Skip to main content
SpringerLink
Log in

CRISPR–Cas-mediated gene editing in lactic acid bacteria

  • Review
  • Published:
Molecular Biology Reports Aims and scope Submit manuscript

Abstract

The high efficiency, convenience and diversity of clustered regular interspaced short palindromic repeats (CRISPR)/CRISPR-associated (Cas) systems are driving a technological revolution in the gene editing of lactic acid bacteria (LAB). Cas-RNA cassettes have been adopted as tools to perform gene deletion, insertion and point mutation in several species of LAB. In this article, we describe the basic mechanisms of the CRISPR–Cas system, and the current gene editing methods available, focusing on the CRISPR–Cas models developed for LAB. We also compare the different types of CRISPR–Cas-based genomic manipulations classified according to the different Cas proteins and the type of recombineering, and discuss the rapidly evolving landscape of CRISPR–Cas application in LAB.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3

Similar content being viewed by others

References

  1. Li H, Cao Y (2010) Lactic acid bacterial cell factories for gamma-aminobutyric acid. Amino Acids 39(5):1107–1116. https://doi.org/10.1007/s00726-010-0582-7

    Article  CAS  PubMed  Google Scholar 

  2. Douillard FP, De Vos WM (2014) Functional genomics of lactic acid bacteria: from food to health. Microb Cell Fact. https://doi.org/10.1186/1475-2859-13-S1-S8

    Article  PubMed  PubMed Central  Google Scholar 

  3. Gaspar P, Carvalho AL, Vinga S, Santos H, Neves AR (2013) From physiology to systems metabolic engineering for the production of biochemicals by lactic acid bacteria. Biotechnol Adv 31(6):764–788. https://doi.org/10.1016/j.biotechadv.2013.03.011

    Article  CAS  PubMed  Google Scholar 

  4. Mazzoli R, Bosco F, Mizrahi I, Bayer EA, Pessione E (2014) Towards lactic acid bacteria-based biorefineries. Biotechnol Adv 32(7):1216–1236. https://doi.org/10.1016/j.biotechadv.2014.07.005

    Article  CAS  PubMed  Google Scholar 

  5. Aktas B, Wolfe TJD, Safdar N, Darien BJ, Steele JL (2016) The impact of Lactobacillus casei on the composition of the cecal microbiota and innate immune system is strain specific. PLoS ONE. https://doi.org/10.1371/journal.pone.0156374

    Article  PubMed  PubMed Central  Google Scholar 

  6. Gleeson M, Bishop NC, Struszczak L (2016) Effects of Lactobacillus casei Shirota ingestion on common cold infection and herpes virus antibodies in endurance athletes: a placebo-controlled, randomized trial. Eur J Appl Physiol 116(8):1555–1563. https://doi.org/10.1007/s00421-016-3415-x

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  7. Kato-Kataoka A, Nishida K, Takada M, Kawai M, Kikuchi-Hayakawa H, Suda K, Ishikawa H, Gondo Y, Shimizu K, Matsuki T (2016) Fermented milk containing Lactobacillus casei strain Shirota preserves the diversity of the gut microbiota and relieves abdominal dysfunction in healthy medical students exposed to academic stress. Appl Environ Microbiol 82(12):3649–3658. https://doi.org/10.1128/AEM.04134-15

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  8. Xiong Z-Q, Kong L-H, Wang G-Q, Xia Y-J, Zhang H, Yin B-X, Ai L-Z (2018) Functional analysis and heterologous expression of bifunctional glutathione synthetase from Lactobacillus. J Dairy Sci 101(8):6937–6945. https://doi.org/10.3168/jds.2017-14142

    Article  CAS  PubMed  Google Scholar 

  9. Wang G, Zhang M, Zhao J, Xia Y, Lai PF-H, Ai L (2018) A surface protein from Lactobacillus plantarum increases the adhesion of Lactobacillus strains to human epithelial cells. Front Microbiol 9:2858. https://doi.org/10.3389/fmicb.2018.02858

