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Wang J, Wang Z, Liu C, Song M, Xu Q, Liu Y, Yan H. Genome analysis of a newly isolated Bacillus velezensis-YW01 for biodegrading acetaldehyde. Biodegradation 2024; 35:539-549. [PMID: 38573500 DOI: 10.1007/s10532-024-10075-4] [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: 12/13/2023] [Accepted: 02/16/2024] [Indexed: 04/05/2024]
Abstract
Acetaldehyde (AL), a primary carcinogen, not only pollutes the environment, but also endangers human health after drinking alcohol. Here a promising bacterial strain was successfully isolated from a white wine cellar pool in the province of Shandong, China, and identified as Bacillus velezensis-YW01 with 16 S rDNA sequence. Using AL as sole carbon source, initial AL of 1 g/L could be completely biodegraded by YW01 within 84 h and the cell-free extracts of YW01 has also been detected to biodegrade the AL, which indicate that YW01 is a high-potential strain for the biodegradation of AL. The optimal culture conditions and the biodegradation of AL of YW01 are at pH 7.0 and 38 °C, respectively. To further analyze the biodegradation mechanism of AL, the whole genome of YW01 was sequenced. Genes ORF1040, ORF1814 and ORF0127 were revealed in KEGG, which encode for acetaldehyde dehydrogenase. Furthermore, ORF0881 and ORF052 encode for ethanol dehydrogenase. This work provides valuable information for exploring metabolic pathway of converting ethanol to AL and subsequently converting AL to carboxylic acid compounds, which opened up potential pathways for the development of microbial catalyst against AL.
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Affiliation(s)
- Jingjing Wang
- School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing, 100083, China
| | - Zhihao Wang
- School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing, 100083, China
| | - Chao Liu
- School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing, 100083, China
| | - Meijie Song
- School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing, 100083, China
| | - Qianqian Xu
- School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing, 100083, China
| | - Yang Liu
- School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing, 100083, China
| | - Hai Yan
- School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing, 100083, China.
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Dong W, Fu X, Zhou D, Teng J, Yang J, Zhen J, Zhao X, Liu Y, Zheng H, Bai W. Extracellular Overexpression of a Neutral Pullulanase in Bacillus subtilis through Multiple Copy Genome Integration and Atypical Secretion Pathway Enhancement. Bioengineering (Basel) 2024; 11:661. [PMID: 39061743 PMCID: PMC11273987 DOI: 10.3390/bioengineering11070661] [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: 06/08/2024] [Revised: 06/21/2024] [Accepted: 06/27/2024] [Indexed: 07/28/2024] Open
Abstract
Neutral pullulanases, having a good application prospect in trehalose production, showed a limited expression level. In order to address this issue, two approaches were utilized to enhance the yield of a new neutral pullulanase variant (PulA3E) in B. subtilis. One involved using multiple copies of genome integration to increase its expression level and fermentation stability. The other focused on enhancing the PulA-type atypical secretion pathway to further improve the secretory expression of PulA3E. Several strains with different numbers of genome integrations, ranging from one to four copies, were constructed. The four-copy genome integration strain PD showed the highest extracellular pullulanase activity. Additionally, the integration sites ytxE, ytrF, and trpP were selected based on their ability to enhance the PulA-type atypical secretion pathway. Furthermore, overexpressing the predicated regulatory genes comEA and yvbW of the PulA-type atypical secretion pathway in PD further improved its extracellular expression. Three-liter fermenter scale-up production of PD and PD-ARY yielded extracellular pullulanase activity of 1767.1 U/mL at 54 h and 2465.1 U/mL at 78 h, respectively. Finally, supplementing PulA3E with 40 U/g maltodextrin in the multi-enzyme catalyzed system resulted in the highest trehalose production of 166 g/L and the substrate conversion rate of 83%, indicating its potential for industrial application.
