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Tian D, Liu Y, Zhang Y, Liu Y, Xia Y, Xu B, Xu J, Yomo T. Implementation of Fluorescent-Protein-Based Quantification Analysis in L-Form Bacteria. Bioengineering (Basel) 2024; 11:81. [PMID: 38247958 PMCID: PMC10813599 DOI: 10.3390/bioengineering11010081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 01/09/2024] [Accepted: 01/12/2024] [Indexed: 01/23/2024] Open
Abstract
Cell-wall-less (L-form) bacteria exhibit morphological complexity and heterogeneity, complicating quantitative analysis of them under internal and external stimuli. Stable and efficient labeling is needed for the fluorescence-based quantitative cell analysis of L-forms during growth and proliferation. Here, we evaluated the expression of multiple fluorescent proteins (FPs) under different promoters in the Bacillus subtilis L-form strain LR2 using confocal microscopy and imaging flow cytometry. Among others, Pylb-derived NBP3510 showed a superior performance for inducing several FPs including EGFP and mKO2 in both the wild-type and L-form strains. Moreover, NBP3510 was also active in Escherichia coli and its L-form strain NC-7. Employing these established FP-labeled strains, we demonstrated distinct morphologies in the L-form bacteria in a quantitative manner. Given cell-wall-deficient bacteria are considered protocell and synthetic cell models, the generated cell lines in our work could be valuable for L-form-based research.
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Affiliation(s)
| | | | | | | | | | | | - Jian Xu
- Laboratory of Biology and Information Science, School of Life Sciences, East China Normal University, Shanghai 200062, China
| | - Tetsuya Yomo
- Laboratory of Biology and Information Science, School of Life Sciences, East China Normal University, Shanghai 200062, China
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2
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Omics-guided bacterial engineering of Escherichia coli ER2566 for recombinant protein expression. Appl Microbiol Biotechnol 2023; 107:853-865. [PMID: 36539564 PMCID: PMC9767853 DOI: 10.1007/s00253-022-12339-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Revised: 12/07/2022] [Accepted: 12/10/2022] [Indexed: 12/24/2022]
Abstract
The goal of bacterial engineering is to rewire metabolic pathways to generate high-value molecules for various applications. However, the production of recombinant proteins is constrained by the complexity of the connections between cellular physiology and recombinant protein synthesis. Here, we used a rational and highly efficient approach to improve bacterial engineering. Based on the complete genome and annotation information of the Escherichia coli ER2566 strain, we compared the transcriptomic profiles of the strain under leaky expression and low temperature-induced stress. Combining the gene ontology (GO) enrichment terms and differentially expressed genes (DEGs) with higher expression, we selected and knocked out 36 genes to determine the potential impact of these genes on protein production. Deletion of bluF, cydA, mngR, and udp led to a significant decrease in soluble recombinant protein production. Moreover, at low-temperature induction, 4 DEGs (gntK, flgH, flgK, flgL) were associated with enhanced expression of the recombinant protein. Knocking out several motility-related DEGs (ER2666-ΔflgH-ΔflgL-ΔflgK) simultaneously improved the protein yield by 1.5-fold at 24 °C induction, and the recombinant strain had the potential to be applied in the expression studies of different exogenous proteins, aiming to improve the yields of soluble form to varying degrees in comparison to the ER2566 strain. Totally, this study focused on the anabolic and stress-responsive hub genes of the adaptation of E. coli to recombinant protein overexpression on the transcriptome level and constructs a series of engineering strains increasing the soluble protein yield of recombinant proteins which lays a solid foundation for the engineering of bacterial strains for recombinant technological advances. KEY POINTS: • Comparative transcriptome analysis shows host responses with altered induction stress. • Deletion of bluF, cydA, mngR, and udp genes was identified to significantly decrease the soluble recombinant protein productions. • Synchronal knockout of flagellar genes in E. coli can enhance recombinant protein yield up to ~ 1.5-fold at 24 °C induction. • Non-model bacterial strains can be re-engineered for recombinant protein expression.
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3
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The potential of cold-shock promoters for the expression of recombinant proteins in microbes and mammalian cells. J Genet Eng Biotechnol 2022; 20:173. [PMID: 36580173 PMCID: PMC9800685 DOI: 10.1186/s43141-022-00455-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2022] [Accepted: 12/15/2022] [Indexed: 12/30/2022]
Abstract
BACKGROUND Low-temperature expression of recombinant proteins may be advantageous to support their proper folding and preserve bioactivity. The generation of expression vectors regulated under cold conditions can improve the expression of some target proteins that are difficult to express in different expression systems. The cspA encodes the major cold-shock protein from Escherichia coli (CspA). The promoter of cspA has been widely used to develop cold shock-inducible expression platforms in E. coli. Moreover, it is often necessary to employ expression systems other than bacteria, particularly when recombinant proteins require complex post-translational modifications. Currently, there are no commercial platforms available for expressing target genes by cold shock in eukaryotic cells. Consequently, genetic elements that respond to cold shock offer the possibility of developing novel cold-inducible expression platforms, particularly suitable for yeasts, and mammalian cells. CONCLUSIONS This review covers the importance of the cellular response to low temperatures and the prospective use of cold-sensitive promoters to direct the expression of recombinant proteins. This concept may contribute to renewing interest in applying white technologies to produce recombinant proteins that are difficult to express.
