Establishment and application of a CRISPR-Cas12a assisted genome-editing system in Zymomonas mobilis

Microbial Cell Factories

Volumn 18, Issue 1, 2019, Pages

  Shen, Wei ^a   Zhang, Jun ^a   Geng, Binan ^a   Qiu, Mengyue ^a   Hu, Mimi ^a   Yang, Qing ^a   Bao, Weiwei ^a   Xiao, Yubei ^a   Zheng, Yanli ^a   Peng, Wenfang ^a   Zhang, Guimin ^a   Ma, Lixin ^a   Yang, Shihui ^a  

^a HUBEI UNIVERSITY   (China)

Author keywords

Cas12a; CRISPR; Genome engineering; In situ mutagenesis; Lactate; ssDNA recombineering; Zymomonas mobilis

Indexed keywords

ALCOHOL; CRISPR ASSOCIATED PROTEIN; ENDONUCLEASE; GUIDE RNA;

ARTICLE; BACTERIAL GENE; BACTERIAL STRAIN; CRISPR CAS SYSTEM; CRISPR CAS12A SYSTEM; DNA CLEAVAGE; FRANCISELLA NOVICIDA; GENE DELETION; GENE EDITING; GENE EXPRESSION; GENE INSERTION; GENE LOCUS; GENETIC ENGINEERING; GENETIC MANIPULATION; METABOLIC ENGINEERING; NONHUMAN; PHENOTYPE; PROMOTER REGION; REPLICON; STRAIN IMPROVEMENT; ZYMOMONAS MOBILIS; BACTERIAL GENOME; CLUSTERED REGULARLY INTERSPACED SHORT PALINDROMIC REPEAT; ENZYMOLOGY; EVALUATION STUDY; FRANCISELLA; GENETICS; METABOLISM; PLASMID; PROCEDURES; ZYMOMONAS;

CLUSTERED REGULARLY INTERSPACED SHORT PALINDROMIC REPEATS; CRISPR-CAS SYSTEMS; ENDONUCLEASES; FRANCISELLA; GENE EDITING; GENOME, BACTERIAL; PLASMIDS; RNA, GUIDE; ZYMOMONAS;

EID: 85072922690     PISSN: None     EISSN: 14752859     Source Type: Journal    
DOI: 10.1186/s12934-019-1219-5     Document Type: Article

References (52)

