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Fu Y, Rao Y, Liao Y, Zhang Q, Ma X, Cai D, Chen S. Protein engineering, expression optimization, and application of alkaline protease from Alkalihalobacillus clausii FYX. Int J Biol Macromol 2025; 307:141891. [PMID: 40064254 DOI: 10.1016/j.ijbiomac.2025.141891] [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: 01/15/2025] [Revised: 02/25/2025] [Accepted: 03/07/2025] [Indexed: 03/14/2025]
Abstract
Alkaline protease has been commercially used in the areas of detergents, food and agriculture, and improving the performance and production of alkaline protease serves as an important role in promoting its market expansion. Here, an alkaline protease AE0 from Alkalihalobacillus clausii FYX was firstly characterized in Bacillus licheniformis DW2△aprE, the optimal temperature and pH of AE0 were 60 °C and 10.5, the Km and Kcat values for casein were 17.25 mg/mL and 60.51 s-1, respectively, as well as the specific activity was 21,365.93 U/mg. Subsequently, six mutants (G113I, H118D, T141Y, S151A, N167S and Q185S) were obtained through semi-rational design, and G113I exhibited the most optimal performance with a specific activity of 28,150.64 U/mg. Furthermore, the double mutant AE0DM1 and triple mutant AE0MM2 were attained, and their specific activities reached 31,026.32 U/mg and 31,868.56 U/mg, respectively. Concurrently, through the evaluation of thermal stability and measurement of reaction kinetic parameters, G113I was advantageous for enhancing the thermal stability of AE0, while H118D and N167S were more beneficial for enhancing the catalytic efficiency. In addition, the enzyme activity of AE0MM2 produced by strain DW2△aprE/RC0-AE0MM2 was increased by 178.5 % through promoter engineering, reached 36,685.33 U/mL, which also showed the wonderful performance on enzymatic hydrolysis of soybean meal to enhance its utilization rate. Taken together, this work provided an alkaline protease with improved thermal stability and catalytic efficiency, as well as an efficient expression system of alkaline protease for industrial application.
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Affiliation(s)
- Yuxi Fu
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Environmental Microbial Technology Center of Hubei Province, College of Life Sciences, Hubei University, Wuhan 430062, PR China
| | - Yi Rao
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Environmental Microbial Technology Center of Hubei Province, College of Life Sciences, Hubei University, Wuhan 430062, PR China
| | - Yongqing Liao
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Environmental Microbial Technology Center of Hubei Province, College of Life Sciences, Hubei University, Wuhan 430062, PR China
| | - Qing Zhang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Environmental Microbial Technology Center of Hubei Province, College of Life Sciences, Hubei University, Wuhan 430062, PR China
| | - Xin Ma
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Environmental Microbial Technology Center of Hubei Province, College of Life Sciences, Hubei University, Wuhan 430062, PR China
| | - Dongbo Cai
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Environmental Microbial Technology Center of Hubei Province, College of Life Sciences, Hubei University, Wuhan 430062, PR China.
| | - Shouwen Chen
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Environmental Microbial Technology Center of Hubei Province, College of Life Sciences, Hubei University, Wuhan 430062, PR China.
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2
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Sadeeq M, Li Y, Wang C, Hou F, Zuo J, Xiong P. Unlocking the power of antimicrobial peptides: advances in production, optimization, and therapeutics. Front Cell Infect Microbiol 2025; 15:1528583. [PMID: 40365533 PMCID: PMC12070195 DOI: 10.3389/fcimb.2025.1528583] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2024] [Accepted: 03/19/2025] [Indexed: 05/15/2025] Open
Abstract
Antimicrobial peptides (AMPs) are critical effectors of innate immunity, presenting a compelling alternative to conventional antibiotics amidst escalating antimicrobial resistance. Their broad-spectrum efficacy and inherent low resistance development are countered by production challenges, including limited yields and proteolytic degradation, which restrict their clinical translation. While chemical synthesis offers precise structural control, it is often prohibitively expensive and complex for large-scale production. Heterologous expression systems provide a scalable, cost-effective platform, but necessitate optimization. This review comprehensively examines established and emerging AMP production strategies, encompassing fusion protein technologies, molecular engineering approaches, rational peptide design, and post-translational modifications, with an emphasis on maximizing yield, bioactivity, stability, and safety. Furthermore, we underscore the transformative role of artificial intelligence, particularly machine learning algorithms, in accelerating AMP discovery and optimization, thereby propelling their expanded therapeutic application and contributing to the global fight against drug-resistant infections.
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Affiliation(s)
| | | | | | | | - Jia Zuo
- Biosynthesis and Bio Transformation Center, School of Life Sciences and Medicine,
Shandong University of Technology (SDUT), Zibo, China
| | - Peng Xiong
- Biosynthesis and Bio Transformation Center, School of Life Sciences and Medicine,
Shandong University of Technology (SDUT), Zibo, China
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3
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Schilling T, Biedendieck R, Moran-Torres R, Saaranen MJ, Ruddock LW, Daniel R, van Dijl JM. Toward Antibody Production in Genome-Minimized Bacillus subtilis Strains. ACS Synth Biol 2025; 14:740-755. [PMID: 40013841 PMCID: PMC11934139 DOI: 10.1021/acssynbio.4c00688] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2024] [Revised: 01/10/2025] [Accepted: 02/13/2025] [Indexed: 02/28/2025]
Abstract
Bacillus subtilis is a bacterial cell factory with outstanding protein secretion capabilities that has been deployed as a workhorse for the production of industrial enzymes for more than a century. Nevertheless, the production of other proteins with B. subtilis, such as antibody formats, has thus far been challenging due to specific requirements that relate to correct protein folding and disulfide bond formation upon export from the cytoplasm. In the present study, we explored the possibility of producing functional antibody formats, such as scFvs and scFabs, using the genome-reduced Midi- and MiniBacillus strain lineage. The applied workflow included selection of optimal chassis strains, appropriate expression vectors, signal peptides, growth media, and analytical methods to verify the functionality of the secreted antibody fragments. The production of scFv fragments was upscaled to the 1 L bioreactor level. As demonstrated for a human C-reactive protein-binding scFv antibody by mass spectrometry, biolayer interferometry, circular dichroism, free thiol cross-linking with N-ethylmaleimide, and nano-differential scanning fluorimetry, MidiBacillus strains can secrete fully functional, natively folded, disulfide-bonded, and thermostable antibody fragments. We therefore conclude that genome-reduced B. subtilis chassis strains are capable of secreting high-quality antibody fragments.
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Affiliation(s)
- Tobias Schilling
- University
Medical Center Groningen, Department of Medical Microbiology, University of Groningen, Hanzeplein 1, P.O. Box 30001, 9700RB Groningen, The Netherlands
| | - Rebekka Biedendieck
- Braunschweig
Centre of Systems Biology (BRICS) and Institute of Microbiology, Technische Universität Braunschweig, Rebenring 56, 38106 Braunschweig, Germany
| | - Rafael Moran-Torres
- Theoretical
Biophysics, Humboldt-Universität
zu Berlin, 10115 Berlin, Germany
| | - Mirva J. Saaranen
- Faculty
of Biochemistry and Molecular Medicine, Protein and Structural Biology
Research Unit, University of Oulu, Aapistie 7B, 90220 Oulu, Finland
| | - Lloyd W. Ruddock
- Faculty
of Biochemistry and Molecular Medicine, Protein and Structural Biology
Research Unit, University of Oulu, Aapistie 7B, 90220 Oulu, Finland
| | - Rolf Daniel
- Institute
of Microbiology and Genetics, Department of Genomic and Applied Microbiology, Georg-August-Universität Göttingen, Grisebachstr. 8, 37077 Göttingen, Germany
| | - Jan Maarten van Dijl
- University
Medical Center Groningen, Department of Medical Microbiology, University of Groningen, Hanzeplein 1, P.O. Box 30001, 9700RB Groningen, The Netherlands
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4
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Li W, Wang X, Chen K, Zhu Y, Yang G, Jin Y, Wang J. Engineered Bacillus subtilis WB600/ZD prevents Salmonella Infantis-induced intestinal inflammation and alters the colon microbiota in a mouse model. Vet Res 2025; 56:35. [PMID: 39920770 PMCID: PMC11806837 DOI: 10.1186/s13567-024-01438-z] [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: 07/13/2024] [Accepted: 11/04/2024] [Indexed: 02/09/2025] Open
Abstract
Antimicrobial peptides (AMPs) are instrumental in maintaining intestinal homeostasis and have emerged as potential therapeutic candidates for ameliorating intestinal bacterial infections. However, the intrinsic instability associated with the in vivo delivery of AMPs constitutes a substantial impediment to their therapeutic efficacy in treating infections. In this study, we genetically modified Bacillus subtilis (B. subtilis) WB600 to express Zophobas atratus defensin (ZD), an antimicrobial peptide with broad-spectrum activity isolated from Zophobas atratus, for oral administration. This engineered strain effectively protects against Salmonella Infantis (S. Infantis) infection in mice. Pretreatment with WB600/ZD prevented NF-κB pathway activation induced by S. Infantis infection and increased expression of antioxidant and tight junction proteins, thus alleviating the severity of intestinal inflammation in both the jejunum and ileum (P < 0.01). Moreover, WB600/ZD pretreatment facilitated the growth of beneficial bacteria such as Lachnospiraceae, Butyricicoccus, Eubacterium_xylanophilum, and Clostridia_UCG-014 while decreasing the abundance of pathogenic bacteria such as Escherichia-Shigella and Salmonella (P < 0.05). In conclusion, this study underscores the protective effects of WB600/ZD on S. Infantis-induced intestinal inflammation, suggesting that oral delivery of B. subtilis WB600/ZD may be a promising prophylactic strategy for combating bacterial infections in the intestine.
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Affiliation(s)
- Wei Li
- College of Veterinary Medicine, China Agricultural University, Beijing, 100193, China
- Sanya Institute of China Agricultural University, Sanya, 572025, Hainan, China
| | - Xue Wang
- College of Veterinary Medicine, Inner Mongolia Agricultural University, Hohhot, 010000, China
| | - Keyuan Chen
- College of Veterinary Medicine, China Agricultural University, Beijing, 100193, China
- Sanya Institute of China Agricultural University, Sanya, 572025, Hainan, China
| | - Yaohong Zhu
- College of Veterinary Medicine, China Agricultural University, Beijing, 100193, China
- Sanya Institute of China Agricultural University, Sanya, 572025, Hainan, China
| | - Guiyan Yang
- College of Veterinary Medicine, China Agricultural University, Beijing, 100193, China
- Sanya Institute of China Agricultural University, Sanya, 572025, Hainan, China
| | - Yipeng Jin
- College of Veterinary Medicine, China Agricultural University, Beijing, 100193, China.
| | - Jiufeng Wang
- College of Veterinary Medicine, China Agricultural University, Beijing, 100193, China.
- Sanya Institute of China Agricultural University, Sanya, 572025, Hainan, China.
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5
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Zhang K, Luo H, Zhu X, Liu W, Yu X, Tao W, Lin H, Hou M, Wu J. Construction of Bacillus subtilis chassis strain with enhanced α-amylase expression capability based on CRISPRi screening. Int J Biol Macromol 2024; 283:137497. [PMID: 39528193 DOI: 10.1016/j.ijbiomac.2024.137497] [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: 06/09/2024] [Revised: 11/08/2024] [Accepted: 11/08/2024] [Indexed: 11/16/2024]
Abstract
Bacillus subtilis has been widely used in the expression of recombinant proteins due to its food safe and powerful secretion characteristic, but the current production level cannot meet the increasing industrial needs. To enhance the production of recombinant protein, we first screened target key genes that are directly or indirectly involved in protein synthesis, using CRISPRi technology targeting the whole genome, with industrial valuable Bacillus stearothermophilus α-amylase as the model protein. Then the screened key genes were combined, yielding a chassis strain that owning enhanced protein expression capability. Following overlaying molecular chaperone GroES/L and peptidoglycan glycosyltransferase PonA, α-amylase activity reached 102,893 U/mL in a 3-L fermenter, the highest level reported till now. Finally, transcriptome analysis showed that the enhanced recombinant expression may be due to more rational allocation of energy and resources. These strategies can be well implicated in engineering other microbial cell factories for higher industrial production.