    Article  PubMed  PubMed Central  Google Scholar 

  10. Xiong Z-Q, Kong L-H, Lai PF-H, Xia Y-J, Liu J-C, Li Q-Y, Ai L-Z (2019) Genomic and phenotypic analyses of exopolysaccharide biosynthesis in Streptococcus thermophilus S-3. J Dairy Sci 102(6):4925–4934. https://doi.org/10.3168/jds.2018-15572

    Article  CAS  PubMed  Google Scholar 

  11. Xiong Z-Q, Kong L-H, Meng H-L, Cui J-M, Xia Y-J, Wang S-J, Ai L-Z (2019) Comparison of gal–lac operons in wild-type galactose-positive and-negative Streptococcus thermophilus by genomics and transcription analysis. J Ind Microbiol Biotechnol 46(5):751–758. https://doi.org/10.1007/s10295-019-02145-x

    Article  CAS  PubMed  Google Scholar 

  12. Doudna JA, Charpentier E (2014) The new frontier of genome engineering with CRISPR-Cas9. Science 346(6213):1258096. https://doi.org/10.1126/science.1258096

    Article  CAS  PubMed  Google Scholar 

  13. Barrangou R, van Pijkeren J-P (2016) Exploiting CRISPR-Cas immune systems for genome editing in bacteria. Curr Opin Biotechnol 37:61–68. https://doi.org/10.1016/j.copbio.2015.10.003

    Article  CAS  PubMed  Google Scholar 

  14. Komor AC, Badran AH, Liu DR (2017) CRISPR-based technologies for the manipulation of eukaryotic genomes. Cell 168(1–2):20–36. https://doi.org/10.1016/j.cell.2016.10.044

    Article  CAS  PubMed  Google Scholar 

  15. Cong L, Ran FA, Cox D, Lin S, Barretto R, Habib N, Hsu PD, Wu X, Jiang W, Marraffini LA (2013) Multiplex genome engineering using CRISPR/Cas systems. Science 339(6121):819–823. https://doi.org/10.1126/science.1231143

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  16. Mali P, Yang L, Esvelt KM, Aach J, Guell M, DiCarlo JE, Norville JE, Church GM (2013) RNA-guided human genome engineering via Cas9. Science 339(6121):823–826. https://doi.org/10.1126/science.1232033

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  17. Liu X, Wu S, Xu J, Sui C, Wei J (2017) Application of CRISPR/Cas9 in plant biology. Acta Pharm Sin B 7(3):292–302. https://doi.org/10.1016/j.apsb.2017.01.002

    Article  PubMed  PubMed Central  Google Scholar 

  18. Wang H, Yang H, Shivalila CS, Dawlaty MM, Cheng AW, Zhang F, Jaenisch R (2013) One-step generation of mice carrying mutations in multiple genes by CRISPR/Cas-mediated genome engineering. Cell 153(4):910–918. https://doi.org/10.1016/j.cell.2013.04.025

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  19. Wang Y, Zhang Z-T, Seo S-O, Lynn P, Lu T, Jin Y-S, Blaschek HP (2016) Bacterial genome editing with CRISPR-Cas9: deletion, integration, single nucleotide modification, and desirable “clean” mutant selection in Clostridium beijerinckii as an example. ACS Synth Biol 5(7):721–732. https://doi.org/10.1021/acssynbio.6b00060

    Article  CAS  PubMed  Google Scholar 

  20. Cobb RE, Wang Y, Zhao H (2015) High-efficiency multiplex genome editing of Streptomyces species using an engineered CRISPR/Cas system. ACS synthetic biology 4(6):723–728. https://doi.org/10.1021/sb500351f

    Article  CAS  PubMed  Google Scholar 

  21. Oh JH, van Pijkeren JP (2014) CRISPR-Cas9-assisted recombineering in Lactobacillus reuteri. Nucleic Acids Res 42(17):e131. https://doi.org/10.1093/nar/gku623

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  22. Douglas GL, Klaenhammer TR (2011) Directed chromosomal integration and expression of the reporter gene gusA3 in Laciobacillus acidophilus NCFM. Appl Environ Microbiol 77(20):7365–7371. https://doi.org/10.1128/AEM.06028-11

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  23. Yang P, Wang J, Qi Q (2015) Prophage recombinases-mediated genome engineering in Lactobacillus plantarum. Microb Cell Fact 14(1):154. https://doi.org/10.1186/s12934-015-0344-z

