Full-length single-stranded PCR product mediated chromosomal integration in intact Bacillus subtilis

Journal of Microbiological Methods

Volumn 92, Issue 3, 2013, Pages 273-277

  Wen, Sai ^a,b   Yang, Jianguo ^a   Tan, Tianwei ^a  

^a BEIJING UNIVERSITY OF CHEMICAL TECHNOLOGY   (China)

^b BEIJING TECHNOLOGY AND BUSINESS UNIVERSITY   (China)

Author keywords

Bacillus subtilis; Full length single stranded DNA; Fusion PCR; Homologous recombination; Lipase

Indexed keywords

DOUBLE STRANDED DNA; SINGLE STRANDED DNA;

AMYE GENE; ARTICLE; BACILLUS SUBTILIS; BACTERIAL GENE; BACTERIAL STRAIN; BACTERIUM IDENTIFICATION; BINDING AFFINITY; BINDING SITE; CELL VIABILITY; CHROMOSOME ANALYSIS; CONTROLLED STUDY; DNA BINDING; DNA SEQUENCE; ELECTROPORATION; GENE DISRUPTION; HOMOLOGOUS RECOMBINATION; MOLECULAR DYNAMICS; NONHUMAN; NUCLEOTIDE SEQUENCE; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; QUANTITATIVE ANALYSIS; SEQUENCE ANALYSIS;

BACILLUS SUBTILIS; DNA, SINGLE-STRANDED; ELECTROPORATION; GENETICS, MICROBIAL; MOLECULAR BIOLOGY; RECOMBINATION, GENETIC; REVERSE TRANSCRIPTASE POLYMERASE CHAIN REACTION; RNA, BACTERIAL;

EID: 84873708128     PISSN: 01677012     EISSN: 18728359     Source Type: Journal    
DOI: 10.1016/j.mimet.2012.11.012     Document Type: Article

References (44)

