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Ferrando J, Miñana-Galbis D, Picart P. The Construction of an Environmentally Friendly Super-Secreting Strain of Bacillus subtilis through Systematic Modulation of Its Secretory Pathway Using the CRISPR-Cas9 System. Int J Mol Sci 2024; 25:6957. [PMID: 39000067 PMCID: PMC11240994 DOI: 10.3390/ijms25136957] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2024] [Revised: 06/12/2024] [Accepted: 06/18/2024] [Indexed: 07/16/2024] Open
Abstract
Achieving commercially significant yields of recombinant proteins in Bacillus subtilis requires the optimization of its protein production pathway, including transcription, translation, folding, and secretion. Therefore, in this study, our aim was to maximize the secretion of a reporter α-amylase by overcoming potential bottlenecks within the secretion process one by one, using a clustered regularly interspaced short palindromic repeat-Cas9 (CRISPR-Cas9) system. The strength of single and tandem promoters was evaluated by measuring the relative α-amylase activity of AmyQ integrated into the B. subtilis chromosome. Once a suitable promoter was selected, the expression levels of amyQ were upregulated through the iterative integration of up to six gene copies, thus boosting the α-amylase activity 20.9-fold in comparison with the strain harboring a single amyQ gene copy. Next, α-amylase secretion was further improved to a 26.4-fold increase through the overexpression of the extracellular chaperone PrsA and the signal peptide peptidase SppA. When the final expression strain was cultivated in a 3 L fermentor for 90 h, the AmyQ production was enhanced 57.9-fold. The proposed strategy allows for the development of robust marker-free plasmid-less super-secreting B. subtilis strains with industrial relevance.
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Affiliation(s)
| | | | - Pere Picart
- Faculty of Pharmacy and Food Science Technology, Department of Biology, Healthcare and the Environment, Microbiology Section, Universitat de Barcelona, Avinguda Diagonal 643, 08028 Barcelona, Spain; (J.F.); (D.M.-G.)
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2
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Chai R, Guo J, Geng Y, Huang S, Wang H, Yao X, Li T, Qiu L. The Influence of Homologous Arm Length on Homologous Recombination Gene Editing Efficiency Mediated by SSB/CRISPR-Cas9 in Escherichia coli. Microorganisms 2024; 12:1102. [PMID: 38930484 PMCID: PMC11205466 DOI: 10.3390/microorganisms12061102] [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: 05/19/2024] [Revised: 05/28/2024] [Accepted: 05/28/2024] [Indexed: 06/28/2024] Open
Abstract
The precise editing of genes mediated by CRISPR-Cas9 necessitates the application of donor DNA with appropriate lengths of homologous arms and fragment sizes. Our previous development, SSB/CRISPR-Cas9, has demonstrated high efficiency in homologous recombination and non-homologous end joining gene editing within bacteria. In this study, we optimized the lengths and sizes of homologous arms of the donor DNA within this system. Two sets of donor DNA constructs were generated: one set comprised donors with only 10-100 bp homologous arms, while the other set included donors with homologous arms ranging from 10-100 bp, between which was a tetracycline resistance expression cassette (1439 bp). These donor constructs were transformed into Escherichia coli MG1655 cells alongside pCas-SSB/pTargetF-lacZ. Notably, when the homologous arms ranged from 10 to 70 bp, the transformation efficiency of non-selectable donors was significantly higher than that of selectable donors. However, within the range of 10-100 bp homologous arm lengths, the homologous recombination rate of selectable donors was significantly higher than that of non-selectable donors, with the gap narrowing as the homologous arm length increased. For selectable donor DNA with homologous arm lengths of 10-60 bp, the homologous recombination rate increased linearly, reaching a plateau when the homologous arm length was between 60-100 bp. Conversely, for non-selectable donor DNA, the homologous recombination rate increased linearly with homologous arm lengths of 10-90 bp, plateauing at 90-100 bp. Editing two loci simultaneously with 100 bp homologous arms, whether selectable or non-selectable, showed no difference in transformation or homologous recombination rates. Editing three loci simultaneously with 100 bp non-selectable homologous arms resulted in a 45% homologous recombination rate. These results suggest that efficient homologous recombination gene editing mediated by SSB/CRISPR-Cas9 can be achieved using donor DNA with 90-100 bp non-selectable homologous arms or 60-100 bp selectable homologous arms.
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Affiliation(s)
- Ran Chai
- School of Environmental Engineering, Yellow River Conservancy Technical Institute, Henan Engineering Technology Research Center of Green Coating Materials, Kaifeng 475004, China; (R.C.)
- College of Life Sciences, Henan Agricultural University, Key Laboratory of Enzyme Engineering of Agricultural Microbiology, Ministry of Agriculture and Rural Affairs, Zhengzhou 450046, China
| | - Jiaxiang Guo
- School of Environmental Engineering, Yellow River Conservancy Technical Institute, Henan Engineering Technology Research Center of Green Coating Materials, Kaifeng 475004, China; (R.C.)
| | - Yue Geng
- School of Environmental Engineering, Yellow River Conservancy Technical Institute, Henan Engineering Technology Research Center of Green Coating Materials, Kaifeng 475004, China; (R.C.)
| | - Shuai Huang
- School of Environmental Engineering, Yellow River Conservancy Technical Institute, Henan Engineering Technology Research Center of Green Coating Materials, Kaifeng 475004, China; (R.C.)
| | - Haifeng Wang
- School of Environmental Engineering, Yellow River Conservancy Technical Institute, Henan Engineering Technology Research Center of Green Coating Materials, Kaifeng 475004, China; (R.C.)
| | - Xinding Yao
- School of Environmental Engineering, Yellow River Conservancy Technical Institute, Henan Engineering Technology Research Center of Green Coating Materials, Kaifeng 475004, China; (R.C.)