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Affiliation(s)
- Kang Zhang
- School of Biotechnology and Key Laboratory of Industrial Biotechnology Ministry of Education, Jiangnan University, 1800 Lihu Avenue, Wuxi, Jiangsu 214122, China; State Key Laboratory of Food Science and Resources, Jiangnan University, 1800 Lihu Avenue, Wuxi, Jiangsu 214122, China; International Joint Laboratory on Food Safety, Jiangnan University, 1800 Lihu Avenue, Wuxi, Jiangsu 214122, China
| | - Hui Luo
- School of Biotechnology and Key Laboratory of Industrial Biotechnology Ministry of Education, Jiangnan University, 1800 Lihu Avenue, Wuxi, Jiangsu 214122, China; State Key Laboratory of Food Science and Resources, Jiangnan University, 1800 Lihu Avenue, Wuxi, Jiangsu 214122, China; International Joint Laboratory on Food Safety, Jiangnan University, 1800 Lihu Avenue, Wuxi, Jiangsu 214122, China
| | - Xuyang Zhu
- School of Biotechnology and Key Laboratory of Industrial Biotechnology Ministry of Education, Jiangnan University, 1800 Lihu Avenue, Wuxi, Jiangsu 214122, China; State Key Laboratory of Food Science and Resources, Jiangnan University, 1800 Lihu Avenue, Wuxi, Jiangsu 214122, China; International Joint Laboratory on Food Safety, Jiangnan University, 1800 Lihu Avenue, Wuxi, Jiangsu 214122, China
| | - Weiqiong Liu
- School of Biotechnology and Key Laboratory of Industrial Biotechnology Ministry of Education, Jiangnan University, 1800 Lihu Avenue, Wuxi, Jiangsu 214122, China; State Key Laboratory of Food Science and Resources, Jiangnan University, 1800 Lihu Avenue, Wuxi, Jiangsu 214122, China; International Joint Laboratory on Food Safety, Jiangnan University, 1800 Lihu Avenue, Wuxi, Jiangsu 214122, China
| | - Xinrui Yu
- School of Biotechnology and Key Laboratory of Industrial Biotechnology Ministry of Education, Jiangnan University, 1800 Lihu Avenue, Wuxi, Jiangsu 214122, China; State Key Laboratory of Food Science and Resources, Jiangnan University, 1800 Lihu Avenue, Wuxi, Jiangsu 214122, China; International Joint Laboratory on Food Safety, Jiangnan University, 1800 Lihu Avenue, Wuxi, Jiangsu 214122, China
| | - Wei Tao
- School of Biotechnology and Key Laboratory of Industrial Biotechnology Ministry of Education, Jiangnan University, 1800 Lihu Avenue, Wuxi, Jiangsu 214122, China; State Key Laboratory of Food Science and Resources, Jiangnan University, 1800 Lihu Avenue, Wuxi, Jiangsu 214122, China; International Joint Laboratory on Food Safety, Jiangnan University, 1800 Lihu Avenue, Wuxi, Jiangsu 214122, China
| | - Huanliu Lin
- School of Biotechnology and Key Laboratory of Industrial Biotechnology Ministry of Education, Jiangnan University, 1800 Lihu Avenue, Wuxi, Jiangsu 214122, China; State Key Laboratory of Food Science and Resources, Jiangnan University, 1800 Lihu Avenue, Wuxi, Jiangsu 214122, China; International Joint Laboratory on Food Safety, Jiangnan University, 1800 Lihu Avenue, Wuxi, Jiangsu 214122, China
| | - Minglei Hou
- School of Biotechnology and Key Laboratory of Industrial Biotechnology Ministry of Education, Jiangnan University, 1800 Lihu Avenue, Wuxi, Jiangsu 214122, China; State Key Laboratory of Food Science and Resources, Jiangnan University, 1800 Lihu Avenue, Wuxi, Jiangsu 214122, China; International Joint Laboratory on Food Safety, Jiangnan University, 1800 Lihu Avenue, Wuxi, Jiangsu 214122, China
| | - Jing Wu
- School of Biotechnology and Key Laboratory of Industrial Biotechnology Ministry of Education, Jiangnan University, 1800 Lihu Avenue, Wuxi, Jiangsu 214122, China; State Key Laboratory of Food Science and Resources, Jiangnan University, 1800 Lihu Avenue, Wuxi, Jiangsu 214122, China; International Joint Laboratory on Food Safety, Jiangnan University, 1800 Lihu Avenue, Wuxi, Jiangsu 214122, China.
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6
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Wang B, Wu Y, Lv X, Liu L, Li J, Du G, Chen J, Liu Y. Synergistic regulation of chassis cell growth and screening of promoters, signal peptides and fusion protein linkers for enhanced recombinant protein expression in Bacillus subtilis. Int J Biol Macromol 2024; 280:136037. [PMID: 39332549 DOI: 10.1016/j.ijbiomac.2024.136037] [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: 07/08/2024] [Revised: 09/24/2024] [Accepted: 09/24/2024] [Indexed: 09/29/2024]
Abstract
Growth-advantageous microbial chassis cells are beneficial for shortening fermentation period and boosting biomolecule productivity. This study focused on enhancing recombinant proteins synthesis efficiency in Bacillus subtilis by CRISPRi-mediated metabolism regulation for improved cell growth and screening expression elements. Specifically, by repressing odhA gene expression to reallocate cellular resource and overexpressing atpC, atpD and atpG genes to reprogram energy metabolism, the growth-advantageous chassis cell with high specific growth rate of 0.63 h-1 and biomass yield of 0.41 g DCW/g glucose in minimum medium was developed, representing 61.54 % and 46.43 % increasements compared to B. subtilis 168. Subsequently, using screened optimal P566 promoter and (EAAAK)3 protein linker, secretory bovine alpha-lactalbumin (α-LA) titer reached 1.02 mg/L. Finally, to test protein synthesis capability of cells, intracellular GFP, secretory α-LA and α-amylase were expressed with P566 promoter, representing 43.76 %, 75.49 % and 82.98 % increasements. The growth-advantageous B. subtilis chassis cells exhibit their potential to boost bioproduction productivity.
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Affiliation(s)
- Bin Wang
- School of Biotechnology and Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China; Science Center for Future Foods, Jiangnan University, Wuxi 214122, China; Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology, Jiangnan University, Wuxi 214122, China; Jiangsu Province Engineering Research Center of Food Synthetic Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Yaokang Wu
- School of Biotechnology and Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China; Science Center for Future Foods, Jiangnan University, Wuxi 214122, China; Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology, Jiangnan University, Wuxi 214122, China; Jiangsu Province Engineering Research Center of Food Synthetic Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Xueqin Lv
- School of Biotechnology and Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China; Science Center for Future Foods, Jiangnan University, Wuxi 214122, China; Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology, Jiangnan University, Wuxi 214122, China; Jiangsu Province Engineering Research Center of Food Synthetic Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Long Liu
- School of Biotechnology and Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China; Science Center for Future Foods, Jiangnan University, Wuxi 214122, China; Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology, Jiangnan University, Wuxi 214122, China; Jiangsu Province Engineering Research Center of Food Synthetic Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Jianghua Li
- Science Center for Future Foods, Jiangnan University, Wuxi 214122, China; Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology, Jiangnan University, Wuxi 214122, China; Jiangsu Province Engineering Research Center of Food Synthetic Biotechnology, Jiangnan University, Wuxi 214122, China.
| | - Guocheng Du
- School of Biotechnology and Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China; Science Center for Future Foods, Jiangnan University, Wuxi 214122, China; Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology, Jiangnan University, Wuxi 214122, China; Jiangsu Province Engineering Research Center of Food Synthetic Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Jian Chen
- Science Center for Future Foods, Jiangnan University, Wuxi 214122, China; Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology, Jiangnan University, Wuxi 214122, China; Jiangsu Province Engineering Research Center of Food Synthetic Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Yanfeng Liu
- School of Biotechnology and Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China; Science Center for Future Foods, Jiangnan University, Wuxi 214122, China; Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology, Jiangnan University, Wuxi 214122, China; Jiangsu Province Engineering Research Center of Food Synthetic Biotechnology, Jiangnan University, Wuxi 214122, China.
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7
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Zhu X, Luo H, Yu X, Lv H, Su L, Zhang K, Wu J. Genome-Wide CRISPRi Screening of Key Genes for Recombinant Protein Expression in Bacillus Subtilis. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2404313. [PMID: 38952047 PMCID: PMC11434012 DOI: 10.1002/advs.202404313] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2024] [Revised: 05/29/2024] [Indexed: 07/03/2024]
Abstract
Bacillus subtilis is an industrially important microorganism that is often used as a microbial cell factory for the production of recombinant proteins due to its food safety, rapid growth, and powerful secretory capacity. However, the lack of data on functional genes related to recombinant protein production has hindered the further development of B. subtilis cell factories. Here, a strategy combining genome-wide CRISPRi screening and targeted CRISPRa activation to enhance recombinant protein expression is proposed. First, a CRISPRi library covering a total of 4225 coding genes (99.7%) in the B. subtilis genome and built the corresponding high-throughput screening methods is constructed. Twelve key genes for recombinant protein expression are identified, including targets without relevant functional annotations. Meanwhile, the transcription of recombinant protein genes by CRISPRa is up-regulated. These screened or selected genes can be easily applied to metabolic engineering by constructing sgRNA arrays. The relationship between differential pathways and recombinant protein expression in engineered strains by transcriptome analysis is also revealed. High-density fermentation and generalisability validation results prove the reliability of the strategy. This method can be extended to other industrial hosts to support functional gene annotation and the design of novel cell factories.
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Affiliation(s)
- Xuyang Zhu
- School of Biotechnology and Key Laboratory of Industrial Biotechnology Ministry of EducationState Key Laboratory of Food Science and ResourcesInternational Joint Laboratory on Food SafetyJiangnan UniversityWuxi214122China
| | - Hui Luo
- School of Biotechnology and Key Laboratory of Industrial Biotechnology Ministry of EducationState Key Laboratory of Food Science and ResourcesInternational Joint Laboratory on Food SafetyJiangnan UniversityWuxi214122China
| | - Xinrui Yu
- School of Biotechnology and Key Laboratory of Industrial Biotechnology Ministry of EducationState Key Laboratory of Food Science and ResourcesInternational Joint Laboratory on Food SafetyJiangnan UniversityWuxi214122China
| | - Huihui Lv
- School of Biotechnology and Key Laboratory of Industrial Biotechnology Ministry of EducationState Key Laboratory of Food Science and ResourcesInternational Joint Laboratory on Food SafetyJiangnan UniversityWuxi214122China
| | - Lingqia Su
- School of Biotechnology and Key Laboratory of Industrial Biotechnology Ministry of EducationState Key Laboratory of Food Science and ResourcesInternational Joint Laboratory on Food SafetyJiangnan UniversityWuxi214122China
| | - Kang Zhang
- School of Biotechnology and Key Laboratory of Industrial Biotechnology Ministry of EducationState Key Laboratory of Food Science and ResourcesInternational Joint Laboratory on Food SafetyJiangnan UniversityWuxi214122China
| | - Jing Wu
- School of Biotechnology and Key Laboratory of Industrial Biotechnology Ministry of EducationState Key Laboratory of Food Science and ResourcesInternational Joint Laboratory on Food SafetyJiangnan UniversityWuxi214122China
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8
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Liu S, Lu SY, Patel M, Qureshi N, Dunlap C, Hoecker E, Skory CD. Production of a Bacteriocin Like Protein PEG 446 from Clostridium tyrobutyricum NRRL B-67062. Probiotics Antimicrob Proteins 2024; 16:1411-1426. [PMID: 38252201 PMCID: PMC11322243 DOI: 10.1007/s12602-023-10211-1] [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] [Accepted: 12/29/2023] [Indexed: 01/23/2024]
Abstract
Clostridium tyrobutyricum strain NRRL B-67062 was previously isolated from an ethanol production facility and shown to produce high yields of butyric acid. In addition, the cell-free supernatant of the fermentation broth from NRRL B-67062 contained antibacterial activity against certain Gram-positive bacteria. To determine the source of this antibacterial activity, we report the genome and genome mining of this strain. The complete genome of NRRL B-67062 showed one circular chromosome of 3,242,608 nucleotides, 3114 predicted coding sequences, 79 RNA genes, and a G+C content of 31.0%. Analyses of the genome data for genes potentially associated with antimicrobial features were sought after by using BAGEL-4 and anti-SMASH databases. Among the leads, a polypeptide of 66 amino acids (PEG 446) contains the DUF4177 domain, which is an uncharacterized highly conserved domain (pfam13783). The cloning and expression of the peg446 gene in Escherichia coli and Bacillus subtilis confirmed the antibacterial property against Lactococcus lactis LM 0230, Limosilactobacillus fermentum 0315-25, and Listeria innocua NRRL B-33088 by gel overlay and well diffusion assays. Molecular modeling suggested that PEG 446 contains one alpha-helix and three anti-parallel short beta-sheets. These results will aid further functional studies and facilitate simultaneously fermentative production of both butyric acid and a putative bacteriocin from agricultural waste and lignocellulosic biomass materials.
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Affiliation(s)
- Siqing Liu
- U.S. Department of Agriculture, Agricultural Research Service, National Center for Agricultural Utilization Research, Renewable Product Technology Research Unit, Peoria, IL, 61604, USA.
| | - Shao-Yeh Lu
- U.S. Department of Agriculture, Agricultural Research Service, National Center for Agricultural Utilization Research, Renewable Product Technology Research Unit, Peoria, IL, 61604, USA
| | - Maulik Patel
- Oak Ridge Institute for Science and Education (ORISE), Oak Ridge, TN, 37830, USA
| | - Nasib Qureshi
- U.S. Department of Agriculture, Agricultural Research Service, National Center for Agricultural Utilization Research, Bioenergy Research Unit, Peoria, IL, 61604, USA
| | - Christopher Dunlap
- U.S. Department of Agriculture, Agricultural Research Service, National Center for Agricultural Utilization Research, Crop Bioprotection Research Unit, Peoria, IL, 61604, USA
| | - Eric Hoecker
- U.S. Department of Agriculture, Agricultural Research Service, National Center for Agricultural Utilization Research, Renewable Product Technology Research Unit, Peoria, IL, 61604, USA
| | - Christopher D Skory
- U.S. Department of Agriculture, Agricultural Research Service, National Center for Agricultural Utilization Research, Renewable Product Technology Research Unit, Peoria, IL, 61604, USA
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9
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Zhao G, Wang J, Tian Y, Wang H, Huang X. Nitroreductase DnrA, Utilizing Strategies Secreted in Bacillus sp. Za and SCK6, Enhances the Detoxification of Acifluorfen. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:15633-15642. [PMID: 38950134 DOI: 10.1021/acs.jafc.4c03397] [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: 07/03/2024]
Abstract
The residues of acifluorfen present a serious threat to the agricultural environment and sensitive crops. DnrA, a nitroreductase, is an intracellular enzyme that restricts the application of wild-type Bacillus sp. Za in environmental remediation. In this study, two strategies were employed to successfully secrete DnrA in strains SCK6 and Za, and the secretion expression conditions were optimized to achieve rapid degradation of acifluorfen. Under the optimal conditions, the relative activities of the DnrA supernatant from strains SCK6-D and Za-W were 3.06-fold and 3.53-fold higher than that of strain Za, respectively. While all three strains exhibited similar tolerance to different concentrations of acifluorfen, strains SCK6-D and Za-W demonstrated significantly faster degradation efficiency compared to strain Za. Furthermore, the DnrA supernatant from strains SCK6-D and Za-W could effectively reduce the toxicity of acifluorfen on maize and cucumber seedlings. This study provides an effective technical approach for the rapid degradation of acifluorfen.