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  24. van Pijkeren J-P, Britton RA (2012) High efficiency recombineering in lactic acid bacteria. Nucleic Acids Res 40(10):e76. https://doi.org/10.1093/nar/gks147

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  25. Russell WM, Klaenhammer TR (2001) Efficient system for directed integration into the Lactobacillus acidophilus and Lactobacillus gasseri chromosomes via homologous recombination. Appl Environ Microbiol 67(9):4361–4364. https://doi.org/10.1128/AEM.67.9.4361-4364.2001

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  26. Biswas I, Gruss A, Ehrlich SD, Maguin E (1993) High-efficiency gene inactivation and replacement system for gram-positive bacteria. J Bacteriol 175(11):3628–3635. https://doi.org/10.1128/jb.175.11.3628-3635.1993

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  27. Solem C, Defoor E, Jensen PR (2008) Plasmid pCS1966, a new selection/counterselection tool for lactic acid bacterium strain construction based on theoroP gene, encoding an orotate transporter from Lactococcus lactis. Appl Environ Microbiol 74(15):4772–4775. https://doi.org/10.1128/AEM.00134-08

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  28. Goh YJ, Azcárate-Peril MA, O'Flaherty S, Durmaz E, Valence F, Jardin J, Lortal S, Klaenhammer TR (2009) Development and application of a upp-based counterselective gene replacement system for the study of the S-layer protein SlpX of Lactobacillus acidophilus NCFM. Appl Environ Microbiol 75(10):3093–3105. https://doi.org/10.1128/AEM.02502-08

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  29. Martinussen J, Hammer K (1994) Cloning and characterization of upp, a gene encoding uracil phosphoribosyltransferase from Lactococcus lactis. J Bacteriol 176(21):6457–6463. https://doi.org/10.1128/jb.176.21.6457-6463.1994

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  30. Martinussen J, Hammer K (1995) Powerful methods to establish chromosomal markers in Lactococcus lactis: an analysis of pyrimidine salvage pathway mutants obtained by positive selections. Microbiology 141(8):1883–1890. https://doi.org/10.1099/13500872-141-8-1883

    Article  CAS  PubMed  Google Scholar 

  31. Xin Y, Guo T, Mu Y, Kong J (2017) Development of a counterselectable seamless mutagenesis system in lactic acid bacteria. Microb Cell Fact 16(1):116. https://doi.org/10.1186/s12934-017-0731-8

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  32. Lambert JM, Bongers RS, Kleerebezem M (2007) Cre-lox-based system for multiple gene deletions and selectable-marker removal in Lactobacillus plantarum. Appl Environ Microbiol 73(4):1126–1135. https://doi.org/10.1128/AEM.01473-06

    Article  CAS  PubMed  Google Scholar 

  33. Datta S, Costantino N, Zhou X, Court DL (2008) Identification and analysis of recombineering functions from Gram-negative and Gram-positive bacteria and their phages. Proc Natl Acad Sci USA 105(5):1626–1631. https://doi.org/10.1073/pnas.0709089105

    Article  PubMed  PubMed Central  Google Scholar 

  34. Swingle B, Bao Z, Markel E, Chambers A, Cartinhour S (2010) Recombineering using RecTE from Pseudomonas syringae. Appl Environ Microbiol 76(5):4960–4968. https://doi.org/10.1128/AEM.00911-10

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  35. Thomason LC, Sawitzke JA, Li X, Costantino N, Court DL (2014) Recombineering: genetic engineering in bacteria using homologous recombination. Curr Protoc Mol Biol. https://doi.org/10.1002/0471142727.mb0116s106

    Article  PubMed  Google Scholar 

  36. Yin J, Zhu H, Xia L (2015) A new recombineering system for Photorhabdus and Xenorhabdus. Nucleic Acids Res 43(6):e36. https://doi.org/10.1093/nar/gku1336

    Article  CAS  PubMed  Google Scholar 

  37. Van Pijkeren JP (2014) Britton RA Precision genome engineering in lactic acid bacteria. Microb Cell Fact. https://doi.org/10.1186/1475-2859-13-S1-S10

