Oligonucleotide recombination in corynebacteria without the expression of exogenous recombinases

Journal of Microbiological Methods

Volumn 105, Issue , 2014, Pages 109-115

  Krylov, Alexander A ^a   Kolontaevsky, Egor E ^a   Mashko, Sergey V ^a  

^a Ajinomoto Genetika Research Institute   (Russian Federation)

Author keywords

Corynebacteria; Oligo; Recombinases; Recombineering

Indexed keywords

OLIGONUCLEOTIDE; RECOMBINASE; SINGLE STRAND DNA ANNEALING PROTEIN; SINGLE STRANDED DNA; UNCLASSIFIED DRUG; DNA BINDING PROTEIN; RIBOSOME PROTEIN; STREPTOMYCIN;

5' UNTRANSLATED REGION; ARTICLE; BACTERIAL GENE; BACTERIAL GROWTH; BACTERIAL STRAIN; CELL VIABILITY; CONCENTRATION (PARAMETERS); CORYNEBACTERIUM GLUTAMICUM; DNA RECOMBINATION; NONHUMAN; PRIORITY JOURNAL; PROCESS OPTIMIZATION; PROTEIN EXPRESSION; PROTEIN PHOSPHORYLATION; RPSL GENE; WILD TYPE; ANTIBIOTIC RESISTANCE; CORYNEBACTERIUM; GENETIC RECOMBINATION; GENETICS; METABOLISM; MICROBIAL GENETICS; MOLECULAR BIOLOGY; PROCEDURES;

CORYNEBACTERIUM; DNA-BINDING PROTEINS; DRUG RESISTANCE, BACTERIAL; GENETICS, MICROBIAL; MOLECULAR BIOLOGY; OLIGONUCLEOTIDES; RECOMBINATION, GENETIC; RIBOSOMAL PROTEINS; STREPTOMYCIN;

EID: 84907319439     PISSN: 01677012     EISSN: 18728359     Source Type: Journal    
DOI: 10.1016/j.mimet.2014.07.028     Document Type: Article

References (60)