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Affiliation(s)
- Guoqiang Zhao
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu 210095, PR China
| | - Juanjuan Wang
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu 210095, PR China
| | - Yanning Tian
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu 210095, PR China
| | - Hancheng Wang
- Guizhou Academy of Tobacco Science, Guiyang, Guizhou 550081, PR China
| | - Xing Huang
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu 210095, PR China
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10
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Senger J, Seitl I, Pross E, Fischer L. Secretion of the cytoplasmic and high molecular weight β-galactosidase of Paenibacillus wynnii with Bacillus subtilis. Microb Cell Fact 2024; 23:170. [PMID: 38867249 PMCID: PMC11167759 DOI: 10.1186/s12934-024-02445-7] [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: 01/18/2024] [Accepted: 05/30/2024] [Indexed: 06/14/2024] Open
Abstract
BACKGROUND The gram-positive bacterium Bacillus subtilis is widely used for industrial enzyme production. Its ability to secrete a wide range of enzymes into the extracellular medium especially facilitates downstream processing since cell disruption is avoided. Although various heterologous enzymes have been successfully secreted with B. subtilis, the secretion of cytoplasmic enzymes with high molecular weight is challenging. Only a few studies report on the secretion of cytoplasmic enzymes with a molecular weight > 100 kDa. RESULTS In this study, the cytoplasmic and 120 kDa β-galactosidase of Paenibacillus wynnii (β-gal-Pw) was expressed and secreted with B. subtilis SCK6. Different strategies were focused on to identify the best secretion conditions. Tailormade codon-optimization of the β-gal-Pw gene led to an increase in extracellular β-gal-Pw production. Consequently, the optimized gene was used to test four signal peptides and two promoters in different combinations. Differences in extracellular β-gal-Pw activity between the recombinant B. subtilis strains were observed with the successful secretion being highly dependent on the specific combination of promoter and signal peptide used. Interestingly, signal peptides of both the general secretory- and the twin-arginine translocation pathway mediated secretion. The highest extracellular activity of 55.2 ± 6 µkat/Lculture was reached when secretion was mediated by the PhoD signal peptide and expression was controlled by the PAprE promoter. Production of extracellular β-gal-Pw was further enhanced 1.4-fold in a bioreactor cultivation to 77.5 ± 10 µkat/Lculture with secretion efficiencies of more than 80%. CONCLUSION For the first time, the β-gal-Pw was efficiently secreted with B. subtilis SCK6, demonstrating the potential of this strain for secretory production of cytoplasmic, high molecular weight enzymes.
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Affiliation(s)
- Jana Senger
- Institute of Food Science and Biotechnology, Department of Biotechnology and Enzyme Science, University of Hohenheim, Garbenstr. 25, 70599, Stuttgart, Germany
| | - Ines Seitl
- Institute of Food Science and Biotechnology, Department of Biotechnology and Enzyme Science, University of Hohenheim, Garbenstr. 25, 70599, Stuttgart, Germany
| | - Eva Pross
- Institute of Food Science and Biotechnology, Department of Biotechnology and Enzyme Science, University of Hohenheim, Garbenstr. 25, 70599, Stuttgart, Germany
| | - Lutz Fischer
- Institute of Food Science and Biotechnology, Department of Biotechnology and Enzyme Science, University of Hohenheim, Garbenstr. 25, 70599, Stuttgart, Germany.
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11
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Kes MB, Wang B, van Ulsen P, Hamoen LW, Luirink J. Development of a split-luciferase assay to establish optimal protein secretion conditions for protein production by Bacillus subtilis. MICROBIOLOGY (READING, ENGLAND) 2024; 170:001460. [PMID: 38847798 PMCID: PMC11261832 DOI: 10.1099/mic.0.001460] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Accepted: 04/26/2024] [Indexed: 07/24/2024]
Abstract
Bacillus subtilis is a Gram-positive bacterium that is frequently used in the bioindustry for the production of various proteins, because of its superior protein secretion capacities. To determine optimal conditions for protein secretion by B. subtilis, a quick and sensitive method for measuring protein secretion is crucial. A fast and universal assay is most useful for detecting diverse proteins in a high-throughput manner. In this study, we introduce a split-luciferase-based method for measuring protein secretion by B. subtilis. The NanoBiT system was used to monitor secretion of four different proteins: xylanase A, amylase M, protein glutaminase A, and GFP nanobody. Our findings underscore the split-luciferase system as a quick, sensitive, and user-friendly method.
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Affiliation(s)
- Mariah B.M.J. Kes
- Molecular Microbiology, Amsterdam Institute of Molecular and Life Sciences, Vrije Universiteit Amsterdam, De Boelelaan 1108, 1081 HZ, Amsterdam, The Netherlands
| | - Biwen Wang
- Bacterial Cell Biology, Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1098 XH, Amsterdam, The Netherlands
| | - Peter van Ulsen
- Molecular Microbiology, Amsterdam Institute of Molecular and Life Sciences, Vrije Universiteit Amsterdam, De Boelelaan 1108, 1081 HZ, Amsterdam, The Netherlands
| | - Leendert W. Hamoen
- Bacterial Cell Biology, Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1098 XH, Amsterdam, The Netherlands
| | - Joen Luirink
- Molecular Microbiology, Amsterdam Institute of Molecular and Life Sciences, Vrije Universiteit Amsterdam, De Boelelaan 1108, 1081 HZ, Amsterdam, The Netherlands
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12
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Saeed M, Yan M, Ni Z, Hussain N, Chen H. Molecular strategies to enhance the keratinase gene expression and its potential implications in poultry feed industry. Poult Sci 2024; 103:103606. [PMID: 38479096 PMCID: PMC10951097 DOI: 10.1016/j.psj.2024.103606] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2024] [Revised: 02/18/2024] [Accepted: 02/27/2024] [Indexed: 03/24/2024] Open
Abstract
The tons of keratin waste are produced by the poultry and meat industry which is an insoluble and protein-rich material found in hair, feathers, wool, and some epidermal wastes. These waste products could be degraded and recycled to recover protein, which can save our environment. One of the potential strategy to achieve this target is use of microbial biotreatment which is more convenient, cost-effective, and environment-friendly by formulating hydrolysate complexes that could be administered as protein supplements, bioactive peptides, or animal feed ingredients. Keratin degradation shows great promise for long-term protein and amino acid recycling. According to the MEROPS database, known keratinolytic enzymes currently belong to at least 14 different protease families, including S1, S8, S9, S10, S16, M3, M4, M14, M16, M28, M32, M36, M38, and M55. In addition to exogenous attack (proteases from families S9, S10, M14, M28, M38, and M55), the various keratinolytic enzymes also function via endo-attack (proteases from families S1, S8, S16, M4, M16, and M36). Biotechnological methods have shown great promise for enhancing keratinase expression in different strains of microbes and different protein engineering techniques in genetically modified microbes such as bacteria and some fungi to enhance keratinase production and activity. Some microbes produce specific keratinolytic enzymes that can effectively degrade keratin substrates. Keratinases have been successfully used in the leather, textile, and pharmaceutical industries. However, the production and efficiency of existing enzymes need to be optimized before they can be used more widely in other processes, such as the cost-effective pretreatment of chicken waste. These can be improved more effectively by using various biotechnological applications which could serve as the best and novel approach for recycling and degrading biomass. This paper provides practical insights about molecular strategies to enhance keratinase expression to effectively utilize various poultry wastes like feathers and feed ingredients like soybean pulp. Furthermore, it describes the future implications of engineered keratinases for environment friendly utilization of wastes and crop byproducts for their better use in the poultry feed industry.
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Affiliation(s)
- Muhammad Saeed
- School of Life Sciences, Jiangsu University, Zhenjiang, 212013, China
| | - Mingchen Yan
- School of Life Sciences, Jiangsu University, Zhenjiang, 212013, China
| | - Zhong Ni
- School of Life Sciences, Jiangsu University, Zhenjiang, 212013, China
| | - Nazar Hussain
- School of Life Sciences, Jiangsu University, Zhenjiang, 212013, China
| | - Huayou Chen
- School of Life Sciences, Jiangsu University, Zhenjiang, 212013, China.
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13
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Gonzalez-de-Miguel J, Montero-Blay A, Ciampi L, Rodriguez-Arce I, Serrano L. Developing a platform for secretion of biomolecules in Mycoplasma feriruminatoris. Microb Cell Fact 2024; 23:124. [PMID: 38689251 PMCID: PMC11059754 DOI: 10.1186/s12934-024-02392-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2024] [Accepted: 04/15/2024] [Indexed: 05/02/2024] Open
Abstract
BACKGROUND Having a simple and fast dividing organism capable of producing and exposing at its surface or secreting functional complex biomolecules with disulphide bridges is of great interest. The mycoplasma bacterial genus offers a set of relevant properties that make it an interesting chassis for such purposes, the main one being the absence of a cell wall. However, due to their slow growth, they have rarely been considered as a potential platform in this respect. This notion may be challenged with the recent discovery of Mycoplasma feriruminatoris, a species with a dividing time close to that of common microbial workhorses. So far, no tools for heterologous protein expression nor secretion have been described for it. RESULTS The work presented here develops the fast-dividing M. feriruminatoris as a tool for secreting functional biomolecules of therapeutic interest that could be used for screening functional mutants as well as potentially for protein-protein interactions. Based on RNAseq, quantitative proteomics and promoter sequence comparison we have rationally designed optimal promoter sequences. Then, using in silico analysis, we have identified putative secretion signals that we validated using a luminescent reporter. The potential of the resulting secretion cassette has been shown with set of active clinically relevant proteins (interleukins and nanobodies). CONCLUSIONS We have engineered Mycoplasma feriruminatoris for producing and secreting functional proteins of medical interest.
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Affiliation(s)
- Javier Gonzalez-de-Miguel
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr Aiguader 88, Barcelona, 08003, Spain
| | - Ariadna Montero-Blay
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr Aiguader 88, Barcelona, 08003, Spain
- Orikine Bio, Dr Aiguader 88, Barcelona, 08003, Spain
| | - Ludovica Ciampi
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr Aiguader 88, Barcelona, 08003, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Irene Rodriguez-Arce
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr Aiguader 88, Barcelona, 08003, Spain.
| | - Luis Serrano
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr Aiguader 88, Barcelona, 08003, Spain.
- Universitat Pompeu Fabra (UPF), Barcelona, Spain.
- ICREA, Pg. Lluis Companys 23, Barcelona, 08010, Spain.
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14
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Ferrero-Bordera B, Bartel J, van Dijl JM, Becher D, Maaß S. From the outer space to the inner cell: deconvoluting the complexity of Bacillus subtilis disulfide stress responses by redox state and absolute abundance quantification of extracellular, membrane, and cytosolic proteins. Microbiol Spectr 2024; 12:e0261623. [PMID: 38358275 PMCID: PMC10986503 DOI: 10.1128/spectrum.02616-23] [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: 06/26/2023] [Accepted: 01/22/2024] [Indexed: 02/16/2024] Open
Abstract
Understanding cellular mechanisms of stress management relies on omics data as a valuable resource. However, the lack of absolute quantitative data on protein abundances remains a significant limitation, particularly when comparing protein abundances across different cell compartments. In this study, we aimed to gain deeper insights into the proteomic responses of the Gram-positive model bacterium Bacillus subtilis to disulfide stress. We determined proteome-wide absolute abundances, focusing on different sub-cellular locations (cytosol and membrane) as well as the extracellular medium, and combined these data with redox state determination. To quantify secreted proteins in the culture medium, we developed a simple and straightforward protocol for the absolute quantification of extracellular proteins in bacteria. We concentrated extracellular proteins, which are highly diluted in the medium, using StrataClean beads along with a set of standard proteins to determine the extent of the concentration step. The resulting data set provides new insights into protein abundances in different sub-cellular compartments and the extracellular medium, along with a comprehensive proteome-wide redox state determination. Our study offers a quantitative understanding of disulfide stress management, protein production, and secretion in B. subtilis. IMPORTANCE Stress responses play a crucial role in bacterial survival and adaptation. The ability to quantitatively measure protein abundances and redox states in different cellular compartments and the extracellular environment is essential for understanding stress management mechanisms. In this study, we addressed the knowledge gap regarding absolute quantification of extracellular proteins and compared protein concentrations in various sub-cellular locations and in the extracellular medium under disulfide stress conditions. Our findings provide valuable insights into the protein production and secretion dynamics of B. subtilis, shedding light on its stress response strategies. Furthermore, the developed protocol for absolute quantification of extracellular proteins in bacteria presents a practical and efficient approach for future studies in the field. Overall, this research contributes to the quantitative understanding of stress management mechanisms and protein dynamics in B. subtilis, which can be used to enhance bacterial stress tolerance and protein-based biotechnological applications.
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Affiliation(s)
- Borja Ferrero-Bordera
- Department of Microbial Proteomics, University of Greifswald, Centre of Functional Genomics of Microbes, Institute of Microbiology, Greifswald, Germany
| | - Jürgen Bartel
- Department of Microbial Proteomics, University of Greifswald, Centre of Functional Genomics of Microbes, Institute of Microbiology, Greifswald, Germany
| | - Jan Maarten van Dijl
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Dörte Becher
- Department of Microbial Proteomics, University of Greifswald, Centre of Functional Genomics of Microbes, Institute of Microbiology, Greifswald, Germany
| | - Sandra Maaß
- Department of Microbial Proteomics, University of Greifswald, Centre of Functional Genomics of Microbes, Institute of Microbiology, Greifswald, Germany
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15
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Guo X, Li X, Feng J, Yue Z, Fu H, Wang J. Engineering of Clostridium tyrobutyricum for butyric acid and butyl butyrate production from cassava starch. BIORESOURCE TECHNOLOGY 2024; 391:129914. [PMID: 37923229 DOI: 10.1016/j.biortech.2023.129914] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Revised: 10/22/2023] [Accepted: 10/23/2023] [Indexed: 11/07/2023]
Abstract
Clostridium tyrobutyricum has been successfully engineered to produce butyrate, butanol, butyl butyrate, and γ-aminobutyric acid. It would be interesting to produce bio-chemicals and bio-fuels directly using starch from non-food crop, e.g., cassava, by engineered C. tyrobutyricum. In this study, heterologous α-amylases were screened and expressed in C. tyrobutyricum, resulting in successfully starch hydrolyzation. Furthermore, α-glucosidase (AgluI) was co-expressed with α-amylases, resulting in enhancement in the capacity of starch hydrolyzation and butyrate production. When increasing the cassava starch concentration to 100 g/L, the engineered strain CTAA05 produced 27.0 g/L butyrate. In addition, when introducing butyl butyrate synthetic pathway, strain MU3-AAV produced 26.8 g/L butyl butyrate with 100 g/L cassava starch as substrate. This study showed a generalizable framework to engineered anaerobes for anaerobic production of bio-chemicals and bio-fuels from starchy biomass.