    Article  PubMed  PubMed Central  Google Scholar 

  38. Bunny K, Liu J, Roth J (2002) Phenotypes of lexA mutations in Salmonella enterica: evidence for a Lethal lexA null phenotype due to the Fels-2 Prophage. J Bacteriol 184(22):6235–6249. https://doi.org/10.1128/JB.184.22.6235-6249.2002

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  39. Hu S, Fu J, Huang F, Ding X, Stewart A, Xia L, Zhang Y (2014) Genome engineering of Agrobacterium tumefaciens using the lambda Red recombination system. Appl Microbiol Biotechnol 98(5):2165–2172. https://doi.org/10.1007/s00253-013-5412-x

    Article  CAS  PubMed  Google Scholar 

  40. Xin Y, Guo T, Mu Y, Kong J (2018) Coupling the recombineering to Cre-lox system enables simplified large-scale genome deletion in Lactobacillus casei. Microb Cell Fact 17(1):21. https://doi.org/10.1186/s12934-018-0872-4

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  41. Costantino N, Court DL (2003) Enhanced levels of lambda Red-mediated recombinants in mismatch repair mutants. Proceedings of the National Academy of Science of the United States of America (No.26):15748–15753. https://doi.org/10.1073/pnas.2434959100

  42. Li X, Costantino N, Lu L, Liu D, Watt R, Cheah K, Court D, Huang J (2003) Identification of factors influencing strand bias in oligonucleotide-mediated recombination inEscherichia coli. Nucleic Acids Res 31(22):6674–6687. https://doi.org/10.1093/nar/gkg844

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  43. Sawitzke JA, Costantino N, Li X-t, Thomason LC, Bubunenko M, Court C, Court DL (2011) Probing cellular processes with oligo-mediated recombination and using the knowledge gained to optimize recombineering. J Mol Biol 407(1):45–59. https://doi.org/10.1016/j.jmb.2011.01.030

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  44. Jinek M, Chylinski K, Fonfara I, Hauer M, Doudna JA, Charpentier E (2012) A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity. Science 337(6096):816–821. https://doi.org/10.1126/science.1225829

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  45. Guo L, Xu K, Liu Z, Zhang C, Xin Y, Zhang Z (2015) Assembling the Streptococcus thermophilus clustered regularly interspaced short palindromic repeats (CRISPR) array for multiplex DNA targeting. Anal Biochem 478:131–133. https://doi.org/10.1016/j.ab.2015.02.028

    Article  CAS  PubMed  Google Scholar 

  46. Gasiunas G, Barrangou R, Horvath P, Siksnys V (2012) Cas9-crRNA ribonucleoprotein complex mediates specific DNA cleavage for adaptive immunity in bacteria. Proceedings of the National Academy of Sciences of the United States of America (No.39):E2579-E2586. https://doi.org/10.1073/pnas.1208507109

  47. Qi LS, Larson MH, Gilbert LA, Doudna JA, Weissman JS, Arkin AP, Lim WA (2013) Repurposing CRISPR as an RNA-guided platform for sequence-specific control of gene expression. Cell 152(5):1173–1183. https://doi.org/10.1016/j.cell.2013.02.022

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  48. Pattanayak V, Lin S, Guilinger JP, Ma E, Doudna JA, Liu DR (2013) High-throughput profiling of off-target DNA cleavage reveals RNA-programmed Cas9 nuclease specificity. Nat Biotechnol 31(9):839. https://doi.org/10.1038/nbt.2673

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  49. Cho SW, Kim S, Kim Y, Kweon J, Kim HS, Bae S, Kim J-S (2014) Analysis of off-target effects of CRISPR/Cas-derived RNA-guided endonucleases and nickases. Genome Res 24(1):132–141. https://doi.org/10.1101/gr.162339.113

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  50. Aras RA, Kang J, Tschumi AI, Harasaki Y, Blaser MJ (2003) Extensive repetitive DNA facilitates prokaryotic genome plasticity. Proc Natl Acad Sci 100(23):13579–13584. https://doi.org/10.1073/pnas.1735481100

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  51. Vinay-Lara E, Wang S, Bai L, Phrommao E, Broadbent JR, Steele JL (2016) Lactobacillus casei as a biocatalyst for biofuel production. J Ind Microbiol Biotechnol 43(9):1205–1213. https://doi.org/10.1007/s10295-016-1797-8