1. Wang X, He Q, Yang Y, Wang J, Haning K, Hu Y, Wu B, He M, Zhang Y, Bao J, et al. Advances and prospects in metabolic engineering of Zymomonas mobilis. Metab Eng. 2018;50:57-73.
2. Yang S, Fei Q, Zhang Y, Contreras LM, Utturkar SM, Brown SD, Himmel ME, Zhang M. Zymomonas mobilis as a model system for production of biofuels and biochemicals. Microb Biotechnol. 2016;9(6):699-717.
3. Panesar PS, Marwaha SS, Kennedy JF. Zymomonas mobilis: an alternative ethanol producer. J Chem Technol Biot. 2006;81(4):623-35.
4. Wu B, Qin H, Yang Y, Duan G, Yang S, Xin F, Zhao C, Shao H, Wang Y, Zhu Q, et al. Engineered Zymomonas mobilis tolerant to acetic acid and low pH via multiplex atmospheric and room temperature plasma mutagenesis. Biotechnol Biofuels. 2019;12:10.
5. Zhang M, Eddy C, Deanda K, Finkelstein M, Picataggio S. Metabolic engineering of a pentose metabolism pathway in ethanologenic Zymomonas mobilis. Science. 1995;267(5195):240-3.
6. Xia J, Yang Y, Liu CG, Yang S, Bai FW. Engineering Zymomonas mobilis for robust cellulosic ethanol production. Trends Biotechnol. 2019;37(9):960-72.
7. Agrawal M, Wang Y, Chen RR. Engineering efficient xylose metabolism into an acetic acid-tolerant Zymomonas mobilis strain by introducing adaptation-induced mutations. Biotechnol Lett. 2012;34(10):1825-32.
8. Chacon-Vargas K, Chirino AA, Davis MM, Debler SA, Haimer WR, Wilbur JJ, Mo X, Worthing BW, Wainblat EG, Zhao S, et al. Genome sequence of Zymomonas mobilis subsp. mobilis NRRL B-1960. Genome Announc. 2017;5(30):e00562.
9. Yang S, Vera JM, Grass J, Savvakis G, Moskvin OV, Yang Y, McIlwain SJ, Lyu Y, Zinonos I, Hebert AS, et al. Complete genome sequence and the expression pattern of plasmids of the model ethanologen Zymomonas mobilis ZM4 and its xylose-utilizing derivatives 8b and 2032. Biotechnol Biofuels. 2018;11:125.
10. Chen C, Wu L, Cao Q, Shao H, Li X, Zhang Y, Wang H, Tan X. Genome comparison of different Zymomonas mobilis strains provides insights on conservation of the evolution. PLoS ONE. 2018;13(4):e0195994.
11. Zhao N, Pan Y, Liu H, Cheng Z. Draft Genome Sequence of Zymomonas mobilis ZM481 (ATCC 31823). Genome Announc. 2016;4(2):e00193.
12. Kouvelis VN, Teshima H, Bruce D, Detter C, Tapia R, Han C, Tampakopoulou VO, Goodwin L, Woyke T, Kyrpides NC, et al. Finished genome of Zymomonas mobilis subsp. mobilis strain CP4, an applied ethanol producer. Genome Announc. 2014;2(1):e00845.
13. Zhao N, Bai Y, Zhao XQ, Yang ZY, Bai FW. Draft genome sequence of the flocculating Zymomonas mobilis strain ZM401 (ATCC 31822). J Bacteriol. 2012;194(24):7008-9.
14. Yang S, Pappas KM, Hauser LJ, Land ML, Chen GL, Hurst GB, Pan C, Kouvelis VN, Typas MA, Pelletier DA, et al. Improved genome annotation for Zymomonas mobilis. Nat Biotechnol. 2009;27(10):893-4.
15. Joung J, Konermann S, Gootenberg JS, Abudayyeh OO, Platt RJ, Brigham MD, Sanjana NE, Zhang F. Genome-scale CRISPR-Cas9 knockout and transcriptional activation screening. Nat Protoc. 2017;12(4):828-63.
16. Pappas KM, Galani I, Typas MA. Transposon mutagenesis and strain construction in Zymomonas mobilis. J Appl Microbiol. 1997;82(3):379-88.
17. Wu Y, Li T, Cao Q, Li X, Zhang Y, Tan X. RecET recombination system driving chromosomal target gene replacement in Zymomonas mobilis. Electron J Biotechnol. 2017;30:118-24.
18. Yan MY, Yan HQ, Ren GX, Zhao JP, Guo XP, Sun YC. CRISPR-Cas12a-Assisted recombineering in bacteria. Appl Environ Microbiol. 2017;83(17):e00947.
19. Zhang J, Hong W, Zong W, Wang P, Wang Y. Markerless genome editing in Clostridium beijerinckii using the CRISPR-Cpf1 system. J Biotechnol. 2018;284:27-30.
20. Barrangou R, Doudna JA. Applications of CRISPR technologies in research and beyond. Nat Biotechnol. 2016;34(9):933-41.
21. Koonin EV, Makarova KS. CRISPR-Cas: an adaptive immunity system in prokaryotes. F1000 Biol Rep. 2009;1:95.
22. Marraffini LA. CRISPR-Cas immunity in prokaryotes. Nature. 2015;526(7571):55-61.
23. Sorek R, Lawrence CM, Wiedenheft B. CRISPR-mediated adaptive immune systems in bacteria and archaea. Annu Rev Biochem. 2013;82:237-66.
24. Yao R, Liu D, Jia X, Zheng Y, Liu W, Xiao Y. CRISPR-Cas9/Cas12a biotechnology and application in bacteria. Synth Syst Biotechnol. 2018;3(3):135-49.
25. Bayat H, Modarressi MH, Rahimpour A. The conspicuity of CRISPR-Cpf1 system as a significant breakthrough in genome editing. Curr Microbiol. 2018;75(1):107-15.
26. Mohanraju P, Makarova KS, Zetsche B, Zhang F, Koonin EV, van der Oost J. Diverse evolutionary roots and mechanistic variations of the CRISPR-Cas systems. Science. 2016;353(6299):5147.
27. Marchisio MA, Huang Z. CRISPR-Cas type II-based synthetic biology applications in eukaryotic cells. RNA Biol. 2017;14(10):1286-93.