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Affiliation(s)
- Xiaolong Guo
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China
| | - Xin Li
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China
| | - Jun Feng
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China
| | - Zhi Yue
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China
| | - Hongxin Fu
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China; Guangdong Provincial Key Laboratory of Fermentation and Enzyme Engineering, South China University of Technology, Guangzhou 510006, China.
| | - Jufang Wang
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China; Guangdong Provincial Key Laboratory of Fermentation and Enzyme Engineering, South China University of Technology, Guangzhou 510006, China.
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16
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Schilling T, Ferrero-Bordera B, Neef J, Maaβ S, Becher D, van Dijl JM. Let There Be Light: Genome Reduction Enables Bacillus subtilis to Produce Disulfide-Bonded Gaussia Luciferase. ACS Synth Biol 2023; 12:3656-3668. [PMID: 38011677 PMCID: PMC10729301 DOI: 10.1021/acssynbio.3c00444] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2023] [Revised: 11/09/2023] [Accepted: 11/17/2023] [Indexed: 11/29/2023]
Abstract
Bacillus subtilis is a major workhorse for enzyme production in industrially relevant quantities. Compared to mammalian-based expression systems, B. subtilis presents intrinsic advantages, such as high growth rates, high space-time yield, unique protein secretion capabilities, and low maintenance costs. However, B. subtilis shows clear limitations in the production of biopharmaceuticals, especially proteins from eukaryotic origin that contain multiple disulfide bonds. In the present study, we deployed genome minimization, signal peptide screening, and coexpression of recombinant thiol oxidases as strategies to improve the ability of B. subtilis to secrete proteins with multiple disulfide bonds. Different genome-reduced strains served as the chassis for expressing the model protein Gaussia Luciferase (GLuc), which contains five disulfide bonds. These chassis lack extracellular proteases, prophages, and key sporulation genes. Importantly, compared to the reference strain with a full-size genome, the best-performing genome-minimized strain achieved over 3000-fold increased secretion of active GLuc while growing to lower cell densities. Our results show that high-level GLuc secretion relates, at least in part, to the absence of major extracellular proteases. In addition, we show that the thiol-disulfide oxidoreductase requirements for disulfide bonding have changed upon genome reduction. Altogether, our results highlight genome-engineered Bacillus strains as promising expression platforms for proteins with multiple disulfide bonds.
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Affiliation(s)
- Tobias Schilling
- Department
of Medical Microbiology, University of Groningen,
University Medical Center Groningen, Hanzeplein 1, P.O. Box 30001, 9700RB Groningen, The Netherlands
| | - Borja Ferrero-Bordera
- Institute
of Microbiology Department of Microbial Proteomics, University of Greifswald, D-17489 Greifswald, Germany
| | - Jolanda Neef
- Department
of Medical Microbiology, University of Groningen,
University Medical Center Groningen, Hanzeplein 1, P.O. Box 30001, 9700RB Groningen, The Netherlands
| | - Sandra Maaβ
- Institute
of Microbiology Department of Microbial Proteomics, University of Greifswald, D-17489 Greifswald, Germany
| | - Dörte Becher
- Institute
of Microbiology Department of Microbial Proteomics, University of Greifswald, D-17489 Greifswald, Germany
| | - Jan Maarten van Dijl
- Department
of Medical Microbiology, University of Groningen,
University Medical Center Groningen, Hanzeplein 1, P.O. Box 30001, 9700RB Groningen, The Netherlands
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17
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Osgerby A, Overton TW. Approaches for high-throughput quantification of periplasmic recombinant proteins. N Biotechnol 2023; 77:149-160. [PMID: 37708933 DOI: 10.1016/j.nbt.2023.09.003] [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: 05/03/2023] [Revised: 09/01/2023] [Accepted: 09/11/2023] [Indexed: 09/16/2023]
Abstract
The Gram-negative periplasm is a convenient location for the accumulation of many recombinant proteins including biopharmaceutical products. It is the site of disulphide bond formation, required by some proteins (such as antibody fragments) for correct folding and function. It also permits simpler protein release and downstream processing than cytoplasmic accumulation. As such, targeting of recombinant proteins to the E. coli periplasm is a key strategy in biologic manufacture. However, expression and translocation of each recombinant protein requires optimisation including selection of the best signal peptide and growth and production conditions. Traditional methods require separation and analysis of protein compositions of periplasmic and cytoplasmic fractions, a time- and labour-intensive method that is difficult to parallelise. Therefore, approaches for high throughput quantification of periplasmic protein accumulation offer advantages in rapid process development.
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Affiliation(s)
- Alexander Osgerby
- School of Chemical Engineering and Institute of Microbiology and Infection, The University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Tim W Overton
- School of Chemical Engineering and Institute of Microbiology and Infection, The University of Birmingham, Edgbaston, Birmingham B15 2TT, UK.
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18
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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: 0.5] [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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19
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Zhou J, Shi Y, Fang J, Gan T, Lu Y, Zhu L, Chen X. Efficient production of α-monoglucosyl hesperidin by cyclodextrin glucanotransferase from Bacillus subtilis. Appl Microbiol Biotechnol 2023:10.1007/s00253-023-12628-8. [PMID: 37335363 DOI: 10.1007/s00253-023-12628-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 05/31/2023] [Accepted: 06/07/2023] [Indexed: 06/21/2023]
Abstract
α-Monoglucosyl hesperidin is a promising food additive with various activities. However, there are a few reports about the production of α-monoglucosyl hesperidin. Here, to develop a practical and safe process for α-monoglucosyl hesperidin synthesis, we used nonpathogenic Bacillus subtilis as a host to express cyclodextrin glucanotransferase (CGTase) from Bacillus sp. A2-5a. The promoters and signal peptides were screened to optimize the transcription and secretion of CGTase in B. subtilis. The results of optimization showed that the best signal peptide and promoter were YdjM and PaprE, respectively. Finally, the enzyme activity increased to 46.5 U mL-1, 8.7 times that of the enzyme expressed from the strain containing pPHpaII-LipA, and the highest yield of α-monoglucosyl hesperidin was 2.70 g L-1 by enzymatic synthesis using the supernatant of the recombinant B. subtilis WB800 harboring the plasmid pPaprE-YdjM. This is the highest α-monoglucosyl hesperidin production level using recombinant CGTase to date. This work provides a generally applicable method for the scaled-up production of α-monoglucosyl hesperidin. KEY POINTS: • A three-step procedure was created for high throughput signal peptide screening. • YdjM and PaprE were screened from 173 signal peptides and 13 promoters. • α-Monoglucosyl hesperidin was synthesized by CGTase with a yield of 2.70 g L-1.
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Affiliation(s)
- Jiawei Zhou
- Institute of Fermentation Engineering, Zhejiang University of Technology, Hangzhou, 310014, China
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014, China
| | - Yuan Shi
- Institute of Fermentation Engineering, Zhejiang University of Technology, Hangzhou, 310014, China
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014, China
| | - Jingyi Fang
- Institute of Fermentation Engineering, Zhejiang University of Technology, Hangzhou, 310014, China
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014, China
| | - Tian Gan
- Institute of Fermentation Engineering, Zhejiang University of Technology, Hangzhou, 310014, China
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014, China
| | - Yuele Lu
- Institute of Fermentation Engineering, Zhejiang University of Technology, Hangzhou, 310014, China
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014, China
| | - Linjiang Zhu
- Institute of Fermentation Engineering, Zhejiang University of Technology, Hangzhou, 310014, China.
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014, China.
| | - Xiaolong Chen
- Institute of Fermentation Engineering, Zhejiang University of Technology, Hangzhou, 310014, China
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014, China
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20
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Zhang P, Gong JS, Xie ZH, Su C, Zhang XM, Rao ZM, Xu ZH, Shi JS. Efficient secretory expression of phospholipase D for the high-yield production of phosphatidylserine and phospholipid derivates from soybean lecithin. Synth Syst Biotechnol 2023; 8:273-280. [PMID: 37033293 PMCID: PMC10073938 DOI: 10.1016/j.synbio.2023.03.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Revised: 03/17/2023] [Accepted: 03/20/2023] [Indexed: 03/30/2023] Open
Abstract
Phospholipase D (PLD) is an essential biocatalyst for the biological production of phosphatidylserine and phospholipid modification. However, the efficient heterologous expression of PLD is limited by its cell toxicity. In this study, a PLD was secretory expressed efficiently in Bacillus subtilis with an activity around 100 U/mL. A secretory expression system containing the signal peptide SPEstA and the dual-promoter PHpaII-SrfA was established, and the extracellular PLD activity further reached 119.22 U/mL through scale-up fermentation, 191.30-fold higher than that of the control. Under optimum reaction conditions, a 61.61% conversion ratio and 21.07 g/L of phosphatidylserine production were achieved. Finally, the synthesis system of PL derivates was established, which could efficiently synthesis novel PL derivates. The results highlight that the secretory expression system constructed in this study provides a promising PLD producing strain in industrial application, and laid the foundation for the biosynthesis of phosphatidylserine and other PL derivates. As far as we know, this work reports the highest level of extracellular PLD expression to date and the enzymatic production of several PL derivates for the first time.
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Affiliation(s)
- Peng Zhang
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Life Sciences and Health Engineering, Jiangnan University, Wuxi, 214122, PR China
- School of Chemical and Material Engineering, Jiangnan University, Wuxi, 214122, PR China
| | - Jin-Song Gong
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Life Sciences and Health Engineering, Jiangnan University, Wuxi, 214122, PR China
- Yixing Institute of Food and Biotechnology Co., Ltd, Yixing, 214200, PR China
- Corresponding author. Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Life Sciences and Health Engineering, Jiangnan University, Wuxi, 214122, PR China.
| | - Zhi-Hao Xie
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Life Sciences and Health Engineering, Jiangnan University, Wuxi, 214122, PR China
- School of Chemical and Material Engineering, Jiangnan University, Wuxi, 214122, PR China
| | - Chang Su
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Life Sciences and Health Engineering, Jiangnan University, Wuxi, 214122, PR China
- Yixing Institute of Food and Biotechnology Co., Ltd, Yixing, 214200, PR China
| | - Xiao-Mei Zhang
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Life Sciences and Health Engineering, Jiangnan University, Wuxi, 214122, PR China
- Yixing Institute of Food and Biotechnology Co., Ltd, Yixing, 214200, PR China
| | - Zhi-Ming Rao
- National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, School of Biotechnology, Jiangnan University, Wuxi, 214122, PR China
| | - Zheng-Hong Xu
- National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, School of Biotechnology, Jiangnan University, Wuxi, 214122, PR China
- Jiangsu Provincial Engineering Research Center for Bioactive Product Processing, Jiangnan University, Wuxi, 214122, PR China
- Yixing Institute of Food and Biotechnology Co., Ltd, Yixing, 214200, PR China
| | - Jin-Song Shi
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Life Sciences and Health Engineering, Jiangnan University, Wuxi, 214122, PR China
- Jiangsu Provincial Engineering Research Center for Bioactive Product Processing, Jiangnan University, Wuxi, 214122, PR China
- Yixing Institute of Food and Biotechnology Co., Ltd, Yixing, 214200, PR China
- Corresponding author. Lihu Avenue No. 1800, Jiangnan University, Wuxi, 214122, PR China.
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21
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Research progress on the degradation mechanism and modification of keratinase. Appl Microbiol Biotechnol 2023; 107:1003-1017. [PMID: 36633625 DOI: 10.1007/s00253-023-12360-3] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 12/23/2022] [Accepted: 12/31/2022] [Indexed: 01/13/2023]
Abstract
Keratin is regarded as the main component of feathers and is difficult to be degraded by conventional proteases, leading to substantial abandonment. Keratinase is the only enzyme with the most formidable potential for degrading feathers. Although there have been in-depth studies in recent years, the large-scale application of keratinase is still associated with many problems. It is relatively challenging to find keratinase not only with high activity but could also meet the industrial application environment, so it is urgent to exploit keratinase with high acid and temperature resistance, strong activity, and low price. Therefore, researchers have been keen to explore the degradation mechanism of keratinases and the modification of existing keratinases for decades. This review critically introduces the basic properties and mechanism of keratinase, and focuses on the current situation of keratinase modification and the direction and strategy of its future application and modification. KEY POINTS: •The research status and mechanism of keratinase were reviewed. •The new direction of keratinase application and modification is discussed. •The existing modification methods and future modification strategies of keratinases are reviewed.
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22
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Alexander LM, van Pijkeren JP. Modes of therapeutic delivery in synthetic microbiology. Trends Microbiol 2023; 31:197-211. [PMID: 36220750 PMCID: PMC9877134 DOI: 10.1016/j.tim.2022.09.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 08/27/2022] [Accepted: 09/06/2022] [Indexed: 02/03/2023]
Abstract
For decades, bacteria have been exploited as vectors for vaccines and therapeutics. However, the bacterial arsenal used has historically been limited to a few strains. Advancements in immunology, combined with the development of genetic tools, have expanded our strategies and capabilities to engineer bacteria using various delivery strategies. Depending on the application, each delivery strategy requires specific considerations, optimization, and safety concerns. Here, we review various modes of therapeutic delivery used to target or vaccinate against a variety of ailments in preclinical models and in clinical trials. We highlight modes of bacteria-derived delivery best suited for different applications. Finally, we discuss current obstacles in bacteria-derived therapies and explore potential improvements of the various modes of therapeutic delivery.
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Affiliation(s)
- Laura M Alexander
- Department of Food Science, University of Wisconsin-Madison, Madison, WI, USA; Microbiology Doctoral Training Program, University of Wisconsin-Madison, Madison, WI, USA
| | - Jan-Peter van Pijkeren
- Department of Food Science, University of Wisconsin-Madison, Madison, WI, USA; Food Research Institute, University of Wisconsin-Madison, Madison, WI, USA.