| | - Tao Li
- College of Applied Engineering, Henan University of Science and Technology, Sanmenxia 472000, China
| | - Liyou Qiu
- College of Life Sciences, Henan Agricultural University, Key Laboratory of Enzyme Engineering of Agricultural Microbiology, Ministry of Agriculture and Rural Affairs, Zhengzhou 450046, China
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3
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Chen Y, Li M, Yan M, Chen Y, Saeed M, Ni Z, Fang Z, Chen H. Bacillus subtilis: current and future modification strategies as a protein secreting factory. World J Microbiol Biotechnol 2024; 40:195. [PMID: 38722426 DOI: 10.1007/s11274-024-03997-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Accepted: 04/19/2024] [Indexed: 05/18/2024]
Abstract
Bacillus subtilis is regarded as a promising microbial expression system in bioengineering due to its high stress resistance, nontoxic, low codon preference and grow fast. The strain has a relatively efficient expression system, as it has at least three protein secretion pathways and abundant molecular chaperones, which guarantee its expression ability and compatibility. Currently, many proteins are expressed in Bacillus subtilis, and their application prospects are broad. Although Bacillus subtilis has great advantages compared with other prokaryotes related to protein expression and secretion, it still faces deficiencies, such as low wild-type expression, low product activity, and easy gene loss, which limit its large-scale application. Over the years, many researchers have achieved abundant results in the modification of Bacillus subtilis expression systems, especially the optimization of promoters, expression vectors, signal peptides, transport pathways and molecular chaperones. An optimal vector with a suitable promoter strength and other regulatory elements could increase protein synthesis and secretion, increasing industrial profits. This review highlights the research status of optimization strategies related to the expression system of Bacillus subtilis. Moreover, research progress on its application as a food-grade expression system is also presented, along with some future modification and application directions.
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Affiliation(s)
- Yanzhen Chen
- School of Life Sciences, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
| | - Miaomiao Li
- School of Life Sciences, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
| | - Mingchen Yan
- School of Life Sciences, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
| | - Yong Chen
- School of Life Sciences, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
| | - Muhammad Saeed
- School of Life Sciences, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
| | - Zhong Ni
- School of Life Sciences, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
| | - Zhen Fang
- School of Life Sciences, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
| | - Huayou Chen
- School of Life Sciences, Jiangsu University, Zhenjiang, 212013, Jiangsu, China.
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4
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Wang X, Xu M, Ren X, Li M, Wang C, Yang F, Li X. High-Level Expression and Biochemical Characterization of a Maltotetraose Amylase in Pichia pastoris X-33 for Maltotetraose Production. Appl Biochem Biotechnol 2024:10.1007/s12010-024-04871-0. [PMID: 38407782 DOI: 10.1007/s12010-024-04871-0] [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] [Accepted: 02/12/2024] [Indexed: 02/27/2024]
Abstract
Maltotetraose amylase, which catalyzes the hydrolysis of amylaceous polysaccharides into maltooligosaccharides with maltotetraose as the main product, is extensively used in the food industry. However, the lack of efficient expression system for maltotetraose amylase has hampered its production and application. In this study, high-level production of a maltotetraose amylase mutant (referred to as Pp-Mta∆CBM) from Pseudomonas saccharophila was achieved in Pichia pastoris X-33. First, the gene of maltotetraose amylase with the carbohydrate-binding module (CBM) removed was codon-optimized and cloned into the pPICZαA vector, followed by transformation into P. pastoris X-33 for expression. Using the promoter PAOX1 and signal peptide α-factor, high-level production of Pp-Mta∆CBM with minimal extracellular impurity proteins was achieved, resulting in an extracellular activity of 367.9 U/mL after 7 days of cultivation in shake flasks. Next, the expressed Pp-Mta∆CBM was purified and characterized. This recombinant enzyme was glycosylated and has maximum activity at 55 ℃ and pH 7.0. Its Km for soluble starch was 4.1 g/L, and its kcat was 3237.6 s-1. Finally, the Pp-Mta∆CBM was found to produce a maximum maltotetraose yield of 57.1% in the presence of 200 g/L of substrate. The findings presented in this study demonstrate the efficient production of Pp-Mta∆CBM in P. pastoris, providing a new expression system for maltotetraose amylase and laying the foundation for its scale-up production and industrial application.
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Affiliation(s)
- Xinyu Wang
- School of Biological Engineering, Dalian Polytechnic University, Dalian, 116034, China
| | - Ming Xu
- School of Biological Engineering, Dalian Polytechnic University, Dalian, 116034, China
| | - Xiaopeng Ren
- School of Biological Engineering, Dalian Polytechnic University, Dalian, 116034, China
| | - Mingyu Li
- School of Biological Engineering, Dalian Polytechnic University, Dalian, 116034, China
| | - Conggang Wang
- School of Biological Engineering, Dalian Polytechnic University, Dalian, 116034, China.
| | - Fan Yang
- School of Biological Engineering, Dalian Polytechnic University, Dalian, 116034, China.
| | - Xianzhen Li
- School of Biological Engineering, Dalian Polytechnic University, Dalian, 116034, China
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Bi M, Li M, Wei J, Meng Z, Wang Z, Ying M, Yang X, Huang L. Genome-scale cis-acting catabolite-responsive element editing confers Bacillus pumilus LG3145 plant-beneficial functions. iScience 2024; 27:108983. [PMID: 38357660 PMCID: PMC10864199 DOI: 10.1016/j.isci.2024.108983] [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: 07/04/2023] [Revised: 10/26/2023] [Accepted: 01/17/2024] [Indexed: 02/16/2024] Open
Abstract
Rhizosphere dwelling microorganism such as Bacillus spp. are helpful for crop growth. However, these functions are adversely affected by long-term synthetic fertilizer application. We developed a modified CRISPR/Cas9 system using non-specific single-guide RNAs to disrupt the genome-wide cis-acting catabolite-responsive elements (cres) in a wild-type Bacillus pumilus strain, which conferred dual plant-benefit properties. Most of the mutations occurred around imperfectly matched cis-acting elements (cre-like sites) in genes that are mainly involved in carbon and secondary metabolism pathways. The comparative metabolomics and transcriptome results revealed that carbon is likely transferred to some pigments, such as riboflavin, carotenoid, and lycopene, or non-ribosomal peptides, such as siderophore, surfactin, myxochelin, and bacilysin, through the pentose phosphate and amino acid metabolism pathways. Collectively, these findings suggested that the mutation of global cre-like sequences in the genome might alter carbon flow, thereby allowing beneficial biological interactions between the rhizobacteria and plants.