28. Su T, Liu F, Gu P, Jin H, Chang Y, Wang Q, Liang Q, Qi Q. A CRISPR-Cas9 assisted non-homologous end-joining strategy for one-step engineering of bacterial genome. Sci Rep. 2016;6:37895.
29. Shmakov S, Smargon A, Scott D, Cox D, Pyzocha N, Yan W, Abudayyeh OO, Gootenberg JS, Makarova KS, Wolf YI, et al. Diversity and evolution of class 2 CRISPR-Cas systems. Nat Rev Microbiol. 2017;15(3):169-82.
30. Peters Jason M, Colavin A, Shi H, Czarny Tomasz L, Larson Matthew H, Wong S, Hawkins John S, Lu Candy HS, Koo B-M, Marta E, et al. A comprehensive, CRISPR-based functional analysis of essential genes in bacteria. Cell. 2016;165(6):1493-506.
31. Jiang Y, Qian F, Yang J, Liu Y, Dong F, Xu C, Sun B, Chen B, Xu X, Li Y, et al. CRISPR-Cpf1 assisted genome editing of Corynebacterium glutamicum. Nat Commun. 2017;8:15179.
32. Ungerer J, Pakrasi HB. Cpf1 is a versatile tool for CRISPR genome editing across diverse species of Cyanobacteria. Sci Rep. 2016;6:39681.
33. Cao QH, Shao HH, Qiu H, Li T, Zhang YZ, Tan XM. Using the CRISPR/Cas9 system to eliminate native plasmids of Zymomonas mobilis ZM4. Biosci Biotechnol Biochem. 2017;81(3):453-9.
34. Zetsche B, Gootenberg JS, Abudayyeh OO, Slaymaker IM, Makarova KS, Essletzbichler P, Volz SE, Joung J, van der Oost J, Regev A, et al. Cpf1 is a single RNA-guided endonuclease of a class 2 CRISPR-Cas system. Cell. 2015;163(3):759-71.
35. Yamano T, Nishimasu H, Zetsche B, Hirano H, Slaymaker IM, Li Y, Fedorova I, Nakane T, Makarova KS, Koonin EV, et al. Crystal structure of Cpf1 in complex with guide RNA and target DNA. Cell. 2016;165(4):949-62.
36. Gao P, Yang H, Rajashankar KR, Huang Z, Patel DJ. Type V CRISPR-Cas Cpf1 endonuclease employs a unique mechanism for crRNA-mediated target DNA recognition. Cell Res. 2016;26(8):901-13.
37. Leenay RT, Maksimchuk KR, Slotkowski RA, Agrawal RN, Gomaa AA, Briner AE, Barrangou R, Beisel CL. Identifying and visualizing functional PAM diversity across CRISPR-Cas systems. Mol Cell. 2016;62(1):137-47.
38. Swarts DC, van der Oost J, Jinek M. Structural basis for guide RNA processing and seed-dependent DNA targeting by CRISPR-Cas12a. Mol Cell. 2017;66(2):221-33.
39. Woolston BM, Emerson DF, Currie DH, Stephanopoulos G. Rediverting carbon flux in Clostridium ljungdahlii using CRISPR interference (CRISPRi). Metab Eng. 2018;48:243-53.
40. Zhang X, Wang J, Cheng Q, Zheng X, Zhao G, Wang J. Multiplex gene regulation by CRISPR-ddCpf1. Cell Discov. 2017;3:17018.
41. Yang Y, Shen W, Huang J, Li R, Xiao Y, Wei H, Chou YC, Zhang M, Himmel ME, Chen S, et al. Prediction and characterization of promoters and ribosomal binding sites of Zymomonas mobilis in system biology era. Biotechnol Biofuels. 2019;12:52.
42. Browne GM, Skotnicki ML, Goodman AE, Rogers PL. Transformation of Zymomonas mobilis by a hybrid plasmid. Plasmid. 1984;12(3):211-4.
43. Talas A, Kulcsar PI, Weinhardt N, Borsy A, Toth E, Szebenyi K, Krausz SL, Huszar K, Vida I, Sturm A, et al. A convenient method to pre-screen candidate guide RNAs for CRISPR/Cas9 gene editing by NHEJ-mediated integration of a 'self-cleaving' GFP-expression plasmid. DNA Res. 2017;24(6):609-21.
44. Kerr AL, Jeon YJ, Svenson CJ, Rogers PL, Neilan BA. DNA restriction-modification systems in the ethanologen, Zymomonas mobilis ZM4. Appl Microbiol Biotechnol. 2011;89(3):761-9.
45. Wang X, He Q, Yang Y, Wang J, Haning K, Hu Y, Wu B, He M, Zhang Y, Bao J, et al. Advances and prospects in metabolic engineering of Zymomonas mobilis. Metab Eng. 2018;50:57-73.
46. Yang S, Pelletier DA, Lu TY, Brown SD. The Zymomonas mobilis regulator hfq contributes to tolerance against multiple lignocellulosic pretreatment inhibitors. BMC Microbiol. 2010;10(1):1-11.
47. Yang S, Tschaplinski TJ, Engle NL, Carroll SL, Martin SL, Davison BH, Palumbo AV, Rodriguez M Jr, Brown SD. Transcriptomic and metabolomic profiling of Zymomonas mobilis during aerobic and anaerobic fermentations. BMC Genomics. 2009;10:34.
48. Yang S, Mohagheghi A, Franden MA, Chou YC, Chen X, Dowe N, Himmel ME, Zhang M. Metabolic engineering of Zymomonas mobilis for 2,3-butanediol production from lignocellulosic biomass sugars. Biotechnol Biofuels. 2016;9(1):189.
49. Hakkila K, Maksimow M, Rosengren A, Karp M, Virta M. Monitoring promoter activity in a single bacterial cell by using green and red fluorescent proteins. J Microbiol Methods. 2003;54(1):75-9.
50. Chudakov DM, Matz MV, Lukyanov S, Lukyanov KA. Fluorescent proteins and their applications in imaging living cells and tissues. Physiol Rev. 2010;90(3):1103-63.
51. Shaner NC, Campbell RE, Steinbach PA, Giepmans BN, Palmer AE, Tsien RY. Improved monomeric red, orange and yellow fluorescent proteins derived from Discosoma sp. red fluorescent protein. Nat Biotechnol. 2004;22(12):1567-72.
52. Telford WG, Hawley T, Subach F, Verkhusha V, Hawley RG. Flow cytometry of fluorescent proteins. Methods. 2012;57(3):318-30.