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Aguilar Suárez R, Kohlstedt M, Öktem A, Neef J, Wu Y, Ikeda K, Yoshida KI, Altenbuchner J, Wittmann C, van Dijl JM. Metabolic Profile of the Genome-Reduced Bacillus subtilis Strain IIG-Bs-27-39: An Attractive Chassis for Recombinant Protein Production. ACS Synth Biol 2024; 13:2199-2214. [PMID: 38981062 PMCID: PMC11264325 DOI: 10.1021/acssynbio.4c00254] [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: 04/20/2024] [Revised: 06/22/2024] [Accepted: 06/26/2024] [Indexed: 07/11/2024]
Abstract
The Gram-positive bacterium Bacillus subtilis is extensively used in the industry for the secretory production of proteins with commercial value. To further improve its performance, this microbe has been the subject of extensive genome engineering efforts, especially the removal of large genomic regions that are dispensable or even counterproductive. Here, we present the genome-reduced B. subtilis strain IIG-Bs-27-39, which was obtained through systematic deletion of mobile genetic elements, as well as genes for extracellular proteases, sporulation, flagella formation, and antibiotic production. Different from previously characterized genome-reduced B. subtilis strains, the IIG-Bs-27-39 strain was still able to grow on minimal media. We used this feature to benchmark strain IIG-Bs-27-39 against its parental strain 168 with respect to heterologous protein production and metabolic parameters during bioreactor cultivation. The IIG-Bs-27-39 strain presented superior secretion of difficult-to-produce staphylococcal antigens, as well as higher specific growth rates and biomass yields. At the metabolic level, changes in byproduct formation and internal amino acid pools were observed, whereas energetic parameters such as the ATP yield, ATP/ADP levels, and adenylate energy charge were comparable between the two strains. Intriguingly, we observed a significant increase in the total cellular NADPH level during all tested conditions and increases in the NAD+ and NADP(H) pools during protein production. This indicates that the IIG-Bs-27-39 strain has more energy available for anabolic processes and protein production, thereby providing a link between strain physiology and production performance. On this basis, we conclude that the genome-reduced strain IIG-Bs-27-39 represents an attractive chassis for future biotechnological applications.
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Affiliation(s)
- Rocío Aguilar Suárez
- Department
of Medical Microbiology, University Medical
Center Groningen-University of Groningen, 9700RB Groningen, The Netherlands
| | - Michael Kohlstedt
- Institute
for Systems Biotechnology, Saarland University, 66123 Saarbrücken, Germany
| | - Ayşegül Öktem
- Department
of Medical Microbiology, University Medical
Center Groningen-University of Groningen, 9700RB Groningen, The Netherlands
| | - Jolanda Neef
- Department
of Medical Microbiology, University Medical
Center Groningen-University of Groningen, 9700RB Groningen, The Netherlands
| | - Yuzheng Wu
- Department
of Science, Technology and Innovation, Kobe
University, 657-8501 Kobe, Japan
| | - Kaiya Ikeda
- Department
of Science, Technology and Innovation, Kobe
University, 657-8501 Kobe, Japan
| | - Ken-Ichi Yoshida
- Department
of Science, Technology and Innovation, Kobe
University, 657-8501 Kobe, Japan
| | - Josef Altenbuchner
- Institute
for Industrial Genetics, University of Stuttgart, 70569 Stuttgart, Germany
| | - Christoph Wittmann
- Institute
for Systems Biotechnology, Saarland University, 66123 Saarbrücken, Germany
| | - Jan Maarten van Dijl
- Department
of Medical Microbiology, University Medical
Center Groningen-University of Groningen, 9700RB Groningen, The Netherlands
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Put H, Gerstmans H, Vande Capelle H, Fauvart M, Michiels J, Masschelein J. Bacillus subtilis as a host for natural product discovery and engineering of biosynthetic gene clusters. Nat Prod Rep 2024; 41:1113-1151. [PMID: 38465694 DOI: 10.1039/d3np00065f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
Covering: up to October 2023Many bioactive natural products are synthesized by microorganisms that are either difficult or impossible to cultivate under laboratory conditions, or that produce only small amounts of the desired compound. By transferring biosynthetic gene clusters (BGCs) into alternative host organisms that are more easily cultured and engineered, larger quantities can be obtained and new analogues with potentially improved biological activity or other desirable properties can be generated. Moreover, expression of cryptic BGCs in a suitable host can facilitate the identification and characterization of novel natural products. Heterologous expression therefore represents a valuable tool for natural product discovery and engineering as it allows the study and manipulation of their biosynthetic pathways in a controlled setting, enabling innovative applications. Bacillus is a genus of Gram-positive bacteria that is widely used in industrial biotechnology as a host for the production of proteins from diverse origins, including enzymes and vaccines. However, despite numerous successful examples, Bacillus species remain underexploited as heterologous hosts for the expression of natural product BGCs. Here, we review important advantages that Bacillus species offer as expression hosts, such as high secretion capacity, natural competence for DNA uptake, and the increasing availability of a wide range of genetic tools for gene expression and strain engineering. We evaluate different strain optimization strategies and other critical factors that have improved the success and efficiency of heterologous natural product biosynthesis in B. subtilis. Finally, future perspectives for using B. subtilis as a heterologous host are discussed, identifying research gaps and promising areas that require further exploration.
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Affiliation(s)
- Hanne Put
- Centre of Microbial and Plant Genetics, KU Leuven, 3001 Leuven, Belgium
- VIB-KU Leuven Center for Microbiology, Flanders Institute for Biotechnology, 3001 Leuven, Belgium.
| | - Hans Gerstmans
- VIB-KU Leuven Center for Microbiology, Flanders Institute for Biotechnology, 3001 Leuven, Belgium.
- Laboratory for Biomolecular Discovery & Engineering, KU Leuven, 3001 Leuven, Belgium
- Biosensors Group, KU Leuven, 3001 Leuven, Belgium
| | - Hanne Vande Capelle
- VIB-KU Leuven Center for Microbiology, Flanders Institute for Biotechnology, 3001 Leuven, Belgium.
- Laboratory for Biomolecular Discovery & Engineering, KU Leuven, 3001 Leuven, Belgium
| | - Maarten Fauvart
- Centre of Microbial and Plant Genetics, KU Leuven, 3001 Leuven, Belgium
- VIB-KU Leuven Center for Microbiology, Flanders Institute for Biotechnology, 3001 Leuven, Belgium.
- imec, 3001 Leuven, Belgium
| | - Jan Michiels
- Centre of Microbial and Plant Genetics, KU Leuven, 3001 Leuven, Belgium
- VIB-KU Leuven Center for Microbiology, Flanders Institute for Biotechnology, 3001 Leuven, Belgium.
| | - Joleen Masschelein
- VIB-KU Leuven Center for Microbiology, Flanders Institute for Biotechnology, 3001 Leuven, Belgium.
- Laboratory for Biomolecular Discovery & Engineering, KU Leuven, 3001 Leuven, Belgium
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Chen Y, Li M, Yan M, Chen Y, Saeed M, Ni Z, Fang Z, Chen H. Bacillus subtilis: current and future modification strategies as a protein secreting factory. World J Microbiol Biotechnol 2024; 40:195. [PMID: 38722426 DOI: 10.1007/s11274-024-03997-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Accepted: 04/19/2024] [Indexed: 05/18/2024]
Abstract
Bacillus subtilis is regarded as a promising microbial expression system in bioengineering due to its high stress resistance, nontoxic, low codon preference and grow fast. The strain has a relatively efficient expression system, as it has at least three protein secretion pathways and abundant molecular chaperones, which guarantee its expression ability and compatibility. Currently, many proteins are expressed in Bacillus subtilis, and their application prospects are broad. Although Bacillus subtilis has great advantages compared with other prokaryotes related to protein expression and secretion, it still faces deficiencies, such as low wild-type expression, low product activity, and easy gene loss, which limit its large-scale application. Over the years, many researchers have achieved abundant results in the modification of Bacillus subtilis expression systems, especially the optimization of promoters, expression vectors, signal peptides, transport pathways and molecular chaperones. An optimal vector with a suitable promoter strength and other regulatory elements could increase protein synthesis and secretion, increasing industrial profits. This review highlights the research status of optimization strategies related to the expression system of Bacillus subtilis. Moreover, research progress on its application as a food-grade expression system is also presented, along with some future modification and application directions.
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Affiliation(s)
- Yanzhen Chen
- School of Life Sciences, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
| | - Miaomiao Li
- School of Life Sciences, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
| | - Mingchen Yan
- School of Life Sciences, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
| | - Yong Chen
- School of Life Sciences, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
| | - Muhammad Saeed
- School of Life Sciences, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
| | - Zhong Ni
- School of Life Sciences, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
| | - Zhen Fang
- School of Life Sciences, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
| | - Huayou Chen
- School of Life Sciences, Jiangsu University, Zhenjiang, 212013, Jiangsu, China.