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Affiliation(s)
- Meiying Bi
- Tianjin Key Laboratory of Organic Solar Cells and Photochemical Conversion, School of Chemistry and Chemical Engineering, Tianjin University of Technology, Tianjin 300384, People’s Republic of China
| | - Mingkun Li
- Tianjin Key Laboratory of Organic Solar Cells and Photochemical Conversion, School of Chemistry and Chemical Engineering, Tianjin University of Technology, Tianjin 300384, People’s Republic of China
| | - Jiaxun Wei
- Tianjin Key Laboratory of Organic Solar Cells and Photochemical Conversion, School of Chemistry and Chemical Engineering, Tianjin University of Technology, Tianjin 300384, People’s Republic of China
| | - Ziwen Meng
- Tianjin Key Laboratory of Organic Solar Cells and Photochemical Conversion, School of Chemistry and Chemical Engineering, Tianjin University of Technology, Tianjin 300384, People’s Republic of China
| | - Zhaoyang Wang
- Tianjin Key Laboratory of Organic Solar Cells and Photochemical Conversion, School of Chemistry and Chemical Engineering, Tianjin University of Technology, Tianjin 300384, People’s Republic of China
| | - Ming Ying
- Tianjin Key Laboratory of Organic Solar Cells and Photochemical Conversion, School of Chemistry and Chemical Engineering, Tianjin University of Technology, Tianjin 300384, People’s Republic of China
| | - Xiurong Yang
- Institute of Plant Protection, Tianjin Academy of Agricultural Sciences, Tianjin 300384, People’s Republic of China
| | - Lei Huang
- Tianjin Key Laboratory of Organic Solar Cells and Photochemical Conversion, School of Chemistry and Chemical Engineering, Tianjin University of Technology, Tianjin 300384, People’s Republic of China
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6
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Lv X, Li Y, Xiu X, Liao C, Xu Y, Liu Y, Li J, Du G, Liu L. CRISPR genetic toolkits of classical food microorganisms: Current state and future prospects. Biotechnol Adv 2023; 69:108261. [PMID: 37741424 DOI: 10.1016/j.biotechadv.2023.108261] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Revised: 09/17/2023] [Accepted: 09/18/2023] [Indexed: 09/25/2023]
Abstract
Production of food-related products using microorganisms in an environmentally friendly manner is a crucial solution to global food safety and environmental pollution issues. Traditional microbial modification methods rely on artificial selection or natural mutations, which require time for repeated screening and reproduction, leading to unstable results. Therefore, it is imperative to develop rapid, efficient, and precise microbial modification technologies. This review summarizes recent advances in the construction of gene editing and metabolic regulation toolkits based on the clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated proteins (CRISPR-Cas) systems and their applications in reconstructing food microorganism metabolic networks. The development and application of gene editing toolkits from single-site gene editing to multi-site and genome-scale gene editing was also introduced. Moreover, it presented a detailed introduction to CRISPR interference, CRISPR activation, and logic circuit toolkits for metabolic network regulation. Moreover, the current challenges and future prospects for developing CRISPR genetic toolkits were also discussed.
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Affiliation(s)
- Xueqin Lv
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China; Science Center for Future Foods, Jiangnan University, Wuxi 214122, China
| | - Yang Li
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China; Science Center for Future Foods, Jiangnan University, Wuxi 214122, China
| | - Xiang Xiu
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China; Science Center for Future Foods, Jiangnan University, Wuxi 214122, China
| | - Chao Liao
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China; Science Center for Future Foods, Jiangnan University, Wuxi 214122, China
| | - Yameng Xu
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China; Science Center for Future Foods, Jiangnan University, Wuxi 214122, China
| | - Yanfeng Liu
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China; Science Center for Future Foods, Jiangnan University, Wuxi 214122, China
| | - Jianghua Li
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China; Science Center for Future Foods, Jiangnan University, Wuxi 214122, China
| | - Guocheng Du
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China; Science Center for Future Foods, Jiangnan University, Wuxi 214122, China
| | - Long Liu
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China; Science Center for Future Foods, Jiangnan University, Wuxi 214122, China; Food Laboratory of Zhongyuan, Jiangnan University, Wuxi 214122, China.