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Greeson EM, Madsen CS, Makela AV, Contag CH. Magnetothermal Control of Temperature-Sensitive Repressors in Superparamagnetic Iron Nanoparticle-Coated Bacillus subtilis. ACS NANO 2022; 16:16699-16712. [PMID: 36200984 DOI: 10.1021/acsnano.2c06239] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Superparamagnetic iron oxide nanoparticles (SPIONs) are used as contrast agents in magnetic resonance imaging (MRI) and magnetic particle imaging (MPI), and resulting images can be used to guide magnetothermal heating. Alternating magnetic fields (AMF) cause local temperature increases in regions with SPIONs, and we investigated the ability of magnetic hyperthermia to regulate temperature-sensitive repressors (TSRs) of bacterial transcription. The TSR, TlpA39, was derived from a Gram-negative bacterium and used here for thermal control of reporter gene expression in Gram-positive, Bacillus subtilis. In vitro heating of B. subtilis with TlpA39 controlling bacterial luciferase expression resulted in a 14.6-fold (12 hours; h) and 1.8-fold (1 h) increase in reporter transcripts with a 10.0-fold (12 h) and 12.1-fold (1 h) increase in bioluminescence. To develop magnetothermal control, B. subtilis cells were coated with three SPION variations. Electron microscopy coupled with energy dispersive X-ray spectroscopy revealed an external association with, and retention of, SPIONs on B. subtilis. Furthermore, using long duration AMF we demonstrated magnetothermal induction of the TSRs in SPION-coated B. subtilis with a maximum of 5.6-fold increases in bioluminescence. After intramuscular injections of SPION-coated B. subtilis, histology revealed that SPIONs remained in the same locations as the bacteria. For in vivo studies, 1 h of AMF is the maximum exposure due to anesthesia constraints. Both in vitro and in vivo, there was no change in bioluminescence after 1 h of AMF treatment. Pairing TSRs with magnetothermal energy using SPIONs for localized heating with AMF can lead to transcriptional control that expands options for targeted bacteriotherapies.
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Affiliation(s)
- Emily M Greeson
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan 48824, United States
- Institute for Quantitative Health Science and Engineering, Michigan State University, East Lansing, Michigan 48824, United States
| | - Cody S Madsen
- Department of Biomedical Engineering, Michigan State University, East Lansing, Michigan 48824, United States
- Institute for Quantitative Health Science and Engineering, Michigan State University, East Lansing, Michigan 48824, United States
| | - Ashley V Makela
- Department of Biomedical Engineering, Michigan State University, East Lansing, Michigan 48824, United States
- Institute for Quantitative Health Science and Engineering, Michigan State University, East Lansing, Michigan 48824, United States
| | - Christopher H Contag
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan 48824, United States
- Department of Biomedical Engineering, Michigan State University, East Lansing, Michigan 48824, United States
- Institute for Quantitative Health Science and Engineering, Michigan State University, East Lansing, Michigan 48824, United States
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5
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An operator-based expression toolkit for Bacillus subtilis enables fine-tuning of gene expression and biosynthetic pathway regulation. Proc Natl Acad Sci U S A 2022; 119:e2119980119. [PMID: 35263224 PMCID: PMC8931375 DOI: 10.1073/pnas.2119980119] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
A gene regulatory system is an important tool for the engineering of biosynthetic pathways of organisms. Here, we report the development of an inducible-ON/OFF regulatory system using a malO operator as a key element. We identified and modulated sequence, position, numbers, and spacing distance of malO operators, generating a series of activating or repressive promoters with tunable strength. The stringency and robustness are both guaranteed in this system, a maximal induction factor of 790-fold was achieved, and nine proteins from different organisms were expressed with high yields. This system can be utilized as a gene switch, promoter enhancer, or metabolic valve in synthetic biology applications. This operator-based engineering strategy can be employed for developing similar regulatory systems in different microorganisms. Genetic elements are key components of metabolic engineering and synthetic biological applications, allowing the development of organisms as biosensors and for manufacturing valuable chemicals and protein products. In contrast to the gram-negative model bacterium Escherichia coli, the gram-positive model bacterium Bacillus subtilis lacks such elements with precise and flexible characteristics, which is a great barrier to employing B. subtilis for laboratory studies and industrial applications. Here, we report the development of a malO-based genetic toolbox that is derived from the operator box in the malA promoter, enabling gene regulation via compatible “ON” and “OFF” switches. This engineered toolbox combines promoter-based mutagenesis and host-specific metabolic engineering of transactivation components upon maltose induction to achieve stringent, robust, and homogeneous gene regulation in B. subtilis. We further demonstrate the synthetic biological applications of the toolbox by utilizing these genetic elements as a gene switch, a promoter enhancer, and an ON-OFF dual-control device in biosynthetic pathway optimization. Collectively, this regulatory system provides a comprehensive genetic toolbox for controlling the expression of genes in biosynthetic pathways and regulatory networks to optimize the production of valuable chemicals and proteins in B. subtilis.