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Zeng M, Sarker B, Howitz N, Shah I, Andrews LB. Synthetic Homoserine Lactone Sensors for Gram-Positive Bacillus subtilis Using LuxR-Type Regulators. ACS Synth Biol 2024; 13:282-299. [PMID: 38079538 PMCID: PMC10805106 DOI: 10.1021/acssynbio.3c00504] [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: 08/18/2023] [Revised: 10/11/2023] [Accepted: 10/18/2023] [Indexed: 01/23/2024]
Abstract
A universal biochemical signal for bacterial cell-cell communication could facilitate programming dynamic responses in diverse bacterial consortia. However, the classical quorum sensing paradigm is that Gram-negative and Gram-positive bacteria generally communicate via homoserine lactones (HSLs) or oligopeptide molecular signals, respectively, to elicit population responses. Here, we create synthetic HSL sensors for Gram-positive Bacillus subtilis 168 using allosteric LuxR-type regulators (RpaR, LuxR, RhlR, and CinR) and synthetic promoters. Promoters were combinatorially designed from different sequence elements (-35, -16, -10, and transcriptional start regions). We quantified the effects of these combinatorial promoters on sensor activity and determined how regulator expression affects its activation, achieving up to 293-fold activation. Using the statistical design of experiments, we identified significant effects of promoter regions and pairwise interactions on sensor activity, which helped to understand the sequence-function relationships for synthetic promoter design. We present the first known set of functional HSL sensors (≥20-fold dynamic range) in B. subtilis for four different HSL chemical signals: p-coumaroyl-HSL, 3-oxohexanoyl-HSL, n-butyryl-HSL, and n-(3-hydroxytetradecanoyl)-HSL. This set of synthetic HSL sensors for a Gram-positive bacterium can pave the way for designable interspecies communication within microbial consortia.
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Affiliation(s)
- Min Zeng
- Department
of Chemical Engineering, University of Massachusetts
Amherst, Amherst, Massachusetts 01003, United States
| | - Biprodev Sarker
- Department
of Chemical Engineering, University of Massachusetts
Amherst, Amherst, Massachusetts 01003, United States
| | - Nathaniel Howitz
- Department
of Chemical Engineering, University of Massachusetts
Amherst, Amherst, Massachusetts 01003, United States
| | - Ishita Shah
- Department
of Chemical Engineering, University of Massachusetts
Amherst, Amherst, Massachusetts 01003, United States
| | - Lauren B. Andrews
- Department
of Chemical Engineering, University of Massachusetts
Amherst, Amherst, Massachusetts 01003, United States
- Molecular
and Cellular Biology Graduate Program, University
of Massachusetts Amherst, Amherst, Massachusetts 01003, United States
- Biotechnology
Training Program, University of Massachusetts
Amherst, Amherst, Massachusetts 01003, United States
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Ma Y, Guo N, Li X, Jiang Z, Zhang D, Guo L, Wang Y. Development of an Efficient Recombinant Protein Expression System in Clostridium saccharoperbutylacetonicum Based on the Bacteriophage T7 System. ACS Synth Biol 2023; 12:3092-3105. [PMID: 37712503 DOI: 10.1021/acssynbio.3c00439] [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] [Indexed: 09/16/2023]
Abstract
Recombinant proteins have broad applications. However, there is a lack of a recombinant protein expression system specifically for large-scale production in anaerobic hosts. Here, we developed a powerful and stringently inducible protein expression system based on the bacteriophage T7 system in the strictly anaerobic solvent-producing Clostridium saccharoperbutylacetonicum. With the integration of a codon optimized T7 RNA polymerase into the chromosome, a single plasmid carrying a T7 promoter could efficiently drive high-level expression of the target gene in an orthogonal manner, which was tightly regulated by a lactose-inducible system. Furthermore, by deleting beta-galactosidase genes involved in lactose metabolism, the transcriptional strength was further improved. In the ultimately optimized strain TM-07, the transcriptional strength of the T7 promoter showed 9.5-fold increase compared to the endogenous strong promoter Pthl. The heterologous NADP+-dependent 3-hydroxybutyryl-CoA dehydrogenase (Hbd1) from C. kluyveri was expressed in TM-07, and the yield of the recombinant protein reached 30.4-42.4% of the total cellular protein, surpassing the strong protein expression systems in other Gram-positive bacteria. The relative activity of Hbd1 in the crude enzyme was 198.0 U/mg, which was 8.3-fold higher than the natural activity in C. kluyveri. The relative activity of the purified enzyme reached 467.4 U/mg. To the best of our knowledge, this study represents the first application of the T7 expression system in Clostridium species, and this optimized expression system holds great potential for large-scale endotoxin-free recombinant protein production under strictly anaerobic conditions. This development paves the way for significant advancements in biotechnology and opens up new avenues for industrial applications.
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Affiliation(s)
- Yuechao Ma
- Department of Biosystems Engineering, Auburn University, Auburn, Alabama 36849, United States
- Center for Bioenergy and Bioproducts, Auburn University, Auburn, Alabama 36849, United States
| | - Na Guo
- Department of Biosystems Engineering, Auburn University, Auburn, Alabama 36849, United States
- Center for Bioenergy and Bioproducts, Auburn University, Auburn, Alabama 36849, United States
| | - Xiao Li
- Department of Crop, Soil and Environmental Sciences, Auburn University, Auburn, Alabama 36849, United States
| | - Zhihua Jiang
- Department of Chemical Engineering, Auburn University, Auburn, Alabama 36849, United States
| | - Dunhua Zhang
- Aquatic Animal Health Research Unit, Agricultural Research Service, USDA, Auburn, Alabama 36832, United States
| | - Liang Guo
- College of Environmental Science and Engineering, Ocean University of China, Qingdao 266100, China
| | - Yi Wang
- Department of Biosystems Engineering, Auburn University, Auburn, Alabama 36849, United States
- Center for Bioenergy and Bioproducts, Auburn University, Auburn, Alabama 36849, United States
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Virginia LJ, Peterbauer C. Localization of Pyranose 2-Oxidase from Kitasatospora aureofaciens: A Step Closer to Elucidate a Biological Role. Int J Mol Sci 2023; 24:ijms24031975. [PMID: 36768294 PMCID: PMC9916811 DOI: 10.3390/ijms24031975] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 01/11/2023] [Accepted: 01/16/2023] [Indexed: 01/20/2023] Open
Abstract
Lignin degradation in fungal systems is well characterized. Recently, a potential for lignin depolymerization and modification employing similar enzymatic activities by bacteria is increasingly recognized. The presence of genes annotated as peroxidases in Actinobacteria genomes suggests that these bacteria should contain auxiliary enzymes such as flavin-dependent carbohydrate oxidoreductases. The only auxiliary activity subfamily with significantly similar representatives in bacteria is pyranose oxidase (POx). A biological role of providing H2O2 for peroxidase activation and reduction of radical degradation products suggests an extracellular localization, which has not been established. Analysis of the genomic locus of POX from Kitasatospora aureofaciens (KaPOx), which is similar to fungal POx, revealed a start codon upstream of the originally annotated one, and the additional sequence was considered a putative Tat-signal peptide by computational analysis. We expressed KaPOx including this additional upstream sequence as well as fusion constructs consisting of the additional sequence, the KaPOx mature domain and the fluorescent protein mRFP1 in Streptomyces lividans. The putative signal peptide facilitated secretion of KaPOx and the fusion protein, suggesting a natural extracellular localization and supporting a potential role in providing H2O2 and reducing radical compounds derived from lignin degradation.
