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Qian J, Wang Y, Hu Z, Shi T, Wang Y, Ye C, Huang H. Bacillus sp. as a microbial cell factory: Advancements and future prospects. Biotechnol Adv 2023; 69:108278. [PMID: 37898328 DOI: 10.1016/j.biotechadv.2023.108278] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Revised: 09/27/2023] [Accepted: 10/25/2023] [Indexed: 10/30/2023]
Abstract
Bacillus sp. is one of the most distinctive gram-positive bacteria, able to grow efficiently using cheap carbon sources and secrete a variety of useful substances, which are widely used in food, pharmaceutical, agricultural and environmental industries. At the same time, Bacillus sp. is also recognized as a safe genus with a relatively clear genetic background, which is conducive to the industrial production of target metabolites. In this review, we discuss the reasons why Bacillus sp. has been so extensively studied and summarize its advances in systems and synthetic biology, engineering strategies to improve microbial cell properties, and industrial applications in several metabolic engineering applications. Finally, we present the current challenges and possible solutions to provide a reliable basis for Bacillus sp. as a microbial cell factory.
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Affiliation(s)
- Jinyi Qian
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing 210023, PR China
| | - Yuzhou Wang
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing 210023, PR China
| | - Zijian Hu
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing 210023, PR China
| | - Tianqiong Shi
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing 210023, PR China.
| | - Yuetong Wang
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing 210023, PR China.
| | - Chao Ye
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing 210023, PR China.
| | - He Huang
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing 210023, PR China.
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Xue F, Ma X, Luo C, Li D, Shi G, Li Y. Construction of a bacteriophage-derived recombinase system in Bacillus licheniformis for gene deletion. AMB Express 2023; 13:89. [PMID: 37633871 PMCID: PMC10460339 DOI: 10.1186/s13568-023-01589-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2023] [Accepted: 07/29/2023] [Indexed: 08/28/2023] Open
Abstract
Bacillus licheniformis and its related strains have found extensive applications in diverse industries, agriculture, and medicine. However, the current breeding methods for this strain primarily rely on natural screening and traditional mutagenesis. The limited availability of efficient genetic engineering tools, particularly recombination techniques, has hindered further advancements in its applications. In this study, we conducted a comprehensive investigation to identify and characterize a recombinase, RecT, derived from a Bacillus phage. Remarkably, the recombinase exhibited a 105-fold enhancement in the recombination efficiency of the strain. To facilitate genome editing, we developed a system based on the conditional expression of RecT using a rhamnose-inducible promoter (Prha). The efficacy of this system was evaluated by deleting the amyL gene, which encodes an α-amylase. Our findings revealed that the induction time and concentration of rhamnose, along with the generation time of the strain, significantly influenced the editing efficiency. Optimal conditions for genome editing were determined as follows: the wild-type strain was initially transformed with the genome editing plasmid, followed by cultivation and induction with 1.5% rhamnose for 8 h. Subsequently, the strain was further cultured for an additional 24 h, equivalent to approximately three generations. Consequently, the recombination efficiency reached an impressive 16.67%. This study represents a significant advancement in enhancing the recombination efficiency of B. licheniformis through the utilization of a RecT-based recombination system. Moreover, it provides a highly effective genome editing tool for genetic engineering applications in this strain.
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Affiliation(s)
- Fang Xue
- Key Laboratory of Chinese Cigar Fermentation, Cigar Technology Innovation Center of China Tobacco, Tobacco Sichuan Industrial Co., Ltd, Chengdu, 610000, P. R. China
| | - Xufan Ma
- National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, Jiangnan University, 1800 Lihu Avenue, Wuxi, Jiangsu, 214122, P. R. China
- Jiangsu Provincial Engineering Research Center for Bioactive Product Processing, Jiangnan University, 1800 Lihu Avenue, Wuxi, Jiangsu, 214122, P. R. China
| | - Cheng Luo
- Key Laboratory of Chinese Cigar Fermentation, Cigar Technology Innovation Center of China Tobacco, Tobacco Sichuan Industrial Co., Ltd, Chengdu, 610000, P. R. China
| | - Dongliang Li
- Key Laboratory of Chinese Cigar Fermentation, Cigar Technology Innovation Center of China Tobacco, Tobacco Sichuan Industrial Co., Ltd, Chengdu, 610000, P. R. China
| | - Guiyang Shi
- National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, Jiangnan University, 1800 Lihu Avenue, Wuxi, Jiangsu, 214122, P. R. China
- Jiangsu Provincial Engineering Research Center for Bioactive Product Processing, Jiangnan University, 1800 Lihu Avenue, Wuxi, Jiangsu, 214122, P. R. China
| | - Youran Li
- National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, Jiangnan University, 1800 Lihu Avenue, Wuxi, Jiangsu, 214122, P. R. China.