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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: 19] [Impact Index Per Article: 6.3] [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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Chen X, Li C, Liu H. Enhanced Recombinant Protein Production Under Special Environmental Stress. Front Microbiol 2021; 12:630814. [PMID: 33935992 PMCID: PMC8084102 DOI: 10.3389/fmicb.2021.630814] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Accepted: 02/19/2021] [Indexed: 01/09/2023] Open
Abstract
Regardless of bacteria or eukaryotic microorganism hosts, improving their ability to express heterologous proteins is always a goal worthy of elaborate study. In addition to traditional methods including intracellular synthesis process regulation and extracellular environment optimization, some special or extreme conditions can also be employed to create an enhancing effect on heterologous protein production. In this review, we summarize some extreme environmental factors used for the improvement of heterologous protein expression, including low temperature, hypoxia, microgravity and high osmolality. The applications of these strategies are elaborated with examples of well-documented studies. We also demonstrated the confirmed or hypothetical mechanisms of environment stress affecting the host behaviors. In addition, multi-omics techniques driving the stress-responsive research for construction of efficient microbial cell factories are also prospected at the end.
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Affiliation(s)
- Xinyi Chen
- Key Laboratory of Medical Molecule Science and Pharmaceutics Engineering, Ministry of Industry and Information Technology, Institute of Biochemical Engineering, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, China
| | - Chun Li
- Key Laboratory of Medical Molecule Science and Pharmaceutics Engineering, Ministry of Industry and Information Technology, Institute of Biochemical Engineering, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, China.,Key Laboratory for Industrial Biocatalysis, Ministry of Education, Department of Chemical Engineering, Tsinghua University, Beijing, China.,Center for Synthetic & Systems Biology, Tsinghua University, Beijing, China
| | - Hu Liu
- Key Laboratory of Medical Molecule Science and Pharmaceutics Engineering, Ministry of Industry and Information Technology, Institute of Biochemical Engineering, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, China
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8
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Highly Efficient Synthesis of Glutathione via a Genetic Engineering Enzymatic Method Coupled with Yeast ATP Generation. Catalysts 2019. [DOI: 10.3390/catal10010033] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Glutathione is a tripeptide compound with many important physiological functions. A new, two-step reaction system has been developed to efficiently synthesize glutathione. In the first step, glutamate and cysteine are condensed to glutamyl-cysteine by endogenous yeast enzymes inside the yeast cell, while consuming ATP. In the second step, the yeast cell membrane is lysed by the permeabilizing agent CTAB (cetyltrimethylammonium bromide) to release the glutamyl-cysteine, upon which added glutathione synthetase converts the glutamyl-cysteine and added glycine into glutathione. The ATP needed for this conversion is supplied by the permeabilized yeast cells of glycolytic pathway. This method provided sufficient ATP, and reduced the feedback inhibition of glutathione for the first-step enzymatic reaction, thereby improving the catalytic efficiency of the enzyme reaction. In addition, the formation of suitable oxidative stress environment in the reaction system can further promote glutathione synthesis. By HPLC analysis of the glutathione, it was found that 2.1 g/L reduced glutathione is produced and 17.5 g/L oxidized glutathione. Therefore, the new reaction system not only increases the total glutathione, but also facilitates the subsequent separation and purification due to the larger proportion of oxidized glutathione in the reaction system.