1. Bailey C.R., Winstanley D.J. Inhibition of restriction in Streptomyces clavuligerus by heat treatment. J. Gen. Microbiol. 1986, 132:2945-2947.
2. Becker J., Wittmann C. Bio-based production of chemicals, materials and fuels-Corynebacterium glutamicum as versatile cell factory. Curr. Opin. Biotechnol. 2012, 23:631-640. 10.1016/j.copbio.2011.11.012.
3. Binder S., Siedler S., Marienhagen J., Bott M., Eggeling L. Recombineering in Corynebacterium glutamicum combined with optical nanosensors: a general strategy for fast producer strain generation. Nucleic Acids Res. 2013, 41:6360-6369. 10.1093/nar/gkt312.
4. Burdett V., Baitinger C., Viswanathan, Lovett S.T., Modrich P. In vivo reauirement for RecJ, ExoVII, ExoI, and ExoX in methyl-directed mismatch repair. Proc. Natl. Acad. Sci. U. S. A. 2001, 98:6765-6770. 10.1073/pnas.121183298.
5. Buschke N., Schäfer R., Becker J., Wittmann C. Metabolic engineering of industrial platform microorganisms for biorefinery applications-optimization of substrate spectrum and process robustness by rational and evolutive strategies. Bioresour. Technol. 2012, 135:544-554. 10.1016/j.biortech.2012.11.047.
6. Carr P.A., Wang H.H., Sterling B., Isaacs F.J., Lajoie M.J., Xu G., Church G.M., Jacobson J.M. Enhanced multiplex genome engineering through co-operative oligonucleotide co-selection. Nucleic Acids Res. 2012, 40:e132.
7. Cha R.S., Zarbl H., Keohavong P., Thilly W.G. Mismatch amplification mutation assay (MAMA): application to the c-H-ras gene. PCR Methods Appl. 1992, 2:14-20.
8. Chase J.W., Richardson C.C. Exonuclease VII of Escherichia coli. Mechanism of action. J. Biol. Chem. 1974, 249:4553-4561.
9. Chittum H.S., Champney W.S. Ribosomal protein gene sequence changes in erythromycin-resistant mutants of Escherichia coli. J. Bacteriol. 1994, 176:6192-6198.
10. Correia A., Martin J.F., Castro J.M. Pulsed-field gel electrophoresis analysis of the genome of amino acid producing corynebacteria: chromosome sizes and diversity of restriction patterns. Microbiology 1994, 140:2841-2847.
11. Datsenko K.A., Wanner B.L. One-step inactivation of chromosomal genes in Escherichia coli K-12 using PCR products. Proc. Natl. Acad. Sci. U. S. A. 2000, 97:6640-6645.
12. Datta S., Costantino N., Zhou X., Court D.L. Identification and analysis of recombineering functions from Gram-negative and Gram-positive bacteria and their phages. Proc. Natl. Acad. Sci. U. S. A. 2008, 105:1626-1631. 10.1073/pnas.0709089105.
13. Eckstein F. Nucleoside phosphorothiotes. Ann. Rev. Biochem. 1985, 54:367-402.
14. Eggeling L., Bott M. Handbook of Corynebacterium glutamicum 2005, CRC Press, New York.
15. Eikmanns B.J., Kircher M., Reinscheid D.J. Discrimination of Corynebacterium glutamicum, Brevibacterium flavum and Brevibacterium lactofermentum by restriction pattern analysis of DNA adjacent to the hom gene. FEMS Microbiol. Lett. 1991, 66:203-207.
16. Ellis H.M., Yu D., DiTizio T., Court D.L. High efficiency mutagenesis, repair, and engineering of chromosomal DNA using single-stranded oligonucleotides. Proc. Natl. Acad. Sci. U. S. A. 2001, 98:6742-6746.
17. Güthlein C., Wanner R.M., Sander P., Davis E.O., Bosshard M., Jiricny J., Böttger E.C., Springer B. Characterization of the mycobacterial NER system reveals novel functions of the uvrD1 helicase. J. Bacteriol. 2009, 191:555-562. 10.1128/JB.00216-08.
18. Hanahan D. Studies on transformation of Escherichia coli with plasmids. J. Mol. Biol. 1983, 166:557-580.
19. Haynes J.A., Britz M.L. Electrotransformation of Brevibacterium lactofermentum and Corynebacterium glutamicum: growth in tween 80 increases transformation frequencies. FEMS Microbiol. Lett. 1989, 61:329-333. 10.1111/j.1574-6968.1989.tb03646.x.
20. Haynes J.A., Britz M.L. The effect of growth conditions of Corynebacterium glutamicum on the transformation frequency obtained by electroporation. Microbiology 1990, 136:255-263. 10.1099/00221287-136-2-255.