1. Aloulou A., Rodriguez J.A., Puccinelli D., Mouz N., Leclaire J., Leblond Y., et al. Purification and biochemical characterization of the LIP2 lipase from Yarrowia lipolytica. BBA-Mol. Cell Biol. Lipids 2007, 1771:228-237.
2. Anagnostopoulos C., Spizizen J. Requirements for transformation in Bacillus subtilis. J. Bacteriol. 1961, 81:741-746.
3. Bordes F., Barbe S., Escalier P., Mourey L., André I., Marty A., et al. Exploring the conformational states and rearrangements of Yarrowia lipolytica lipase. Biophys. J. 2010, 99:2225-2234.
4. Brans A., Filee P., Chevigne A., Claessens A., Joris B. New integrative method to generate Bacillus subtilis recombinant strains free of selection markers. Appl. Environ. Microbiol. 2004, 70:7241-7250.
5. Cao G.Q., Zhang X.H., Zhong L., Lu Z.X. A modified electro-transformation method for Bacillus subtilis and its application in the production of antimicrobial lipopeptides. Biotechnol. Lett. 2011, 33:1047-1051.
6. Contente S., Dubnau D. Marker rescue transformation by linear plasmid DNA in Bacillus subtilis. Plasmid 1979, 2:555-571.
7. Cutting S.M., Vander Horn P.B. Molecular Biological Methods for Bacillus 1990, John Wiley & Sons, Chichester, UK.
8. Dubnau D. Genetic competence in Bacillus subtilis. Microbiol. Rev. 1991, 55:395-424.
9. Dubnau D. Genetic exchange and homologues recombination. Bacillus subtilis and Other Gram-Positive Bacteria: Biochemistry, Physiology and Molecular Genetics 1993, 555-584. ASM Press, Washington, D.C. A. Sonenshein, J. Hoch, R. Losick (Eds.).
10. Dubnau D., Lovett C.M.J. Transformation and recombination. In Bacillus subtilis and Its Closest Relatives: From Genes to Cells 2002, 453-471. ASM Press, Washington, D.C. A.L. Sonenshein, J.A. Hoch, R. Losick (Eds.).
11. Fabret C., Dusko Ehrlich S., Noirot P. A new mutation delivery system for genome-scale approaches in Bacillus subtilis. Mol. Microbiol. 2002, 46:25-36.
12. Fickers P., Marty A., Nicaud J.M. The lipases from Yarrowia lipolytica: genetics, production, regulation, biochemical characterization and biotechnological applications. Biotechnol. Adv. 2011, 29:632-644.
13. Guieysse D., Sandoval G., Faure L., Nicaud J.-M., Monsan P., Marty A. New efficient lipase from Yarrowia lipolytica for the resolution of 2-bromo-arylacetic acid esters. Tetrahedron: Asymmetry 2004, 15:3539-3543.
14. Gupta N., Rathi P., Gupta R. Simplified para-nitrophenyl palmitate assay for lipases and esterases. Anal. Biochem. 2002, 311:98-99.
15. Harwood C.R. Bacillus subtilis and its relatives: molecular biological and industrial workhorses. Trends Biotechnol. 1992, 10:247-256.
16. Harwood C.R., Cranenburgh R. Bacillus protein secretion: an unfolding story. Trends Microbiol. 2008, 16:73-79.
17. Horton R.M., Hunt H.D., Ho S.N., Pullen J.K., Pease L.R. Engineering hybrid genes without the use of restriction enzymes gene splicing by overlap extension. Gene 1989, 77:61-68.
18. Kharazmi M., Hammes W.P., Hertel C. Construction of a marker rescue system in Bacillus subtilis for detection of horizontal gene transfer in food. Syst. Appl. Microbiol. 2002, 25:471-477.
19. Liu S., Endo K., Ara K., Ozaki K., Ogasawara N. Introduction of marker-free deletions in Bacillus subtilis using the AraR repressor and the ara promoter. Microbiology 2008, 154:2562-2570.
20. Maresca M., Erler A., Fu J., Friedrich A., Zhang Y., Stewart A.F. Single-stranded heteroduplex intermediates in λ Red homologous recombination. BMC Mol. Biol. 2010, 11:54.
21. McDonald I.R., Riley P.W., Sharp R.J., McCarthy A.J. Factors affecting the electroporation of Bacillus subtilis. J. Appl. Bacteriol. 1995, 79:213-218.
22. Melnikov A., Youngman P.J. Random mutagenesis by recombinational capture of PCR products in Bacillus subtilis and Acinetobacter calcoaceticus. Nucleic Acids Res. 1999, 27:1056-1062.
23. Michel B., Niaudet B., Ehrlich S.D. Intermolecular recombination during transformation of Bacillus subtilis competent cells by monomeric and dimeric plasmids. Plasmid 1983, 10:1-10.
24. Morimoto T., Ara K., Ozaki K., Ogasawara N. A new simple method to introduce marker-free deletions in the Bacillus subtilis genome. Genes Genet. Syst. 2009, 84:315-318.
25. Mosberg J.A., Lajoie M.J., Church G.M. Lambda Red recombineering in Escherichia coli occurs through a fully single-stranded intermediate. Genetics 2010, 186:791-799.
26. Nie K., Xie F., Wang F., Tan T. Lipase catalyzed methanolysis to produce biodiesel: optimization of the biodiesel production. J. Mol. Catal. B: Enzym. 2006, 43:142-147.
27. Sanchez J.A., Pierce K.E., Rice J.E., Wangh L.J. Linear-After-The-Exponential (LATE)-PCR: an advanced method of asymmetric PCR and its uses in quantitative real-time analysis. PANS 2003, 101:1933-1938.
28. Sanchez H., Cozar M.C., Martinez-Jimenez M.I. Targeting the Bacillus subtilis genome: an efficient and clean method for gene disruption. J. Microbiol. Methods 2007, 70:389-394.
29. Shevchuk N.A., Bryksin A.V., Nusinovich Y.A., Cabello F.C., Sutherland M., Ladisch S. Construction of long DNA molecules using long PCR-based fusion of several fragments simultaneously. Nucleic Acids Res. 2004, 32:e19.
30. Stephenson M., Jarrett P. Transformation of Bacillus subtilis by electroporation. Biotechnol. Tech. 1991, 5:9-12.
31. Tomita S., Tsuge K., Kikuchi Y., Itaya M. Targeted isolation of a designated region of the Bacillus subtilis genome by recombinational transfer. Appl. Environ. Microbiol. 2004, 70:2508-2513.
32. Tsuge K., Matsui K., Itaya M. One step assembly of multiple DNA fragments with a designed order and orientation in Bacillus subtilis plasmid. Nucleic Acids Res. 2003, 31:e133.
33. Turgeon N., Laflamme C., Ho J., Duchaine C. Elaboration of an electroporation protocol for Bacillus cereus ATCC 14579. J. Microbiol. Methods 2006, 67:543-548.
34. Wang H.H., Xu G., Vonner A.J., Church G. Modified bases enable high-efficiency oligonucleotide-mediated allelic replacement via mismatch repair evasion. Nucleic Acids Res. 2011, 39:7336-7347.
35. Wang Y., Weng J., Waseem R., Yin X., Zhang R., Shen Q. Bacillus subtilis genome editing using ssDNA with short homology regions. Nucleic Acids Res. 2012, 40:e91.
36. Weinrauch Y., Dubnau D. Plasmid marker rescue transformation in Bacillus subtilis. J. Bacteriol. 1983, 154:1077-1087.
37. Wen S., Tan T., Yu M. Immobilized lipase YlLip2-catalyzed resolution of (±)α-phenylethyl amine in a medium with organic cosolvent. Process. Biochem. 2008, 43:1259-1264.
38. Xue G.-P., Johnson J.S., Dalrymple B.P. High osmolarity improves the electro-transformation efficiency of the Gram-positive bacteria Bacillus subtilis and Bacillus licheniformis. J. Microbiol. Methods 1999, 34:183-191.
39. Yan X., Yu H.J., Hong Q., Li S.P. Cre/lox system and PCR-based genome engineering in Bacillus subtilis. Appl. Environ. Microbiol. 2008, 74:5556-5562.
40. Yu M., Lange S., Richter S., Tan T., Schmid R.D. High-level expression of extracellular lipase Lip2 from Yarrowia lipolytica in Pichia pastoris and its purification and characterization. Protein Expr. Purif. 2007, 53:255-263.
41. Yu M., Wen S., Tan T. Enhancing production of Yarrowia lipolytica lipase Lip2 in Pichia pastoris. Eng. Life Sci. 2010, 10:458-464.
42. Zhang X.-Z., Zhang Y.H.P. Simple, fast and high-efficiency transformation system for directed evolution of cellulase in Bacillus subtilis. Microb. Biotechnol. 2011, 4:98-105.
43. Zhang X.Z., Yan X., Cui Z.-L., Hong Q., Li S.-P. mazF, a novel counter-selectable marker for unmarked chromosomal manipulation in Bacillus subtilis. Nucleic Acids Res. 2006, 34:e71.
44. Zyprian E., Matzura H. Characterization of signals promoting gene expression on the Staphylococcus aureus plasmid pUB110 and development of a Gram-positive expression vector system. DNA 1986, 3:219-225.