    Article  CAS  PubMed  Google Scholar 

  52. Sybesma W, Burgess C, Starrenburg M, van Sinderen D, Hugenholtz J (2004) Multivitamin production in Lactococcus lactis using metabolic engineering. Metab Eng 6(2):109–115. https://doi.org/10.1016/j.ymben.2003.11.002

    Article  CAS  PubMed  Google Scholar 

  53. Song X, Huang H, Xiong Z, Ai L, Yang S (2017) CRISPR-Cas 9(D10A) Nickase-assisted genome editing in Lactobacillus casei. Appl Environ Microbiol. https://doi.org/10.1128/AEM.01259-17

    Article  PubMed  PubMed Central  Google Scholar 

  54. Bravo D, Landete JM (2017) Genetic engineering as a powerful tool to improve probiotic strains. Biotechnol Genet Eng Rev 33(2):173–189. https://doi.org/10.1080/02648725.2017.1408257

    Article  CAS  PubMed  Google Scholar 

  55. Leenay RT, Vento JM, Shah M, Martino ME, Leulier F, Beisel CL (2019) Genome editing with CRISPR-Cas9 in Lactobacillus plantarum revealed that editing outcomes can vary across strains and between methods. Biotechnol J 14(3):1700583. https://doi.org/10.1002/biot.201700583

    Article  CAS  Google Scholar 

  56. Cui L, Bikard D (2016) Consequences of Cas9 cleavage in the chromosome of Escherichia coli. Nucleic Acids Res 44(9):4243–4251. https://doi.org/10.1093/nar/gkw223

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  57. Altenbuchner J (2016) Editing of the Bacillus subtilis genome by the CRISPR-Cas9 system. Appl Environ Microbiol 82(17):5421–5427. https://doi.org/10.1128/AEM.01453-16

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  58. Huang H, Zheng G, Jiang W, Hu H, Lu Y (2015) One-step high-efficiency CRISPR/Cas9-mediated genome editing in Streptomyces. Acta Biochim Biophys Sin 47(4):231–243. https://doi.org/10.1093/abbs/gmv007

    Article  CAS  PubMed  Google Scholar 

  59. Jiang W, Bikard D, Cox D, Zhang F, Marraffini LA (2013) RNA-guided editing of bacterial genomes using CRISPR-Cas systems. Nat Biotechnol 31(3):233. https://doi.org/10.1038/nbt.2508

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  60. Selle K, Klaenhammer TR, Barrangou R (2015) CRISPR-based screening of genomic island excision events in bacteria. Proc Natl Acad Sci USA 112(26):8076–8081. https://doi.org/10.1073/pnas.1508525112

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  61. Vercoe RB, Chang JT, Dy RL, Taylor C, Gristwood T, Clulow JS, Richter C, Przybilski R, Pitman AR, Fineran PC (2013) Cytotoxic chromosomal targeting by CRISPR/Cas systems can reshape bacterial genomes and expel or remodel pathogenicity islands. PLoS Genet 9(4):e1003454. https://doi.org/10.1371/journal.pgen.1003454

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  62. Martino ME, Joncour P, Leenay R, Gervais H, Shah M, Hughes S, Gillet B, Beisel C, Leulier F (2018) Bacterial adaptation to the host's diet is a key evolutionary force shaping Drosophila-Lactobacillus symbiosis. Cell Host Microbe 24(1):109–119.e106. https://doi.org/10.1016/j.chom.2018.06.001

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  63. Siedler S, Rau MH, Bidstrup S, Vento JM, Aunsbjerg SD, Bosma EF, McNair LM, Beisel CL, Neves AR (2020) Competitive exclusion is a major bioprotective mechanism of lactobacilli against fungal spoilage in fermented milk products. Appl Environ Microbiol. https://doi.org/10.1128/AEM.02312-19

    Article  PubMed  PubMed Central  Google Scholar 

  64. Huang H, Song X, Yang S (2019) Development of a RecE/T-assisted CRISPR-Cas9 toolbox for Lactobacillus. Biotechnol J 14(7):1800690. https://doi.org/10.1002/biot.201800690