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23
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Xu T, Li Z, Gu Z, Li C, Cheng L, Hong Y, Ban X. The N-terminus of 1,4-α-glucan branching enzyme plays an important role in its non-classical secretion in Bacillus subtilis. FOOD BIOSCI 2023. [DOI: 10.1016/j.fbio.2023.102491] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/22/2023]
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24
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Aguilar M, Isla A, Barrientos CA, Flores-Martin SN, Blanco JA, Enríquez R, Figueroa J, Yañez AJ. Genomic and proteomic aspects of p57 protein from Renibacterium salmoninarum: Characteristics in virulence patterns. Microb Pathog 2023; 174:105932. [PMID: 36473669 DOI: 10.1016/j.micpath.2022.105932] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2022] [Revised: 12/02/2022] [Accepted: 12/02/2022] [Indexed: 12/07/2022]
Abstract
Renibacterium salmoninarum is one of the oldest known fish bacterial pathogens. This Gram-positive bacterium is the causative agent of Bacterial Kidney Disease (BKD), a chronic infection that primarily infects salmonids at low temperatures. Externally, infected fish may show exophthalmos, skin blisters, ulcerations, and hemorrhages at the base of the fins and along the lateral line. Internally, the kidney, heart, spleen, and liver may show signs of inflammation. The best characterized virulence factor of R. salmoninarum is p57, a 57 kDa protein located on the bacterial cell surface and secreted into surrounding fish tissue. The p57 protein in fish is the main mediator in suppressing the immune system, reducing antibody production, and intervening in cytokine activity. In this review, we will discuss aspects such as single nucleotide polymorphisms (SNPs) that modify the DNA sequence, variants in the number of copies of MSA genes, physical-chemical properties of the signal peptides, and the limited iron conditions that can modify p57 expression and increase the virulence of R. salmoninarum.
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Affiliation(s)
- Marcelo Aguilar
- Laboratorio de Diagnostico y Terapia, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile
| | - Adolfo Isla
- Laboratorio de Diagnostico y Terapia, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile; Departamento de Ciencias Básicas, Facultad de Ciencias, Universidad Santo Tomás, Valdivia, Chile; Center for Aquaculture Research (INCAR), Concepción, Chile
| | - Claudia A Barrientos
- Laboratorio de Diagnostico y Terapia, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile
| | - Sandra N Flores-Martin
- Laboratorio de Diagnostico y Terapia, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile
| | - Jose A Blanco
- Laboratorio de Diagnostico y Terapia, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile
| | - Ricardo Enríquez
- Laboratorio de Inmunología y Estrés de Organismos Acuáticos, Instituto de Patología Animal, Facultad de Ciencias Veterinarias, Universidad Austral de Chile, Chile
| | - Jaime Figueroa
- Center for Aquaculture Research (INCAR), Concepción, Chile; Instituto de Bioquímica y Microbiología, Universidad Austral de Chile, Valdivia, Chile
| | - Alejandro J Yañez
- Laboratorio de Diagnostico y Terapia, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile; Center for Aquaculture Research (INCAR), Concepción, Chile.
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25
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Miao H, Zhe Y, Xiang X, Cao Y, Han N, Wu Q, Huang Z. Enhanced Extracellular Expression of a Ca 2+- and Mg 2+-Dependent Hyperthermostable Protease EA1 in Bacillus subtilis via Systematic Screening of Optimal Signal Peptides. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:15830-15839. [PMID: 36480738 DOI: 10.1021/acs.jafc.2c06741] [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: 06/17/2023]
Abstract
Proteases have been widely applied in various industries, including tanning, silk, feed, medicine, food, and environmental protection. Herein, the protease EA1 (GenBank accession no. U25630.1) was successfully expressed in Bacillus subtilis and demonstrated to function as a Ca2+- and Mg2+-dependent hyperthermostable neutral protease. At 80 °C, its half-life (t1/2) in the presence of 10 mM Mg2+ and Ca2+ was 50.4-fold longer than that in their absence (7.4 min), which can be explained by structural analysis. Compared with the currently available commercial proteases, protease EA1 has obvious advantages in heat resistance. The largest peptide library was used to enhance the extracellular expression of protease EA1 via constructing and screening 244 signal peptides (SPs). Eleven SPs with high yields of protease EA1 were identified from 5000 clones using a high-throughput assay. Specifically, the enzyme activity of protease produced by the strain (217.6 U/mL) containing the SP XynD was 5.2-fold higher than that of the strain with the initial SP. In brief, the protease is a potential candidate for future use in the high-temperature industry.
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Affiliation(s)
- Huabiao Miao
- Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Ministry of Education, Kunming 650500, China
- School of Life Science, Yunnan Normal University, Kunming 650500, China
| | - Yuanyuan Zhe
- School of Life Science, Yunnan Normal University, Kunming 650500, China
| | - Xia Xiang
- School of Life Science, Yunnan Normal University, Kunming 650500, China
| | - Yan Cao
- School of Life Science, Yunnan Normal University, Kunming 650500, China
| | - Nanyu Han
- Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Ministry of Education, Kunming 650500, China
- School of Life Science, Yunnan Normal University, Kunming 650500, China
| | - Qian Wu
- Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Ministry of Education, Kunming 650500, China
- School of Life Science, Yunnan Normal University, Kunming 650500, China
| | - Zunxi Huang
- Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Ministry of Education, Kunming 650500, China
- School of Life Science, Yunnan Normal University, Kunming 650500, China
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26
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Jiang Z, Zhang L, Zhou W, Li H, Li Y, Qin W, Wang F, Wei D, Gao B. The Rational Modification of the Secretion Pathway: The Bidirectional Grinding Strategy on Signal Peptide and SecA in Bacillus subtilis. Biochem Eng J 2022. [DOI: 10.1016/j.bej.2022.108769] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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27
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Jamali N, Vahedi F, Soltani Fard E, Taheri-Anganeh M, Taghvimi S, Khatami SH, Ghasemi H, Movahedpour A. Nattokinase: Structure, applications and sources. BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY 2022. [DOI: 10.1016/j.bcab.2022.102564] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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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: 14] [Impact Index Per Article: 4.7] [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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Jiang C, Ye C, Liu Y, Huang K, Jiang X, Zou D, Li L, Han W, Wei X. Genetic engineering for enhanced production of a novel alkaline protease BSP-1 in Bacillus amyloliquefaciens. Front Bioeng Biotechnol 2022; 10:977215. [PMID: 36110310 PMCID: PMC9468883 DOI: 10.3389/fbioe.2022.977215] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Accepted: 08/08/2022] [Indexed: 11/13/2022] Open
Abstract
Alkaline protease has been widely applied in food, medicine, environmental protection and other industrial fields. However, the current activity and yield of alkaline protease cannot meet the demand. Therefore, it is important to identify new alkaline proteases with high activity. In this study, we cloned a potential alkaline protease gene bsp-1 from a Bacillus subtilis strain isolated in our laboratory. BSP-1 shows the highest sequence similarity to subtilisin NAT (S51909) from B. subtilis natto. Then, we expressed BSP-1 in Bacillus amyloliquefaciens BAX-9 and analyzed the protein expression level under a collection of promoters. The results show that the P43 promoter resulted in the highest transcription level, protein level and enzyme activity. Finally, we obtained a maximum activity of 524.12 U/mL using the P43 promoter after fermentation medium optimization. In conclusion, this study identified an alkaline protease gene bsp-1 from B. subtilis and provided a new method for high-efficiency alkaline protease expression in B. amyloliquefaciens.
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Affiliation(s)
- Cong Jiang
- State Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Changwen Ye
- Zhengzhou Tobacco Research Institute of China National Tobacco Corporation, Zhengzhou, China
| | - Yongfeng Liu
- GeneMind Biosciences Company Limited, Shenzhen, China
| | - Kuo Huang
- Zhengzhou Tobacco Research Institute of China National Tobacco Corporation, Zhengzhou, China
| | - Xuedeng Jiang
- State Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Dian Zou
- State Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Lu Li
- Sericultural & Argi-Food Research Institute, Guangdong Academy of Agricultural Sciences/Key Laboratory of Functional Foods, Ministry of Agriculture and Rural Affairs/Guangdong Key Laboratory of Agricultural Products Processing, Guangzhou, China
| | - Wenyuan Han
- State Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Xuetuan Wei
- State Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
- *Correspondence: Xuetuan Wei,
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Chen H, Wu J, Huang X, Feng X, Ji H, Zhao L, Wang J. Overexpression of Bacillus circulans alkaline protease in Bacillus subtilis and its potential application for recovery of protein from soybean dregs. Front Microbiol 2022; 13:968439. [PMID: 36090104 PMCID: PMC9459226 DOI: 10.3389/fmicb.2022.968439] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Accepted: 07/21/2022] [Indexed: 11/13/2022] Open
Abstract
Proteases are important for decomposition of proteins to generate peptides or amino acids and have a broad range of applications in different industries. Herein, a gene encoding an alkaline protease (AprBcp) from Bacillus circulans R1 was cloned and bioinformatics analyzed. In addition, a series of strategies were applied to achieve high-level expression of AprBcp in Bacillus subtilis. The maximum activity of AprBcp reached 165,870 U/ml after 60 h fed-batch cultivation in 50 l bioreactor. The purified recombinant AprBcp exhibited maximum activity at 60°C and pH 10.0, and remained stable in the range from pH 8.0 to 11.0 and 30 to 45°C. Metal ions Ca2+, Mn2+, and Mg2+ could improve the stability of AprBcp. Furthermore, the recombinant AprBcp displayed great potential application on the recovery of protein from soybean dregs. The results of this study will provide an effective method to prepare AprBcp in B. subtilis and its potential application on utilization of soybean dregs.
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Affiliation(s)
- Hao Chen
- College of Food and Chemical Engineering, Shaoyang University, Shaoyang, China
- Hunan Provincial Key Laboratory of Soybean Products Processing and Safety Control, Shaoyang, China
- College of Food Science and Technology, Guangdong Ocean University, Zhanjiang, China
- Guangdong Provincial Key Laboratory of Aquatic Product Processing and Safety, Zhanjiang, China
| | - Jie Wu
- College of Food and Chemical Engineering, Shaoyang University, Shaoyang, China
- Hunan Provincial Key Laboratory of Soybean Products Processing and Safety Control, Shaoyang, China
| | - Xiaodan Huang
- College of Food Science and Technology, Guangdong Ocean University, Zhanjiang, China
- Guangdong Provincial Key Laboratory of Aquatic Product Processing and Safety, Zhanjiang, China
| | - Xuzhong Feng
- Shenzhen Shanggutang Food Development Co., Ltd.,Shenzhen, China
| | - Hongwu Ji
- College of Food Science and Technology, Guangdong Ocean University, Zhanjiang, China
- Guangdong Provincial Key Laboratory of Aquatic Product Processing and Safety, Zhanjiang, China
| | - Liangzhong Zhao
- College of Food and Chemical Engineering, Shaoyang University, Shaoyang, China
- Hunan Provincial Key Laboratory of Soybean Products Processing and Safety Control, Shaoyang, China
- *Correspondence: Liangzhong Zhao,
| | - Jianrong Wang
- College of Food and Chemical Engineering, Shaoyang University, Shaoyang, China
- Hunan Provincial Key Laboratory of Soybean Products Processing and Safety Control, Shaoyang, China
- Shenzhen Raink Ecology and Environment Co., Ltd.,Shenzhen, China
- Jianrong Wang,
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Zou Y, Qiu L, Xie A, Han W, Zhang S, Li J, Zhao S, Li Y, Liang Y, Hu Y. Development and application of a rapid all-in-one plasmid CRISPR-Cas9 system for iterative genome editing in Bacillus subtilis. Microb Cell Fact 2022; 21:173. [PMID: 35999638 PMCID: PMC9400229 DOI: 10.1186/s12934-022-01896-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2022] [Accepted: 08/14/2022] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND Bacillus subtilis, an important industrial microorganism, is commonly used in the production of industrial enzymes. Genome modification is often necessary to improve the production performance of cell. The dual-plasmid CRISPR-Cas9 system suitable for iterative genome editing has been applied in Bacillus subtilis. However, it is limited by the selection of knockout genes, long editing cycle and instability. RESULTS To address these problems, we constructed an all-in-one plasmid CRISPR-Cas9 system, which was suitable for iterative genome editing of B. subtilis. The PEG4000-assisted monomer plasmid ligation (PAMPL) method greatly improved the transformation efficiency of B. subtilis SCK6. Self-targeting sgRNArep transcription was tightly controlled by rigorous promoter PacoR, which could induce the elimination of plasmids after genome editing and prepare for next round of genome editing. Our system achieved 100% efficiency for single gene deletions and point mutations, 96% efficiency for gene insertions, and at least 90% efficiency for plasmid curing. As a proof of concept, two extracellular protease genes epr and bpr were continuously knocked out using this system, and it only took 2.5 days to complete one round of genome editing. The engineering strain was used to express Douchi fibrinolytic enzyme DFE27, and its extracellular enzyme activity reached 159.5 FU/mL. CONCLUSIONS We developed and applied a rapid all-in-one plasmid CRISPR-Cas9 system for iterative genome editing in B. subtilis, which required only one plasmid transformation and curing, and accelerated the cycle of genome editing. To the best of our knowledge, this is the rapidest iterative genome editing system for B. subtilis. We hope that the system can be used to reconstruct the B. subtilis cell factory for the production of various biological molecules.
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Affiliation(s)
- Yu Zou
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China
| | - Lu Qiu
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China
| | - Aowen Xie
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China
| | - Wenyuan Han
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China
| | - Shangbo Zhang
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China
| | - Jinshan Li
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China.,Bioengineering Center, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Shumiao Zhao
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China
| | - Yingjun Li
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China
| | - Yunxiang Liang
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China
| | - Yongmei Hu
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China.