21. Holloway B.W. Variations in restriction and modification following increase of growth temperature in Pseudomonas aeruginosa. Virology 1965, 25:634-642.
22. Holo H., Nes I.F. High-frequencytransformation, by electroporation, of Lactococcus lactis subsp. cremoris grown with glycine in osmotically stabilized media. Appl. Environ. Microbiol. 1989, 55:3119-3123.
23. Jiang W., Bikard D., Cox D., Zhang F., Marraffini L.A. RNA-guided editing of bacterial genomes using CRISPR-Cas system. Nat. Biotechnol. 2013, 31:233-239. 10.1038/nbt.2508.
24. Katashkina J.I., Hara Y., Golubeva L.I., Andreeva I.G., Kuvaeva T.M., Mashko S.V. Use of the lambda Red-recombineering method for genetic engineering of Pantoea ananatis. BMC Mol. Biol. 2009, 10:34. 10.1186/1471-2199-10-34.
25. Kim I.K., Jeong W.K., Lim S.H., Hwang I.K., Kim Y.H. The small ribosomal protein S12P gene rpsL as an efficient positive selection marker in allelic exchange mutation systems for Corynebacterium glutamicum. J. Microbiol. Methods 2011, 84:128-130. 10.1016/j.mimet.2010.10.007.
26. Li X.T., Costantino N., Lu L.Y., Liu D.P., Watt R.M., Cheah K.S., Court D.L., Huang J.D. Identification of factors influencing strand bias in oligonucleotide-mediated recombination in Escherichia coli. Nucleic Acids Res. 2003, 31:6674-6687.
27. Li X.T., Thomason L.C., Sawitzke J.A., Costantino N., Court D.L. Bacterial DNA polymerases participate in oligonucleotide recombination. Mol. Microbiol. 2013, 88:906-920. 10.1111/mmi.12231.
28. Lieb W., Ehrmann M., Ludwig W., Schleifer K.H. Transfer of Brevibacterium divaricatum DSM 20297T, "Brevibacterium flavum" DSM 20411, "Brevibacterium lactofermentum" DSM 20412 and DSM 1412, and Corynebacterium glutamicum and their distinction by rRNA gene restriction patterns. Int. J. Syst. Bacteriol. 1991, 41:255-260.
29. Maresca M., Erler A., Fu J., Friedrich A., Zhang Y., Stewart A.F. Single-stranded heteroduplex intermediates in λRed homologous recombination. BMC Mol. Biol. 2010, 11:54. 10.1186/1471-2199-11-54.
30. Miwa K., Matsui K., Terabe M., Ito K., Nakamori S., Sano K., Momose H. Cryptic plasmid in glutamic acid producing bacteria. Agric. Biol. Chem. 1984, 48:2901-2903.
31. Mizrahi V., Andersen S.J. DNA repair in Mycobacterium tuberculosis. What have we learnt from the genome sequence?. Mol. Microbiol. 1998, 29:1331-1339.
32. 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. 10.1534/genetics.110.120782.
33. Mosberg J.A., Gregg C.J., Lajoie M.J., Wang H.H., Church G.M. Improving lambda Red genome engineering in Escherichia coli via rational removal of endogenous nucleases. PLoS One 2012, 7:e44638. 10.1371/journal.pone.0044638.
34. Muniyappa K., Radding C.M. The homologous recombination system of phage lambda. Pairing activities of beta protein. J. Biol. Chem. 1986, 261:7472-7478.
35. Murphy K.C., Marinus M.G. RecA-independent single-stranded DNA oligonucleotide-mediated mutagenesis. Biol. Rep. 2010, 2:56. (F1000). 10.3410/B2-56.
36. Murphy K.C., Campellone K.G., Poteete A.R. PCR-mediated gene replacement in Escherichia coli. Gene 2000, 246:321-330.
37. Nakamura J., Hirano S., Ito H., June 2006. L-glutamic acid producing microorganism and a method for producing L-glutamic acid. U.S. patent US20060141588A1.
38. Nešvera J., Pátek M. Tools for genetic manipulations in Corynebacterium glutamicum and their applications. Appl. Microbiol. Biotechnol. 2011, 90:1641-1654. 10.1007/s00253-011-3272-9.
39. Powell I.B., Achen M.G., Hillier A.J., Davidson B.E. A simple and rapid method for genetic transformation of lactic streptococci by electroporation. Appl. Environ. Microbiol. 1988, 54:655-660.
40. Pyne M.E., Moo-Young M., Chung D.A., Chou C.P. Development of an electrotransformation protocol for genetic manipulation of Clostridium pasteurianum. Biotechnol. Biofuels 2013, 6:50. 10.1186/1754-6834-6-50.