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9
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Zhou C, Ye B, Cheng S, Zhao L, Liu Y, Jiang J, Yan X. Promoter engineering enables overproduction of foreign proteins from a single copy expression cassette in Bacillus subtilis. Microb Cell Fact 2019; 18:111. [PMID: 31200722 PMCID: PMC6570832 DOI: 10.1186/s12934-019-1159-0] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2019] [Accepted: 06/09/2019] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND Bacillus subtilis is developed to be an attractive expression host to produce both secreted and cytoplasmic proteins owing to its prominent biological characteristics. Chromosomal integration is a stable expression strategy while the expression level is not ideal compared with plasmid expression. Thus, to meet the requirement of protein overexpression, promoter, as one of the key elements, is important. It is necessary to obtain an ideal promoter for overproduction of foreign proteins from a single copy expression cassette. RESULTS The activity of promoter Pylb was further enhanced by optimizing the - 35, - 10 core region and upstream sequence (UP) by substituting both sequences with consensus sequences. The final engineered promoter exhibited almost 26-fold in β-galactosidase (BgaB) activity and 195-fold in super-folded green fluorescent protein (sfGFP) intensity than that of WT. The two proteins account for 43% and 30% of intracellular proteins, respectively. The promoter was eventually tested by successful extracellular overproduction of Methyl Parathion Hydrolase (MPH) and Chlorothalonil hydrolytic dehalogenase (Chd) to a level of 0.3 g/L (144 U/mL) and 0.27 g/L (4.4 U/mL) on shake-flask culture condition. CONCLUSIONS A strong promoter was engineered for efficient chromosomally integrated expression of heterologous proteins.
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Affiliation(s)
- Chaoyang Zhou
- Department of Microbiology, College of Life Sciences, Key Laboratory for Microbiological Engineering of Agricultural, Environment of Ministry of Agriculture, Nanjing Agricultural University, 6 Tongwei Road, Nanjing, 210095, Jiangsu, People's Republic of China
| | - Bin Ye
- Department of Microbiology, College of Life Sciences, Key Laboratory for Microbiological Engineering of Agricultural, Environment of Ministry of Agriculture, Nanjing Agricultural University, 6 Tongwei Road, Nanjing, 210095, Jiangsu, People's Republic of China
| | - Shan Cheng
- Department of Microbiology, College of Life Sciences, Key Laboratory for Microbiological Engineering of Agricultural, Environment of Ministry of Agriculture, Nanjing Agricultural University, 6 Tongwei Road, Nanjing, 210095, Jiangsu, People's Republic of China
| | - Leizhen Zhao
- Department of Microbiology, College of Life Sciences, Key Laboratory for Microbiological Engineering of Agricultural, Environment of Ministry of Agriculture, Nanjing Agricultural University, 6 Tongwei Road, Nanjing, 210095, Jiangsu, People's Republic of China
| | - Yuanxin Liu
- Department of Microbiology, College of Life Sciences, Key Laboratory for Microbiological Engineering of Agricultural, Environment of Ministry of Agriculture, Nanjing Agricultural University, 6 Tongwei Road, Nanjing, 210095, Jiangsu, People's Republic of China
| | - Jiandong Jiang
- Department of Microbiology, College of Life Sciences, Key Laboratory for Microbiological Engineering of Agricultural, Environment of Ministry of Agriculture, Nanjing Agricultural University, 6 Tongwei Road, Nanjing, 210095, Jiangsu, People's Republic of China
| | - Xin Yan
- Department of Microbiology, College of Life Sciences, Key Laboratory for Microbiological Engineering of Agricultural, Environment of Ministry of Agriculture, Nanjing Agricultural University, 6 Tongwei Road, Nanjing, 210095, Jiangsu, People's Republic of China.
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Liu H, Wang X, Yang S, Wang R, Wang T. Saturation mutagenesis and self-inducible expression of trehalose synthase in Bacillus subtilis. Biotechnol Prog 2019; 35:e2826. [PMID: 31021505 DOI: 10.1002/btpr.2826] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Revised: 02/12/2019] [Accepted: 04/19/2019] [Indexed: 01/27/2023]
Abstract
Trehalose is a nonreducing disaccharide synthesized by trehalose synthase (TreS), which catalyzes the reversible interconversion of maltose and trehalose. We aimed to enhance the catalytic conversion of maltose to trehalose by saturation mutagenesis, and constructed a self-inducible TreS expression system by generating a robust Bacillus subtilis recombinant. We found that the conversion yield and enzymatic activity of TreS was enhanced by saturation mutations, especially by the combination of V407M and K490L mutations. At the same time, these saturation mutations were contributing to reducing by-products in the reaction. Compared to WT TreS, the conversion yield of maltose to trehalose was increased by 11.9%, and the kcat /Km toward trehalose was 1.33 times higher in the reaction catalyzed by treSV407M-K490L . treSV407M-K490L expression was further observed in the recombinant B. subtilis W800N(ΔσF ) under the influence of PsrfA , Pcry3Aa , and PsrfA-cry3Aa promoters without an inducer. It was shown that PsrfA-cry3Aa was evidently a stronger promoter for treSV407M-K490L expression, with the intracellular enzymatic activity of recombinant treSV407M-K490L being over 5,800 U/g at 35 hr in TB medium. These results suggested the combination of two mutations, V407M and K490L, was conducive for the production of trehalose. In addition, the self-inducible TreSV407M/K490L mutant in the B. subtilis host provides a low-cost choice for the industrial production of endotoxin-free trehalose with high yields.