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Saldarriaga-Córdoba M, Avendaño-Herrera R. Comparative pan-genomic analysis of 51 Renibacterium salmoninarum indicates heterogeneity in the principal virulence factor, the 57 kDa protein. JOURNAL OF FISH DISEASES 2022; 45:1173-1188. [PMID: 35604683 DOI: 10.1111/jfd.13653] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 04/28/2022] [Accepted: 05/02/2022] [Indexed: 06/15/2023]
Abstract
Renibacterium salmoninarum, a Gram-positive intracellular pathogen, is the causative agent of bacterial kidney disease (BKD), the impacts of which are high mortalities and economic losses for the salmon industry. This study provides novel analyses for the whole-genome sequences of 50 R. salmoninarum isolates and the reference strain ATCC 33209 using a pan-genomic approach to elucidate phylogenomic relationships and identify unique and shared genes associated with pathogenicity and infection mechanisms. Genome size varied from 3,061,638 to 3,155,332 bp; gene count from 3452 to 3580; and predicted coding sequences from 3402 to 3527. Comparative analyses revealed an open, but approaching closed, pan-genome. The pan-genome analysis recovered 4064 genes, with a core genome containing 3306 genes. Phylogenetic analysis of R. salmoninarum showed high genomic homogeneity, apart from one isolate obtained from Salmo trutta in Norway. All genomes presented the 57-kDa protein (p57). Strain ATCC 33209 and the Chilean isolates H-2 and DJ2R presented two copies of the msa gene, while the remaining isolates had one copy. The pan-genome analysis further identified differences in the number of copies and length of the signalling peptide for p57, the principal virulence factor reported for this bacterium. This heterogeneity could be associated with the secretion levels of p57, potentially influencing virulence. Additionally identified were numerous common genes related to iron uptake, the stress response and regulation, and cell signalling-all of which constitute the pathogenic repertoire of R. salmoninarum. This investigation provides information that is applicable in future studies for identifying therapeutic targets and/or for designing new strategies (e.g., vaccines) to prevent BKD infections in salmon farming.
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Affiliation(s)
- Mónica Saldarriaga-Córdoba
- Centro de Investigación en Recursos Naturales y Sustentabilidad, Universidad Bernardo O'Higgins, Santiago, Chile
- Centro FONDAP, Interdisciplinary Center for Aquaculture Research (INCAR), Universidad Andrés Bello, Viña del Mar, Chile
| | - Ruben Avendaño-Herrera
- Centro FONDAP, Interdisciplinary Center for Aquaculture Research (INCAR), Universidad Andrés Bello, Viña del Mar, Chile
- Laboratorio de Patología de Organismos Acuáticos y Biotecnología Acuícola, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Viña del Mar, Chile
- Centro de Investigaciones Marina Quintay (CIMARQ), Universidad Andés Bello, Quintay, Chile
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Müller C, Bakkes PJ, Lenz P, Waffenschmidt V, Helleckes LM, Jaeger KE, Wiechert W, Knapp A, Freudl R, Oldiges M. Accelerated strain construction and characterization of C. glutamicum protein secretion by laboratory automation. Appl Microbiol Biotechnol 2022; 106:4481-4497. [PMID: 35759036 PMCID: PMC9259529 DOI: 10.1007/s00253-022-12017-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Revised: 06/01/2022] [Accepted: 06/04/2022] [Indexed: 11/02/2022]
Abstract
Secretion of bacterial proteins into the culture medium simplifies downstream processing by avoiding cell disruption for target protein purification. However, a suitable signal peptide for efficient secretion needs to be identified, and currently, there are no tools available to predict optimal combinations of signal peptides and target proteins. The selection of such a combination is influenced by several factors, including protein biosynthesis efficiency and cultivation conditions, which both can have a significant impact on secretion performance. As a result, a large number of combinations must be tested. Therefore, we have developed automated workflows allowing for targeted strain construction and secretion screening using two platforms. Key advantages of this experimental setup include lowered hands-on time and increased throughput. In this study, the automated workflows were established for the heterologous production of Fusarium solani f. sp. pisi cutinase in Corynebacterium glutamicum. The target protein was monitored in culture supernatants via enzymatic activity and split GFP assay. Varying spacer lengths between the Shine-Dalgarno sequence and the start codon of Bacillus subtilis signal peptides were tested. Consistent with previous work on the secretory cutinase production in B. subtilis, a ribosome binding site with extended spacer length to up to 12 nt, which likely slows down translation initiation, does not necessarily lead to poorer cutinase secretion by C. glutamicum. The best performing signal peptides for cutinase secretion with a standard spacer length were identified in a signal peptide screening. Additional insights into the secretion process were gained by monitoring secretion stress using the C. glutamicum K9 biosensor strain. KEY POINTS: • Automated workflows for strain construction and screening of protein secretion • Comparison of spacer, signal peptide, and host combinations for cutinase secretion • Signal peptide screening for secretion by C. glutamicum using the split GFP assay.
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Affiliation(s)
- Carolin Müller
- Institute of Bio- and Geosciences IBG-1, Biotechnology, Forschungszentrum Jülich GmbH, 52425, Jülich, Germany.,Institute of Biotechnology, RWTH Aachen University, 52062, Aachen, Germany
| | - Patrick J Bakkes
- Institute of Bio- and Geosciences IBG-1, Biotechnology, Forschungszentrum Jülich GmbH, 52425, Jülich, Germany
| | - Patrick Lenz
- Institute of Molecular Enzyme Technology, Heinrich Heine University Düsseldorf, Forschungszentrum Jülich, 52425, Jülich, Germany
| | - Vera Waffenschmidt
- Institute of Bio- and Geosciences IBG-1, Biotechnology, Forschungszentrum Jülich GmbH, 52425, Jülich, Germany
| | - Laura M Helleckes
- Institute of Bio- and Geosciences IBG-1, Biotechnology, Forschungszentrum Jülich GmbH, 52425, Jülich, Germany.,Institute of Biotechnology, RWTH Aachen University, 52062, Aachen, Germany
| | - Karl-Erich Jaeger
- Institute of Bio- and Geosciences IBG-1, Biotechnology, Forschungszentrum Jülich GmbH, 52425, Jülich, Germany.,Institute of Molecular Enzyme Technology, Heinrich Heine University Düsseldorf, Forschungszentrum Jülich, 52425, Jülich, Germany
| | - Wolfgang Wiechert
- Institute of Bio- and Geosciences IBG-1, Biotechnology, Forschungszentrum Jülich GmbH, 52425, Jülich, Germany.,Computational Systems Biotechnology (AVT.CSB), RWTH Aachen University, 52062, Aachen, Germany
| | - Andreas Knapp
- Institute of Molecular Enzyme Technology, Heinrich Heine University Düsseldorf, Forschungszentrum Jülich, 52425, Jülich, Germany.,Castrol Germany GmbH, 41179, Mönchengladbach, Germany
| | - Roland Freudl
- Institute of Bio- and Geosciences IBG-1, Biotechnology, Forschungszentrum Jülich GmbH, 52425, Jülich, Germany
| | - Marco Oldiges
- Institute of Bio- and Geosciences IBG-1, Biotechnology, Forschungszentrum Jülich GmbH, 52425, Jülich, Germany. .,Institute of Biotechnology, RWTH Aachen University, 52062, Aachen, Germany.
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Holec PV, Camacho KV, Breuckman KC, Mou J, Birnbaum ME. Proteome-Scale Screening to Identify High-Expression Signal Peptides with Minimal N-Terminus Biases via Yeast Display. ACS Synth Biol 2022; 11:2405-2416. [PMID: 35687717 DOI: 10.1021/acssynbio.2c00101] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Signal peptides are critical for the efficient expression and routing of extracellular and secreted proteins. Most protein production and screening technologies rely upon a relatively small set of signal peptides. Despite their central role in biotechnology, there are limited studies comprehensively examining the interplay between signal peptides and expressed protein sequences. Here, we describe a high-throughput method to screen novel signal peptides that maintain a high degree of surface expression across a range of protein scaffolds with highly variable N-termini. We find that the canonical signal peptide used in yeast surface display, derived from Aga2p, fails to achieve high surface expression for 42.5% of constructs containing diverse N-termini. To circumvent this, we have identified two novel signal peptides derived from endogenous yeast proteins, SRL1 and KISH, which are highly tolerant to diverse N-terminal sequences. This pipeline can be used to expand our understanding of signal peptide function, identify improved signal peptides for protein expression, and refine the computational tools used for signal peptide prediction.
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Affiliation(s)
- Patrick V Holec
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States.,Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Karen V Camacho
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States.,Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Kathryn C Breuckman
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Jody Mou
- Harvard-MIT Program in Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Michael E Birnbaum
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States.,Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States.,Ragon Institute of MGH, MIT, and Harvard, Cambridge, Massachusetts 02139, United States
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35
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Mayer J, Knuuti T, Baumgarten L, Menke E, Bischoff L, Bunk B, Biedendieck R. Construction and Application of a Plasmid-Based Signal Peptide Library for Improved Secretion of Recombinant Proteins with Priestia megaterium. Microorganisms 2022; 10:microorganisms10040777. [PMID: 35456829 PMCID: PMC9032162 DOI: 10.3390/microorganisms10040777] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Revised: 03/31/2022] [Accepted: 04/01/2022] [Indexed: 02/04/2023] Open
Abstract
The secretion of recombinant proteins plays an important role in their economic production and purification. The secretion efficiency depends on the responsible signal peptide (SP) in combination with the target protein and the given host and cannot be predicted so far. Due to its high plasmid stability, the lack of alkaline extracellular proteases and only few contaminating extracellular host proteins, Priestia megaterium provides a promising alternative to common Bacillus species. For the development of an easy and fast cloning and screening system to identify the SP best suited to a distinct protein, a plasmid-based SP library containing all predicted 182 Sec-dependent SPs from P. megaterium was established. The splitting of the SPs into 10 groups of individual multi-SP plasmids (pMSPs) allows their grouped amplification and application in screening approaches. The functionality of the whole library was demonstrated by enhancing the amount of the already well-secreted α-amylase AmyE by 1.6-fold. The secretion of a novel penicillin G acylase, which remained as insoluble protein inside the cells, as its native SP is unsuitable for secretion in P. megaterium, could be enhanced even up to 29-fold. Overall, only around 170 recombinant P. megaterium clones based on 50 inserted SPs had to be screened to achieve sufficient amounts for further enzyme characterizations. Thus, this newly developed plasmid-based genetic tool applicable for P. megaterium and also other Bacillus species facilitates the identification of suitable SPs for secretion of recombinant proteins.
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Affiliation(s)
- Janine Mayer
- Institute of Microbiology and Braunschweig Integrated Centre of Systems Biology (BRICS), Technische Universität Braunschweig, Rebenring 56, 38106 Braunschweig, Germany; (J.M.); (T.K.); (L.B.); (E.M.); (L.B.)
| | - Tobias Knuuti
- Institute of Microbiology and Braunschweig Integrated Centre of Systems Biology (BRICS), Technische Universität Braunschweig, Rebenring 56, 38106 Braunschweig, Germany; (J.M.); (T.K.); (L.B.); (E.M.); (L.B.)
| | - Lisa Baumgarten
- Institute of Microbiology and Braunschweig Integrated Centre of Systems Biology (BRICS), Technische Universität Braunschweig, Rebenring 56, 38106 Braunschweig, Germany; (J.M.); (T.K.); (L.B.); (E.M.); (L.B.)
| | - Elise Menke
- Institute of Microbiology and Braunschweig Integrated Centre of Systems Biology (BRICS), Technische Universität Braunschweig, Rebenring 56, 38106 Braunschweig, Germany; (J.M.); (T.K.); (L.B.); (E.M.); (L.B.)
| | - Lena Bischoff
- Institute of Microbiology and Braunschweig Integrated Centre of Systems Biology (BRICS), Technische Universität Braunschweig, Rebenring 56, 38106 Braunschweig, Germany; (J.M.); (T.K.); (L.B.); (E.M.); (L.B.)
| | - Boyke Bunk
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7, 38124 Braunschweig, Germany;
| | - Rebekka Biedendieck
- Institute of Microbiology and Braunschweig Integrated Centre of Systems Biology (BRICS), Technische Universität Braunschweig, Rebenring 56, 38106 Braunschweig, Germany; (J.M.); (T.K.); (L.B.); (E.M.); (L.B.)
- Correspondence: ; Tel.: +49-531-391-55291
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Chao S, Liu Y, Ding N, Lin Y, Wang Q, Tan J, Li W, Zheng Y, Hu X, Li J. Highly Expressed Soluble Recombinant Anti-GFP VHHs in Escherichia coli via Optimized Signal Peptides, Strains, and Inducers. Front Mol Biosci 2022; 9:848829. [PMID: 35359590 PMCID: PMC8960375 DOI: 10.3389/fmolb.2022.848829] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Accepted: 01/31/2022] [Indexed: 11/13/2022] Open
Abstract
Antigen-binding variable domains of the H chain of heavy-chain antibodies (VHHs), also known as nanobodies (Nbs), are of great interest in imaging technique, disease prevention, diagnosis, and therapy. High-level expression of soluble Nbs is very important for its industrial production. In this study, we optimized the expression system of anti-green fluorescent protein (GFP) VHHs with three different signal peptides (SPs), outer-membrane protein A (OmpA), pectate lyase B (PelB), and L-asparaginase II SP (L-AsPsII), in different Escherichia coli strains via isopropyl β-D-thiogalactoside (IPTG) induction and auto-induction, respectively. The solubility of recombinant anti-GFP VHHs with PelB or OmpA was significantly enhanced to the same extent by IPTG induction and auto-induction in BL21 (DE3) E. coli strain and the maximum yield of target protein reached approximately 0.4 mg/l in a shake flask. The binding activity of recombinant anti-GFP VHHs was also confirmed to be retained by native-polyacrylamide gel electrophoresis (PAGE). These results suggest that SPs like OmpA and PelB could efficiently improve the recombinant anti-GFP VHH solubility without changing its bioactivity, providing a novel strategy to optimize the E. coli expression system of soluble VHHs, and lay the foundation for the industrial production of soluble recombinant anti-GFP VHHs and the research of other VHHs in the future.
