Multigene disruption in undomesticated Bacillus subtilis ATCC 6051a using the CRISPR/Cas9 system

Scientific Reports

Volumn 6, Issue , 2016, Pages

  Zhang, Kang ^a   Duan, Xuguo ^a   Wu, Jing ^a  

^a JIANGNAN UNIVERSITY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

BACILLUS SUBTILIS; CRISPR CAS SYSTEM; ENZYMOLOGY; GENE DELETION; GENE KNOCKOUT; GENETICS; GROWTH, DEVELOPMENT AND AGING; METABOLIC ENGINEERING; METABOLISM; MICROBIOLOGY; PLASMID; PROCEDURES; STREPTOCOCCUS PYOGENES;

BACILLUS SUBTILIS; CRISPR-CAS SYSTEMS; GENE DELETION; GENE KNOCKOUT TECHNIQUES; INDUSTRIAL MICROBIOLOGY; METABOLIC ENGINEERING; PLASMIDS; STREPTOCOCCUS PYOGENES;

EID: 84975061735     PISSN: None     EISSN: 20452322     Source Type: Journal    
DOI: 10.1038/srep27943     Document Type: Article

References (59)

1. Zeigler, D. R. et al. The origins of 168, W23, and other Bacillus subtilis legacy strains. J Bacteriol. 190, 6983-6995 (2008).
2. Wu, S. C. et al. Functional production and characterization of a fibrin-specific single-chain antibody fragment from Bacillus subtilis: effects of molecular chaperones and a wall-bound protease on antibody fragment production. Appl Environ Microbiol. 68, 3261-3269 (2002).
3. Skolpap, W., Scharer, J. M., Douglas, P. L. & Moo-Young, M. Fed-batch optimization of alpha-amylase and protease-producing Bacillus subtilis using Markov chain methods. Biotechnol Bioeng. 86, 706-717 (2004).
4. Widner, B. et al. Development of marker-free strains of Bacillus subtilis capable of secreting high levels of industrial enzymes. J Ind Microbiol Biot. 25, 204-212 (2000).
5. Coutte, F. et al. Effect of pps disruption and constitutive expression of srfA on surfactin productivity, spreading and antagonistic properties of Bacillus subtilis 168 derivatives. J Appl Microbiol. 109, 480-491 (2010).
6. Clarke, S. & Mandelstam, J. Regulation of stage II of sporulation in Bacillus subtilis. J Gen Appl Microbiol. 133, 2371-2380 (1987).
7. Kawabata, Y., Kimura, K. & Funane, K. Extracellular production of cycloisomaltooligosaccharide glucanotransferase and cyclodextran by a protease-deficient Bacillus subtilis host-vector system. Appl Microbiol Biot. 93, 1877-1884 (2012).
8. Wu, X. C., Lee, W., Tran, L. & Wong, S. L. Engineering a Bacillus subtilis expression-system with a strain deficient in 6 extracellular proteases J Bacteriol. 173, 4952-4958 (1991).
9. Gupta, M. & Rao, K. K. Phosphorylation of DegU is essential for activation of amyE expression in Bacillus subtilis. J Biosci. 39, 747-752 (2014).
10. Konkol, M. A., Blair, K. M. & Kearns, D. B. Plasmid-encoded ComI inhibits competence in the ancestral 3610 strain of Bacillus subtilis. J Bacteriol. 195, 4085-4093 (2013).
11. Jeong, H., Sim, Y. M., Park, S.-H. & Choi, S.-K. Complete genome sequence of Bacillus subtilis strain ATCC 6051a, a potential host for high-level secretion of industrial enzymes. Genome announcements. 3, doi: 10. 1128/genomeA. 00532-15 (2015).
12. Sorek, R., Lawrence, C. M. & Wiedenheft, B. in Annual Review of Biochemistry Vol. 82 (ed R. D. Kornberg) 237-266 (Annual Reviews, 2013).
13. Brouns, S. J. et al. Small CRISPR RNAs guide antiviral defense in prokaryotes. Science. 321, 960-964 (2008).
14. Jiang, W., Bikard, D., Cox, D., Zhang, F. & Marraffini, L. A. RNA-guided editing of bacterial genomes using CRISPR-Cas systems. Nat biotechnol. 31, 233-239 (2013).
15. Deltcheva, E. et al. CRISPR RNA maturation by trans-encoded small RNA and host factor RNase III. Nature. 471, 602-607 (2011).
16. Jinek, M. et al. A Programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity. Science. 337, 816-821 (2012).