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Affiliation(s)
- Ludovika Jessica Virginia
- Food Biotechnology Laboratory, Department of Food Science and Technology, BOKU—University of Natural Resources and Life Sciences, Muthgasse 11, 1190 Vienna, Austria
- Doctoral Programme BioToP—Biomolecular Technology of Proteins, BOKU—University of Natural Resources and Life Sciences, Muthgasse 11, 1190 Vienna, Austria
| | - Clemens Peterbauer
- Food Biotechnology Laboratory, Department of Food Science and Technology, BOKU—University of Natural Resources and Life Sciences, Muthgasse 11, 1190 Vienna, Austria
- Doctoral Programme BioToP—Biomolecular Technology of Proteins, BOKU—University of Natural Resources and Life Sciences, Muthgasse 11, 1190 Vienna, Austria
- Correspondence: ; Tel.: +43-1-47654-75212
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Ye J, Li Y, Bai Y, Zhang T, Jiang W, Shi T, Wu Z, Zhang YHPJ. A facile and robust T7-promoter-based high-expression of heterologous proteins in Bacillus subtilis. BIORESOUR BIOPROCESS 2022; 9:56. [PMID: 38647747 PMCID: PMC10991129 DOI: 10.1186/s40643-022-00540-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2022] [Accepted: 04/27/2022] [Indexed: 11/10/2022] Open
Abstract
To mimic the Escherichia coli T7 protein expression system, we developed a facile T7 promoter-based protein expression system in an industrial microorganism Bacillus subtilis. This system has two parts: a new B. subtilis strain SCK22 and a plasmid pHT7. To construct strain SCK22, the T7 RNA polymerase gene was inserted into the chromosome, and several genes, such as two major protease genes, a spore generation-related gene, and a fermentation foam generation-related gene, were knocked out to facilitate good expression in high-density cell fermentation. The gene of a target protein can be subcloned into plasmid pHT7, where the gene of the target protein was under tight control of the T7 promoter with a ribosome binding site (RBS) sequence of B. subtilis (i.e., AAGGAGG). A few recombinant proteins (i.e., green fluorescent protein, α-glucan phosphorylase, inositol monophosphatase, phosphoglucomutase, and 4-α-glucanotransferase) were expressed with approximately 25-40% expression levels relative to the cellular total proteins estimated by SDS-PAGE by using B. subtilis SCK22/pHT7-derived plasmid. A fed-batch high-cell density fermentation was conducted in a 5-L fermenter, producing up to 4.78 g/L inositol monophosphatase. This expression system has a few advantageous features, such as, wide applicability for recombinant proteins, high protein expression level, easy genetic operation, high transformation efficiency, good genetic stability, and suitability for high-cell density fermentation.
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Affiliation(s)
- Jing Ye
- Tianjin Key Laboratory of Food Science and Biotechnology, College of Biotechnology and Food Science, Tianjin University of Commerce, Tianjin, China
| | - Yunjie Li
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin Airport Economic Area, Tianjin, 300308, China
| | - Yuqing Bai
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin Airport Economic Area, Tianjin, 300308, China
| | - Ting Zhang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin Airport Economic Area, Tianjin, 300308, China
| | - Wei Jiang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin Airport Economic Area, Tianjin, 300308, China
| | - Ting Shi
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin Airport Economic Area, Tianjin, 300308, China.
| | - Zijian Wu
- Tianjin Key Laboratory of Food Science and Biotechnology, College of Biotechnology and Food Science, Tianjin University of Commerce, Tianjin, China.
| | - Yi-Heng P Job Zhang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin Airport Economic Area, Tianjin, 300308, China.
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Zhang Q, Kobras CM, Gebhard S, Mascher T, Wolf D. Regulation of heterologous subtilin production in Bacillus subtilis W168. Microb Cell Fact 2022; 21:57. [PMID: 35392905 PMCID: PMC8991943 DOI: 10.1186/s12934-022-01782-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Accepted: 03/25/2022] [Indexed: 11/30/2022] Open
Abstract
Background Subtilin is a peptide antibiotic (lantibiotic) natively produced by Bacillus subtilis ATCC6633. It is encoded in a gene cluster spaBTCSIFEGRK (spa-locus) consisting of four transcriptional units: spaS (subtilin pre-peptide), spaBTC (modification and export), spaIFEG (immunity) and spaRK (regulation). Despite the pioneer understanding on subtilin biosynthesis, a robust platform to facilitate subtilin research and improve subtilin production is still a poorly explored spot. Results In this work, the intact spa-locus was successfully integrated into the chromosome of Bacillus subtilis W168, which is the by far best-characterized Gram-positive model organism with powerful genetics and many advantages in industrial use. Through systematic analysis of spa-promoter activities in B. subtilis W168 wild type and mutant strains, our work demonstrates that subtilin is basally expressed in B. subtilis W168, and the transition state regulator AbrB strongly represses subtilin biosynthesis in a growth phase-dependent manner. The deletion of AbrB remarkably enhanced subtilin gene expression, resulting in comparable yield of bioactive subtilin production as for B. subtilis ATCC6633. However, while in B. subtilis ATCC6633 AbrB regulates subtilin gene expression via SigH, which in turn activates spaRK, AbrB of B. subtilis W168 controls subtilin gene expression in SigH-independent manner, except for the regulation of spaBTC. Furthermore, the work shows that subtilin biosynthesis in B. subtilis W168 is regulated by the two-component regulatory system SpaRK and strictly relies on subtilin itself as inducer to fulfill the autoregulatory circuit. In addition, by incorporating the subtilin-producing system (spa-locus) and subtilin-reporting system (PpsdA-lux) together, we developed “online” reporter strains to efficiently monitor the dynamics of subtilin biosynthesis. Conclusions Within this study, the model organism B. subtilis W168 was successfully established as a novel platform for subtilin biosynthesis and the underlying regulatory mechanism was comprehensively characterized. This work will not only facilitate genetic (engineering) studies on subtilin, but also pave the way for its industrial production. More broadly, this work will shed new light on the heterologous production of other lantibiotics. Supplementary Information The online version contains supplementary material available at 10.1186/s12934-022-01782-9.
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Affiliation(s)
- Qian Zhang
- Institute of Microbiology, Technische Universität Dresden, 01217, Dresden, Germany
| | - Carolin M Kobras
- Department Biology I, Ludwig-Maximilians-Universität München, 82152, Planegg-Martinsried, Germany.,School of Biosciences, The University of Sheffield, Sheffield, S10 2TN, UK
| | - Susanne Gebhard
- Department Biology I, Ludwig-Maximilians-Universität München, 82152, Planegg-Martinsried, Germany.,Department of Biology & Biochemistry, Milner Centre for Evolution, University of Bath, Bath, BA2 7AY, UK
| | - Thorsten Mascher
- Institute of Microbiology, Technische Universität Dresden, 01217, Dresden, Germany
| | - Diana Wolf
- Institute of Microbiology, Technische Universität Dresden, 01217, Dresden, Germany.
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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: 26] [Impact Index Per Article: 13.0] [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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Redirected Stress Responses in a Genome-Minimized 'midi Bacillus' Strain with Enhanced Capacity for Protein Secretion. mSystems 2021; 6:e0065521. [PMID: 34904864 PMCID: PMC8670375 DOI: 10.1128/msystems.00655-21] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Genome engineering offers the possibility to create completely novel cell factories with enhanced properties for biotechnological applications. In recent years, genome minimization was extensively explored in the Gram-positive bacterial cell factory Bacillus subtilis, where up to 42% of the genome encoding dispensable functions was removed. Such studies showed that some strains with minimized genomes gained beneficial features, especially for secretory protein production. However, strains with the most minimal genomes displayed growth defects. This focused our attention on strains with less extensive genomic deletions that display close-to-wild-type growth properties while retaining the acquired beneficial traits in secretory protein production. A strain of this category is B. subtilis IIG-Bs27-47-24, here referred to as midiBacillus, which lacks 30.95% of the parental genome. To date, it was unknown how the altered genomic configuration of midiBacillus impacts cell physiology in general, and protein secretion in particular. The present study bridges this knowledge gap through comparative quantitative proteome analyses with focus on protein secretion. Interestingly, the results show that the secretion stress responses of midiBacillus, as elicited by high-level expression of the immunodominant staphylococcal antigen A, are completely different from secretion stress responses that occur in the parental strain 168. We further show that midiBacillus has an increased capacity for translation and that a variety of critical Sec secretion machinery components is present at elevated levels. Altogether, our observations demonstrate that high-level protein secretion has different consequences for wild-type and genome-engineered Bacillus strains, dictated by the altered genomic and proteomic configurations. IMPORTANCE Our present study showcases a genome-minimized nonpathogenic bacterium, the so-called midiBacillus, as a chassis for the development of future industrial strains that serve in the production of high-value difficult-to-produce proteins. In particular, we explain how midiBacillus, which lacks about one-third of the original genome, effectively secretes a protein of the major human pathogen Staphylococcus aureus that cannot be produced by the parental Bacillus subtilis strain. This is important, because the secreted S. aureus protein is exemplary for a range of targets that can be implemented in future antistaphylococcal immunotherapies. Accordingly, we anticipate that midiBacillus chassis will contribute to the development of vaccines that protect both humans and livestock against diseases caused by S. aureus, a bacterial pathogen that is increasingly difficult to fight with antibiotics, because it has accumulated resistances to essentially all antibiotics that are currently in clinical practice.