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Affiliation(s)
- Hongling Liu
- State Key Laboratory of Biobased Material and Green Papermaking (LBMP), Qilu University of Technology (Shandong Academy of Sciences), Jinan, Shandong, People's Republic of China.,Key Laboratory of Shandong Microbial Engineering, School of Bioengineering, QiLu University of Technology (Shandong Academy of Sciences), Jinan, Shandong, People's Republic of China.,Key Laboratory of Industrial Fermentation Microbiology (Tianjin University of Science &Technology), Ministry of Education, Tianjin, People's Republic of China
| | - Xihui Wang
- State Key Laboratory of Biobased Material and Green Papermaking (LBMP), Qilu University of Technology (Shandong Academy of Sciences), Jinan, Shandong, People's Republic of China.,Key Laboratory of Shandong Microbial Engineering, School of Bioengineering, QiLu University of Technology (Shandong Academy of Sciences), Jinan, Shandong, People's Republic of China
| | - Shaojie Yang
- State Key Laboratory of Biobased Material and Green Papermaking (LBMP), Qilu University of Technology (Shandong Academy of Sciences), Jinan, Shandong, People's Republic of China.,Key Laboratory of Shandong Microbial Engineering, School of Bioengineering, QiLu University of Technology (Shandong Academy of Sciences), Jinan, Shandong, People's Republic of China
| | - Ruiming Wang
- State Key Laboratory of Biobased Material and Green Papermaking (LBMP), Qilu University of Technology (Shandong Academy of Sciences), Jinan, Shandong, People's Republic of China.,Key Laboratory of Shandong Microbial Engineering, School of Bioengineering, QiLu University of Technology (Shandong Academy of Sciences), Jinan, Shandong, People's Republic of China
| | - Tengfei Wang
- State Key Laboratory of Biobased Material and Green Papermaking (LBMP), Qilu University of Technology (Shandong Academy of Sciences), Jinan, Shandong, People's Republic of China.,Key Laboratory of Shandong Microbial Engineering, School of Bioengineering, QiLu University of Technology (Shandong Academy of Sciences), Jinan, Shandong, People's Republic of China
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11
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Uhoraningoga A, Kinsella GK, Henehan GT, Ryan BJ. The Goldilocks Approach: A Review of Employing Design of Experiments in Prokaryotic Recombinant Protein Production. Bioengineering (Basel) 2018; 5:E89. [PMID: 30347746 PMCID: PMC6316313 DOI: 10.3390/bioengineering5040089] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Revised: 10/09/2018] [Accepted: 10/12/2018] [Indexed: 02/06/2023] Open
Abstract
The production of high yields of soluble recombinant protein is one of the main objectives of protein biotechnology. Several factors, such as expression system, vector, host, media composition and induction conditions can influence recombinant protein yield. Identifying the most important factors for optimum protein expression may involve significant investment of time and considerable cost. To address this problem, statistical models such as Design of Experiments (DoE) have been used to optimise recombinant protein production. This review examines the application of DoE in the production of recombinant proteins in prokaryotic expression systems with specific emphasis on media composition and culture conditions. The review examines the most commonly used DoE screening and optimisation designs. It provides examples of DoE applied to optimisation of media and culture conditions.
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Affiliation(s)
| | | | - Gary T Henehan
- Dublin Institute of Technology, Dublin D01 HV58, Ireland.
| | - Barry J Ryan
- Dublin Institute of Technology, Dublin D01 HV58, Ireland.
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12
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Yang S, Du G, Chen J, Kang Z. Characterization and application of endogenous phase-dependent promoters in Bacillus subtilis. Appl Microbiol Biotechnol 2017; 101:4151-4161. [DOI: 10.1007/s00253-017-8142-7] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2016] [Revised: 01/05/2017] [Accepted: 01/20/2017] [Indexed: 01/01/2023]
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13
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Construction of a novel, stable, food-grade expression system by engineering the endogenous toxin-antitoxin system in Bacillus subtilis. J Biotechnol 2016; 219:40-7. [DOI: 10.1016/j.jbiotec.2015.12.029] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2015] [Revised: 11/03/2015] [Accepted: 12/16/2015] [Indexed: 12/28/2022]
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14
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Bjerga GEK, Lale R, Williamson AK. Engineering low-temperature expression systems for heterologous production of cold-adapted enzymes. Bioengineered 2015; 7:33-8. [PMID: 26710170 PMCID: PMC4878266 DOI: 10.1080/21655979.2015.1128589] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
Production of psychrophilic enzymes in the commonly used mesophilic expression systems is hampered by low intrinsic stability of the recombinant enzymes at the optimal host growth temperatures. Unless strategies for low-temperature expression are advanced, research on psychrophilic enzymes may end up being biased toward those that can be stably produced in commonly used mesophilic host systems. Two main strategies are currently being explored for the development of low-temperature expression in bacterial hosts: (i) low-temperature adaption of existing mesophilic expression systems, and (ii) development of new psychrophilic hosts. These developments include genetic engineering of the expression cassettes to optimize the promoter/operator systems that regulate heterologous expression. In this addendum we present our efforts in the development of such low-temperature expression systems, and speculate about future advancements in the field and potential applications.