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Affiliation(s)
- Wenkang Dong
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, The College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China (Y.L.)
| | - Xiaoping Fu
- National Technology Innovation Center of Synthetic Biology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
- Industrial Enzymes National Engineering Research Center, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
- Tianjin Key Laboratory for Industrial Biological Systems and Bioprocessing Engineering, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Dasen Zhou
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, The College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China (Y.L.)
| | - Jia Teng
- Industrial Enzymes National Engineering Research Center, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Jun Yang
- Industrial Enzymes National Engineering Research Center, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Jie Zhen
- National Technology Innovation Center of Synthetic Biology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
- Industrial Enzymes National Engineering Research Center, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
- Tianjin Key Laboratory for Industrial Biological Systems and Bioprocessing Engineering, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Xingya Zhao
- National Technology Innovation Center of Synthetic Biology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
- Industrial Enzymes National Engineering Research Center, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
- Tianjin Key Laboratory for Industrial Biological Systems and Bioprocessing Engineering, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Yihan Liu
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, The College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China (Y.L.)
| | - Hongchen Zheng
- National Technology Innovation Center of Synthetic Biology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
- Industrial Enzymes National Engineering Research Center, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
- Tianjin Key Laboratory for Industrial Biological Systems and Bioprocessing Engineering, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
- Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Wenqin Bai
- National Technology Innovation Center of Synthetic Biology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
- Industrial Enzymes National Engineering Research Center, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
- Tianjin Key Laboratory for Industrial Biological Systems and Bioprocessing Engineering, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
- Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
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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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Yao D, Han X, Gao H, Wang B, Fang Z, Li H, Fang W, Xiao Y. Enhanced extracellular production of raw starch-degrading α-amylase in Bacillus subtilis through expression regulatory element modification and fermentation optimization. Microb Cell Fact 2023; 22:118. [PMID: 37381017 DOI: 10.1186/s12934-023-02116-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Accepted: 05/17/2023] [Indexed: 06/30/2023] Open
Abstract
BACKGROUND Raw starch-degrading α-amylase (RSDA) can hydrolyze raw starch at moderate temperatures, thus contributing to savings in starch processing costs. However, the low production level of RSDA limits its industrial application. Therefore, improving the extracellular expression of RSDA in Bacillus subtilis, a commonly used industrial expression host, has great value. RESULTS In this study, the extracellular production level of Pontibacillus sp. ZY raw starch-degrading α-amylase (AmyZ1) in B. subtilis was enhanced by expression regulatory element modification and fermentation optimization. As an important regulatory element of gene expression, the promoter, signal peptide, and ribosome binding site (RBS) sequences upstream of the amyZ1 gene were sequentially optimized. Initially, based on five single promoters, the dual-promoter Pveg-PylB was constructed by tandem promoter engineering. Afterward, the optimal signal peptide SPNucB was obtained by screening 173 B. subtilis signal peptides. Then, the RBS sequence was optimized using the RBS Calculator to obtain the optimal RBS1. The resulting recombinant strain WBZ-VY-B-R1 showed an extracellular AmyZ1 activity of 4824.2 and 41251.3 U/mL during shake-flask cultivation and 3-L fermenter fermentation, which were 2.6- and 2.5-fold greater than those of the original strain WBZ-Y, respectively. Finally, the extracellular AmyZ1 activity of WBZ-VY-B-R1 was increased to 5733.5 U/mL in shake flask by optimizing the type and concentration of carbon source, nitrogen source, and metal ions in the fermentation medium. On this basis, its extracellular AmyZ1 activity was increased to 49082.1 U/mL in 3-L fermenter by optimizing the basic medium components as well as the ratio of carbon and nitrogen sources in the feed solution. This is the highest production level reported to date for recombinant RSDA production. CONCLUSIONS This study represents a report on the extracellular production of AmyZ1 using B. subtilis as a host strain, and achieved the current highest expression level. The results of this study will lay a foundation for the industrial application of RSDA. In addition, the strategies employed here also provide a promising way for improving other protein production in B. subtilis.