- Jiangsu Provincial Engineering Research Center for Bioactive Product Processing, Jiangnan University, 1800 Lihu Avenue, Wuxi, Jiangsu, 214122, P. R. China.
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He H, Yu Q, Ding Z, Zhang L, Shi G, Li Y. Biotechnological and food synthetic biology potential of platform strain: Bacillus licheniformis. Synth Syst Biotechnol 2023; 8:281-291. [PMID: 37090063 PMCID: PMC10119484 DOI: 10.1016/j.synbio.2023.03.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Revised: 03/22/2023] [Accepted: 03/22/2023] [Indexed: 04/01/2023] Open
Abstract
Bacillus licheniformis is one of the most characteristic Gram-positive bacteria. Its unique genetic background and safety characteristics make it have important biologic applications in the food industry, including, the biosynthesis of high value-added bioproducts, probiotic functions, biological treatment of wastes derived from food production, etc. In this review, these recent advances are summarized and presented systematically for the first time. In addition, we highlight synthetic biology strategies as a potential driver of developing this strain for wider and more efficient application in the food industry. Finally, we present the current challenges faced and provide our unique perspective on relevant future research directions. In summary, this review will provide an illuminating and comprehensive perspective that will allow an in-depth understanding of B. licheniformis and promote its more effective development in the food industry.
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Song Y, He S, Jopkiewicz A, Setroikromo R, van Merkerk R, Quax WJ. Development and application of CRISPR-based genetic tools in Bacillus species and Bacillus phages. J Appl Microbiol 2022; 133:2280-2298. [PMID: 35797344 PMCID: PMC9796756 DOI: 10.1111/jam.15704] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 07/02/2022] [Accepted: 07/06/2022] [Indexed: 01/07/2023]
Abstract
Recently, the clustered regularly interspaced short palindromic repeats (CRISPR) system has been developed into a precise and efficient genome editing tool. Since its discovery as an adaptive immune system in prokaryotes, it has been applied in many different research fields including biotechnology and medical sciences. The high demand for rapid, highly efficient and versatile genetic tools to thrive in bacteria-based cell factories accelerates this process. This review mainly focuses on significant advancements of the CRISPR system in Bacillus subtilis, including the achievements in gene editing, and on problems still remaining. Next, we comprehensively summarize this genetic tool's up-to-date development and utilization in other Bacillus species, including B. licheniformis, B. methanolicus, B. anthracis, B. cereus, B. smithii and B. thuringiensis. Furthermore, we describe the current application of CRISPR tools in phages to increase Bacillus hosts' resistance to virulent phages and phage genetic modification. Finally, we suggest potential strategies to further improve this advanced technique and provide insights into future directions of CRISPR technologies for rendering Bacillus species cell factories more effective and more powerful.
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Affiliation(s)
- Yafeng Song
- Department of Chemical and Pharmaceutical BiologyGroningen Research Institute of Pharmacy, University of GroningenGroningenThe Netherlands,Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern ChinaInstitute of Microbiology, Guangdong Acadamy of SciencesGuangzhouChina
| | - Siqi He
- Department of Chemical and Pharmaceutical BiologyGroningen Research Institute of Pharmacy, University of GroningenGroningenThe Netherlands
| | - Anita Jopkiewicz
- Department of Chemical and Pharmaceutical BiologyGroningen Research Institute of Pharmacy, University of GroningenGroningenThe Netherlands
| | - Rita Setroikromo
- Department of Chemical and Pharmaceutical BiologyGroningen Research Institute of Pharmacy, University of GroningenGroningenThe Netherlands
| | - Ronald van Merkerk
- Department of Chemical and Pharmaceutical BiologyGroningen Research Institute of Pharmacy, University of GroningenGroningenThe Netherlands
| | - Wim J. Quax
- Department of Chemical and Pharmaceutical BiologyGroningen Research Institute of Pharmacy, University of GroningenGroningenThe Netherlands
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Zocca VFB, Corrêa GG, Lins MRDCR, de Jesus VN, Tavares LF, Amorim LADS, Kundlatsch GE, Pedrolli DB. The CRISPR toolbox for the gram-positive model bacterium Bacillus subtilis. Crit Rev Biotechnol 2021; 42:813-826. [PMID: 34719304 DOI: 10.1080/07388551.2021.1983516] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
CRISPR has revolutionized the way we engineer genomes. Its simplicity and modularity have enabled the development of a great number of tools to edit genomes and to control gene expression. This powerful technology was first adapted to Bacillus subtilis in 2016 and has been intensely upgraded since then. Many tools have been successfully developed to build a CRISPR toolbox for this Gram-positive model and important industrial chassis. The toolbox includes tools, such as double-strand and single-strand cutting CRISPR for point mutation, gene insertion, and gene deletion up to 38 kb. Moreover, catalytic dead Cas proteins have been used for base editing, as well as for the control of gene expression (CRISPRi and CRISPRa). Many of these tools have been used for multiplex CRISPR with the most successful one targeting up to six loci simultaneously for point mutation. However, tools for efficient multiplex CRISPR for other functionalities are still missing in the toolbox. CRISPR engineering has already resulted in efficient protein and metabolite-producing strains, demonstrating its great potential. In this review, we cover all the important additions made to the B. subtilis CRISPR toolbox since 2016, and strain developments fomented by the technology.