17. Cong, L. et al. Multiplex genome engineering using CRISPR/Cas Systems. Science. 339, 819-823 (2013).
18. Mali, P. et al. RNA-guided human genome engineering via cas9. Science. 339, 823-826 (2013).
19. Huang, H., Zheng, G., Jiang, W., Hu, H. & Lu, Y. One-step high-efficiency CRISPR/Cas9-mediated genome editing in Streptomyces. Acta Bioch Bioph Sin. 47, 231-243 (2015).
20. DiCarlo, J. E. et al. Genome engineering in Saccharomyces cerevisiae using CRISPR-Cas systems. Nucleic Acids Res. 41, 4336-4343 (2013).
21. Oh, J.-H. & van Pijkeren, J.-P. CRISPR-Cas9-assisted recombineering in Lactobacillus reuteri. Nucleic Acids Res. 42, doi: 10. 1093/nar/ gku623 (2014).
22. Wang, Y. et al. The CRISPR/Cas System mediates efficient genome engineering in Bombyx mori. Cell Res. 23, 1414-1416 (2013).
23. Yu, Z. et al. Highly efficient genome modifications mediated by CRISPR/Cas9 in Drosophila. Genetics. 195, 289-291 (2013).
24. Shen, B. et al. Generation of gene-modified mice via Cas9/RNA-mediated gene targeting. Cell Res. 23, 720-723 (2013).
25. Ong, R. M. et al. Cloning, extracellular expression and characterization of a predominant beta-CGTase from Bacillus sp G1 in E-coli. J Ind Microbiol Biot. 35, 1705-1714 (2008).
26. Ye, R. Q. et al. High-level secretory production of intact, biologically active staphylokinase from Bacillus subtilis. Biotechnol Bioeng. 62, 87-96 (1999).
27. Weller, G. R. et al. Identification of a DNA nonhomologous end-joining complex in bacteria. Science. 297, 1686-1689 (2002).
28. Yan, X., Yu, H.-J., Hong, Q. & Li, S.-P. Cre/lox system and PCR-based genome engineering in Bacillus subtilis. Appl Environ Micro. 74, 5556-5562 (2008).
29. de Jong, I. G., Veening, J. W. & Kuipers, O. P. Heterochronic phosphorelay gene expression as a source of heterogeneity in Bacillus subtilis spore formation. J Bacteriol. 192, 2053-2067 (2010).
30. Pandey, R. et al. Live cell Imaging of germination and outgrowth of individual Bacillus subtilis spores; the effect of heat stress quantitatively analyzed with spore tracker. Plos One. 8, doi: 10. 1371/journal. pone. 0058972 (2013).
31. Jonas, R. M. & Haldenwang, W. G. Influence of spo mutations on sigma E synthesis in Bacillus subtilis. J Bacteriol. 171, 5226-5228 (1989).
32. Pereira, F. C. et al. The spore differentiation pathway in the enteric pathogen Clostridium difficile. Plos Genet. 9, doi: 10. 1371/journal. pgen. 1003782 (2013).
33. Pishdadian, K., Fimlaid, K. A. & Shen, A. SpoIIID-mediated regulation of sigmaK function during Clostridium difficile sporulation. Mol Microbiol. 95, 189-208 (2015).
34. Feng, J. et al. Recruiting a new strategy to improve levan production in Bacillus amyloliquefaciens. Sci Rep. 5, 13814, doi: 10. 1038/ srep13814 (2015).
35. Pretorius, I. S., de Kock, M. J., Britz, T. J., Potgieter, H. J. & Lategan, P. M. Numerical taxonomy of alpha-amylase producing Bacillus species. J Appl Microbiol. 60, 351-360 (1986).
36. Anders, C., Niewoehner, O., Duerst, A. & Jinek, M. Structural basis of PAM-dependent target DNA recognition by the Cas9 endonuclease. Nature. 513, 569-573 (2014).
37. Fu, Y. et al. High-frequency off-target mutagenesis induced by CRISPR-Cas nucleases in human cells. Nat biotechnol. 31, 822-826 (2013).
38. Morton, J. T., Freed, S. D., Lee, S. W. & Friedberg, I. A large scale prediction of bacteriocin gene blocks suggests a wide functional spectrum for bacteriocins. BMC bioinformatics. 16, doi: 10. 1186/s12859-015-0792-9 (2015).
39. Ran, F. A. et al. Double nicking by RNA-guided CRISPR Cas9 for enhanced genome editing specificity. Cell. 154, 1380-1389 (2013).