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7
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Jiang M, Liu Y, Xue H, Wang Y, Wang C, Yang F, Li X. Expression and biochemical characterization of a Bacillus subtilis catalase in Pichia pastoris X-33. Protein Expr Purif 2023; 208-209:106277. [PMID: 37100104 DOI: 10.1016/j.pep.2023.106277] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 04/20/2023] [Accepted: 04/21/2023] [Indexed: 04/28/2023]
Abstract
Catalase, which catalyzes the decomposition of H2O2 to H2O and O2, is widely used to reduce H2O2 in industrial applications, such as in food processing, textile dyeing and wastewater treatment. In this study, the catalase (KatA) from Bacillus subtilis was cloned and expressed in the yeast Pichia pastoris X-33. The effect of the promoter in the expression plasmid on the activity level of the secreted KatA protein was also studied. First, the gene encoding KatA was cloned and inserted into a plasmid containing an inducible alcohol oxidase 1 promoter (pAOX1) or a constitutive glyceraldehyde-3-phosphate dehydrogenase promoter (pGAP). The recombinant plasmids were validated by colony PCR and sequencing and then linearized and transformed into the yeast P. pastoris X-33 for expression. With the promoter pAOX1, the maximum yield of KatA in the culture medium reached 338.8 ± 9.6 U/mL in 2 days of shake flask cultivation, which was approximately 2.1-fold greater than the maximum yield obtained with the promoter pGAP. The expressed KatA was then purified from the culture medium by anion exchange chromatography, and its specific activity was determined to be 14826.58 U/mg. Finally, the purified KatA exhibited optimum activity at 25 °C and pH 11.0. Its Km for hydrogen peroxide was 10.9 ± 0.5 mM, and its kcat/Km was 5788.1 ± 25.6 s-1 mM-1. Through the work presented in this article, we have therefore demonstrated efficient expression and purification of KatA in P. pastoris, which might be advantageous for scaling up the production of KatA for use in a variety of biotechnological applications.
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Affiliation(s)
- Mengtong Jiang
- School of Biological Engineering, Dalian Polytechnic University, Dalian, 116034, China
| | - Yuxin Liu
- School of Biological Engineering, Dalian Polytechnic University, Dalian, 116034, China
| | - Hongjian Xue
- School of Biological Engineering, Dalian Polytechnic University, Dalian, 116034, China
| | - Yiqi Wang
- School of Biological Engineering, Dalian Polytechnic University, Dalian, 116034, China
| | - Conggang Wang
- School of Biological Engineering, Dalian Polytechnic University, Dalian, 116034, China.
| | - Fan Yang
- School of Biological Engineering, Dalian Polytechnic University, Dalian, 116034, China.
| | - Xianzhen Li
- School of Biological Engineering, Dalian Polytechnic University, Dalian, 116034, China
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Zhang G, Lin M, Qin M, Xie Q, Liang M, Jiang J, Dai H, Xu S, Feng S, Liao M. Establishing Heterologous Production of Microcins J25 and Y in Bacillus subtilis. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:5600-5613. [PMID: 36995900 DOI: 10.1021/acs.jafc.3c00675] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Microcin J25 (MccJ25) and microcin Y (MccY) are lasso peptides and considered potential alternatives to antibiotics and harmful preservatives. The combination of these two microcins can provide a wide antimicrobial spectrum against food-borne Salmonella. Currently, MccJ25 and MccY are produced using Escherichia coli expression systems; however, the entire production process is accompanied by negative effects from endotoxins. In this study, we identified Bacillus subtilis as a suitable host for MccJ25 and MccY production. High-level production of microcins was achieved by promoter optimization, host strain selection, and recombinant expression. The engineered strains produced maximum yields of 2.827 μM MccJ25 and 1.481 μM MccY. This is the first study to demonstrate the expression of MccJ25 and MccY in B. subtilis, and it offers a few engineered strains that are without antibiotic resistance markers, inducer-free, sporulation-deficient, and free of the negative effects of endotoxins for antibacterial therapy and food preservation.
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Affiliation(s)
- Guangwen Zhang
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, P. R. China
| | - Min Lin
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, P. R. China
| | - Miaomiao Qin
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, P. R. China
| | - Qianmei Xie
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, P. R. China
| | - Mingzhi Liang
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, P. R. China
| | - Jinfei Jiang
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, P. R. China
| | - Huilin Dai
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, P. R. China
| | - Siqi Xu
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, P. R. China
| | - Saixiang Feng
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, P. R. China
- Key Laboratory of Zoonosis Prevention and Control of Guangdong Province, Guangzhou 510642, P. R. China
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou 510642, P. R. China
- Key Laboratory of Veterinary Vaccine Innovation of the Ministry of Agriculture, Guangzhou 510642, P. R. China
- National and Regional Joint Engineering Laboratory for Medicament of Zoonosis Prevention and Control, Guangzhou 510642, P. R. China
| | - Ming Liao
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, P. R. China
- Key Laboratory of Zoonosis Prevention and Control of Guangdong Province, Guangzhou 510642, P. R. China
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou 510642, P. R. China
- Key Laboratory of Veterinary Vaccine Innovation of the Ministry of Agriculture, Guangzhou 510642, P. R. China
- National and Regional Joint Engineering Laboratory for Medicament of Zoonosis Prevention and Control, Guangzhou 510642, P. R. China
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9
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Chu PTB, Phan TTP, Nguyen TTT, Truong TTT, Schumann W, Nguyen HD. Potent IPTG-inducible integrative expression vectors for production of recombinant proteins in Bacillus subtilis. World J Microbiol Biotechnol 2023; 39:143. [PMID: 37004690 DOI: 10.1007/s11274-023-03566-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Accepted: 03/03/2023] [Indexed: 04/04/2023]
Abstract
The IPTG-inducible promoter family, Pgrac, allows high protein expression levels in an inducible manner. In this study, we constructed IPTG-inducible expression vectors containing strong Pgrac promoters that allow integration of the transgene at either the amyE or lacA locus or both loci in Bacillus subtilis. Our novel integrative expression vectors based on Pgrac promoters could control the repression of protein production in the absence and the induction in the presence of an inducer, IPTG. The β-galactosidase (BgaB) protein levels were 9.0%, 15% and 30% of the total cellular protein in the B. subtilis strains carrying single cassettes with the Pgrac01, Pgrac100 or Pgrac212 promoters, respectively. The maximal induction ratio of Pgrac01-bgaB was 35.5 while that of Pgrac100-bgaB was 7.5 and that of Pgrac212-bgaB was 9. The inducible expression of GFP and BgaB protein was stably maintained for 24 h, with the highest yield of GFP being 24% of cell total protein while the maximum amount of BgaB was found to be 38%. A dual integration of two copies of the gfp+ gene into the B. subtilis genome at the lacA and amyE loci resulted in a yield of about 40% of total cellular protein and a 1.74-fold increase in GFP compared with single-integrated strains containing the same Pgrac212 promoter. The capability of protein production from low to high levels of these inducible integrative systems is useful for fundamental and applied research in B. subtilis.
