Using the CRISPR/Cas9 system to eliminate native plasmids of Zymomonas mobilis ZM4Footnote

Abbreviations: CRISPR, clustered regularly interspaced short palindromic repeats; sgRNA, single-guide RNA; tracrRNA, trans-activating CRISPR RNA; crRNA, CRISPR RNA; Cas, CRISPR-associated; PAM, Protospacer-Adjacent Motif; qPCR, quantitative (real time) PCR; RMG, Rich medium with glucose.

References

• Lee KY, Park JM, Kim TY, et al. The genome-scale metabolic network analysis of Zymomonas mobilis ZM4 explains physiological features and suggests ethanol and succinic acid production strategies. Microb. Cell Fact. 2010;9:2–12.10.1186/1475-2859-9-94
   PubMed Web of Science ®Google Scholar
• Seo JS, Chong H, Park HS, et al. The genome sequence of the ethanologenic bacterium Zymomonas mobilis ZM4. Nat. Biotechnol. 2005;23:63–68.10.1038/nbt1045
   PubMed Web of Science ®Google Scholar
• He MX, Wu B, Shui ZX, et al. Transcriptome profiling of Zymomonas mobilis under ethanol stress. Appl. Microbiol. Biotechnol. 2012;95:189–199.10.1007/s00253-012-4155-4
   PubMed Web of Science ®Google Scholar
• He MX, Wu B, Qin H, et al. Zymomonas mobilis: a novel platform for future biorefineries. Biotechnol. Biofuels. 2014;7:2–15.10.1186/1754-6834-7-101
   PubMed Web of Science ®Google Scholar
• Ran FA, Hsu PD, Lin CY, et al. Genome engineering using the CRISPR-Cas9 system. Cell. 2013;154:1380–1389.10.1016/j.cell.2013.08.021
   PubMed Web of Science ®Google Scholar
• Shen B, Zhang J, Wu H, et al. Generation of gene-modified mice via Cas9/RNA-mediated gene targeting. Cell Res. 2013;23:720–723.10.1038/cr.2013.46
   PubMed Web of Science ®Google Scholar
• Jiang W, Bikard D, Cox D, et al. RNA-guided editing of bacterial genomes using CRISPR-Cas systems. Nat. Biotechnol. 2013;31:233–239.10.1038/nbt.2508
   PubMed Web of Science ®Google Scholar
• Jinek M, Chylinski K, Fonfara I, et al. A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity. Science. 2012;337:816–821.10.1126/science.1225829
   PubMed Web of Science ®Google Scholar
• Fineran PC, Gerritzen MJ, Suárez-Diez M, et al. Degenerate target sites mediate rapid primed CRISPR adaptation. Proc. Natl. Acad. Sci. 2014;111:E1629–E1638.10.1073/pnas.1400071111
   PubMed Web of Science ®Google Scholar
• Garneau JE, Dupuis M-È, Villion M, et al. The CRISPR/Cas bacterial immune system cleaves bacteriophage and plasmid DNA. Nature. 2010;468:67–71.10.1038/nature09523
   PubMed Web of Science ®Google Scholar
• Swarts DC, Mosterd C, van Passel M, et al. CRISPR interference directs strand specific spacer acquisition. PLoS ONE. 2012;7:e35888.10.1371/journal.pone.0035888
   PubMed Web of Science ®Google Scholar
• Bikard D, Euler CW, Jiang W, et al. Exploiting CRISPR-Cas nucleases to produce sequence-specific antimicrobials, Nat. Biotechnol. 2014, 32:1146–1150.
   PubMed Web of Science ®Google Scholar
• Goodman Amanda E., Rogers Peter L., et al. Minimal medium for isolation of auxotrophic Zymomonas mutants. Appl. Environ. Microbiol. 1982;44:496–498.
   PubMed Web of Science ®Google Scholar
• Sambrook J, David WR, David WR. Molecular cloning: a laboratory manual (3-volume set). Cold Spring Harbor, NY: Cold spring harbor laboratory press; 2001;999.
   Google Scholar
• Cao QH, Li T, Shao HH, et al. Three new shuttle vectors for heterologous expression in Zymomonas mobilis. Electron. J. Biotechnol. 2016;19:33–40.http://dx.doi.org/10.1016/j.ejbt.2015.11.004
   Web of Science ®Google Scholar
• Wang GJ, Wang ZS, Zhang YW, et al. Cloning and expression of amyE gene from Bacillus subtilis in Zymomonas mobilis and direct production of ethanol from soluble starch. Biotechnol. Bioproc. Eng. 2012;17:780–786.10.1007/s12257-011-0490-z
   Web of Science ®Google Scholar
• Afendra AS, Vartholomatos G, Arvanitis N, et al. Characterization of the mobilization region of the Zymomonas mobilis ATCC10988 plasmid pZMO3. Plasmid. 1999;41:73–77.10.1006/plas.1998.1374
   PubMed Web of Science ®Google Scholar
• Arvanitis N, Pappas KM, Kolios G, et al. Characterization and replication properties of the Zymomonas mobilis ATCC 10988 plasmids pZMO1 and pZMO2. Plasmid. 2000;44:127–137.10.1006/plas.2000.1480
   PubMed Web of Science ®Google Scholar
• Li MZ, Elledge SJ. Harnessing homologous recombination in vitro to generate recombinant DNA via SLIC. Nat. Methods. 2007;4:251–256.10.1038/nmeth1010
   PubMed Web of Science ®Google Scholar
• Wang GJ, He C, Zhang YZ. Improvement of the sequence and ligation independent cloning (SLIC) method. J. Sichuan Univ. (Nat. Sci. Ed). 2010;47:893–898.
   Google Scholar
• Datsenko KA, Wanner BL. One-step inactivation of chromosomal genes in Escherichia coli K-12 using PCR products. Proc. Natl. Acad. Sci. 2000;97:6640–6645.10.1073/pnas.120163297
   PubMed Web of Science ®Google Scholar
• Fujii W, Kawasaki K, Sugiura K, et al. Efficient generation of genome-modified mice via offset-nicking by CRISPR/Cas system. Nucleic Acids Res. 2013;41:e187–e187.10.1093/nar/gkt772
   PubMed Web of Science ®Google Scholar
• Škulj M, Okršlar V, Jalen Š, et al. Improved determination of plasmid copy number using quantitative real-time PCR for monitoring fermentation processes. Microb. Cell Fact. 2008;7:1–12.
   PubMed Web of Science ®Google Scholar
• So LY, Chen WY, Lacap-Bugler DC, et al. pZMO7-Derived shuttle vectors for heterologous protein expression and proteomic applications in the ethanol-producing bacterium Zymomonas mobilis. BMC Microbiol. 2014;14:2–16.10.1186/1471-2180-14-68
   PubMed Web of Science ®Google Scholar
• Livak KJ, Schmittgen TD. Analysis of relative gene expression data using real-time quantitative pcr and the 2−ΔΔCT method. Methods. 2001;25:402–408.10.1006/meth.2001.1262
   PubMed Web of Science ®Google Scholar
• Yang M, Li X, Bu C, et al. Pyruvate decarboxylase and alcohol dehydrogenase overexpression in Escherichia coli resulted in high ethanol production and rewired metabolic enzyme networks. World J. Microb. Biot. 2014;30:2871–2883.10.1007/s11274-014-1713-1
   PubMed Web of Science ®Google Scholar
• Khan SA. Rolling-circle replication of bacterial plasmids. Microbiol. Mol. Biol. Rev. 1997;61:442–455.
   PubMed Web of Science ®Google Scholar