    Article  CAS  Google Scholar 

  65. van Kessel JC, Hatfull GF (2007) Recombineering in Mycobacterium tuberculosis. Nat Methods 4(2):147–152. https://doi.org/10.1038/nmeth996

    Article  CAS  PubMed  Google Scholar 

  66. Binder S, Siedler S, Marienhagen J, Bott M, Eggeling L (2013) Recombineering in Corynebacterium glutamicum combined with optical nanosensors: a general strategy for fast producer strain generation. Nucleic Acids Res 41(12):6360–6369. https://doi.org/10.1093/nar/gkt312

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  67. Sun Z, Deng A, Hu T, Wu J, Sun Q, Bai H, Zhang G, Wen T (2015) A high-efficiency recombineering system with PCR-based ssDNA in Bacillus subtilis mediated by the native phage recombinase GP35. Appl Microbiol Biotechnol 99(12):5151–5162. https://doi.org/10.1007/s00253-015-6485-5

    Article  CAS  PubMed  Google Scholar 

  68. Aparicio T, Jensen SI, Nielsen AT, de Lorenzo V, Martínez-García E (2016) The Ssr protein (T1E_1405) from Pseudomonas putida DOT-T1E enables oligonucleotide-based recombineering in platform strain P. putida EM42. Biotechnol J 11(10):1309–1319. https://doi.org/10.1002/biot.201600317

    Article  CAS  PubMed  Google Scholar 

  69. Ellis HM, Yu D, DiTizio T (2001) High efficiency mutagenesis, repair, and engineering of chromosomal DNA using single-stranded oligonucleotides. Proc Natl Acad Sci USA 98(12):6742–6746. https://doi.org/10.1073/pnas.121164898

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  70. Zhou D, Jiang Z, Pang Q, Zhu Y, Wang Q, Qi Q (2019) CRISPR/Cas9-assisted seamless genome editing in Lactobacillus plantarum and its application in N-Acetylglucosamine production. Appl Environ Microbiol. https://doi.org/10.1128/AEM.01367-19

    Article  PubMed  PubMed Central  Google Scholar 

  71. Berlec A, Skrlec K, Kocjan J (2018) Single plasmid systems for inducible dual protein expression and for CRISPR-Cas9/CRISPRi gene regulation in lactic acid bacterium Lactococcus lactis. Sci Rep. https://doi.org/10.1038/s41598-018-19402-1

    Article  PubMed  PubMed Central  Google Scholar 

  72. Guo T, Xin Y, Zhang Y, Gu X, Kong J (2019) A rapid and versatile tool for genomic engineering in Lactococcus lactis. Microb Cell Fact 18(1):22. https://doi.org/10.1186/s12934-019-1075-3

    Article  PubMed  PubMed Central  Google Scholar 

  73. van der Els S, James JK, Kleerebezem M, Bron PA (2018) Versatile Cas9-driven subpopulation selection toolbox for Lactococcus lactis. Appl Environ Microbiol 84(8):e02752–e12717. https://doi.org/10.1128/AEM.02752-17

    Article  PubMed  PubMed Central  Google Scholar 

  74. Xiong ZQ, Wei YY, Kong LH, Song X, Yi HX, Ai LZ (2019) Short communication: An inducible CRISPR/dCas9 gene repression system in Lactococcus lactis. J Dairy Sci. https://doi.org/10.3168/jds.2019-17346

    Article  PubMed  Google Scholar 

  75. Zhao C, Shu X, Sun B (2017) Construction of a gene knockdown system based on catalytically inactive (“dead”) Cas9 (dCas9) in Staphylococcus aureus. Appl Environ Microbiol 83(12):e00291–e1217. https://doi.org/10.1128/AEM.00291-17

    Article  PubMed  PubMed Central  Google Scholar 

  76. Kocak DD, Josephs EA, Bhandarkar V, Adkar SS, Kwon JB, Gersbach CA (2019) Increasing the specificity of CRISPR systems with engineered RNA secondary structures. Nat Biotechnol 37(6):657–666. https://doi.org/10.1038/s41587-019-0095-1