41. Resende B.C., Rebelato A.B., D'Afonseca V., Santos A.R., Stutzman T., Azevedo V.A., Santos L.L., Miyoshi A., Lopes D.O. DNA repair in Corynebacterium model. Gene 2011, 482:1-7. 10.1016/j.gene.2011.03.008.
42. Sambrook J., Russell D.W. Molecular Cloning: a laboratory manual 2001, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York. third ed.
43. Sawitzke J.A., Thomason L.C., Costantino N., Bubunenko M., Datta S., Court D.L. Recombineering: in vivo genetic engineering in E. coli, S. enterica, and beyond. Methods Enzymol. 2007, 421:171-199.
44. Sawitzke J.A., Costantino N., Li X.T., Thomason L.C., Bubunenko M., Court C., Court D.L. Probing cellular processes with oligo-mediated recombination and using the knowledge gained to optimize recombineering. J. Mol. Biol. 2011, 407:45-59. 10.1016/j.jmb.2011.01.030.
45. Schäfer A., Tauch A., Jäger W., Kalinowski J., Thierbach G., Pühler A. Small mobilizable multi-purpose cloning vectors derived from the Escherichia coli plasmids pK18 and pK19: selection of defined deletions in the chromosome of Corynebacterium glutamicum. Gene 1994, 145(1):69-73.
46. Shimomura-Shimizu M., Karube I. Applications of microbial cell sensors. Adv. Biochem. Eng. Biotechnol. 2010, 118:1-30. 10.1007/10_2009_19.
47. Shirai T., Fujimura K., Furusawa C., Nagahisa K., Shioya S., Shimizu H. Study on roles of anaplerotic pathways in glutamate overproduction of Corynebacterium glutamicum by metabolic flux analysis. Microb. Cell Fact. 2007, 6:19.
48. Swingle B., Bao Z., Markel E., Chambers A., Cartinhour S. Recombineering using RecTE from Pseudomonas syringae. Appl. Environ. Microbiol. 2010, 76:4960-4968. 10.1128/AEM.00911-10.
49. Swingle B., Markel E., Cartinhour S. Oligonucleotide recombination: a hidden treasure. Bioeng. Bugs 2010, 1:263-266. 10.4161/bbug.1.4.12098.
50. Swingle B., Markel E., Costantino N., Bubunenko M.G., Cartinhour S., Court D.L. Oligonucleotide recombination in Gram-negative bacteria. Mol. Microbiol. 2010, 75:138-148. 10.1111/j.1365-2958.2009.06976.x.
51. Van der Rest M.E., Lange C., Molenaar D. A heat shock following electroporation induces highly efficient transformation of Corynebacterium glutamicum with xenogeneic plasmid DNA. Appl. Microbiol. Biotechnol. 1999, 52:541-545.
52. Van Kessel J.C., Hatfull G.F. Recombineering in Mycobacterium tuberculosis. Nat. Methods 2007, 4:147-152. 10.1038/nmeth996.
53. Van Kessel J.C., Hatfull G.F. Efficient point mutagenesis in mycobacteria using single-stranded DNA recombineering: characterization of antimycobacterial drug targets. Mol. Microbiol. 2008, 67:1094-1107. 10.1111/j.1365-2958.2008.06109.x.
54. Van Pijkeren J.P., Britton R.A. High efficiency recombineering in lactic acid bacteria. Nucleic Acids Res. 2012, 40:e76. 10.1093/nar/gks147.
55. Van Pijkeren J.P., Neoh K.M., Sirias D., Findley A.S., Britton R.A. Exploring optimization parameters to increase ssDNA recombineering in Lactococcus lactis and Lactobacillus reuteri. Bioengineered 2012, 3:209-217. 10.4161/bioe.21049.
56. Wang H.H., Isaacs F.J., Carr P.A., Sun Z.Z., Xu G., Forest C.R., Church G.M. Programming cells by multiplex genome engineering and accelerated evolution. Nature 2009, 460:894-898. 10.1038/nature08187.
57. 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. 10.1093/nar/gks248.
58. Yu D., Ellis H.M., Lee E.C., Jenkins N.A., Copeland N.G., Court D.L. An efficient recombination system for chromosome engineering in Escherichia coli. Proc. Natl. Acad. Sci. U. S. A. 2000, 97:5978-5983.
59. Zaman S., Fitzpatrick M., Lindahl L., Zengel J. Novel mutations in ribosomal proteins L4 and L22 that confer erythromycin resistance in Escherichia coli. Mol. Microbiol. 2007, 66:1039-1050.
60. Zhang Y., Buchholz F., Muyrers J.P., Stewart A.F. A new logic for DNA engineering using recombination in Escherichia coli. Nat. Genet. 1998, 20:123-128.