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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: 0.7] [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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12
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Goosens VJ, Walker KT, Aragon SM, Singh A, Senthivel VR, Dekker L, Caro-Astorga J, Buat MLA, Song W, Lee KY, Ellis T. Komagataeibacter Tool Kit (KTK): A Modular Cloning System for Multigene Constructs and Programmed Protein Secretion from Cellulose Producing Bacteria. ACS Synth Biol 2021; 10:3422-3434. [PMID: 34767345 DOI: 10.1021/acssynbio.1c00358] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Bacteria proficient at producing cellulose are an attractive synthetic biology host for the emerging field of Engineered Living Materials (ELMs). Species from the Komagataeibacter genus produce high yields of pure cellulose materials in a short time with minimal resources, and pioneering work has shown that genetic engineering in these strains is possible and can be used to modify the material and its production. To accelerate synthetic biology progress in these bacteria, we introduce here the Komagataeibacter tool kit (KTK), a standardized modular cloning system based on Golden Gate DNA assembly that allows DNA parts to be combined to build complex multigene constructs expressed in bacteria from plasmids. Working in Komagataeibacter rhaeticus, we describe basic parts for this system, including promoters, fusion tags, and reporter proteins, before showcasing how the assembly system enables more complex designs. Specifically, we use KTK cloning to reformat the Escherichia coli curli amyloid fiber system for functional expression in K. rhaeticus, and go on to modify it as a system for programming protein secretion from the cellulose producing bacteria. With this toolkit, we aim to accelerate modular synthetic biology in these bacteria, and enable more rapid progress in the emerging ELMs community.
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Affiliation(s)
- Vivianne J. Goosens
- Imperial College Centre for Synthetic Biology, Imperial College London, London SW7 2AZ, U.K
- Department of Bioengineering, Imperial College London, London SW7 2AZ, U.K
| | - Kenneth T. Walker
- Imperial College Centre for Synthetic Biology, Imperial College London, London SW7 2AZ, U.K
- Department of Bioengineering, Imperial College London, London SW7 2AZ, U.K
| | - Silvia M. Aragon
- Imperial College Centre for Synthetic Biology, Imperial College London, London SW7 2AZ, U.K
- Department of Life Sciences, Imperial College London, London SW7 2AZ, U.K
| | - Amritpal Singh
- Imperial College Centre for Synthetic Biology, Imperial College London, London SW7 2AZ, U.K
- Department of Bioengineering, Imperial College London, London SW7 2AZ, U.K
| | - Vivek R. Senthivel
- Imperial College Centre for Synthetic Biology, Imperial College London, London SW7 2AZ, U.K
- Department of Bioengineering, Imperial College London, London SW7 2AZ, U.K
| | - Linda Dekker
- Imperial College Centre for Synthetic Biology, Imperial College London, London SW7 2AZ, U.K
- Department of Life Sciences, Imperial College London, London SW7 2AZ, U.K
| | - Joaquin Caro-Astorga
- Imperial College Centre for Synthetic Biology, Imperial College London, London SW7 2AZ, U.K
- Department of Bioengineering, Imperial College London, London SW7 2AZ, U.K
| | | | - Wenzhe Song
- Department of Aeronautics, Imperial College London, London SW7 2AZ, U.K
| | - Koon-Yang Lee
- Department of Aeronautics, Imperial College London, London SW7 2AZ, U.K
| | - Tom Ellis
- Imperial College Centre for Synthetic Biology, Imperial College London, London SW7 2AZ, U.K
- Department of Bioengineering, Imperial College London, London SW7 2AZ, U.K
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13
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Lazar JT, Tabor JJ. Bacterial two-component systems as sensors for synthetic biology applications. CURRENT OPINION IN SYSTEMS BIOLOGY 2021; 28:100398. [PMID: 34917859 PMCID: PMC8670732 DOI: 10.1016/j.coisb.2021.100398] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/12/2023]
Abstract
Two-component systems (TCSs) are a ubiquitous family of signal transduction pathways that enable bacteria to sense and respond to diverse physical, chemical, and biological stimuli outside and inside the cell. Synthetic biologists have begun to repurpose TCSs for applications in optogenetics, materials science, gut microbiome engineering, and soil nutrient biosensing, among others. New engineering methods including genetic refactoring, DNA-binding domain swapping, detection threshold tuning, and phosphorylation cross-talk insulation are being used to increase the reliability of TCS sensor performance and tailor TCS signaling properties to the requirements of specific applications. There is now potential to combine these methods with large-scale gene synthesis and laboratory screening to discover the inputs sensed by many uncharacterized TCSs and develop a large new family of genetically-encoded sensors that respond to an unrivaled breadth of stimuli.
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Affiliation(s)
- John T Lazar
- Department of Chemical and Biomolecular Engineering, Rice University, Houston, TX, USA
| | - Jeffrey J Tabor
- Department of Bioengineering, Rice University, Houston, TX, USA
- PhD Program in Systems, Synthetic, and Physical Biology, Rice University, Houston, TX, USA
- Department of Biosciences, Rice University, Houston, TX, USA
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14
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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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15
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Bernal-Cabas M, Miethke M, Antelo-Varela M, Aguilar Suárez R, Neef J, Schön L, Gabarrini G, Otto A, Becher D, Wolf D, van Dijl JM. Functional association of the stress-responsive LiaH protein and the minimal TatAyCy protein translocase in Bacillus subtilis. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2020; 1867:118719. [DOI: 10.1016/j.bbamcr.2020.118719] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Revised: 04/07/2020] [Accepted: 04/09/2020] [Indexed: 01/07/2023]
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16
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van Tilburg AY, van Heel AJ, Stülke J, de Kok NAW, Rueff AS, Kuipers OP. Mini Bacillus PG10 as a Convenient and Effective Production Host for Lantibiotics. ACS Synth Biol 2020; 9:1833-1842. [PMID: 32551553 PMCID: PMC7372594 DOI: 10.1021/acssynbio.0c00194] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Efficient bacterial cell factories are important for the screening and characterization of potent antimicrobial peptides such as lantibiotics. Although lantibiotic production systems have been established in Lactococcus lactis and Escherichia coli, the industrial workhorse Bacillus subtilis has been left relatively unexplored as a lantibiotic production host. Therefore, we tested different B. subtilis strains for their ability to produce lantibiotic peptides by using the subtilin modification and transport enzymes derived from the natural subtilin producer B. subtilis ATCC 6633. Our study shows that although B. subtilis ATCC 6633 and 168 are able to produce various processed lantibiotic peptides, an evident advantage of using either the 8-fold protease-deficient strain WB800 or the genome-minimized B. subtilis 168 strain PG10 is the lack of extracellular serine protease activity. Consequently, leader processing of lantibiotic precursor peptides is circumvented and thus potential toxicity toward the production host is prevented. Furthermore, PG10 provides a clean secondary metabolic background and therefore appears to be the most promising B. subtilis lantibiotic production host. We demonstrate the production of various lantibiotic precursor peptides by PG10 and show different options for their in vitro activation. Our study thus provides a convenient B. subtilis-based lantibiotic production system, which facilitates the search for novel antimicrobial peptides.
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Affiliation(s)
- Amanda Y. van Tilburg
- Department of Molecular Genetics, University of Groningen, Groningen, 9747AG, The Netherlands
| | - Auke J. van Heel
- Department of Molecular Genetics, University of Groningen, Groningen, 9747AG, The Netherlands
| | - Jörg Stülke
- Institute of Microbiology and Genetics, Georg-August University Göttingen, Göttingen, 37077, Germany
| | - Niels A. W. de Kok
- Department of Molecular Genetics, University of Groningen, Groningen, 9747AG, The Netherlands
| | - Anne-Stéphanie Rueff
- Department of Molecular Genetics, University of Groningen, Groningen, 9747AG, The Netherlands
| | - Oscar P. Kuipers
- Department of Molecular Genetics, University of Groningen, Groningen, 9747AG, The Netherlands
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17
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Label-Free Multiple Reaction Monitoring, a Promising Method for Quantification Analyses of Specific Proteins in Bacteria. Int J Mol Sci 2020; 21:ijms21144924. [PMID: 32664686 PMCID: PMC7404251 DOI: 10.3390/ijms21144924] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Revised: 07/09/2020] [Accepted: 07/10/2020] [Indexed: 02/06/2023] Open
Abstract
Bacillus subtilis produces eight industrially important exo-proteases. For the detection of proteases, the activity- and antibody-based assays are normally used. Current activity-based assays require expensive multiplex chemical substrates which allow specificity determination of each enzyme. In this study, we provide evidences pertaining to the usefulness of the label-free multiple reaction monitoring (MRM) assay for a rapid identification and quantitation of specific proteins in bacteria. We used wild-type B. pumilus cells producing at least two serine proteases, subtilisin-like protease (AprBp) and glutamyl endopeptidase (GseBp), as well as optimized recombinant B. subtilis cells containing the same protease genes under control of the LIKE expression system. The Skyline software was used for the selection of three specific proteotypic peptides and their fragment ions for quantification and confirmation of AprBp and GseBp in complex mixtures. MRM indicated that the production of AprBp and GseBp exo-enzymes were respectively 0.9- and 26.6-fold higher in the culture medium of B. pumilus strain in comparison to the recombinant B. subtilis strains carrying optimized LIKE expression systems under identical conditions. The developed procedure in this study is fast, easy to perform and dependable. Additionally, it achieves accurate proteins identification and quantification in complex mixture.