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Affiliation(s)
- Shuangying Chao
- Medical College, Dalian University, Dalian, China
- DalianKey Laboratory of Oligosaccharide Recombination and Recombinant Protein Modification, Dalian, China
| | - Yuhang Liu
- Medical College, Dalian University, Dalian, China
- DalianKey Laboratory of Oligosaccharide Recombination and Recombinant Protein Modification, Dalian, China
| | - Ning Ding
- Medical College, Dalian University, Dalian, China
- DalianKey Laboratory of Oligosaccharide Recombination and Recombinant Protein Modification, Dalian, China
| | - Yue Lin
- Medical College, Dalian University, Dalian, China
- DalianKey Laboratory of Oligosaccharide Recombination and Recombinant Protein Modification, Dalian, China
| | - Qian Wang
- Medical College, Dalian University, Dalian, China
- DalianKey Laboratory of Oligosaccharide Recombination and Recombinant Protein Modification, Dalian, China
| | - Junwen Tan
- Medical College, Dalian University, Dalian, China
- DalianKey Laboratory of Oligosaccharide Recombination and Recombinant Protein Modification, Dalian, China
| | - Wei Li
- Medical College, Dalian University, Dalian, China
- DalianKey Laboratory of Oligosaccharide Recombination and Recombinant Protein Modification, Dalian, China
| | - Yang Zheng
- Medical College, Dalian University, Dalian, China
- DalianKey Laboratory of Oligosaccharide Recombination and Recombinant Protein Modification, Dalian, China
- *Correspondence: Yang Zheng, ; Xuejun Hu, ; Junming Li,
| | - Xuejun Hu
- Medical College, Dalian University, Dalian, China
- DalianKey Laboratory of Oligosaccharide Recombination and Recombinant Protein Modification, Dalian, China
- *Correspondence: Yang Zheng, ; Xuejun Hu, ; Junming Li,
| | - Junming Li
- Department of Clinical Laboratory, Yantai Yuhuangding Hospital, Yantai, China
- *Correspondence: Yang Zheng, ; Xuejun Hu, ; Junming Li,
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Zhang K, Su L, Wu J. Enhancing Extracellular Pullulanase Production in Bacillus subtilis Through dltB Disruption and Signal Peptide Optimization. Appl Biochem Biotechnol 2022; 194:1206-1220. [PMID: 34652585 DOI: 10.1007/s12010-021-03617-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Accepted: 07/12/2021] [Indexed: 10/20/2022]
Abstract
Bacillus subtilis has many attributes that make it a popular host for recombinant protein production. Although its protein production ability has been enhanced through protease gene disruption, residual proteases like quality control HtrA and HtrB can limit protein yield by degrading inadequately folded proteins present during overexpression. In this study, two strategies were employed to increase production of industrial enzyme pullulanase: enhancing extracellular pullulanase folding and optimizing its signal peptide. The hypothesis was that disruption of dltB gene of expression host B. subtilis WS9 would enhance recombinant extracellular folding by increasing cation binding to the cell's outer envelope. Consistent with this hypothesis, disrupting dltB enhanced pullulanase production by 49% in shake-flask cultures. The disruption also enhanced extracellular α-CGTase and β-CGTase production by 25% and 35%, respectively. Then, more effective signal peptide for pullulanase production was identified through high-throughput screening of 173 unique B. subtilis signal peptides. Replacing the native signal peptide of pullulanase with that encoded by ywtF increased extracellular pullulanase activity by an additional 12%. Three-liter fermenter scale-up production yielded the highest extracellular pullulanase activity reported to date: 8037.91 U·mL-1. This study highlights the usefulness of dltB deletion and signal peptide optimization in enhancing extracellular protein production.
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Affiliation(s)
- Kang Zhang
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi, 214122, China
- School of Biotechnology and Key Laboratory of Industrial Biotechnology Ministry of Education, Jiangnan University, 1800 Lihu Avenue, Wuxi, 214122, China
- International Joint Laboratory On Food Safety, Jiangnan University, 1800 Lihu Avenue, Wuxi, 214122, China
| | - Lingqia Su
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi, 214122, China
- School of Biotechnology and Key Laboratory of Industrial Biotechnology Ministry of Education, Jiangnan University, 1800 Lihu Avenue, Wuxi, 214122, China
- International Joint Laboratory On Food Safety, Jiangnan University, 1800 Lihu Avenue, Wuxi, 214122, China
| | - Jing Wu
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi, 214122, China.
- School of Biotechnology and Key Laboratory of Industrial Biotechnology Ministry of Education, Jiangnan University, 1800 Lihu Avenue, Wuxi, 214122, China.
- International Joint Laboratory On Food Safety, Jiangnan University, 1800 Lihu Avenue, Wuxi, 214122, China.
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Peng C, Guo Y, Ren S, Li C, Liu F, Lu F. SPSED: A Signal Peptide Secretion Efficiency Database. Front Bioeng Biotechnol 2022; 9:819789. [PMID: 35118058 PMCID: PMC8804277 DOI: 10.3389/fbioe.2021.819789] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Accepted: 12/20/2021] [Indexed: 11/13/2022] Open
Affiliation(s)
- Chong Peng
- Key Laboratory of Industrial Fermentation Microbiology, Education Ministry of China, Tianjin, China
- National Engineering Laboratory for Industrial Enzymes (NELIE), Tianjin, China
- Tianjin Key Laboratory of Industrial Microbiology, Tianjin, China
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China
| | - Yixue Guo
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China
| | - Shaodong Ren
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China
| | - Cen Li
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China
| | - Fufeng Liu
- Key Laboratory of Industrial Fermentation Microbiology, Education Ministry of China, Tianjin, China
- National Engineering Laboratory for Industrial Enzymes (NELIE), Tianjin, China
- Tianjin Key Laboratory of Industrial Microbiology, Tianjin, China
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China
| | - Fuping Lu
- Key Laboratory of Industrial Fermentation Microbiology, Education Ministry of China, Tianjin, China
- National Engineering Laboratory for Industrial Enzymes (NELIE), Tianjin, China
- Tianjin Key Laboratory of Industrial Microbiology, Tianjin, China
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China
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Chen B, Loo BZL, Cheng YY, Song P, Fan H, Latypov O, Kittelmann S. Genome-wide high-throughput signal peptide screening via plasmid pUC256E improves protease secretion in Lactiplantibacillus plantarum and Pediococcus acidilactici. BMC Genomics 2022; 23:48. [PMID: 35021997 PMCID: PMC8756648 DOI: 10.1186/s12864-022-08292-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Accepted: 01/03/2022] [Indexed: 11/30/2022] Open
Abstract
BACKGROUND Proteases catalyze the hydrolysis of peptide bonds of proteins, thereby improving dietary protein digestibility, nutrient availability, as well as flavor and texture of fermented food and feed products. The lactobacilli Lactiplantibacillus plantarum (formerly Lactobacillus plantarum) and Pediococcus acidilactici are widely used in food and feed fermentations due to their broad metabolic capabilities and safe use. However, extracellular protease activity in these two species is low. Here, we optimized protease expression and secretion in L. plantarum and P. acidilactici via a genetic engineering strategy. RESULTS To this end, we first developed a versatile and stable plasmid, pUC256E, which can propagate in both L. plantarum and P. acidilactici. We then confirmed expression and secretion of protease PepG1 as a functional enzyme in both strains with the aid of the previously described L. plantarum-derived signal peptide LP_0373. To further increase secretion of PepG1, we carried out a genome-wide experimental screening of signal peptide functionality. A total of 155 predicted signal peptides originating from L. plantarum and 110 predicted signal peptides from P. acidilactici were expressed and screened for extracellular proteolytic activity in the two different strains, respectively. We identified 12 L. plantarum signal peptides and eight P. acidilactici signal peptides that resulted in improved yield of secreted PepG1. No significant correlation was found between signal peptide sequence properties and its performance with PepG1. CONCLUSION The vector developed here provides a powerful tool for rapid experimental screening of signal peptides in both L. plantarum and P. acidilactici. Moreover, the set of novel signal peptides identified was widely distributed across strains of the same species and even across some closely related species. This indicates their potential applicability also for the secretion of other proteins of interest in other L. plantarum or P. acidilactici host strains. Our findings demonstrate that screening a library of homologous signal peptides is an attractive strategy to identify the optimal signal peptide for the target protein, resulting in improved protein export.
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Affiliation(s)
- Binbin Chen
- Wilmar International Limited, WIL@NUS Corporate Laboratory, Centre for Translational Medicine, National University of Singapore, Singapore, Singapore
| | - Bryan Zong Lin Loo
- Wilmar International Limited, WIL@NUS Corporate Laboratory, Centre for Translational Medicine, National University of Singapore, Singapore, Singapore
| | - Ying Ying Cheng
- Wilmar International Limited, WIL@NUS Corporate Laboratory, Centre for Translational Medicine, National University of Singapore, Singapore, Singapore
| | - Peng Song
- Wilmar International Limited, Wilmar (Shanghai) Biotechnology Research and Development Center Co. Ltd., Shanghai, China
| | - Huan Fan
- Wilmar International Limited, WIL@NUS Corporate Laboratory, Centre for Translational Medicine, National University of Singapore, Singapore, Singapore
- Present Address: Huan Fan, Center for Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Yunnan, People's Republic of China
| | - Oleg Latypov
- Wilmar International Limited, WIL@NUS Corporate Laboratory, Centre for Translational Medicine, National University of Singapore, Singapore, Singapore.
| | - Sandra Kittelmann
- Wilmar International Limited, WIL@NUS Corporate Laboratory, Centre for Translational Medicine, National University of Singapore, Singapore, Singapore.
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Falkenberg KB, Mol V, de la Maza Larrea AS, Pogrebnyakov I, Nørholm MHH, Nielsen AT, Jensen SI. The ProUSER2.0 Toolbox: Genetic Parts and Highly Customizable Plasmids for Synthetic Biology in Bacillus subtilis. ACS Synth Biol 2021; 10:3278-3289. [PMID: 34793671 DOI: 10.1021/acssynbio.1c00130] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Versatile DNA assembly standards and compatible, well-characterized part libraries are essential tools for creating effective designs in synthetic biology. However, to date, vector standards for Gram-positive hosts have limited flexibility. As a result, users often revert to PCR-based methods for building the desired genetic constructs. These methods are inherently prone to introducing mutations, which is problematic considering vector backbone parts are often left unsequenced in cloning workflows. To circumvent this, we present the ProUSER2.0 toolbox: a standardized vector platform for building both integrative and replicative shuttle vectors forBacillus subtilis. The ProUSER2.0 vectors consist of a ProUSER cassette for easy and efficient insertion of cargo sequences and six exchangeable modules. Furthermore, the standard is semicompatible with several previously developed standards, allowing the user to utilize the parts developed for these. To provide parts for the toolbox, seven novel integration sites and six promoters were thoroughly characterized in B. subtilis. Finally, the capacity of the ProUSER2.0 system was demonstrated through the construction of signal peptide libraries for two industrially relevant proteins. Altogether, the ProUSER2.0 toolbox is a powerful and flexible framework for use in B. subtilis.
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Affiliation(s)
- Kristoffer Bach Falkenberg
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet Building 220, Kongens Lyngby 2800, Denmark
| | - Viviënne Mol
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet Building 220, Kongens Lyngby 2800, Denmark
| | - Arrate Sainz de la Maza Larrea
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet Building 220, Kongens Lyngby 2800, Denmark
| | - Ivan Pogrebnyakov
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet Building 220, Kongens Lyngby 2800, Denmark
| | - Morten H. H. Nørholm
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet Building 220, Kongens Lyngby 2800, Denmark
| | - Alex Toftgaard Nielsen
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet Building 220, Kongens Lyngby 2800, Denmark
| | - Sheila Ingemann Jensen
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet Building 220, Kongens Lyngby 2800, Denmark
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Kupriyanova EV, Sinetova MA, Leusenko AV, Voronkov AS, Los DA. A leader peptide of the extracellular cyanobacterial carbonic anhydrase ensures the efficient secretion of recombinant proteins in Escherichia coli. J Biotechnol 2021; 344:11-23. [PMID: 34921977 DOI: 10.1016/j.jbiotec.2021.12.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Revised: 12/11/2021] [Accepted: 12/13/2021] [Indexed: 10/19/2022]
Abstract
Several forms of EcaA protein, correspondent to the extracellular α-class carbonic anhydrase (CA) of cyanobacterium Crocosphaera subtropica ATCC 51142 were expressed in Escherichia coli. The recombinant proteins with no leader peptide (EcaA and its fusion with thioredoxin or glutathione S-transferase) were allocated inside cells in a full-length form; these cells did not display any extracellular CA activity. Soluble proteins (including that of periplasmic space) of E. coli cells that expressed both ЕсаА equipped with its native leader peptide (L-EcaA) as well as L-EcaA fused with thioredoxin or glutathione S-transferase at N-terminus, mainly contained the processed EcaA. The appearance of mature ЕсаА in outer layers of E. coli cells expressed leader peptide-containing forms of recombinant proteins, has been directly confirmed by immunofluorescent microscopy. Those cells also displayed high extracellular CA activity. In addition, the mature EcaA protein was detected in the culture medium. This suggests that cyanobacterial signal peptide is recognized by the secretory machinery and by the leader peptidase of E. coli even as a part of a fusion protein. The efficiency of EcaA leader peptide was comparable to that of PelB and TorA signal peptides, commonly used for biotechnological production of extracellular recombinant proteins in E. coli.
