Research Progress of CRISPR -based Bacillus Subtilis System

Siyu Liu; Wenke Zhou

doi:10.54097/g8ec3v45

Authors

Siyu Liu
Wenke Zhou

DOI:

https://doi.org/10.54097/g8ec3v45

Keywords:

Bacillus Subtilis; CRISPR; Metabolic Engineering.

Abstract

As a typical industrial model of food safety, the Bacillus Subtilis has the characteristics of non -pathogenicity, strong extracellular secretion protein ability, and no obvious password preferences, which have been widely used in the field of metabolic engineering. In recent years, with the rapid development of molecular biology and genetic engineering technology, various technologies have been applied to Bacillus Subtilis, thereby synthesizing biological products. This article detailed the application of CRISPR and CRISPR on Bacillus Subtilis, and summarized the biological products of Bacillus Subtilis in related fields and the outlook on its future research direction.

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References

[1] M. Maki, K. T. Leung and W. S. Qin: The prospects of cellulase-producing bacteria for the bioconversion of lignocellulosic biomass, International Journal of Biological Sciences, Vol. 5 (2009) No.5, p.500-516.

[2] M. S. Ou, N. Mohammed, L. O. Ingram and K. T. Shanmugam: Thermophilic Bacillus coagulans Requires Less Cellulases for Simultaneous Saccharification and Fermentation of Cellulose to Products than Mesophilic Microbial Biocatalysts, Applied Biochemistry and Biotechnology, Vol. 155 (2009) No.1-3, p.379-385.

[3] C. Michon, C. M. Kang, S. Karpenko, K. Tanaka, S. Ishikawa and K. Yoshida: A bacterial cell factory converting glucose into scyllo-inositol, a therapeutic agent for Alzheimer's disease, Communications Biology, Vol. 3 (2020) No.1, p.93-99.

[4] K. Tanaka, A. Natsume, S. Ishikawa, S. Takenaka and K. Yoshida: A new-generation of Bacillus subtilis cell factory for further elevated scyllo-inositol production, Microbial Cell Factories, Vol. 16 (2017), p.67-74.

[5] L. Liu, Y. F. Liu, H. D. Shin, R. R. Chen, N. S. Wang, J. H. Li, G. C. Du and J. Chen: Developing Bacillus spp. as a cell factory for production of microbial enzymes and industrially important biochemicals in the context of systems and synthetic biology, Applied Microbiology and Biotechnology, Vol. 97 (2013) No.14, p.6113-6127.

[6] Z. Guan, D. Xue, Abdallah, II, L. Dijkshoorn, R. Setroikromo, G. Y. Lv and W. J. Quax: Metabolic engineering of Bacillus subtilis for terpenoid production, Applied Microbiology and Biotechnology, Vol. 99 (2015) No.22, p.9395-9406.

[7] Y. F. Song, Z. Guan, R. van Merkerk, H. Pramastya, Abdallah, II, R. Setroikromo and W. J. Quax: Production of Squalene in Bacillus subtilis by Squalene Synthase Screening and Metabolic Engineering, Journal of Agricultural and Food Chemistry, Vol. 68 (2015) No.15, p.4447-4455.

[8] K. Zhou, R. Y. Zou, C. Q. Zhang, G. Stephanopoulos and H. P. Too: Optimization of Amorphadiene Synthesis in Bacillus Subtilis Via Transcriptional, Translational, and Media Modulation, Biotechnology and Bioengineering, Vol. 110 (2015) No.9, p.2556-2561.

[9] Y. F. Liu, H. Link, L. Liu, G. C. Du, J. Chen and U. Sauer: A dynamic pathway analysis approach reveals a limiting futile cycle in N-acetylglucosamine overproducing Bacillus subtilis, Nature Communications, Vol. 7 (2016), p.11933-11940.

[10] T. F. Niu, Y. F. Liu, J. H. Li, M. Koffas, G. C. Du, H. S. Alper and L. Liu: Engineering a Glucosamine-6-phosphate Responsive glmS Ribozyme Switch Enables Dynamic Control of Metabolic Flux in Bacillus subtilis for Overproduction of Acetylglucosamine, Acs Synthetic Biology, Vol. 7 (2018) No.10, p.2423-2435.

[11] Y. F. Liu, L. Liu, H. D. Shin, R. R. Chen, J. H. Li, G. C. Du and J. Chen: Pathway engineering of Bacillus subtilis for microbial production of acetylglucosamine, Metabolic Engineering, Vol. 19 (2013), p.107-115.

[12] Y. Gu, X. Q. Lv, Y. F. Liu, J. H. Li, G. C. Du, J. Chen, L. A. Rodrigo and L. Liu: Synthetic redesign of central carbon and redox metabolism for high yield production of acetylglucosamine in Bacillus subtilis, Metabolic Engineering, Vol. 51 (2019), p.59-69.

[13] S. Yang, Y. Wang, C. B. Wei, Q. T. Liu, X. R. Jin, G. C. Du, J. Chen and Z. Kang: A new sRNA-mediated posttranscriptional regulation system for Bacillus subtilis, Biotechnology and Bioengineering, Vol. 115 (2018) No.12, p.2986-2995.

[14] P. Jin, L. P. Zhang, P. H. Yuan, Z. Kang, G. C. Du and J. Chen: Efficient biosynthesis of polysaccharides chondroitin and heparosan by metabolically engineered Bacillus subtilis, Carbohydrate Polymers, Vol. 140 (2018), p.424-432.

[15] S. X. Cui, X. Q. Lv, Y. K. Wu, J. H. Li, G. C. Du, R. Ledesma-Amaro and L. Liu: Engineering a Bifunctional Phr60-Rap60-Spo0A Quorum-Sensing Molecular Switch for Dynamic Fine-Tuning of Menaquinone-7 Synthesis in Bacillus subtilis, Acs Synthetic Biology, Vol. 8 (2019) No.8, p.1826-1837.