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Affiliation(s)
- Dongbang Yao
- School of Life Sciences, Anhui University, Hefei, 230601, China
- Anhui Key Laboratory of Modern Biomanufacturing, Hefei, 230601, China
- Anhui Provincial Engineering Technology Research Center of Microorganisms and Biocatalysis, Hefei, 230601, China
- AHU Green Industry Innovation Research Institute, Hefei, 230088, China
| | - Xudong Han
- School of Life Sciences, Anhui University, Hefei, 230601, China
- Anhui Key Laboratory of Modern Biomanufacturing, Hefei, 230601, China
- Anhui Provincial Engineering Technology Research Center of Microorganisms and Biocatalysis, Hefei, 230601, China
- AHU Green Industry Innovation Research Institute, Hefei, 230088, China
| | - Huanhuan Gao
- School of Life Sciences, Anhui University, Hefei, 230601, China
- Anhui Key Laboratory of Modern Biomanufacturing, Hefei, 230601, China
- Anhui Provincial Engineering Technology Research Center of Microorganisms and Biocatalysis, Hefei, 230601, China
- AHU Green Industry Innovation Research Institute, Hefei, 230088, China
| | - Bin Wang
- School of Life Sciences, Anhui University, Hefei, 230601, China
- Anhui Key Laboratory of Modern Biomanufacturing, Hefei, 230601, China
- Anhui Provincial Engineering Technology Research Center of Microorganisms and Biocatalysis, Hefei, 230601, China
- AHU Green Industry Innovation Research Institute, Hefei, 230088, China
| | - Zemin Fang
- School of Life Sciences, Anhui University, Hefei, 230601, China
- Anhui Key Laboratory of Modern Biomanufacturing, Hefei, 230601, China
- Anhui Provincial Engineering Technology Research Center of Microorganisms and Biocatalysis, Hefei, 230601, China
- AHU Green Industry Innovation Research Institute, Hefei, 230088, China
| | - He Li
- School of Life Sciences, Anhui University, Hefei, 230601, China
- Anhui Key Laboratory of Modern Biomanufacturing, Hefei, 230601, China
- Anhui Provincial Engineering Technology Research Center of Microorganisms and Biocatalysis, Hefei, 230601, China
- AHU Green Industry Innovation Research Institute, Hefei, 230088, China
| | - Wei Fang
- School of Life Sciences, Anhui University, Hefei, 230601, China.
- Anhui Key Laboratory of Modern Biomanufacturing, Hefei, 230601, China.
- Anhui Provincial Engineering Technology Research Center of Microorganisms and Biocatalysis, Hefei, 230601, China.
- AHU Green Industry Innovation Research Institute, Hefei, 230088, China.
| | - Yazhong Xiao
- School of Life Sciences, Anhui University, Hefei, 230601, China.
- Anhui Key Laboratory of Modern Biomanufacturing, Hefei, 230601, China.
- Anhui Provincial Engineering Technology Research Center of Microorganisms and Biocatalysis, Hefei, 230601, China.
- AHU Green Industry Innovation Research Institute, Hefei, 230088, China.
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Li Y, Wu Y, Liu Y, Li J, Du G, Lv X, Liu L. A genetic toolkit for efficient production of secretory protein in Bacillus subtilis. BIORESOURCE TECHNOLOGY 2022; 363:127885. [PMID: 36064082 DOI: 10.1016/j.biortech.2022.127885] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 08/27/2022] [Accepted: 08/29/2022] [Indexed: 06/15/2023]
Abstract
Bacillus subtilis is a microbial cell factory widely used to produce recombinant proteins, but the expression of heterologous proteins is often severely hampered. This study constructed a genetic toolkit for improving the secretory efficiency of heterologous proteins in Bacillus subtilis. First, the protease-deficient hosts were reconstructed. Then, two endogenous constitutive promoters, Phag and PspovG, were screened. Next, a method called systemic combinatorial optimization of ribosome binding site (RBS) equipped with signal peptide (SCORES) was designed for optimizing the secretion and translation of the heterologous protein. Finally, Serratia marcescens nonspecific endonuclease (SMNE), which causes cell death by degrading nucleic acids, was expressed. The enzyme activity in the shake flask reached 7.5 × 106 U/L, which was 7.5-times that of the control RBS and signal peptide combination (RS0). This study not only expanded on the synthetic biology toolbox in B. subtilis but also provided strategies to create a prokaryotic protein expression system.
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Affiliation(s)
- 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
| | - Yaokang Wu
- 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
| | - 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
| | - 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.
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