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Affiliation(s)
- Elena V Kupriyanova
- К.А. Timiryazev Institute of Plant Physiology, Russian Academy of Sciences, Botanicheskaya Street 35, Moscow 127276, Russia.
| | - Maria A Sinetova
- К.А. Timiryazev Institute of Plant Physiology, Russian Academy of Sciences, Botanicheskaya Street 35, Moscow 127276, Russia
| | - Anna V Leusenko
- К.А. Timiryazev Institute of Plant Physiology, Russian Academy of Sciences, Botanicheskaya Street 35, Moscow 127276, Russia
| | - Alexander S Voronkov
- К.А. Timiryazev Institute of Plant Physiology, Russian Academy of Sciences, Botanicheskaya Street 35, Moscow 127276, Russia
| | - Dmitry A Los
- К.А. Timiryazev Institute of Plant Physiology, Russian Academy of Sciences, Botanicheskaya Street 35, Moscow 127276, Russia
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Yang H, Qu J, Zou W, Shen W, Chen X. An overview and future prospects of recombinant protein production in Bacillus subtilis. Appl Microbiol Biotechnol 2021; 105:6607-6626. [PMID: 34468804 DOI: 10.1007/s00253-021-11533-2] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 08/12/2021] [Accepted: 08/15/2021] [Indexed: 12/27/2022]
Abstract
Bacillus subtilis is a well-characterized Gram-positive bacterium and a valuable host for recombinant protein production because of its efficient secretion ability, high yield, and non-toxicity. Here, we comprehensively review the recent studies on recombinant protein production in B. subtilis to update and supplement other previous reviews. We have focused on several aspects, including optimization of B. subtilis strains, enhancement and regulation of expression, improvement of secretion level, surface display of proteins, and fermentation optimization. Among them, optimization of B. subtilis strains mainly involves undirected chemical/physical mutagenesis and selection and genetic manipulation; enhancement and regulation of expression comprises autonomous plasmid and integrated expression, promoter regulation and engineering, and fine-tuning gene expression based on proteases and molecular chaperones; improvement of secretion level predominantly involves secretion pathway and signal peptide screening and optimization; surface display of proteins includes surface display of proteins on spores or vegetative cells; and fermentation optimization incorporates medium optimization, process condition optimization, and feeding strategy optimization. Furthermore, we propose some novel methods and future challenges for recombinant protein production in B. subtilis.Key points• A comprehensive review on recombinant protein production in Bacillus subtilis.• Novel techniques facilitate recombinant protein expression and secretion.• Surface display of proteins has significant potential for different applications.
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Affiliation(s)
- Haiquan Yang
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, China.
| | - Jinfeng Qu
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, China
| | - Wei Zou
- College of Bioengineering, Sichuan University of Science & Engineering, Yibin, 644000, Sichuan, China
| | - Wei Shen
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, China
| | - Xianzhong Chen
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, China.
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Miao H, Jiang R, Han N, Ma Y, Wu Q, Mu Y, Huang Z. Enhanced extracellular expression of α-Amylase DL3-4-1 in Bacillus subtilis via systematic screening of optimal signal peptides. Process Biochem 2021. [DOI: 10.1016/j.procbio.2021.06.018] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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Appelbaum M, Schweder T. Metabolic Engineering of
Bacillus
– New Tools, Strains, and Concepts. Metab Eng 2021. [DOI: 10.1002/9783527823468.ch13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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45
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Enhanced extracellular Bacillus stearothermophilus α-amylase production in Bacillus subtilis by balancing the entire secretion process in an optimal strain. Biochem Eng J 2021. [DOI: 10.1016/j.bej.2021.107948] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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46
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Khadye VS, Sawant S, Shaikh K, Srivastava R, Chandrayan S, Odaneth AA. Optimal secretion of thermostable Beta-glucosidase in Bacillus subtilis by signal peptide optimization. Protein Expr Purif 2021; 182:105843. [PMID: 33631310 DOI: 10.1016/j.pep.2021.105843] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Revised: 01/29/2021] [Accepted: 02/09/2021] [Indexed: 10/22/2022]
Abstract
Commercial applications of β-glucosidase (BGL) demands its purity and availability on a large scale. In the present study, we aim to optimize the expression and secretion of a thermostable BGL from Pyrococcus furiosus (PfuBGL) in B. subtilis strain RIK1285. Initial studies with base strain BV002 harboring aprE signal peptide (aprESP) showed PfuBGL yield of 0.743 ± 0.19 pNP U/ml only. A library of 173 different homologous SPs from B. subtilis 168 genome was fused with target PfuBGL gene (PF0073) in pBE-S vector and extracellularly expressed in RIK1285 strain to identify optimal SP for PfuBGL secretion. High-throughput screening of the resulting SP library for BGL activity with a synthetic substrate followed by systematic scaling of the clones yielded a gene construct with CitHSP reporting a sixteen fold enhancement of PfuBGL secretion in comparison to base strain. Batch fermentation (7.5 L scale) PfuBGL yield of the BV003 strain with CitHSP-PF0073 fusion was observed to be 12.08 ± 0.21 pNP U/ml with specific activity of 35.52 ± 0.53 U/mg. Thus, the study represents report on the secretory expression of thermostable PfuBGL using B. subtilis as a host organism and demonstrating its high potential for industrial production of any protein/enzyme.
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Affiliation(s)
- Vishwanath S Khadye
- DBT-ICT Centre for Energy Biosciences, Institute of Chemical Technology (formerly UDCT), Nathalal Parekh Marg, Matunga, Mumbai, 400019, India.
| | - Sneha Sawant
- DBT-ICT Centre for Energy Biosciences, Institute of Chemical Technology (formerly UDCT), Nathalal Parekh Marg, Matunga, Mumbai, 400019, India.
| | - Kurshedaktar Shaikh
- DBT-ICT Centre for Energy Biosciences, Institute of Chemical Technology (formerly UDCT), Nathalal Parekh Marg, Matunga, Mumbai, 400019, India.
| | - Ritika Srivastava
- DBT-ICT Centre for Energy Biosciences, Institute of Chemical Technology (formerly UDCT), Nathalal Parekh Marg, Matunga, Mumbai, 400019, India.
| | - Sanjeev Chandrayan
- DBT-ICT Centre for Energy Biosciences, Institute of Chemical Technology (formerly UDCT), Nathalal Parekh Marg, Matunga, Mumbai, 400019, India.
| | - Annamma A Odaneth
- DBT-ICT Centre for Energy Biosciences, Institute of Chemical Technology (formerly UDCT), Nathalal Parekh Marg, Matunga, Mumbai, 400019, India.
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Lin Y, Guan Y, Dong X, Ma Y, Wang X, Leng Y, Wu F, Ye JW, Chen GQ. Engineering Halomonas bluephagenesis as a chassis for bioproduction from starch. Metab Eng 2021; 64:134-145. [PMID: 33577951 DOI: 10.1016/j.ymben.2021.01.014] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2020] [Revised: 12/22/2020] [Accepted: 01/30/2021] [Indexed: 10/22/2022]
Abstract
Halomonas bluephagenesis has been successfully engineered to produce multiple products under open unsterile conditions utilizing costly glucose as the carbon source. It would be highly interesting to investigate if H. bluephagenesis, a chassis for the Next Generation Industrial Biotechnology (NGIB), can be reconstructed to become an extracellular hydrolytic enzyme producer replacing traditional enzyme producer Bacillus spp. If successful, cost of bulk hydrolytic enzymes such as amylase and protease, can be significantly reduced due to the contamination resistant and robust growth of H. bluephagenesis. This also allows H. bluephagenesis to be able to grow on low cost substrates such as starch. The modularized secretion machinery was constructed and fine-tuned in H. bluephagenesis using codon-optimized gene encoding α-amylase from Bacillus lichenifomis. Screening of suitable signal peptides and linkers based on super-fold green fluorescence protein (sfGFP) for enhanced expression in H. bluephagenesis resulted in a 7-fold enhancement of sfGFP secretion in the recombinant H. bluephagenesis. When the gene encoding sfGFP was replaced by α-amylase encoding gene, recombinant H. bluephagenesis harboring this amylase secretory system was able to produce poly(3-hydroxybutyrate) (PHB), poly(3-hydroxybutyrate-co-4-hydroxybutyrate) (P34HB), poly(3-hydroxybutyrate-co-3-hydroxyvalerate) (PHBV), ectoine and L-threonine utilizing starch as the growth substrate, respectively. Recombinant H. bluephagenesis TN04 expressing genes encoding α-amylase and glucosidase on chromosome and plasmid-based systems, respectively, was able to grow on corn starch to approximately 10 g/L cell dry weight containing 51% PHB when grown in shake flasks. H. bluephagenesis was demonstrated to be a chassis for productions of extracellular enzymes and multiple products from low cost corn starch.
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Affiliation(s)
- Yina Lin
- Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China; Tsinghua-Peking Center for Life Sciences, 100084, China
| | - Yuying Guan
- Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Xu Dong
- Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Yueyuan Ma
- Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Xuan Wang
- Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China; Tsinghua-Peking Center for Life Sciences, 100084, China
| | - Yuchen Leng
- Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Fuqing Wu
- Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China; Tsinghua-Peking Center for Life Sciences, 100084, China; MOE Key Lab of Industrial Biocatalysis, Tsinghua University, Beijing, 100084, China
| | - Jian-Wen Ye
- Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China; Tsinghua-Peking Center for Life Sciences, 100084, China; Center for Materials Synthetic Biology, CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China.
| | - Guo-Qiang Chen
- Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China; Tsinghua-Peking Center for Life Sciences, 100084, China; MOE Key Lab of Industrial Biocatalysis, Tsinghua University, Beijing, 100084, China.
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Rational design of signal peptides for improved MtC1LPMO production in Bacillus amyloliquefaciens. Int J Biol Macromol 2021; 175:262-269. [PMID: 33561461 DOI: 10.1016/j.ijbiomac.2021.02.034] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2020] [Revised: 02/04/2021] [Accepted: 02/04/2021] [Indexed: 11/21/2022]
Abstract
A high-throughput screening system was established by employing enhanced green fluorescent protein as a screenable fusion tag to evaluate the expression and secretion of a lytic polysaccharide monooxygenase (MtC1LPMO) using 20 Sec-type signal peptides (SPs) from Bacillus amyloliquefaciens 111018. Among these, 10 SPs were found to be better than the native SP of MtC1LPMO. The protein expression and secretion levels using SP12 (MNITNWAAILQLQSMALQSISNTGTASS) were the highest among all SPs, with 4.1- and 2.1-fold increases over the native SP, respectively. Then, the amino acids of the 10 best SPs were analyzed, and the results indicated that the most abundant amino acid of the N-region was K, those of the H-region were L, F, A and V, and the C-region contained an AXA motif. Additionally, we found that the protein expression level gradually improved along with the increasing folding free energies of the SP-encoding part of the mRNA. Finally, the SPs were rationally designed to improve the expression and secretion level of MtC1LPMO. An increased positive charge of the SP N-region was found to enhance the protein expression and secretion level, as long as the folding free energy of the mRNA did not change significantly.
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Zhang J, Xu X, Li X, Chen X, Zhou C, Liu Y, Li Y, Lu F. Reducing the cell lysis to enhance yield of acid-stable alpha amylase by deletion of multiple peptidoglycan hydrolase-related genes in Bacillus amyloliquefaciens. Int J Biol Macromol 2020; 167:777-786. [PMID: 33278447 DOI: 10.1016/j.ijbiomac.2020.11.193] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Revised: 11/26/2020] [Accepted: 11/29/2020] [Indexed: 11/30/2022]
Abstract
Bacillus amyloliquefaciens is a major industrial host for extracellular protein production, with great potential in the enzyme industry. However, the strain has accelerated the autolysis drawback in the process of secreting extracellular enzymes, which can significantly lower the density of cells and decrease the product yield. To identify target genes, we employed comparative transcriptome sequencing and KEGG analysis to indicate the increased expression of peptidoglycan hydrolase-regulated genes from the exponential phase to the apoptotic phase of growth; this was further confirmed by quantitative RT-PCR. By deleting lytD, lytE, and sigD genes, cell lysis was reduced and the production of acid-stable Bacillus licheniformis alpha-amylase was enhanced. After 36 h of culture, multiple deletion mutant BA ΔSDE had significantly more viable cells compared to the control strain BA Δupp, and flow cytometry analysis indicated that 48.43% and 64.03% of the cells were lysed in cultures of BA ΔSDE and BA Δupp, respectively. In a 2-L fed-batch fermenter, viable cell number of the triple deletion mutant BA ΔSDE increased by 2.79 Log/cfu/mL, and the activity of acid-stable alpha-amylase increased by 48.4%, compared to BA Δupp. Systematic multiple peptidoglycan hydrolases deletion relieved the autolysis and increased the production of industrial enzymes, and provided a useful strategy for guiding efforts to manipulate the genomes of other B. amyloliquefaciens used for chassis host.
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Affiliation(s)
- Jinfang Zhang
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, The College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, PR China
| | - Xiaojian Xu
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, The College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, PR China
| | - Xinyue Li
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, The College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, PR China
| | - Xuejia Chen
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, The College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, PR China
| | - Cuixia Zhou
- School of Biology and Brewing Engineering, Taishan University, Taian 271018, PR China
| | - Yihan Liu
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, The College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, PR China.
| | - Yu Li
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, The College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, PR China.
| | - Fuping Lu
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, The College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, PR China.
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50
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Su C, Gong JS, Qin J, Li H, Li H, Xu ZH, Shi JS. The tale of a versatile enzyme: Molecular insights into keratinase for its industrial dissemination. Biotechnol Adv 2020; 45:107655. [PMID: 33186607 DOI: 10.1016/j.biotechadv.2020.107655] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2020] [Revised: 10/30/2020] [Accepted: 11/02/2020] [Indexed: 01/02/2023]
Abstract
Keratinases are unique among proteolytic enzymes for their ability to degrade recalcitrant insoluble proteins, and they are of critical importance in keratin waste management. Over the past few decades, researchers have focused on discovering keratinase producers, as well as producing and characterizing keratinases. The application potential of keratinases has been investigated in the feed, fertilizer, leathering, detergent, cosmetic, and medical industries. However, the commercial availability of keratinases is still limited due to poor productivity and properties, such as thermostability, storage stability and resistance to organic reagents. Advances in molecular biotechnology have provided powerful tools for enhancing the production and functional properties of keratinase. This critical review systematically summarizes the application potential of keratinase, and in particular certain newly discovered catalytic capabilities. Furthermore, we provide comprehensive insight into mechanistic and molecular aspects of keratinases including analysis of gene sequences and protein structures. In addition, development and current advances in protein engineering of keratinases are summarized and discussed, revealing that the engineering of protein domains such as signal peptides and pro-peptides has become an important strategy to increase production of keratinases. Finally, prospects for further development are also proposed, indicating that advanced protein engineering technologies will lead to improved and additional commercial keratinases for various industrial applications.
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Affiliation(s)
- Chang Su
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Pharmaceutical Sciences, 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
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark
| | - Heng Li
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Pharmaceutical Sciences, 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
| | - 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
| | - Jin-Song Shi
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Pharmaceutical Sciences, Jiangnan University, Wuxi 214122, PR China.
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