[16] S. B. Shi, T. Chen, Z. G. Zhang, X. Chen and X. M. Zhao: Transcriptome analysis guided metabolic engineering of Bacillus subtilis for riboflavin production, Metabolic Engineering, Vol. 11 (2009) No.4-5, p.243-252.

[17] T. Shi, Y. C. Wang, Z. W. Wang, G. L. Wang, D. Y. Liu, J. Fu, T. Chen and X. M. Zhao: Deregulation of purine pathway in Bacillus subtilis and its use in riboflavin biosynthesis, Microbial Cell Factories, Vol. 13 (2014), p.101-116.

[18] Abdallah, II, H. Pramastya, R. Van Merkerk, Sukrasno and W. J. Quax: Metabolic Engineering of Bacillus subtilis Toward Taxadiene Biosynthesis as the First Committed Step for Taxol Production, Frontiers in Microbiology, Vol. 10 (2019), p.218-228.

[19] Y. Gu, X. H. Xu, Y. K. Wu, T. F. Niu, Y. F. Liu, J. H. Li, G. C. Du and L. Liu: Advances and prospects of Bacillus subtilis cellular factories: From rational design to industrial applications, Metabolic Engineering, Vol. 50 (2018) No.4, p.109-121.

[20] Y. F. Liu, L. Liu, J. H. Li, G. C. Du and J. Che: Synthetic Biology Toolbox and Chassis Development in Bacillus subtilis, Trends in Biotechnology, Vol. 37 (2019) No.5, p.548-562.

[21] M. J. Xiang, Q. Kang and D. W. Zhang: Advances on systems metabolic engineering of Bacillus subtilis as a chassis cell, Synthetic and Systems Biotechnology, Vol. 5 (2020) No.4, p.245-251.

[22] S. Yang, Z. Kang, W. L. Cao, G. C. Du and J. Chen: Construction of a novel, stable, food-grade expression system by engineering the endogenous toxin-antitoxin system in Bacillus subtilis, Journal of Biotechnology, Vol. 219 (2022), p.40-47.

[23] L. A. Flórez, S. F. Roppel, A. G. Schmeisky, C. R. Lammers and J. Stülke: A community-curated consensual annotation that is continuously updated: the Bacillus subtilis centred wiki Subti Wiki, Database-the Journal of Biological Databases and Curation, Vol. 2009 (2009), p.9.

[24] T. Ishii, K. Yoshida, G. Terai, Y. Fujita and K. Nakai: DBTBS: a database of Bacillus subtilis promoters and transcription factors, Nucleic acids research, Vol. 29 (2001) No.1, p.278-80.

[25] P. D. Karp, C. A. Ouzounis, C. Moore-Kochlacs, L. Goldovsky, P. Kaipa, D. Ahren, S. Tsoka, N. Darzentas, V. Kunin and N. Lopez-Bigas: Expansion of the BioCyc collection of pathway/genome databases to 160 genomes, Nucleic acids research, Vol. 33 (2005) No.19, p.6083-9.

[26] M. X. Zhang, X. C. Zhao, X. Chen, M. Y. Li and X. D. Wang: Enhancement of riboflavin production in Bacillus subtilis via in vitro and in vivo metabolic engineering of pentose phosphate pathway, Biotechnology Letters, Vol. 43 (2021) No.12, p.2209-2216.

[27] P. Jin, Z. Kang, P. H. Yuan, G. C. Du and J. Chen: Production of specific-molecular-weight hyaluronan by metabolically engineered Bacillus subtilis 168, Metabolic Engineering, Vol. 35 (2016), p.21-30

[28] Y. Wang, J. Weng, R. Waseem, X. H. Yin, R. F. Zhang and Q. R. Shen: Bacillus subtilis genome editing using ssDNA with short homology regions, Nucleic Acids Research 2012, 40: 9

[29] X. Yan, H. J. Yu, Q. Hong and S. P. Li: Crelox system and PCR-based genome engineering in Bacillus subtilis, Applied and Environmental Microbiology, Vol. 74 (2008) No.17, p.5556-62.

[30] P. F. Popp, M. Dotzler, J. Radeck, J. Bartels and T. Mascher: The Bacillus BioBrick Box 2.0: expanding the genetic toolbox for the standardized work with Bacillus subtilis, Scientific Reports, Vol. 7 (2017) No.15058, p.16

[31] A. W. Westbrook, M. Moo-Young and C. P. Chou: Development of a CRISPR-Cas9 Tool Kit for Comprehensive Engineering of Bacillus subtilis, Applied and Environmental Microbiology, Vol. 82 (2016) No.16, p.4876-4895.

[32] K. Zhang, X. G. Duan and J. Wu: Multigene disruption in undomesticated Bacillus subtilis ATCC 6051a using the CRISPR/Cas9 system, Scientific Reports, Vol. 6 (2016), p.27943-27953.

[33] Y. So, S. Y. Park, E. H. Park, S. H. Park, E. J. Kim, J. G. Pan and S. K. Choi: A Highly Efficient CRISPR-Cas9-Mediated Large Genomic Deletion in Bacillus subtilis, Frontiers in Microbiology, Vol. 8 (2017), p.1167-1178.

[34] D. Y. Liu, C. Huang, J. X. Guo, P. J. Zhang, T. Chen, Z. W. Wang and X. M. Zhao: Development and characterization of a CRISPR/Cas9n-based multiplex genome editing system for Bacillus subtilis, Biotechnology for Biofuels, Vol. 12 (2019) No.1, p.197-213.