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Affiliation(s)
- Phuong Thi Bich Chu
- Center for Bioscience and Biotechnology, University of Science, Ho Chi Minh City, Vietnam
- Vietnam National University, Ho Chi Minh City, Vietnam
- Faculty of Pharmacy, HUTECH University, Ho Chi Minh City, Vietnam
| | - Trang Thi Phuong Phan
- Center for Bioscience and Biotechnology, University of Science, Ho Chi Minh City, Vietnam.
- Vietnam National University, Ho Chi Minh City, Vietnam.
- Laboratory of Molecular Biotechnology, University of Science, Ho Chi Minh City, Vietnam.
| | - Tam Thi Thanh Nguyen
- Center for Bioscience and Biotechnology, University of Science, Ho Chi Minh City, Vietnam
- Vietnam National University, Ho Chi Minh City, Vietnam
- Faculty of Pharmacy, HUTECH University, Ho Chi Minh City, Vietnam
| | - Tuom Thi Tinh Truong
- Center for Bioscience and Biotechnology, University of Science, Ho Chi Minh City, Vietnam
- Vietnam National University, Ho Chi Minh City, Vietnam
- Cancer Research Laboratory, University of Science, Ho Chi Minh City, Vietnam
| | - Wolfgang Schumann
- Center for Bioscience and Biotechnology, University of Science, Ho Chi Minh City, Vietnam
- Vietnam National University, Ho Chi Minh City, Vietnam
- Institute of Genetics, University of Bayreuth, 95440, Bayreuth, Germany
| | - Hoang Duc Nguyen
- Center for Bioscience and Biotechnology, University of Science, Ho Chi Minh City, Vietnam.
- Vietnam National University, Ho Chi Minh City, Vietnam.
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Kalathinathan P, Sain A, Pulicherla K, Kodiveri Muthukaliannan G. A Review on the Various Sources of β-Galactosidase and Its Lactose Hydrolysis Property. Curr Microbiol 2023; 80:122. [PMID: 36862237 DOI: 10.1007/s00284-023-03220-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Accepted: 02/10/2023] [Indexed: 03/03/2023]
Abstract
β-Galactosidase is a glycoside hydrolase enzyme that possesses both hydrolytic and transgalactosylation properties and has several benefits and advantages in the food and dairy industries. The catalytic process of β-galactosidase involves the transfer of a sugar residue from a glycosyl donor to an acceptor via a double-displacement mechanism. Hydrolysis prevails when water acts as an acceptor, resulting in the production of lactose-free products. Transgalactosylation prevails when lactose acts as an acceptor, resulting in the production of prebiotic oligosaccharides. β-Galactosidase is also obtained from many sources including bacteria, yeast, fungi, plants, and animals. However, depending on the origin of the β-galactosidase, the monomer composition and their bonds may differ, thereby influencing their properties and prebiotic efficacy. Thus, the increasing demand for prebiotics in the food industry and the search for new oligosaccharides have compelled researchers to search for novel sources of β-galactosidase with diverse properties. In this review, we discuss the properties, catalytic mechanisms, various sources and lactose hydrolysis properties of β-galactosidase.
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Affiliation(s)
- Pooja Kalathinathan
- School of BioSciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, India
| | - Avtar Sain
- Centre for Bio-Separation Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, India
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11
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Ferrando J, Filluelo O, Zeigler DR, Picart P. Barriers to simultaneous multilocus integration in Bacillus subtilis tumble down: development of a straightforward screening method for the colorimetric detection of one-step multiple gene insertion using the CRISPR-Cas9 system. Microb Cell Fact 2023; 22:21. [PMID: 36721198 PMCID: PMC9890709 DOI: 10.1186/s12934-023-02032-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Accepted: 01/25/2023] [Indexed: 02/02/2023] Open
Abstract
BACKGROUND Despite recent advances in genetic engineering tools for effectively regulating and manipulating genes, efficient simultaneous multigene insertion methods have not been established in Bacillus subtilis. To date, multilocus integration systems in B. subtilis, which is one of the main industrial enzyme producers and a GRAS (generally regarded as safe) microbial host, rely on iterative rounds of plasmid construction for sequential insertions of genes into the B. subtilis chromosome, which is tedious and time consuming. RESULTS In this study, we present development and proof-of-concept of a novel CRISPR-Cas9-based genome-editing strategy for the colorimetric detection of one-step multiple gene insertion in B. subtilis. First, up to three copies of the crtMN operon from Staphylococcus aureus, encoding a yellow pigment, were incorporated at three ectopic sites within the B. subtilis chromosome, rendering engineered strains able to form yellow colonies. Second, a single CRISPR-Cas9-based plasmid carrying a highly specific single guide RNA (sgRNA) targeting crtMN operon and a changeable editing template was constructed to facilitate simultaneous insertion of multiple gene-copies through homology-directed repair (HDR). Upon transformation of engineered strains with engineered plasmids, strains harboring up to three gene copies integrated into the chromosome formed white colonies because of the removal of the crtMN operon, clearly distinguishable from yellow colonies harboring undesired genetic modifications. As a result, construction of a plasmid-less, marker-free, high-expression stable producer B. subtilis strain can be completed in only seven days, demonstrating the potential that the implementation of this technology may bring for biotechnology purposes. CONCLUSIONS The novel technology expands the genome-editing toolset for B. subtilis and means a substantial improvement over current methodology, offering new application possibilities that we envision should significantly boost the development of B. subtilis as a chassis in the field of synthetic biology.