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Affiliation(s)
- Gro Elin Kjæreng Bjerga
- a University of Tromsø, Norstruct, Department of Chemistry, Faculty of Science and Technology , Tromsø , Norway
| | - Rahmi Lale
- b Norwegian University of Science and Technology , Department of Biotechnology , Trondheim , Norway
| | - Adele Kim Williamson
- a University of Tromsø, Norstruct, Department of Chemistry, Faculty of Science and Technology , Tromsø , Norway
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15
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Guan C, Cui W, Cheng J, Zhou L, Guo J, Hu X, Xiao G, Zhou Z. Construction and development of an auto-regulatory gene expression system in Bacillus subtilis. Microb Cell Fact 2015; 14:150. [PMID: 26392346 PMCID: PMC4578258 DOI: 10.1186/s12934-015-0341-2] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2015] [Accepted: 09/12/2015] [Indexed: 01/24/2023] Open
Abstract
BACKGROUND Bacillus subtilis is an all-important Gram-positive bacterium of valuable biotechnological utility that has been widely used to over-produce industrially and pharmaceutically relevant proteins. There are a variety of expression systems in terms of types of transcriptional patterns, among which the auto-inducible and growth-phase-dependent promoters are gaining increasing favor due to their inducer-independent feature, allowing for the potential to industrially scale-up. To expand the applicability of the auto-inducible expression system, a novel auto-regulatory expression system coupled with cell density was constructed and developed in B. subtilis using the quorum-sensing related promoter srfA (PsrfA). RESULTS The promoter of the srf operon was used to construct an expression plasmid with the green fluorescent protein (GFP) downstream of PsrfA. The expression displayed a cell-density-dependent pattern in that GFP had a fairly low expression level at the early exponential stage and was highly expressed at the late exponential as well as the stationary stages. Moreover, the recombinant system had a similar expression pattern in wild-type B. subtilis 168, WB600, and WB800, as well as in B. subtilis 168 derivative strain 1681, with the complete deletion of PsrfA, indicating the excellent compatibility of this system. Noticeably, the expression strength of PsrfA was enhanced by optimizing the -10 and -35 core sequence by substituting both sequences with consensus sequences. Importantly, the expression pattern was successfully developed in an auto-regulatory cell-density coupling system by the simple addition of glucose in which GFP could not be strongly expressed until glucose was depleted, resulting in a greater amount of the GFP product and increased cell density. The expression system was eventually tested by the successful over-production of aminopeptidase to a desired level. CONCLUSION The auto-regulatory cell density coupling system that is mediated by PsrfA is a novel expression system that has an expression pattern that is split between cell-growth and over-expression, leading to an increase in cell density and elevating the overall expression levels of heterologously expressed proteins. The broad applicability of this system and inducer-free expression property in B. subtilis facilitate the industrial scale-up and medical applications for the over-production of a variety of desired proteins.
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Affiliation(s)
- Chengran Guan
- School of Biotechnology, Key Laboratory of Industrial Biotechnology (Ministry of Education), Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, China.
| | - Wenjing Cui
- School of Biotechnology, Key Laboratory of Industrial Biotechnology (Ministry of Education), Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, China.
| | - Jintao Cheng
- School of Biotechnology, Key Laboratory of Industrial Biotechnology (Ministry of Education), Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, China.
| | - Li Zhou
- School of Biotechnology, Key Laboratory of Industrial Biotechnology (Ministry of Education), Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, China.
| | - Junling Guo
- School of Biotechnology, Key Laboratory of Industrial Biotechnology (Ministry of Education), Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, China.
| | - Xu Hu
- School of Biotechnology, Key Laboratory of Industrial Biotechnology (Ministry of Education), Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, China.
| | - Guoping Xiao
- Wuxi Biortus Bioscience Co., Ltd, Wuxi, Jiangsu, 214122, China.
| | - Zhemin Zhou
- School of Biotechnology, Key Laboratory of Industrial Biotechnology (Ministry of Education), Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, China.
