Precision genome engineering in lactic acid bacteria

Microbial Cell Factories

Volumn 13, Issue 1, 2014, Pages

  van Pijkeren, Jan Peter ^a   Britton, Robert A ^b  

^a UNIVERSITY OF WISCONSIN MADISON   (United States)

^b Department of Microbiology and Molecular Genetics ^*  (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL DNA; OLIGONUCLEOTIDE; RECOMBINASE; RECT PROTEIN; SINGLE STRANDED DNA; BACTERIAL PROTEIN; ENDONUCLEASE;

ACCURACY; ARTICLE; ESCHERICHIA COLI; GENETIC ENGINEERING; GENOME ENGINEERING; HUMAN; LACTIC ACID BACTERIUM; LACTOBACILLUS REUTERI; LACTOCOCCUS LACTIS; MISMATCH REPAIR; MUTATIONAL ANALYSIS; NONHUMAN; NUCLEOTIDE SEQUENCE; PROTEIN EXPRESSION; RECOMBINEERING; TRANSGENIC ORGANISM; BACTERIAL GENOME; CLUSTERED REGULARLY INTERSPACED SHORT PALINDROMIC REPEAT; GENETICS; METABOLISM;

BACTERIA (MICROORGANISMS); ESCHERICHIA COLI; LACTOBACILLUS REUTERI; LACTOCOCCUS LACTIS;

BACTERIAL PROTEINS; CLUSTERED REGULARLY INTERSPACED SHORT PALINDROMIC REPEATS; ENDONUCLEASES; GENETIC ENGINEERING; GENOME, BACTERIAL; LACTOBACILLUS REUTERI; RECOMBINASES;

EID: 84906828539     PISSN: None     EISSN: 14752859     Source Type: Journal    
DOI: 10.1186/1475-2859-13-S1-S10     Document Type: Article

References (39)