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Affiliation(s)
- Jordi Ferrando
- grid.5841.80000 0004 1937 0247Microbiology Section, Department of Biology, Healthcare and Environment, Faculty of Pharmacy and Food Sciences, Universitat de Barcelona, Barcelona, Catalonia Spain
| | - Oriana Filluelo
- grid.5841.80000 0004 1937 0247Microbiology Section, Department of Biology, Healthcare and Environment, Faculty of Pharmacy and Food Sciences, Universitat de Barcelona, Barcelona, Catalonia Spain
| | | | - Pere Picart
- grid.5841.80000 0004 1937 0247Microbiology Section, Department of Biology, Healthcare and Environment, Faculty of Pharmacy and Food Sciences, Universitat de Barcelona, Barcelona, Catalonia Spain
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12
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Greeson EM, Madsen CS, Makela AV, Contag CH. Magnetothermal Control of Temperature-Sensitive Repressors in Superparamagnetic Iron Nanoparticle-Coated Bacillus subtilis. ACS NANO 2022; 16:16699-16712. [PMID: 36200984 DOI: 10.1021/acsnano.2c06239] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Superparamagnetic iron oxide nanoparticles (SPIONs) are used as contrast agents in magnetic resonance imaging (MRI) and magnetic particle imaging (MPI), and resulting images can be used to guide magnetothermal heating. Alternating magnetic fields (AMF) cause local temperature increases in regions with SPIONs, and we investigated the ability of magnetic hyperthermia to regulate temperature-sensitive repressors (TSRs) of bacterial transcription. The TSR, TlpA39, was derived from a Gram-negative bacterium and used here for thermal control of reporter gene expression in Gram-positive, Bacillus subtilis. In vitro heating of B. subtilis with TlpA39 controlling bacterial luciferase expression resulted in a 14.6-fold (12 hours; h) and 1.8-fold (1 h) increase in reporter transcripts with a 10.0-fold (12 h) and 12.1-fold (1 h) increase in bioluminescence. To develop magnetothermal control, B. subtilis cells were coated with three SPION variations. Electron microscopy coupled with energy dispersive X-ray spectroscopy revealed an external association with, and retention of, SPIONs on B. subtilis. Furthermore, using long duration AMF we demonstrated magnetothermal induction of the TSRs in SPION-coated B. subtilis with a maximum of 5.6-fold increases in bioluminescence. After intramuscular injections of SPION-coated B. subtilis, histology revealed that SPIONs remained in the same locations as the bacteria. For in vivo studies, 1 h of AMF is the maximum exposure due to anesthesia constraints. Both in vitro and in vivo, there was no change in bioluminescence after 1 h of AMF treatment. Pairing TSRs with magnetothermal energy using SPIONs for localized heating with AMF can lead to transcriptional control that expands options for targeted bacteriotherapies.
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Affiliation(s)
- Emily M Greeson
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan 48824, United States
- Institute for Quantitative Health Science and Engineering, Michigan State University, East Lansing, Michigan 48824, United States
| | - Cody S Madsen
- Department of Biomedical Engineering, Michigan State University, East Lansing, Michigan 48824, United States
- Institute for Quantitative Health Science and Engineering, Michigan State University, East Lansing, Michigan 48824, United States
| | - Ashley V Makela
- Department of Biomedical Engineering, Michigan State University, East Lansing, Michigan 48824, United States
- Institute for Quantitative Health Science and Engineering, Michigan State University, East Lansing, Michigan 48824, United States
| | - Christopher H Contag
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan 48824, United States
- Department of Biomedical Engineering, Michigan State University, East Lansing, Michigan 48824, United States
- Institute for Quantitative Health Science and Engineering, Michigan State University, East Lansing, Michigan 48824, United States
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13
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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: 6] [Impact Index Per Article: 3.0] [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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14
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Singh RV, Sambyal K. β-galactosidase as an industrial enzyme: production and potential. CHEMICAL PAPERS 2022. [DOI: 10.1007/s11696-022-02507-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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15
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Xin Q, Chen Y, Chen Q, Wang B, Pan L. Development and application of a fast and efficient CRISPR-based genetic toolkit in Bacillus amyloliquefaciens LB1ba02. Microb Cell Fact 2022; 21:99. [PMID: 35643496 PMCID: PMC9148480 DOI: 10.1186/s12934-022-01832-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Accepted: 05/17/2022] [Indexed: 01/19/2023] Open
Abstract
Abstract
Background
Bacillus amyloliquefaciens is generally recognized as food safe (GRAS) microbial host and important enzyme-producing strain in the industry. B.amyloliquefaciens LB1ba02 is a production strain suitable for secreting mesophilic α-amylase in the industry. Nevertheless, due to the low transformation efficiency and restriction-modification system, the development of its CRISPR tool lags far behind other species and strains from the genus Bacillus. This work was undertaken to develop a fast and efficient gene-editing tool in B.amyloliquefaciens LB1ba02.
Results
In this study, we fused the nuclease-deficient mutant Cas9n (D10A) of Cas9 with activation-induced cytidine deaminase (AID) and developed a fast and efficient base editing system for the first time in B. amyloliquefaciens LB1ba02. The system was verified by inactivating the pyrF gene coding orotidine 5'-phosphate decarboxylase and the mutant could grow normally on M9 medium supplemented with 5-fluoroorotic acid (5-FOA) and uridine (U). Our base editing system has a 6nt editing window consisting of an all-in-one temperature-sensitive plasmid that facilitates multiple rounds of genome engineering in B. amyloliquefaciens LB1ba02. The total editing efficiency of this method reached 100% and it achieved simultaneous editing of three loci with an efficiency of 53.3%. In addition, based on the base editing CRISPR/Cas9n-AID system, we also developed a single plasmid CRISPR/Cas9n system suitable for rapid gene knockout and integration. The knockout efficiency for a single gene reached 93%. Finally, we generated 4 genes (aprE, nprE, wprA, and bamHIR) mutant strain, LB1ba02△4. The mutant strain secreted 1.25-fold more α-amylase into the medium than the wild-type strain.