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18
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Panneerselvam P, Senapati A, Kumar U, Sharma L, Lepcha P, Prabhukarthikeyan SR, Jahan A, Parameshwaran C, Govindharaj GPP, Lenka S, Nayak PK, Mitra D, Sagarika MS, Thangappan S, Sivakumar U. Antagonistic and plant-growth promoting novel Bacillus species from long-term organic farming soils from Sikkim, India. 3 Biotech 2019; 9:416. [PMID: 31696021 DOI: 10.1007/s13205-019-1938-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Accepted: 10/03/2019] [Indexed: 01/13/2023] Open
Abstract
Three bacteria namely Bacillus luciferensis K2, Bacillus amyloliquefaciens K12 and Bacillus subtilis BioCWB possessing plant growth promotion and biocontrol potential against phytopathogens and rice leaf folder were identified from organic soils of Sikkim, India. The results revealed significant higher production of phytohormones IAA (97.1 μg mL-1) and GA3 (10.6 μg mL-1) was found in K2, whereas BioCWB had higher phosphate solubilization (570.0 μg mL-1) efficacy and also possessed nitrogen fixation ability (5.34 log copy number mL-1 culture). All these bacteria had higher antagonistic activities against phytopathogens viz. Rhizoctonia solani, Fusarium proliferatum, Athelia rolfsii and Colletotrichum gloeosporioides and also had higher larvicidal activity against rice leaf folder Cnaphalocrocis medinalis (Guenne) under in vitro conditions. Molecular insights into the antagonistic mechanisms of Bacillus strains deciphered the presence of several antimicrobial peptides (ericin, subtilin, surfactin, iturin, bacilysin, subtilosin, fengycin and bacillomycin), volatiles (dimethyl disulphide, methyl-Furan, acetic acid, Z-1,3-pentadiene and 3-hexyn-2-ol) and soluble metabolites (9-octadecenamide, E-15-heptadecenal, E-3-eicosene and 5-octadecene). Furthermore, liquid microbial inoculum prepared using the bacterial strains (K2, K12 and BioCWB) were evaluated under glass house (rice) and field condition (capsicum), which significantly enhanced plant growth in rice and yield in capsicum compared to control. The present study revealed the combination of Bacillus spp. (K2, K12 and BioCWB) can be used as bio-inoculants for improving agricultural production in Sikkim. Moreover, for the first time, we demonstrated plant growth promoting (PGP) traits, antifungal and insecticidal properties of B. luciferensis.
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Affiliation(s)
| | - Ansuman Senapati
- 1Crop Production Division, ICAR-National Rice Research Institute, Cuttack, 753006 Odisha India
| | - Upendra Kumar
- 1Crop Production Division, ICAR-National Rice Research Institute, Cuttack, 753006 Odisha India
| | - Laxuman Sharma
- 2Department of Horticulture, Sikkim University, Gangtok, 737102 Sikkim India
| | - Pinky Lepcha
- 2Department of Horticulture, Sikkim University, Gangtok, 737102 Sikkim India
| | - S R Prabhukarthikeyan
- 1Crop Production Division, ICAR-National Rice Research Institute, Cuttack, 753006 Odisha India
| | - Afrin Jahan
- 1Crop Production Division, ICAR-National Rice Research Institute, Cuttack, 753006 Odisha India
| | | | | | - Srikanta Lenka
- 1Crop Production Division, ICAR-National Rice Research Institute, Cuttack, 753006 Odisha India
| | - Prafulla Kumar Nayak
- 1Crop Production Division, ICAR-National Rice Research Institute, Cuttack, 753006 Odisha India
| | - Debasis Mitra
- 2Department of Horticulture, Sikkim University, Gangtok, 737102 Sikkim India
| | | | - Sugitha Thangappan
- 3Tamil Nadu Agricultural University, Coimbatore, 641003 Tamil Nadu India
| | - Utthandi Sivakumar
- 3Tamil Nadu Agricultural University, Coimbatore, 641003 Tamil Nadu India
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van Tilburg AY, Cao H, van der Meulen SB, Solopova A, Kuipers OP. Metabolic engineering and synthetic biology employing Lactococcus lactis and Bacillus subtilis cell factories. Curr Opin Biotechnol 2019; 59:1-7. [DOI: 10.1016/j.copbio.2019.01.007] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Revised: 12/05/2018] [Accepted: 01/16/2019] [Indexed: 12/11/2022]
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20
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Jin L, Li L, Zhou L, Zhang R, Xu Y, Li J. Improving Expression of Bovine Lactoferrin N-Lobe by Promoter Optimization and Codon Engineering in Bacillus subtilis and Its Antibacterial Activity. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2019; 67:9749-9756. [PMID: 31415718 DOI: 10.1021/acs.jafc.9b02350] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Bovine lactoferrin N-lobe plays an important key in the nonimmunological defense system. In this work, the most suitable promoter Pveg was selected and the fragment coding bovine lactoferrin N-lobe was optimized according to codon bias of Bacillus. The recombinant plasmid pMA0911-Pveg-mBLF-N was introduced into Baicillus subtilis 168 to create B. subtilis/pMA0911-Pveg-mBLF-N. The bovine lactoferrin N-lobe was highly expressed at 28 °C for 15 h. Its purified protein was obtained with 16.5 mg/L and a purity of 93.6% using ammonium sulfate precipitation, Ni-NTA, and molecular exclusion. About 200 ng/mL purified bovine lactoferrin N-lobe completely inhibited cell-growth of Escherichia coli JM109 (DE3), 70.3% of Pseudomonas aeruginosa CGMCC 1.6740, and 41.5% of Staphylococcus aureus CGMCC 1.282. To our knowledge, this is the first report about active expression, purification, and characterization of bovine lactoferrin N-lobe in safe bacterium B. subtilis, which opens an available application way in the biomedical and food industries.
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Affiliation(s)
- Liang Jin
- Key Laboratory of Industrial Biotechnology of Ministry of Education & School of Biotechnology , Jiangnan University , Wuxi 214122 , P. R. China
| | - Lihong Li
- Key Laboratory of Industrial Biotechnology of Ministry of Education & School of Biotechnology , Jiangnan University , Wuxi 214122 , P. R. China
| | - Lixian Zhou
- Key Laboratory of Industrial Biotechnology of Ministry of Education & School of Biotechnology , Jiangnan University , Wuxi 214122 , P. R. China
| | - Rongzhen Zhang
- Key Laboratory of Industrial Biotechnology of Ministry of Education & School of Biotechnology , Jiangnan University , Wuxi 214122 , P. R. China
| | - Yan Xu
- Key Laboratory of Industrial Biotechnology of Ministry of Education & School of Biotechnology , Jiangnan University , Wuxi 214122 , P. R. China
| | - Jiming Li
- Key Laboratory of Industrial Biotechnology of Ministry of Education & School of Biotechnology , Jiangnan University , Wuxi 214122 , P. R. China
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21
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Castillo-Hair SM, Fujita M, Igoshin OA, Tabor JJ. An Engineered B. subtilis Inducible Promoter System with over 10 000-Fold Dynamic Range. ACS Synth Biol 2019; 8:1673-1678. [PMID: 31181163 DOI: 10.1021/acssynbio.8b00469] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Bacillus subtilis is the leading model Gram-positive bacterium, and a widely used chassis for industrial protein production. However, B. subtilis research is limited by a lack of inducible promoter systems with low leakiness and high dynamic range. Here, we engineer an inducible promoter system based on the T7 RNA Polymerase (T7 RNAP), the lactose repressor LacI, and the chimeric promoter PT7lac, integrated as a single copy in the B. subtilis genome. In the absence of IPTG, LacI strongly represses T7 RNAP and PT7lac and minimizes leakiness. Addition of IPTG derepresses PT7lac and simultaneously induces expression of T7RNAP, which results in very high output expression. Using green fluorescent and β-galactosidase reporter proteins, we estimate that this LacI-T7 system can regulate expression with a dynamic range of over 10 000, by far the largest reported for an inducible B. subtilis promoter system. Furthermore, LacI-T7 responds to similar IPTG concentrations and with similar kinetics as the widely used Phy-spank IPTG-inducible system, which we show has a dynamic range of at most 300 in a similar genetic context. Due to its superior performance, our LacI-T7 system should have broad applications in fundamental B. subtilis biology studies and biotechnology.
