25. Lopes, A., J. Amarir-Bouhram, G. Faure, M. A. Petit, and R. Guerois. 1 March 2010. Detection of novel recombinases in bacteriophage genomes unveils Rad52, Rad51 and Gp2.5 remote homologs. Nucleic Acids Res. [Epub ahead of print.] doi:10.1093/nar/gkq096.
26. Marchler-Bauer, A., J. B. Anderson, F. Chitsaz, M. K. Derbyshire, C. DeWeese-Scott, J. H. Fong, L. Y. Geer, R. C. Geer, N. R. Gonzales, M. Gwadz, S. He, D. I. Hurwitz, J. D. Jackson, Z. Ke, C. J. Lanczycki, C. A. Liebert, C. Liu, F. Lu, S. Lu, G. H. Marchler, M. Mullokandov, J. S. Song, A. Tasneem, N. Thanki, R. A. Yamashita, D. Zhang, N. Zhang, and S. H. Bryant. 2009. CDD: specific functional annotation with the Conserved Domain Database. Nucleic Acids Res. 37:D205-D210.
27. Mascher, T., N. G. Margulis, T. Wang, R. W. Ye, and J. D. Helmann. 2003. Cell wall stress responses in Bacillus subtilis: the regulatory network of the bacitracin stimulon. Mol. Microbiol. 50:1591-1604.
28. Murphy, K. C. 2009. Chromosomal engineering strategies, p. 7-1-7-28. In C. D. Smolke (ed.), The metabolic pathway engineering handbook, vol. 2. CRC Press, Boca Raton, FL.
29. Murphy, K. C. 1998. Use of bacteriophage λ recombination functions to promote gene replacement in Escherichia coli. J. Bacteriol. 180:2063-2071.
30. Muyrers, J. P., Y. Zhang, F. Buchholz, and A. F. Stewart. 2000. RecE/RecT and Redalpha/Redbeta initiate double-stranded break repair by specifically interacting with their respective partners. Genes Dev. 14:1971-1982.
31. Mythili, E., K. A. Kumar, and K. Muniyappa. 1996. Characterization of the DNA-binding domain of beta protein, a component of phage lambda redpathway, by UV catalyzed cross-linking. Gene 182:81-87.
32. Noirot, P., and R. D. Kolodner. 1998. DNA strand invasion promoted by Escherichia coli RecT protein. J. Biol. Chem. 273:12274-12280.
33. Ried, J. L., and A. Collmer. 1987. An nptI-sacB-sacR cartridge for constructing directed, unmarked mutations in gram-negative bacteria by marker exchange-eviction mutagenesis. Gene 57:239-246.
34. Swingle, B., E. Markel, N. Costantino, M. G. Bubunenko, S. Cartinhour, and D. L. Court. 2010. Oligonucleotide recombination in Gram-negative bacteria. Mol. Microbiol. 75:138-148.
35. Swingle, B., D. There, M. Moll, C. R. Myers, D. J. Schneider, and S. Cartinhour. 2008. Characterization of the PvdS-regulated promoter motif in Pseudomonas syringae pv. tomato DC3000 reveals regulon members andinsights regarding PvdS function in other pseudomonads. Mol. Microbiol. 68:871-889.
36. van Kessel, J. C., and G. F. Hatfull. 2008. Efficient point mutagenesis in mycobacteria using single-stranded DNA recombineering: characterization of antimycobacterial drug targets. Mol. Microbiol. 67:1094-1107.
37. van Kessel, J. C., and G. F. Hatfull. 2007. Recombineering in Mycobacterium tuberculosis. Nat. Methods 4:147-152.
38. van Kessel, J. C., L. J. Marinelli, and G. F. Hatfull. 2008. Recombineering mycobacteria and their phages. Nat. Rev. Microbiol. 6:851-857.
39. Wach, A. 1996. PCR-synthesis of marker cassettes with long flanking homology regions for gene disruptions in S. cerevisiae. Yeast 12:259-265.
40. West, S. E., H. P. Schweizer, C. Dall, A. K. Sample, and L. J. RunyenJanecky. 1994. Construction of improved Escherichia-Pseudomonas shuttle vectors derived from pUC18/19 and sequence of the region required for their replication in Pseudomonas aeruginosa. Gene 148:81-86.
41. Yu, D., H. M. Ellis, E. C. Lee, N. A. Jenkins, N. G. Copeland, and D. L. Court. 2000. An efficient recombination system for chromosome engineering in Escherichia coli. Proc. Natl. Acad. Sci. U. S. A. 97:5978-5983.
42. Zhang, J., X. Xing, A. B. Herr, and C. E. Bell. 2009. Crystal structure of E. coli RecE protein reveals a toroidal tetramer for processing double-stranded DNA breaks. Structure 17:690-702.
43. Zhang, Y., F. Buchholz, J. P. Muyrers, and A. F. Stewart. 1998. A new logic for DNA engineering using recombination in Escherichia coli. Nat. Genet. 20:123-128.