1. Fang F, O'Toole PW: Genetic tools for investigating the biology of commensal lactobacilli. Front Biosci (Landmark Ed) 2009, 14:3111-3127.
2. Sharan SK, Thomason LC, Kuznetsov SG, Court DL: Recombineering: a homologous recombination-based method of genetic engineering. Nat Protoc 2009, 4:206-223. 10.1038/nprot.2008.227
3. Murphy KC: Phage recombinases and their applications. Adv Virus Res 2012, 83:367-414.
4. Kuhlman TE, Cox EC: Site-specific chromosomal integration of large synthetic constructs. Nucleic Acids Res 2010, 38:e92. 10.1093/nar/gkp1193
5. Fu J, Bian X, Hu S, Wang H, Huang F, Seibert PM, Plaza A, Xia L, Muller R, Stewart AF, Zhang Y: Full-length RecE enhances linear-linear homologous recombination and facilitates direct cloning for bioprospecting. Nat Biotechnol 2012, 30:440-446. 10.1038/nbt.2183
6. Muyrers JP, Zhang Y, Testa G, Stewart AF: Rapid modification of bacterial artificial chromosomes by ET-recombination. Nucleic Acids Res 1999, 27:1555-1557. 10.1093/nar/27.6.1555
7. Sawitzke JA, Thomason LC, Bubunenko M, Li X, Costantino N, Court DL: Recombineering: using drug cassettes to knock out genes in vivo. Methods Enzymol 2013, 533:79-102.
8. Costantino N, Court DL: Enhanced levels of lambda Red-mediated recombinants in mismatch repair mutants. Proc Natl Acad Sci USA 2003, 100:15748-15753. 10.1073/pnas.2434959100
9. Li XT, Costantino N, Lu LY, Liu DP, Watt RM, Cheah KS, Court DL, Huang JD: Identification of factors influencing strand bias in oligonucleotide-mediated recombination in Escherichia coli. Nucleic Acids Res 2003, 31:6674-6687. 10.1093/nar/gkg844
10. Sawitzke JA, Costantino N, Li XT, Thomason LC, Bubunenko M, Court C, Court DL: 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
11. Ellis HM, Yu D, DiTizio T, Court DL: High efficiency mutagenesis, repair, and engineering of chromosomal DNA using single-stranded oligonucleotides. Proc Natl Acad Sci USA 2001, 98:6742-6746. 10.1073/pnas.121164898
12. Sakabe K, Okazaki R: A unique property of the replicating region of chromosomal DNA. Biochim Biophys Acta 1966, 129:651-654. 10.1016/0005-2787(66)90088-8
13. Maresca M, Erler A, Fu J, Friedrich A, Zhang Y, Stewart AF: Single-stranded heteroduplex intermediates in lambda Red homologous recombination. BMC Mol Biol 2010, 11:54. 10.1186/1471-2199-11-54
14. Mosberg JA, Gregg CJ, Lajoie MJ, Wang HH, Church GM: Improving lambda red genome engineering in Escherichia coli via rational removal of endogenous nucleases. PLoS One 2012, 7:e44638. 10.1371/journal.pone.0044638
15. Mosberg JA, Lajoie MJ, Church GM: Lambda red recombineering in Escherichia coli occurs through a fully single-stranded intermediate. Genetics 2010, 186:791-799. 10.1534/genetics.110.120782
16. Van Pijkeren JP, Neoh KM, Sirias D, Findley AS, Britton RA: Exploring optimization parameters to increase ssDNA recombineering in Lactococcus lactis and Lactobacillus reuteri. Bioengineered 2012, 3:209-217. 10.4161/bioe.21049
17. Wang HH, Isaacs FJ, Carr PA, Sun ZZ, Xu G, Forest CR, Church GM: Programming cells by multiplex genome engineering and accelerated evolution. Nature 2009, 460:894-898. 10.1038/nature08187
18. Datta S, Costantino N, Zhou X, Court DL: Identification and analysis of recombineering functions from Gram-negative and Gram-positive bacteria and their phages. Proc Natl Acad Sci USA 2008, 105:1626-1631. 10.1073/pnas.0709089105
19. van Pijkeren JP, Britton RA: High efficiency recombineering in lactic acid bacteria. Nucleic Acids Res 2012, 40:e76. 10.1093/nar/gks147
20. Yu D, Ellis HM, Lee EC, Jenkins NA, Copeland NG, Court DL: An efficient recombination system for chromosome engineering in Escherichia coli. Proc Natl Acad Sci USA 2000, 97:5978-5983. 10.1073/pnas.100127597
21. Murphy KC, Campellone KG: Lambda Red-mediated recombinogenic engineering of enterohemorrhagic and enteropathogenic E. coli. BMC Mol Biol 2003, 4:11. 10.1186/1471-2199-4-11
22. Eichenbaum Z, Federle MJ, Marra D, de Vos WM, Kuipers OP, Kleerebezem M, Scott JR: Use of the lactococcal nisA promoter to regulate gene expression in gram-positive bacteria: comparison of induction level and promoter strength. Appl Environ Microbiol 1998, 64:2763-2769.
23. Kleerebezem M, Beerthuyzen MM, Vaughan EE, de Vos WM, Kuipers OP: Controlled gene expression systems for lactic acid bacteria: transferable nisin-inducible expression cassettes for Lactococcus, Leuconostoc, and Lactobacillus spp. Appl Environ Microbiol 1997, 63:4581-4584.
24. Sorvig E, Mathiesen G, Naterstad K, Eijsink VG, Axelsson L: High-level, inducible gene expression in Lactobacillus sakei and Lactobacillus plantarum using versatile expression vectors. Microbiology 2005, 151:2439-2449. 10.1099/mic.0.28084-0
25. van Kessel JC, Hatfull GF: 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
26. Wang HH, Church GM: Multiplexed genome engineering and genotyping methods applications for synthetic biology and metabolic engineering. Methods Enzymol 2011, 498:409-426.
27. Wang HH, Xu G, Vonner AJ, Church G: Modified bases enable high-efficiency oligonucleotide-mediated allelic replacement via mismatch repair evasion. Nucleic Acids Res 2011, 39:7336-7347. 10.1093/nar/gkr183
28. Cha RS, Zarbl H, Keohavong P, Thilly WG: Mismatch amplification mutation assay (MAMA): application to the c-H-ras gene. PCR Methods Appl 1992, 2:14-20. 10.1101/gr.2.1.14
29. Cong L, Ran FA, Cox D, Lin S, Barretto R, Habib N, Hsu PD, Wu X, Jiang W, Marraffini LA, Zhang F: Multiplex genome engineering using CRISPR/Cas systems. Science 2013, 339:819-823. 10.1126/science.1231143
30. Jiang W, Bikard D, Cox D, Zhang F, Marraffini LA: RNA-guided editing of bacterial genomes using CRISPR-Cas systems. Nat Biotechnol 2013, 31:233-239. 10.1038/nbt.2508
31. Mali P, Esvelt KM, Church GM: Cas9 as a versatile tool for engineering biology. Nat Methods 2013, 10:957-963. 10.1038/nmeth.2649
32. Mali P, Yang L, Esvelt KM, Aach J, Guell M, DiCarlo JE, Norville JE, Church GM: RNA-guided human genome engineering via Cas9. Science 2013, 339:823-826. 10.1126/science.1232033
33. Sander JD, Joung JK: CRISPR-Cas systems for editing, regulating and targeting genomes. Nat Biotechnol 2014.
34. Barrangou R: CRISPR-Cas systems and RNA-guided interference. Wiley Interdiscip Rev RNA 2013, 4:267-278. 10.1002/wrna.1159
35. Horvath P, Barrangou R: CRISPR/Cas, the immune system of bacteria and archaea. Science 2010, 327:167-170. 10.1126/science.1179555
36. Wiedenheft B, Sternberg SH, Doudna JA: RNA-guided genetic silencing systems in bacteria and archaea. Nature 2012, 482:331-338. 10.1038/nature10886
37. Sorek R, Lawrence CM, Wiedenheft B: CRISPR-mediated adaptive immune systems in bacteria and archaea. Annu Rev Biochem 2013, 82:237-266. 10.1146/annurev-biochem-072911-172315
38. Esvelt KM, Mali P, Braff JL, Moosburner M, Yaung SJ, Church GM: Orthogonal Cas9 proteins for RNA-guided gene regulation and editing. Nat Methods 2013, 10:1116-1121. 10.1038/nmeth.2681
39. Walsh RM, Hochedlinger K: A variant CRISPR-Cas9 system adds versatility to genome engineering. Proc Natl Acad Sci USA 2013, 110:15514-15515. 10.1073/pnas.1314697110