Conclusions
The CRISPR/Cas9n-AID and CRISPR/Cas9n systems developed in this work proved to be a fast and efficient genetic manipulation tool in a restriction-modification system and poorly transformable strain.
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16
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Wang ZK, Gong JS, Qin J, Li H, Lu ZM, Shi JS, Xu ZH. Improving the Intensity of Integrated Expression for Microbial Production. ACS Synth Biol 2021; 10:2796-2807. [PMID: 34738786 DOI: 10.1021/acssynbio.1c00334] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Chromosomal integration of exogenous genes is preferred for industrially related fermentation, as plasmid-mediated fermentation leads to extra metabolic burden and genetic instability. Moreover, with the development and advancement of genome engineering and gene editing technologies, inserting genes into chromosomes has become more convenient; integration expression is extensively utilized in microorganisms for industrial bioproduction and expected to become the trend of recombinant protein expression. However, in actual research and application, it is important to enhance the expression of heterologous genes at the host genome level. Herein, we summarized the basic principles and characteristics of genomic integration; furthermore, we highlighted strategies to improve the expression of chromosomal integration of genes and pathways in host strains from three aspects, including chassis cell optimization, regulation of expression elements in gene expression cassettes, optimization of gene dose level and integration sites on chromosomes. Moreover, we reviewed and summarized the relevant studies on the application of integrated expression in the exploration of gene function and the various types of industrial microorganism production. Consequently, this review would serve as a reference for the better application of integrated expression.
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Affiliation(s)
- Zi-Kai Wang
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Pharmaceutical Sciences, Jiangnan University, Wuxi 214122, PR China
- National Engineering Laboratory for Cereal Fermentation Technology, School of Biotechnology, Jiangnan University, Wuxi 214122, PR China
- Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, Wuxi 214122, PR China
| | - Jin-Song Gong
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Pharmaceutical Sciences, Jiangnan University, Wuxi 214122, PR China
| | - Jiufu Qin
- Science Center for Future Foods, Jiangnan University, Wuxi 214122, PR China
| | - Hui Li
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Pharmaceutical Sciences, Jiangnan University, Wuxi 214122, PR China
| | - Zhen-Ming Lu
- National Engineering Laboratory for Cereal Fermentation Technology, School of Biotechnology, Jiangnan University, Wuxi 214122, PR China
| | - Jin-Song Shi
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Pharmaceutical Sciences, Jiangnan University, Wuxi 214122, PR China
| | - Zheng-Hong Xu
- National Engineering Laboratory for Cereal Fermentation Technology, School of Biotechnology, Jiangnan University, Wuxi 214122, PR China
- Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, Wuxi 214122, PR China
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17
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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: 9] [Impact Index Per Article: 3.0] [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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18
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Liao C, Ayansola H, Ma Y, Ito K, Guo Y, Zhang B. Advances in Enhanced Menaquinone-7 Production From Bacillus subtilis. Front Bioeng Biotechnol 2021; 9:695526. [PMID: 34354987 PMCID: PMC8330505 DOI: 10.3389/fbioe.2021.695526] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Accepted: 07/01/2021] [Indexed: 12/02/2022] Open
Abstract
The production of nutraceutical compounds through biosynthetic approaches has received considerable attention in recent years. For example, Menaquinone-7 (MK-7), a sub-type of Vitamin K2, biosynthesized from Bacillus subtilis (B. subtilis), proved to be more efficiently produced than the conventional chemical synthesis techniques. This is possible due to the development of B. subtilis as a chassis cell during the biosynthesis stages. Hence, it is imperative to provide insights on the B. subtilis membrane permeability modifications, biofilm reactors, and fermentation optimization as advanced techniques relevant to MK-7 production. Although the traditional gene-editing method of homologous recombination improves the biosynthetic pathway, CRISPR-Cas9 could potentially resolve the drawbacks of traditional genome editing techniques. For these reasons, future studies should explore the applications of CRISPRi (CRISPR interference) and CRISPRa (CRISPR activation) system gene-editing tools in the MK-7 anabolism pathway.
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Affiliation(s)
- Chaoyong Liao
- State Key Laboratory of Animal Nutrition, Department of Animal Nutrition and Feed Science, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Hammed Ayansola
- State Key Laboratory of Animal Nutrition, Department of Animal Nutrition and Feed Science, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Yanbo Ma
- Henan International Joint Laboratory of Animal Welfare and Health Breeding, Department of Animal Physiology, College of Animal Science and Technology, Henan University of Science and Technology, Luoyang, China
| | - Koichi Ito
- Department of Food and Physiological Models, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Ibaraki, Japan
| | - Yuming Guo
- State Key Laboratory of Animal Nutrition, Department of Animal Nutrition and Feed Science, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Bingkun Zhang
- State Key Laboratory of Animal Nutrition, Department of Animal Nutrition and Feed Science, College of Animal Science and Technology, China Agricultural University, Beijing, China
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19
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Zou D, Maina SW, Zhang F, Yan Z, Ding L, Shao Y, Xin Z. Mining New Plipastatins and Increasing the Total Yield Using CRISPR/Cas9 in Genome-Modified Bacillus subtilis 1A751. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2020; 68:11358-11367. [PMID: 32930578 DOI: 10.1021/acs.jafc.0c03694] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
CRISPR/Cas9 is one of the robust and effective gene manipulation tools which has been widely applied in various organisms. In this study, the plipastatin gene cluster was successfully expressed in genome-modified Bacillus subtilis 1A751 by disrupting the surfactin operon (srf) through CRISPR/Cas9 technology. The presumed plipastatin biosynthetic pathway was proposed based on the analysis of its biosynthetic gene cluster. Two new plipastatins were identified by a combination of ultra-high performance liquid chromatography-coupled electron spray ionization-tandem mass spectrometry and gas chromatography-mass spectrometry analyses, together with nine known plipastatins or their derivatives. The yield of plipastatin was as high as 1600 mg/L which is the highest reported to date. Antimicrobial experiments revealed that its methanolic extracts exhibited powerful inhibitory effects on the growth of the tested pathogens and fungi. The results from this investigation highlight the remarkable utility of CRISPR/Cas9 in mining new plipastatins and increasing the total plipastatin yield, providing a new pipeline for the industrial application of plipastatin.
