Genome engineering of Agrobacterium tumefaciens using the lambda Red recombination system

Applied Microbiology and Biotechnology

Volumn 98, Issue 5, 2014, Pages 2165-2172

  Hu, Shengbiao ^a,b   Fu, Jun ^b   Huang, Fan ^a,b   Ding, Xuezhi ^a   Stewart, A Francis ^b   Xia, Liqiu ^a   Zhang, Youming ^a,c  

^a HUNAN NORMAL UNIVERSITY   (China)

^b DRESDEN UNIVERSITY OF TECHNOLOGY   (Germany)

^c SHANDONG UNIVERSITY   (China)

Author keywords

Agrobacterium tumefaciens; Gene targeting; Homology arm; Recombineering; Red recombinase

Indexed keywords

AGROBACTERIUM TUMEFACIENS; GENE TARGETING; HOMOLOGY ARM; RECOMBINEERING; RED RECOMBINASE;

DNA; GENETIC ENGINEERING;

GENES;

BACTERIAL ENZYME; LAMBDA RED RECOMBINASE; TETRACYCLINE; UNCLASSIFIED DRUG;

BACTERIUM; CHROMOSOME; ENZYME ACTIVITY; GENE EXPRESSION; GENETIC ENGINEERING; GENOME; GENOMICS; RECOMBINATION;

AGROBACTERIUM TUMEFACIENS; ARTICLE; BACTERIAL GENOME; BACTERIAL STRAIN; CHROMOSOME; FUNCTIONAL GENOMICS; GENETIC ENGINEERING; GENETIC RECOMBINATION; LAMBDA RED RECOMBINATION SYSTEM; NONHUMAN; NUCLEOTIDE SEQUENCE; OPERON; PLASMID;

AGROBACTERIUM TUMEFACIENS;

AGROBACTERIUM TUMEFACIENS; BACTERIOPHAGE LAMBDA; GENETIC ENGINEERING; GENETIC VECTORS; GENETICS, MICROBIAL; GENOME, BACTERIAL; OPERON; PLASMIDS; RECOMBINATION, GENETIC;

EID: 84896724199     PISSN: 01757598     EISSN: 14320614     Source Type: Journal    
DOI: 10.1007/s00253-013-5412-x     Document Type: Article

References (45)