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Affiliation(s)
| | - Masaya Fujita
- Department of Biology and Biochemistry, University of Houston, 4800 Calhoun Road, Houston, Texas 77004, United States
| | - Oleg A. Igoshin
- Department of Bioengineering, Rice University, 6100 Main Street, Houston, Texas 77005, United States
- Department of Biosciences, Rice University, 6100 Main Street, Houston, Texas 77005, United States
- Center for Theoretical Biophysics, Rice University, 6100 Main Street, Houston, Texas 77005, United States
| | - Jeffrey J. Tabor
- Department of Bioengineering, Rice University, 6100 Main Street, Houston, Texas 77005, United States
- Department of Biosciences, Rice University, 6100 Main Street, Houston, Texas 77005, United States
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22
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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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Lastochkina O, Seifikalhor M, Aliniaeifard S, Baymiev A, Pusenkova L, Garipova S, Kulabuhova D, Maksimov I. Bacillus Spp.: Efficient Biotic Strategy to Control Postharvest Diseases of Fruits and Vegetables. PLANTS 2019; 8:plants8040097. [PMID: 31013814 PMCID: PMC6524353 DOI: 10.3390/plants8040097] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/24/2019] [Revised: 03/30/2019] [Accepted: 04/03/2019] [Indexed: 12/13/2022]
Abstract
: Postharvest diseases significantly reduce the shelf-life of harvested fruits/vegetables worldwide. Bacillus spp. are considered to be an eco-friendly and bio-safe alternative to traditional chemical fungicides/bactericides due to their intrinsic ability to induce native anti-stress pathways in plants. This review compiles information from multiple scientific databases (Scopus, ScienceDirect, GoogleScholar, ResearchGate, etc.) using the keywords "postharvest diseases", "Bacillus", "Bacillus subtilis", "biocontrol", "storage", "losses", and "fruits/vegetables". To date, numerous examples of successful Bacillus spp. application in controlling various postharvest-emerged pathogens of different fruits/vegetables during handling, transportation, and storage have been described in the literature. The mechanism/s of such action is/are still largely unknown; however, it is suggested that they include: i) competition for space/nutrients with pathogens; ii) production of various bio-active substances with antibiotic activity and cell wall-degrading compounds; and iii) induction of systemic resistance. With that, Bacillus efficiency may depend on various factors including strain characteristics (epiphytes or endophytes), application methods (before or after harvest/storage), type of pathogens/hosts, etc. Endophytic B. subtilis-based products can be more effective because they colonize internal plant tissues and are less dependent on external environmental factors while protecting cells inside. Nevertheless, the mechanism/s of Bacillus action on harvested fruits/vegetables is largely unknown and requires further detailed investigations to fully realize their potential in agricultural/food industries.
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Affiliation(s)
- Oksana Lastochkina
- Bashkir Research Institute of Agriculture, Ufa Federal Research Centre of the Russian Academy of Sciences, 450059 Ufa, Russia.
- Institute of Biochemistry and Genetics, Ufa Federal Research Centre of the Russian Academy of Sciences, 450054 Ufa, Russia.
| | - Maryam Seifikalhor
- Department of Plant Biology, Center of Excellence in Phylogeny of Living Organisms in Iran, School of Biology, College of Science, University of Tehran, Tehran 14155, Iran.
| | - Sasan Aliniaeifard
- Department of Horticulture, College of Aburaihan, University of Tehran, Pakdasht, Tehran 3391653775, Iran.
| | - Andrey Baymiev
- Institute of Biochemistry and Genetics, Ufa Federal Research Centre of the Russian Academy of Sciences, 450054 Ufa, Russia.
- Department of Biology, Bashkir State University, 450076 Ufa, Russia.
| | - Ludmila Pusenkova
- Bashkir Research Institute of Agriculture, Ufa Federal Research Centre of the Russian Academy of Sciences, 450059 Ufa, Russia.
| | - Svetlana Garipova
- Bashkir Research Institute of Agriculture, Ufa Federal Research Centre of the Russian Academy of Sciences, 450059 Ufa, Russia.
- Department of Biology, Bashkir State University, 450076 Ufa, Russia.
| | - Darya Kulabuhova
- Bashkir Research Institute of Agriculture, Ufa Federal Research Centre of the Russian Academy of Sciences, 450059 Ufa, Russia.
| | - Igor Maksimov
- Institute of Biochemistry and Genetics, Ufa Federal Research Centre of the Russian Academy of Sciences, 450054 Ufa, Russia.
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25
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Aguilar Suárez R, Stülke J, van Dijl JM. Less Is More: Toward a Genome-Reduced Bacillus Cell Factory for "Difficult Proteins". ACS Synth Biol 2019; 8:99-108. [PMID: 30540431 PMCID: PMC6343112 DOI: 10.1021/acssynbio.8b00342] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
![]()
The availability of complete genome
sequences and the definition
of essential gene sets were fundamental in the start of the genome
engineering era. In a recent study, redundant and unnecessary genes
were systematically deleted from the Gram-positive bacterium Bacillus subtilis, an industrial production host of high-value
secreted proteins. This culminated in strain PG10, which lacks about
36% of the genome, thus representing the most minimal Bacillus chassis currently available. Here, we show that this “miniBacillus” strain has synthetic traits that are favorable
for producing “difficult-to-produce proteins”. As exemplified
with different staphylococcal antigens, PG10 overcomes several bottlenecks
in protein production related to the secretion process and instability
of the secreted product. These findings show for the first time that
massive genome reduction can substantially improve secretory protein
production by a bacterial expression host, and underpin the high potential
of genome-engineered strains as future cell factories.
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Affiliation(s)
- Rocío Aguilar Suárez
- University Medical Center Groningen, University of Groningen, 9712 CP Groningen, The Netherlands
| | - Jörg Stülke
- Institute of Microbiology and Genetics, Georg-August University Göttingen, 37077 Göttingen, Germany
| | - Jan Maarten van Dijl
- University Medical Center Groningen, University of Groningen, 9712 CP Groningen, The Netherlands
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26
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Waites W, Mısırlı G, Cavaliere M, Danos V, Wipat A. A Genetic Circuit Compiler: Generating Combinatorial Genetic Circuits with Web Semantics and Inference. ACS Synth Biol 2018; 7:2812-2823. [PMID: 30408409 PMCID: PMC6305556 DOI: 10.1021/acssynbio.8b00201] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
A central strategy of synthetic biology is to understand the basic processes of living creatures through engineering organisms using the same building blocks. Biological machines described in terms of parts can be studied by computer simulation in any of several languages or robotically assembled in vitro. In this paper we present a language, the Genetic Circuit Description Language (GCDL) and a compiler, the Genetic Circuit Compiler (GCC). This language describes genetic circuits at a level of granularity appropriate both for automated assembly in the laboratory and deriving simulation code. The GCDL follows Semantic Web practice, and the compiler makes novel use of the logical inference facilities that are therefore available. We present the GCDL and compiler structure as a study of a tool for generating κ-language simulations from semantic descriptions of genetic circuits.
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Affiliation(s)
- William Waites
- School
of Informatics, University of Edinburgh, Edinburgh EH8 9YL, U.K.,E-mail:
| | - Göksel Mısırlı
- School
of Computing and Mathematics, Keele University, Newcastle ST5 5BG, U.K.
| | - Matteo Cavaliere
- School
of Computing & Mathematics, Manchester
Metropolitan University, Manchester M15 6BH, U.K.
| | - Vincent Danos
- School
of Informatics, University of Edinburgh, Edinburgh EH8 9YL, U.K.,École
Normale Supérieure, Paris, CNRS, 75005 Paris, France
| | - Anil Wipat
- School
of Computing Science, Newcastle University, Newcastle upon Tyne NE1
7RU, U.K.
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27
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Advances and prospects of Bacillus subtilis cellular factories: From rational design to industrial applications. Metab Eng 2018; 50:109-121. [DOI: 10.1016/j.ymben.2018.05.006] [Citation(s) in RCA: 115] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2017] [Revised: 05/02/2018] [Accepted: 05/10/2018] [Indexed: 01/29/2023]
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28
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Liu X, Wang H, Wang B, Pan L. High-level extracellular protein expression in Bacillus subtilis by optimizing strong promoters based on the transcriptome of Bacillus subtilis and Bacillus megaterium. Protein Expr Purif 2018; 151:72-77. [DOI: 10.1016/j.pep.2018.06.006] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Revised: 06/08/2018] [Accepted: 06/08/2018] [Indexed: 10/14/2022]
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29
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Exploitation of Bacillus subtilis as a robust workhorse for production of heterologous proteins and beyond. World J Microbiol Biotechnol 2018; 34:145. [DOI: 10.1007/s11274-018-2531-7] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Accepted: 09/05/2018] [Indexed: 10/28/2022]
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30
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Dade-Robertson M, Mitrani H, Corral JR, Zhang M, Hernan L, Guyet A, Wipat A. Design and modelling of an engineered bacteria-based, pressure-sensitive soil. BIOINSPIRATION & BIOMIMETICS 2018; 13:046004. [PMID: 29652250 DOI: 10.1088/1748-3190/aabe15] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
In this paper, we describe the first steps in the design of a synthetic biological system based on the use of genetically modified bacteria to detect elevated pressures in soils and respond by cementing soil particles. Such a system might, for example, enable a self- constructed foundation to form in response to load using engineered bacteria which could be seeded and grown in the soils. This process would reduce the need for large-scale excavations and may be the basis for a new generation of self-assembling and responsive bio-based materials. A prototype computational model is presented which integrates experimental data from a pressure sensitive gene within Escherichia coli bacteria with geotechnical models of soil loading and pore water pressure. The results from the integrated model are visualised by mapping expected gene expression values onto the soil volume. We also use our experimental data to design a two component system where one type of bacteria acts as a sensor and signals to another material synthesis bacteria. The simulation demonstrates the potential of computational models which integrate multiple scales from macro stresses in soils to the expression of individual genes to inform new types of design process. The work also illustrates the combination of in silico (silicon based computing) computation with in vivo (in the living) computation.