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Affiliation(s)
- Vitoria Fernanda Bertolazzi Zocca
- Department of Bioprocess Engineering and Biotechnology, School of Pharmaceutical Sciences, Universidade Estadual Paulista (UNESP), Araraquara, Brazil
| | - Graciely Gomes Corrêa
- Department of Bioprocess Engineering and Biotechnology, School of Pharmaceutical Sciences, Universidade Estadual Paulista (UNESP), Araraquara, Brazil
| | - Milca Rachel da Costa Ribeiro Lins
- Department of Bioprocess Engineering and Biotechnology, School of Pharmaceutical Sciences, Universidade Estadual Paulista (UNESP), Araraquara, Brazil
| | - Victor Nunes de Jesus
- Department of Bioprocess Engineering and Biotechnology, School of Pharmaceutical Sciences, Universidade Estadual Paulista (UNESP), Araraquara, Brazil
| | - Leonardo Ferro Tavares
- Department of Bioprocess Engineering and Biotechnology, School of Pharmaceutical Sciences, Universidade Estadual Paulista (UNESP), Araraquara, Brazil
| | - Laura Araujo da Silva Amorim
- Department of Bioprocess Engineering and Biotechnology, School of Pharmaceutical Sciences, Universidade Estadual Paulista (UNESP), Araraquara, Brazil
| | - Guilherme Engelberto Kundlatsch
- Department of Bioprocess Engineering and Biotechnology, School of Pharmaceutical Sciences, Universidade Estadual Paulista (UNESP), Araraquara, Brazil
| | - Danielle Biscaro Pedrolli
- Department of Bioprocess Engineering and Biotechnology, School of Pharmaceutical Sciences, Universidade Estadual Paulista (UNESP), Araraquara, Brazil
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Muras A, Romero M, Mayer C, Otero A. Biotechnological applications of Bacillus licheniformis. Crit Rev Biotechnol 2021; 41:609-627. [PMID: 33593221 DOI: 10.1080/07388551.2021.1873239] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Bacillus licheniformis is a Gram positive spore-forming bacterial species of high biotechnological interest with numerous present and potential uses, including the production of bioactive compounds that are applied in a wide range of fields, such as aquaculture, agriculture, food, biomedicine, and pharmaceutical industries. Its use as an expression vector for the production of enzymes and other bioproducts is also gaining interest due to the availability of novel genetic manipulation tools. Furthermore, besides its widespread use as a probiotic, other biotechnological applications of B. licheniformis strains include: bioflocculation, biomineralization, biofuel production, bioremediation, and anti-biofilm activity. Although authorities have approved the use of B. licheniformis as a feed additive worldwide due to the absence of toxigenic potential, some probiotics containing this bacterium are considered unsafe due to the possible transference of antibiotic resistance genes. The wide variability in biological activities and genetic characteristics of this species makes it necessary to establish an exact protocol for describing the novel strains, in order to evaluate its biotechnological potential.
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Affiliation(s)
- Andrea Muras
- Departmento de Microbioloxía e Parasitoloxía, Facultade de Bioloxía-CIBUS, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - Manuel Romero
- School of Life Sciences, Centre for Biomolecular Sciences, University of Nottingham, Nottingham, UK
| | - Celia Mayer
- Departmento de Microbioloxía e Parasitoloxía, Facultade de Bioloxía-CIBUS, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - Ana Otero
- Departmento de Microbioloxía e Parasitoloxía, Facultade de Bioloxía-CIBUS, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
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