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Affiliation(s)
- Dandan Zou
- Key Laboratory of Food Processing and Quality Control, College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, P. R. China
| | - Sarah Wanjiku Maina
- Key Laboratory of Food Processing and Quality Control, College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, P. R. China
| | - Fengmin Zhang
- Testing Center, Yangzhou University, Wenhui East Road 48, Yangzhou 225009, China
| | - Zhenzhen Yan
- Key Laboratory of Food Processing and Quality Control, College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, P. R. China
| | - Liping Ding
- Key Laboratory of Food Processing and Quality Control, College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, P. R. China
| | - Yuting Shao
- Key Laboratory of Food Processing and Quality Control, College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, P. R. China
| | - Zhihong Xin
- Key Laboratory of Food Processing and Quality Control, College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, P. R. China
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20
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Su Y, Liu C, Fang H, Zhang D. Bacillus subtilis: a universal cell factory for industry, agriculture, biomaterials and medicine. Microb Cell Fact 2020; 19:173. [PMID: 32883293 PMCID: PMC7650271 DOI: 10.1186/s12934-020-01436-8] [Citation(s) in RCA: 142] [Impact Index Per Article: 35.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2020] [Accepted: 08/27/2020] [Indexed: 12/18/2022] Open
Abstract
Due to its clear inherited backgrounds as well as simple and diverse genetic manipulation systems, Bacillus subtilis is the key Gram-positive model bacterium for studies on physiology and metabolism. Furthermore, due to its highly efficient protein secretion system and adaptable metabolism, it has been widely used as a cell factory for microbial production of chemicals, enzymes, and antimicrobial materials for industry, agriculture, and medicine. In this mini-review, we first summarize the basic genetic manipulation tools and expression systems for this bacterium, including traditional methods and novel engineering systems. Secondly, we briefly introduce its applications in the production of chemicals and enzymes, and summarize its advantages, mainly focusing on some noteworthy products and recent progress in the engineering of B. subtilis. Finally, this review also covers applications such as microbial additives and antimicrobials, as well as biofilm systems and spore formation. We hope to provide an overview for novice researchers in this area, offering them a better understanding of B. subtilis and its applications.
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Affiliation(s)
- Yuan Su
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin, 300457, China.,Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
| | - Chuan Liu
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China.,Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
| | - Huan Fang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China.,Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
| | - Dawei Zhang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China. .,Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China. .,University of Chinese Academy of Sciences, Beijing, 100049, China.
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21
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Challenges of in vitro genome editing with CRISPR/Cas9 and possible solutions: A review. Gene 2020; 753:144813. [DOI: 10.1016/j.gene.2020.144813] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2020] [Revised: 04/26/2020] [Accepted: 05/23/2020] [Indexed: 12/20/2022]
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22
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Yu S, Price MA, Wang Y, Liu Y, Guo Y, Ni X, Rosser SJ, Bi C, Wang M. CRISPR-dCas9 Mediated Cytosine Deaminase Base Editing in Bacillus subtilis. ACS Synth Biol 2020; 9:1781-1789. [PMID: 32551562 DOI: 10.1021/acssynbio.0c00151] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Base editing technology based on clustered regularly interspaced short palindromic repeats/associated protein 9 (CRISPR/Cas9) is a recent addition to the family of CRISPR technologies. Compared with the traditional CRISPR/Cas9 technology, it does not rely on DNA double strand break and homologous recombination, and can realize gene inactivation and point mutation more quickly and simply. Herein, we first developed a base editing method for genome editing in Bacillus subtilis utilizing CRISPR/dCas9 (a fully nuclease-deficient mutant of Cas9 from S. pyogenes) and activation-induced cytidine deaminase (AID). This method achieved three and four loci simultaneous editing with editing efficiency up to 100% and 50%, respectively. Our base editing system in B. subtilis has a 5 nt editing window, which is similar to previously reported base editing in other microorganisms. We demonstrated that the plasmid curing rate is almost 100%, which is advantageous for multiple rounds of genome engineering in B. subtilis. Finally, we applied multiplex genome editing to generate a B. subtilis 168 mutant strain with eight inactive extracellular protease genes in just two rounds of base editing and plasmid curing, suggesting that it is a powerful tool for gene manipulation in B. subtilis and industrial applications in the future.
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Affiliation(s)
- Sili Yu
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
- Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Marcus A. Price
- Centre for Synthetic and Systems Biology and UK Centre for Mammalian Synthetic Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH8 9YL, U.K
| | - Yu Wang
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
- Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Yang Liu
- Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Yanmei Guo
- Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Xiaomeng Ni
- Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Susan J. Rosser
- Centre for Synthetic and Systems Biology and UK Centre for Mammalian Synthetic Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH8 9YL, U.K
| | - Changhao Bi
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
- Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Meng Wang
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
- Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
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