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Affiliation(s)
- Martyn Dade-Robertson
- School of Architecture Planning and Landscape, Newcastle University, Newcastle upon Tyne, NE1 7RU, United Kingdom
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31
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Bartholomae M, Buivydas A, Viel JH, Montalbán-López M, Kuipers OP. Major gene-regulatory mechanisms operating in ribosomally synthesized and post-translationally modified peptide (RiPP) biosynthesis. Mol Microbiol 2017; 106:186-206. [DOI: 10.1111/mmi.13764] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Revised: 08/02/2017] [Accepted: 08/03/2017] [Indexed: 02/06/2023]
Affiliation(s)
- Maike Bartholomae
- Department of Molecular Genetics; University of Groningen, Nijenborgh 7; 9747AG Groningen The Netherlands
| | - Andrius Buivydas
- Department of Molecular Genetics; University of Groningen, Nijenborgh 7; 9747AG Groningen The Netherlands
| | - Jakob H. Viel
- Department of Molecular Genetics; University of Groningen, Nijenborgh 7; 9747AG Groningen The Netherlands
| | - Manuel Montalbán-López
- Department of Microbiology; University of Granada, C. Fuentenueva s/n; 18071 Granada Spain
| | - Oscar P. Kuipers
- Department of Molecular Genetics; University of Groningen, Nijenborgh 7; 9747AG Groningen The Netherlands
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32
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Yan S, Wu G. Bottleneck in secretion of α-amylase in Bacillus subtilis. Microb Cell Fact 2017; 16:124. [PMID: 28724440 PMCID: PMC5518135 DOI: 10.1186/s12934-017-0738-1] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2017] [Accepted: 07/10/2017] [Indexed: 11/10/2022] Open
Abstract
Amylase plays an important role in biotechnology industries, and Gram-positive bacterium Bacillus subtilis is a major host to produce heterogeneous α-amylases. However, the secretion stress limits the high yield of α-amylase in B. subtilis although huge efforts have been made to address this secretion bottleneck. In this question-oriented review, every effort is made to answer the following questions, which look simple but are long-standing, through reviewing of literature: (1) Does α-amylase need a specific and dedicated chaperone? (2) What signal sequence does CsaA recognize? (3) Does CsaA require ATP for its operation? (4) Does an unfolded α-amylase is less soluble than a folded one? (5) Does α-amylase aggregate before transporting through Sec secretion system? (6) Is α-amylase sufficient stable to prevent itself from misfolding? (7) Does α-amylase need more disulfide bonds to be stabilized? (8) Which secretion system does PrsA pass through? (9) Is PrsA ATP-dependent? (10) Is PrsA reused after folding of α-amylase? (11) What is the fate of PrsA? (12) Is trigger factor (TF) ATP-dependent? The literature review suggests that not only the most of those questions are still open to answers but also it is necessary to calculate ATP budget in order to better understand how B. subtilis uses its energy for production and secretion.
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Affiliation(s)
- Shaomin Yan
- National Engineering Research Center for Non-food Biorefinery, Guangxi Academy of Sciences, 98 Daling Road, Nanning, 530007, Guangxi, China
| | - Guang Wu
- National Engineering Research Center for Non-food Biorefinery, Guangxi Academy of Sciences, 98 Daling Road, Nanning, 530007, Guangxi, China.
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33
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Yue J, Fu G, Zhang D, Wen J. A new maltose-inducible high-performance heterologous expression system in Bacillus subtilis. Biotechnol Lett 2017; 39:1237-1244. [PMID: 28527120 DOI: 10.1007/s10529-017-2357-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2017] [Accepted: 05/11/2017] [Indexed: 11/26/2022]
Abstract
OBJECTIVES To improve heterologous proteins production, we constructed a maltose-inducible expression system in Bacillus subtilis. RESULTS An expression system based on the promoter for maltose utilization constructed in B. subtilis. Successively, to improve the performance of the P malA -derived system, mutagenesis was employed by gradually shortening the length of P malA promoter and altering the spacing between the predicted MalR binding site and the -35 region. Furthermore, deletion of the maltose utilization genes (malL and yvdK) improved the P malA promoter activity. Finally, using this efficient maltose-inducible expression system, we enhanced the production of luciferase and D-aminoacylase, compared with the P hpaII system. CONCLUSIONS A maltose-inducible expression system was constructed and evaluated. It could be used for high level expression of heterologous proteins production.
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Affiliation(s)
- Jie Yue
- Department of Biological Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, People's Republic of China
- Tianjin Institutes of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, People's Republic of China
- Key Laboratories of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, People's Republic of China
| | - Gang Fu
- Tianjin Institutes of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, People's Republic of China
- Key Laboratories of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, People's Republic of China
| | - Dawei Zhang
- Tianjin Institutes of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, People's Republic of China.
- Key Laboratories of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, People's Republic of China.
| | - Jianping Wen
- Department of Biological Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, People's Republic of China
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34
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Cell surface engineering of Bacillus subtilis improves production yields of heterologously expressed α-amylases. Microb Cell Fact 2017; 16:56. [PMID: 28376879 PMCID: PMC5379735 DOI: 10.1186/s12934-017-0674-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2017] [Accepted: 03/31/2017] [Indexed: 11/24/2022] Open
Abstract
Background Bacillus subtilis is widely used as a cell factory for numerous heterologous proteins of commercial value and medical interest. To explore the possibility of further enhancing the secretion potential of this model bacterium, a library of engineered strains with modified cell surface components was constructed, and the corresponding influences on protein secretion were investigated by analyzing the secretion of α-amylase variants with either low-, neutral- or high- isoelectric points (pI). Results Relative to the wild-type strain, the presence of overall anionic membrane phospholipids (phosphatidylglycerol and cardiolipin) increased dramatically in the PssA-, ClsA- and double KO mutants, which resulted in an up to 47% higher secretion of α-amylase. Additionally, we demonstrated that the appropriate net charge of secreted targets (AmyTS-23, AmyBs and AmyBm) was beneficial for secretion efficiency as well. Conclusions In B. subtilis, the characteristics of cell membrane phospholipid bilayer and the pIs of heterologous α-amylases appear to be important for their secretion efficiency. These two factors can be engineered to reduce the electrostatic interaction between each other during the secretion process, which finally leads to a better secretion yield of α-amylases.
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35
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Iris Betsabee OS, José Luis SS, Juan Arturo RS, Montserrat CS. Evaluation of the toxicity and pathogenicity of biocontrol agents in murine models, chicken embryos and dermal irritation in rabbits. Toxicol Res (Camb) 2017; 6:188-198. [PMID: 30090489 PMCID: PMC6060713 DOI: 10.1039/c6tx00275g] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Accepted: 11/04/2016] [Indexed: 11/21/2022] Open
Abstract
Biological control has emerged as an alternative to the use of crop fungicides in fields and postharvest. It has already been demonstrated that strains of Candida famata, Bacillus subtilis Pla10, Meyerozyma guilliermondii, Meyerozyma caribbica and Debaryomyces hansenii are effective in controlling fungal diseases in tropical fruits. However, in order to develop applications on a field-scale, it is necessary to show that these biocontrol agents are innocuous to humans. In this study, three common toxicity studies were carried out to measure the safety of their use in food products: acute oral toxicity in adult Wistar rats, chicken embryo lethality and skin irritation studies in rabbits using concentrations of 1 and 10 mg of microbial extracts and the administration of 3 and 6 × 108 cells per mL of live cells for each one of the tested strains used for each model. The rats showed no toxic symptoms and none died during testing. The extracts and strain cells under study did not produce a life-cycle interruption in chicken embryos. For the skin irritation studies in rabbits, the substance being studied produced no skin alteration in the animals. With these results it was concluded that the lyophilized extracts in concentrations of 1 and 10 mg, as well as the cells of the studied strains in concentrations of 3 and 6 × 108 cells per mL, were safe in the studied models. Therefore, their use in controlling postharvest diseases in tropical fruits is possible. Their efficiency in controlling plagues in fields and their possible effects on humans, however, require further study.