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  77. Anzalone AV, Randolph PB, Davis JR, Sousa AA, Koblan LW, Levy JM, Chen PJ, Wilson C, Newby GA, Raguram A, Liu DR (2019) Search-and-replace genome editing without double-strand breaks or donor DNA. Nature 576(7785):149–157. https://doi.org/10.1038/s41586-019-1711-4

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  78. Strecker J, Ladha A, Gardner Z, Schmid-Burgk JL, Makarova KS, Koonin EV, Zhang F (2019) RNA-guided DNA insertion with CRISPR-associated transposases. Science 365(6448):48–53. https://doi.org/10.1126/science.aax9181

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  79. Klompe S, Vo P, Halpin-Healy T, Sternberg S (2019) Transposon-encoded CRISPR–Cas systems direct RNA-guided DNA integration. Nature 571(7764):219–225. https://doi.org/10.1038/s41586-019-1323-z

    Article  CAS  PubMed  Google Scholar 

  80. Walton RT, Christie KA, Whittaker MN, Kleinstiver BP (2020) Unconstrained genome targeting with near-PAMless engineered CRISPR-Cas9 variants. Science 368(6488):290–296. https://doi.org/10.1126/science.aba8853

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  81. Tong Y, Charusanti P, Zhang L, Weber T, Lee SY (2015) CRISPR-Cas9 based engineering of actinomycetal genomes. ACS Synth Biol 4(9):1020–1029. https://doi.org/10.1021/acssynbio.5b00038

    Article  CAS  PubMed  Google Scholar 

  82. Xu T, Li Y, Shi Z, Hemme CL, Li Y, Zhu Y, Van Nostrand JD, He Z, Zhou J (2015) Efficient genome editing in Clostridium cellulolyticum via CRISPR-Cas9 nickase. Appl Environ Microbiol 81(13):4423–4431. https://doi.org/10.1128/AEM.00873-15

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  83. Li Q, Chen J, Minton NP, Zhang Y, Wen Z, Liu J, Yang H, Zeng Z, Ren X, Yang J (2016) CRISPR-based genome editing and expression control systems in Clostridium acetobutylicum and Clostridium beijerinckii. Biotechnol J 11(7):961–972. https://doi.org/10.1002/biot.201600053

    Article  CAS  PubMed  Google Scholar 

Download references

Acknowledgements

This work was supported by the Shanghai Agriculture Applied Technology Development Program, China [Grant No. 2019-02-08-00-07-F01152]; the Natural Science Foundation of China [Grant No. 31871757]; Shanghai Technical Standard Program, China [18DZ2200200]; Shanghai Engineering Research Center of food microbiology program [19DZ2281100].

Author information

Author notes

  1. Xin Song and Xiao-yu Zhang contributed equally to this work.

Authors and Affiliations

  1. Shanghai Engineering Research Center of Food Microbiology, School of Medical Instrument and Food Engineering, University of Shanghai for Science and Technology, Shanghai, 200093, China

    Xin Song, Xiao-yu Zhang, Zhi-qiang Xiong, Xin-xin Liu, Yong-jun Xia & Lian-zhong Ai

  2. College of Bioscience and Bioengineering, Hebei University of Science and Technology, Shijiazhuang, 050018, Hebei, China

    Shi-jie Wang

  3. Shijiazhuang Junlebao Dairy Co. Ltd.,, Shijiazhuang, 050211, China

    Shi-jie Wang

Authors
  1. Xin Song
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Xiao-yu Zhang
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Zhi-qiang Xiong
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Xin-xin Liu
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Yong-jun Xia
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Shi-jie Wang
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Lian-zhong Ai
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Lian-zhong Ai.

Ethics declarations

Conflict of interest

The authors declare that they have no conflicts of interest.

Ethics approval

This article does not contain any studies with human or animal subjects performed by any of the authors.

Consent for participation and publication

Approved by all authors for participation and publication.

Additional information

Publisher's Note

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Song, X., Zhang, Xy., Xiong, Zq. et al. CRISPR–Cas-mediated gene editing in lactic acid bacteria. Mol Biol Rep 47, 8133–8144 (2020). https://doi.org/10.1007/s11033-020-05820-w

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s11033-020-05820-w

Keywords

Search

Navigation