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Phan TTP, Tran LT, Schumann W, Nguyen HD. Development of Pgrac100-based expression vectors allowing high protein production levels in Bacillus subtilis and relatively low basal expression in Escherichia coli. Microb Cell Fact 2015; 14:72. [PMID: 25990516 PMCID: PMC4446860 DOI: 10.1186/s12934-015-0255-z] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2015] [Accepted: 05/06/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND In general, fusion of recombinant genes to strong inducible promoters allowing intracellular expression in Bacillus subtilis is a two-step process. The ligation products are transformed into Escherichia coli, followed by identification of the correct plasmid, and this plasmid is subsequently transformed into B. subtilis. This raises the problem that basal level of expression of the recombinant gene could be harmful for E. coli cells. Based on the Pgrac promoter, we optimized the UP element, the -35, 15, -10 and the +1 region to enhance the promoter activity in B. subtilis after induction. However, detailed investigations for a promoter to develop expression vectors that allows high protein production levels in B. subtilis and a relatively low basal expression levels in E. coli has not been studied yet. RESULTS We screened the previously constructed library of E. coli - B. subtilis shuttle vectors for high level expression in B. subtilis and low basal level in E. coli. Promoter Pgrac100 turned out to meet these criteria, in which ß-galactosidase expression level of Pgrac100-bgaB is about 9.2 times higher than Pgrac01-bgaB in B. subtilis and the ratio of those in induced B. subtilis over un-induced E. coli from Pgrac100-bgaB is 1.3 times higher than Pgrac01-bgaB. Similarly, GFP expression level of Pgrac100-gfp is about 27 times higher than that of Pgrac01-gfp and the ratio from Pgrac100-gfp is 35.5 times higher than Pgrac01-gfp. This promoter was used as a basis for the construction of three novel vectors, pHT253 (His-tag-MCS), pHT254 (MCS-His-tag) and pHT255 (MCS-Strep-tag). Expression of the reporter proteins BgaB and GFP using these expression vectors in B. subtilis at a low IPTG concentration were measured and the fusion proteins could be purified easily in a single step by using Strep-Tactin or IMAC-Ni columns. CONCLUSIONS This paper describes the construction and analysis of an IPTG-inducible expression vector termed Pgrac100 for the high level production of intracellular recombinant proteins in B. subtilis and a relatively low basal expression level in E. coli. Based on this vector, the derivative vectors, Pgrac100-His-tag-MCS, Pgrac100-MCS-His-tag and Pgrac100-MCS-Strep-tag have been constructed.
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Affiliation(s)
- Trang Thi Phuong Phan
- Center for Bioscience and Biotechnology, VNUHCMC-University of Science, 227 Nguyen Van Cu District 5, Hochiminh, Vietnam. .,Laboratory of Molecular Biotechnology, VNUHCMC-University of Science, 227 Nguyen Van Cu District 5, Hochiminh, Vietnam.
| | - Linh Thuoc Tran
- Laboratory of Molecular Biotechnology, VNUHCMC-University of Science, 227 Nguyen Van Cu District 5, Hochiminh, Vietnam.
| | - Wolfgang Schumann
- Center for Bioscience and Biotechnology, VNUHCMC-University of Science, 227 Nguyen Van Cu District 5, Hochiminh, Vietnam. .,Institute of Genetics, Universität of Bayreuth, Bayreuth, D-95440, Germany.
| | - Hoang Duc Nguyen
- Center for Bioscience and Biotechnology, VNUHCMC-University of Science, 227 Nguyen Van Cu District 5, Hochiminh, Vietnam. .,Laboratory of Molecular Biotechnology, VNUHCMC-University of Science, 227 Nguyen Van Cu District 5, Hochiminh, Vietnam. .,Department of Microbiology, VNUHCMC-University of Science, 227 Nguyen Van Cu District 5, Hochiminh, Vietnam.
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Welsch N, Homuth G, Schweder T. Stepwise optimization of a low-temperature Bacillus subtilis expression system for “difficult to express” proteins. Appl Microbiol Biotechnol 2015; 99:6363-76. [DOI: 10.1007/s00253-015-6552-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2015] [Revised: 03/13/2015] [Accepted: 03/17/2015] [Indexed: 10/23/2022]
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Jajesniak P, Seng Wong T. From genetic circuits to industrial-scale biomanufacturing: bacterial promoters as a cornerstone of biotechnology. AIMS BIOENGINEERING 2015. [DOI: 10.3934/bioeng.2015.3.277] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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San-Miguel T, Pérez-Bermúdez P, Gavidia I. Production of soluble eukaryotic recombinant proteins in E. coli is favoured in early log-phase cultures induced at low temperature. SPRINGERPLUS 2013; 2:89. [PMID: 23525091 PMCID: PMC3602615 DOI: 10.1186/2193-1801-2-89] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/20/2012] [Accepted: 03/04/2013] [Indexed: 11/16/2022]
Abstract
Background Producing recombinant plant proteins expressed in Escherichia coli produce in high yields and in a soluble and functional form can be difficult. Under overexpression conditions, proteins frequently accumulate as insoluble aggregates (inclusion bodies) within the producing bacteria. We evaluated how the initial culture density, temperature and duration of the expression stage affect the production of some eukaryotic enzymes in E. coli. Findings A high yield of active soluble proteins was obtained by combining early-log phase cultures and low temperatures for protein induction. When IPTG was added at OD600 = 0.1 and cultures were maintained at 4°C for 48-72 h, the soluble protein yield was 3 fold higher than that obtained in the mid-log phase (OD600 = 0.6). Besides, the target protein expression increased and the endogenous bacterial proteins reduced, thus making the protein purification process easier and more efficient. Conclusions The protocol can be widely applied to proteins with a heterologous expression which was limited by loss of activity at high temperatures or by low soluble recombinant protein yield.