1. Alper H, Miyaoku K, Stephanopoulos G (2005) Construction of lycopene-overproducing E. coli strains by combining systematic and combinatorial gene knockout targets. Nat Biotechnol 23:612-616. doi:10.1038/nbt1083 (Pubitemid 41724901)
2. Baba T, Huan HC, Datsenko K, Wanner BL, Mori H (2008) The applications of systematic in-frame, single-gene knockout mutant collection of Escherichia coli K-12. In: Osterman AL, Gerdes SY (eds) Microbial gene essentiality: protocols and bioinformatics. Humana, Totowa, pp 183-194. doi:10.1007/978-1-59745-321-9:12
3. Close TJ, Zaitlin D, Kado CI (1984) Design and development of amplifiable broad-host-range cloning vectors: analysis of the vir region of Agrobacterium tumefaciens plasmid pTiC58. Plasmid 12:111-118. doi:10.1016/0147-619X(84)90057-X
4. Datsenko KA, Wanner BL (2000) One-step inactivation of chromosomal genes in Escherichia coli K-12 using PCR products. Proc Natl Acad Sci U S A 97:6640-6645. doi:10.1073/pnas.120163297 (Pubitemid 30412767)
5. de Groot MJ, Bundock P, Hooykaas PJ, Beijersbergen AG (1998) Agrobacterium tumefaciens-mediated transformation of filamentous fungi. Nat Biotechnol 16:839-842. doi:10.1038/nbt0998-839 (Pubitemid 28405853)
6. den Dulk-Ras A, Hooykaas PJ (1995) Electroporation of Agrobacterium tumefaciens. Methods Mol Biol 55:63-72. doi:10.1385/0-89603-328-7:63
7. Derbise A, Lesic B, Dacheux D, Ghigo JM, Carniel E (2003) A rapid and simple method for inactivating chromosomal genes in Yersinia. FEMS Immunol Med Microbiol 38:113-116. doi:10.1016/S0928-8244(03)00181-0 (Pubitemid 37297836)
8. Drecktrah D, Douglas JM, Samuels DS (2010) Use of rpsL as a counterselectable marker in Borrelia burgdorferi. Appl Environ Microbiol 76:985-987. doi:10.1128/AEM.02172-09
9. Ellis HM, Yu D, DiTizio T, Court DL (2001) High efficiency mutagenesis, repair, and engineering of chromosomal DNA using single-stranded oligonucleotides. Proc Natl Acad Sci USA 98:6742-6746. doi:10.1073/pnas. 121164898 (Pubitemid 32538287)
10. Erler A, Wegmann S, Elie-Caille C, Bradshaw CR, Maresca M, Seidel R, Habermann B, Müller DJ, Stewart AF (2009) Conformational adaptability of Redß during DNA annealing and implications for its structural relationship with Rad52. JMol Biol 391:586-598. doi:10.1016/j.jmb.2009.06.030
11. Hendrickson W, Petithory J, Schleif R (1983) Spacing mutations between the Escherichia coli pBAD RNA polymerase binding site and the araC (I) induction site. Nucleic Acids Res 11:1873-1880. doi:10.1093/nar/11.6.1873
12. Hill SA, Stahl MM, Stahl FW (1997) Single-strand DNA intermediates in phage λ's Red recombination pathway. Proc Natl Acad Sci U S A 94:2951-2956 (Pubitemid 27157245)
13. Hood EE, Gelvin SB, Melchers LS, Hoekema A (1993) New Agrobacterium helper plasmids for gene transfer to plants. Transgenic Res 2:208-218. doi:10.1007/BF01977351
14. Husseiny MI, Hensel M (2005) Rapid method for the construction of Salmonella enterica serovar typhimurium vaccine carrier strains. Infect Immun 73:1598-1605. doi:10.1128/IAI.73.3.1598-1605.2005 (Pubitemid 40470747)
15. Karakousis G, Ye N, Li Z, Chiu S, Reddy G, Radding C (1998) The beta protein of phage λ binds preferentially to an intermediate in DNA renaturation. J Mol Biol 276:721-731. doi:10.1006/jmbi.1997.1573 (Pubitemid 28122285)
16. Karnezis T, Epa VC, Stone BA, Stanisich VA (2003) Topological characterization of an inner membrane (1→3)-β-D-glucan (curdlan) synthase from Agrobacterium sp. strain ATCC31749. Glycobiology 13:693-706. doi:10.1093/glycob/cwg093 (Pubitemid 37337050)
17. Katashkina J, Hara Y, Golubeva L, Andreeva I, Kuvaeva T, Mashko S (2009) Use of the λ Red-recombineering method for genetic engineering of Pantoea ananatis. BMC Mol Biol 10:34-38. doi:10.1186/1471-2199-10-34
18. Kües U, Stahl U (1989) Replication of plasmids in gram-negative bacteria. Microbiol Rev 53:491-516 (Pubitemid 20006369)
19. Kunik T, Tzfira T, Kapulnik Y, Gafni Y, Dingwall C, Citovsky V (2001) Genetic transformation of HeLa cells by Agrobacterium. Proc Natl Acad Sci U S A 98:1871-1876. doi:10.1073/pnas.98.4.1871 (Pubitemid 32165590)
20. Lee LY (2006) Integration of genes into the chromosome of Agrobacterium tumefaciens C58. Agrobacterium protocols. Meth Mol Biol 343:55-66
21. Lesic B, Rahme LG (2008) Use of the lambda Red recombinase system to rapidly generate mutants in Pseudomonas aeruginosa. BMC Mol Biol 9:20. doi:10.1186/1471-2199-9-20
22. Li Z, Karakousis G, Chiu S, Reddy G, Radding C (1998) The beta protein of phage λ promotes strand exchange. J Mol Biol 276:733-744. doi:10.1006/jmbi.1997.1572 (Pubitemid 28122286)