40. Willenbacher, J., Rau, J.-T., Rogalla, J., Syldatk, C. & Hausmann, R. Foam-free production of surfactin via anaerobic fermentation of Bacillus subtilis DSM 10(T). Bba-Mol Cell Res. 5, doi: 10. 1186/s13568-015-0107-6 (2015).
41. Vater, J., Wilde, C. & Kell, H. In situ detection of the intermediates in the biosynthesis of surfactin, a lipoheptapeptide from Bacillus subtilis OKB 105, by whole-cell cell matrix-assisted laser desorption/ionization time-of-flight mass spectrometry in combination with mutant analysis. Rapid Commun Mass Sp. 23, 1493-1498 (2009).
42. Ullrich, C., Kluge, B., Palacz, Z. & Vater, J. Cell-free biosynthesis of surfactin, a cyclic lipopeptide produced by Bacillus subtilis. Biochemistry. 30, 6503-6508 (1991).
43. Steller, S. et al. Initiation of surfactin biosynthesis and the role of the SrfD-thioesterase protein. Biochemistry. 43, 11331-11343 (2004).
44. Gutierrez, J., Smith, R. & Pogliano, K. SpoIID-mediated peptidoglycan degradation is required throughout engulfment during Bacillus subtilis sporulation. J Bacteriol. 192, 3174-3186 (2010).
45. Westers, L., Westers, H. & Quax, W. J. Bacillus subtilis as cell factory for pharmaceutical proteins: A biotechnological approach to optimize the host organism. Bba-Mol Cell Res. 1694, 299-310 (2004).
46. Wu, X. C., Ng, S. C., Near, R. I. & Wong & S. L. Efficient production of a functional single-chain antidigoxin antibody via an engineered Bacillus subtilis expression-secretion system. Bio-Technology. 11, 71-76 (1993).
47. Waldeck, J. et al. Targeted deletion of genes encoding extracellular enzymes in Bacillus licheniformis and the impact on the secretion capability. J Biotechnol. 130, 124-132 (2007).
48. Knegtel, R. M. K. et al. Crystallographic studies of cyclodextrin glycosyltransferase from Bacillus-circulans strain-251 with natural substrates and products. J Biol Chem. 270, 29256-29264 (1995).
49. Qi, L. S. et al. Repurposing CRISPR as an RNA-guided platform for sequence-specific control of gene expression. Cell. 152, 1173-1183 (2013).
50. Sleight, S. C. & Sauro, H. M. BioBrick assembly using the in-fusion PCR cloning kit. Methods Mol Biol. 1073, 19-30 (2013).
51. Anagnostopoulos, C. & Spizizen, J. Requirements for transformation in Bacillus subtilis. J Bacteriol. 81, 741-746 (1961).
52. Dempsey, L. A. & Dubnau, D. A. Localization of the replication origin of plasmid pE194. J Bacteriol. 171, 2866-2869 (1989).
53. Ochi, K., Kandala, J. C. & Freese, E. Initiation of Bacillus subtilis sporulation by the stringent response to partial amino acid deprivation. J Biol Chem. 256, 6866-6875 (1981).
54. Kasana, R. C. & Yadav, S. K. Isolation of a psychrotrophic Exiguobacterium sp SKPB5 (MTCC 7803) and characterization of its alkaline protease. Curr Microbiol. 54, 224-229 (2007).
55. Zhang, X.-Z., Yan, X., Cui, Z.-L., Hong, Q. & Li, S.-P. MazF, a novel counter-selectable marker for unmarked chromosomal manipulation in Bacillus subtilis. Nucleic Acids Res. 34, doi: 10. 1093/nar/gkl358 (2006).
56. Makela, M., Korpela, T. & Laakso, S. Colorimetric determination of beta-cyclodextrin: Two assay modifications based on molecular complexation of phenolphtalein. J Biochem Bioph Meth. 14, 85-92 (1987).
57. Penninga, D. et al. The raw starch binding domain of cyclodextrin glycosyltransferase from Bacillus circulans strain 251. J Biol Chem. 271, 32777-32784 (1996).
58. Biswas, I., Gruss, A., Ehrlich, S. D. & Maguin, E. High-efficiency gene inactivation and replacement system for gram-positive bacteria. J Bacteriol. 175, 3628-3635 (1993).
59. Reyrat, J. M., Pelicic, V., Gicquel, B. & Rappuoli, R. Counterselectable markers: Untapped tools for bacterial genetics and pathogenesis. Infection and Immunity. 66, 4011-4017 (1998).