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Affiliation(s)
- Teresa San-Miguel
- Departamento de Biología Vegetal, Facultad de Farmacia, Universidad de Valencia, Av. VA Estellés s/n, Burjasot, 46100 Spain
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Toymentseva AA, Schrecke K, Sharipova MR, Mascher T. The LIKE system, a novel protein expression toolbox for Bacillus subtilis based on the liaI promoter. Microb Cell Fact 2012; 11:143. [PMID: 23110498 PMCID: PMC3567932 DOI: 10.1186/1475-2859-11-143] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2012] [Accepted: 10/15/2012] [Indexed: 11/17/2022] Open
Abstract
Background Bacillus subtilis is a very important Gram-positive model organism of high biotechnological relevance, which is widely used as a host for the production of both secreted and cytoplasmic proteins. We developed a novel and efficient expression system, based on the liaI promoter (PliaI) from B. subtilis, which is under control of the LiaRS antibiotic-inducible two-component system. In the absence of a stimulus, this promoter is kept tightly inactive. Upon induction by cell wall antibiotics, it shows an over 100-fold increase in activity within 10 min. Results Based on these traits of PliaI, we developed a novel LiaRS-controlled gene expression system for B. subtilis (the “LIKE" system). Two expression vectors, the integrative pLIKE-int and the replicative pLIKE-rep, were constructed. To enhance the performance of the PliaI-derived system, site-directed mutagenesis was employed to optimize the ribosome binding site and alter its spacing to the initiation codon used for the translational fusion. The impact of these genetic modifications on protein production yield was measured using GFP as a model protein. Moreover, a number of tailored B. subtilis expression strains containing different markerless chromosomal deletions of the liaIH region were constructed to circumvent undesired protein production, enhance the positive autoregulation of the LiaRS system and thereby increase target gene expression strength from the PliaI promoter. Conclusions The LIKE protein expression system is a novel protein expression system, which offers a number of advantages over existing systems. Its major advantages are (i) a tightly switched-off promoter during exponential growth in the absence of a stimulus, (ii) a concentration-dependent activation of PliaI in the presence of suitable inducers, (iii) a very fast but transient response with a very high dynamic range of over 100-fold (up to 1,000-fold) induction, (iv) a choice from a range of well-defined, commercially available, and affordable inducers and (v) the convenient conversion of LIKE-derived inducible expression strains into strong constitutive protein production factories.
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Affiliation(s)
- Anna A Toymentseva
- Department of Biology I, Microbiology, Ludwig-Maximilians-University Munich, Munich, Germany
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Stress-responsive systems set specific limits to the overproduction of membrane proteins in Bacillus subtilis. Appl Environ Microbiol 2009; 75:7356-64. [PMID: 19820159 DOI: 10.1128/aem.01560-09] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Essential membrane proteins are generally recognized as relevant potential drug targets due to their exposed localization in the cell envelope. Unfortunately, high-level production of membrane proteins for functional and structural analyses is often problematic. This is mainly due to their high overall hydrophobicity. To develop new concepts for membrane protein overproduction, we investigated whether the biogenesis of overproduced membrane proteins is affected by stress response-related proteolytic systems in the membrane. For this purpose, the well-established expression host Bacillus subtilis was used to overproduce eight essential membrane proteins from B. subtilis and Staphylococcus aureus. The results show that the sigma(W) regulon (responding to cell envelope perturbations) and the CssRS two-component regulatory system (responding to unfolded exported proteins) set critical limits to membrane protein production in large quantities. The identified sigW or cssRS mutant B. subtilis strains with significantly improved capacity for membrane protein production are interesting candidate expression hosts for fundamental research and biotechnological applications. Importantly, our results pinpoint the interdependent expression and function of membrane-associated proteases as key parameters in bacterial membrane protein production.
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Schumann W. Production of Recombinant Proteins in Bacillus subtilis. ADVANCES IN APPLIED MICROBIOLOGY 2007; 62:137-89. [PMID: 17869605 DOI: 10.1016/s0065-2164(07)62006-1] [Citation(s) in RCA: 116] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Wolfgang Schumann
- Institute of Genetics, University of Bayreuth, Bayreuth D-95440, Germany
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