23. Liu P, Jenkins NA, Copeland NG (2001) Efficient Cre-loxP-induced mitotic recombination in mouse embryonic stem cells. Nat Genet 30:66-72. doi:10.1038/ng788
24. Luo ZQ, Clemente TE, Farrand SK (2001) Construction of a derivative of Agrobacterium tumefaciens C58 that does not mutate to tetracycline resistance. Mol Plant Microbe Interact 14:98-103. doi:10.1094/MPMI.2001.14.1.98 (Pubitemid 32062634)
25. Maresca M, Erler A, Fu J, Friedrich A, Zhang Y, Stewart AF (2010) Single-stranded heteroduplex intermediates in λ Red homologous recombination. BMC Mol Biol 11:54. doi:10.1186/1471-2199-11-54
26. Marx CJ (2008) Development of a broad-host-range sacB-based vector for unmarked allelic exchange. BMC Res Notes 1:1. doi:10.1186/1756-0500-1-1
27. Murphy KC (2007) The λ Gam protein inhibits RecBCD binding to dsDNA ends. J Mol Biol 371:19-24. doi:10.1016/j.jmb.2007.05.085
28. Murphy KC, Campellone KG, Poteete AR (2000) PCR-mediated gene replacement in Escherichia coli. Gene 246:321-330. doi:10.1016/S0378-1119(00)00071-8 (Pubitemid 30190186)
29. Muyrers JP, Zhang Y, Testa G, Stewart AF (1999) Rapid modification of bacterial artificial chromosomes by ET-recombination. Nucleic Acids Res 27:1555-1557. doi:10.1093/nar/27.6.1555 (Pubitemid 29206301)
30. Mythili E, Kumar KA, Muniyappa K (1996) Characterization of the DNA-binding domain of β protein, a component of phage λ Red-pathway, by UV catalyzed cross-linking. Gene 182:81-87. doi:10.1016/S0378-1119(96)00518- 5 (Pubitemid 27007169)
31. Pazour GJ, Das A (1990) virG, an Agrobacterium tumefaciens transcriptional activator, initiates translation at a UUG codon and is a sequence-specific DNA-binding protein. J Bacteriol 172:1241-1249 (Pubitemid 20085941)
32. Piers KL, Heath JD, Liang X, Stephens KM, Nester EW (1996) Agrobacterium tumefaciens-mediated transformation of yeast. Proc Natl Acad Sci U S A 93:1613-1618 (Pubitemid 26075174)
33. Sergueev K, Yu D, Austin S (2001) Cell toxicity caused by products of the pL operon of bacteriophage lambda. Gene 272:227-235. doi:10.1016/S0378-1119(01) 00535-2 (Pubitemid 32695416)
34. Sugui JA, Chang YC, Kwon-Chung K (2005) Agrobacterium tumefaciens-mediated transformation of Aspergillus fumigatus: an efficient tool for insertional mutagenesis and targeted gene disruption. Appl Environ Microbiol 71:1798-1802. doi:10.1128/AEM.71.4.1798-1802.2005 (Pubitemid 40546095)
35. Terpe K (2006) Overview of bacterial expression systems for heterologous protein production: from molecular and biochemical fundamentals to commercial systems. Appl Microbiol Biot 72:211-222. doi:10.1007/s00253-006-0465-8
36. Ülker B, Li Y, Rosso MG, Logemann E, Somssich IE, Weisshaar B (2008) T-DNA-mediated transfer of Agrobacterium tumefaciens chromosomal DNA into plants. Nat Biotechnol 26:1015-1017. doi:10.1038/nbt.1491
37. Wang J, Sarov M, Rientjes J,Hu J, Hollak H, Kranz H, Xie Y, Stewart AF, Zhang Y (2006) An improved recombineering approach by adding RecA to λ red recombination. Mol Biotechnol 32:43-53. doi:10.1385/MB:32:1:043 (Pubitemid 43022767)
38. Wood DW, Setubal JC, Kaul R, Monks DE, Kitajima JP, Okura VK, Zhou Y, Chen L, Wood GE, Almeida NF (2001) The genome of the natural genetic engineer Agrobacterium tumefaciens C58. Science 294:2317-2323. doi:10.1126/science. 1066804 (Pubitemid 33140549)
39. Wray L, Jorgensen R, Reznikoff W (1981) Identification of the tetracycline resistance promoter and repressor in transposon Tn10. J Bacteriol 147:297-304 (Pubitemid 12226867)
40. Xiang C, Han P, Lutziger I, Wang K, Oliver DJ (1999) A mini binary vector series for plant transformation. Plant Mol Biol 40:711-717. doi:10.1023/A:1006201910593
41. Yao J, Lambowitz AM (2007) Gene targeting in gram-negative bacteria by use of a mobile group II intron ("targetron") expressed from a broad-host-range vector. Appl Environ Microbiol 73:2735-2743. doi:10.1128/AEM.02829-06 (Pubitemid 46668768)
42. Yu D, Ellis HM, Lee E-C, Jenkins NA, Copeland NG (2000) An efficient recombination system for chromosome engineering in Escherichia coli. Proc Natl Acad Sci U S A 97:5978-5983. doi:10.1073/pnas.100127597 (Pubitemid 30367509)
43. Yu D, Sawitzke JA, Ellis H (2003) Recombineering with overlapping single-stranded DNA oligonucleotides: testing a recombination intermediate. Proc Natl Acad Sci U S A 100:7207-7212. doi:10.1073/pnas.1232375100 (Pubitemid 36706417)
44. Zhang Y, Buchholz F, Muyrers JP, Stewart AF (1998) A new logic for DNA engineering using recombination in Escherichia coli. Nat Genet 20:123-128. doi:10.1038/2417 (Pubitemid 28455443)
45. Zhang Y, Muyrers JP, Testa G, Stewart AF (2000) DNA cloning by homologous recombination in Escherichia coli. Nat Biotechnol 12:1314-1317. doi:10.1038/82449