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Affiliation(s)
- Ocampo-Suarez Iris Betsabee
- Laboratorio Integral de Investigación en Alimentos , Instituto Tecnológico de Tepic , Av. Tecnológico 2595 C. P. 63175 , Tepic , Nayarit , México .
| | - Sanchez-Salas José Luis
- Laboratorio de Microbiología y Biología Molecular del Departamento de Ciencias Químico-Biológicas , Universidad de las Américas Puebla , Ex-Hacienda Sta. Catarina Martir , C. P. 72810 , Cholula , Puebla
| | - Ragazzo-Sánchez Juan Arturo
- Laboratorio Integral de Investigación en Alimentos , Instituto Tecnológico de Tepic , Av. Tecnológico 2595 C. P. 63175 , Tepic , Nayarit , México .
| | - Calderón-Santoyo Montserrat
- Laboratorio Integral de Investigación en Alimentos , Instituto Tecnológico de Tepic , Av. Tecnológico 2595 C. P. 63175 , Tepic , Nayarit , México .
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36
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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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37
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Cui W, Cheng J, Miao S, Zhou L, Liu Z, Guo J, Zhou Z. Comprehensive characterization of a theophylline riboswitch reveals two pivotal features of Shine-Dalgarno influencing activated translation property. Appl Microbiol Biotechnol 2016; 101:2107-2120. [DOI: 10.1007/s00253-016-7988-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2016] [Revised: 09/29/2016] [Accepted: 11/05/2016] [Indexed: 01/08/2023]
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38
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Screening of Heterologous Signal Peptides for Optimization of the LIKE-Expression System. BIONANOSCIENCE 2016. [DOI: 10.1007/s12668-016-0357-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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39
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Guan C, Cui W, Cheng J, Zhou L, Liu Z, Zhou Z. Development of an efficient autoinducible expression system by promoter engineering in Bacillus subtilis. Microb Cell Fact 2016; 15:66. [PMID: 27112779 PMCID: PMC4845504 DOI: 10.1186/s12934-016-0464-0] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2015] [Accepted: 04/13/2016] [Indexed: 11/11/2022] Open
Abstract
Background Bacillus subtilis, a Gram-positive organism, has been developed to be an attractive expression platform to produce both secreted and cytoplasmic proteins owing to its prominent biological characteristics. We previously developed an auto-inducible expression system containing the srfA promoter (PsrfA) which was activated by the signal molecules acting in the quorum-sensing pathway for competence. The PsrfA promoter exhibited the unique property of inducer-free activity that is closely correlated with cell density. Results To improve the PsrfA-mediated expression system to the high-cell-density fermentation for industrial production in the B. subtilis mutant strain that is unable to sporulate, a spore mutant strain BSG1682 was developed, and the PsrfA promoter was enhanced by promoter engineering. Using green fluorescent protein (GFP) as the reporter, higher fluorescent intensity was observed in BSG1682 with expression from either plasmid or chromosome than that of the wild type B. subtilis 168. Thereafter, the PsrfA was engineered, yielding a library of PsrfA derivatives varied in the strength of GFP expression. The P23 promoter exhibited the best performance, almost twofold stronger than that of PsrfA. Two heterologous proteins, aminopeptidase (AP) and nattokinase (NK), were successfully overproduced under the control of P23 in BSG1682. Finally, the capacity of the expression system was demonstrated in batch fermentation in a 5-L fermenter. Conclusions The expression system demonstrates prominence in the activity of the auto-inducible promoter. Desired proteins could be highly and stably produced by integrating the corresponding genes downstream of the promoter on the plasmid or the chromosome in strain BSG1682. The expression system is conducive to the industrial production of pharmaceuticals and heterologous proteins in high-cell-density fermentation in BSG1682.
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Affiliation(s)
- Chengran Guan
- School of Biotechnology, Key Laboratory of Industrial Biotechnology (Ministry of Education), Jiangnan University, 1800 Lihu Avenue, Wuxi, 214122, Jiangsu, China
| | - Wenjing Cui
- School of Biotechnology, Key Laboratory of Industrial Biotechnology (Ministry of Education), Jiangnan University, 1800 Lihu Avenue, Wuxi, 214122, Jiangsu, China.
| | - Jintao Cheng
- School of Biotechnology, Key Laboratory of Industrial Biotechnology (Ministry of Education), Jiangnan University, 1800 Lihu Avenue, Wuxi, 214122, Jiangsu, China
| | - Li Zhou
- School of Biotechnology, Key Laboratory of Industrial Biotechnology (Ministry of Education), Jiangnan University, 1800 Lihu Avenue, Wuxi, 214122, Jiangsu, China
| | - Zhongmei Liu
- School of Biotechnology, Key Laboratory of Industrial Biotechnology (Ministry of Education), Jiangnan University, 1800 Lihu Avenue, Wuxi, 214122, Jiangsu, China
| | - Zhemin Zhou
- School of Biotechnology, Key Laboratory of Industrial Biotechnology (Ministry of Education), Jiangnan University, 1800 Lihu Avenue, Wuxi, 214122, Jiangsu, China.
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Wolf D, Mascher T. The applied side of antimicrobial peptide-inducible promoters from Firmicutes bacteria: expression systems and whole-cell biosensors. Appl Microbiol Biotechnol 2016; 100:4817-29. [PMID: 27102123 DOI: 10.1007/s00253-016-7519-3] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2016] [Revised: 03/23/2016] [Accepted: 03/25/2016] [Indexed: 11/28/2022]
Abstract
The cell envelope is an essential bacterial structure that consists of the cytoplasmic membrane, the cell wall, and-in Gram-negative bacteria-the outer membrane. Because of its crucial functions, it represents a prime antibiotic target. Monitoring and maintaining its integrity are therefore keys to survival, especially in competitive environments where antibiotics represent one means of suppressing the growth of competitors. Resistance against external antibiotic threat, as well as auto-immunity against self-produced antibiotics, is often mediated by two-component systems (2CSs). They respond to antibiotic threat by inducing gene expression that results in the production of specific resistance determinants. The underlying transcriptional control is exhibited at the level of specific target promoters, which usually share a number of relevant features: They are tightly controlled and only induced in the presence of specific (sets of) antibiotics. This induction is dose dependent and often very sensitive, that is, it occurs well below inhibitory antibiotic concentrations. Because of these characteristics, a number of well-characterized cell envelope stress-inducible promoters have been developed for two different applied purposes: first, as whole-cell biosensors for antibiotic detection and mechanism-of-action studies, and second, as antibiotic-inducible expression systems for biotechnological purposes. The current state of research in both fields will be discussed in this review, focusing on 2CS-regulated promoters from Firmicutes bacteria that are induced to mediate resistance against antimicrobial peptides (AMPs) targeting the cell envelope.
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Affiliation(s)
- Diana Wolf
- Institute of Microbiology, Technische Universität (TU) Dresden, 01062, Dresden, Germany
| | - Thorsten Mascher
- Institute of Microbiology, Technische Universität (TU) Dresden, 01062, Dresden, Germany.
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Promchai R, Promdonkoy B, Tanapongpipat S, Visessanguan W, Eurwilaichitr L, Luxananil P. A novel salt-inducible vector for efficient expression and secretion of heterologous proteins in Bacillus subtilis. J Biotechnol 2016; 222:86-93. [DOI: 10.1016/j.jbiotec.2016.02.019] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2015] [Revised: 01/18/2016] [Accepted: 02/08/2016] [Indexed: 12/01/2022]
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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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Construction of a highly active secretory expression system via an engineered dual promoter and a highly efficient signal peptide in Bacillus subtilis. N Biotechnol 2016; 33:372-9. [PMID: 26820123 DOI: 10.1016/j.nbt.2016.01.005] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2015] [Revised: 01/13/2016] [Accepted: 01/18/2016] [Indexed: 11/21/2022]
Abstract
A strong promoter and highly efficient signal peptides are essential for the secretory overproduction of recombinant proteins in Bacillus subtilis. To enhance the limited overexpression capability of natural promoters, various strategies for promoter engineering have been developed and used to construct gene expression systems in B. subtilis and other hosts. By applying a semi-rational approach for promoter engineering, a series of expression plasmids containing single and dual promoters were constructed using aminopeptidase (AP) with an intrinsic signal peptide as the reporter protein. Of the single and dual promoters investigated, the dual promoter PgsiB-PHpaII gave the best performance. To optimize secretion efficiency, the signal peptide YncM was selected after screening a library containing 19 different Sec-type signal peptides. The AP activity detected in the supernatants of a recombinant strain containing the plasmid pBSG24-YncM was as high as 88.86U/mL. The capacity of the expression plasmid pBSG24-YncM was also evaluated with batch fermentation in a 5-L fermentor. Increased production of AP (205U/mL, equal to 1.7g/L) was achieved after 45h of fermentation. These results suggest that this expression system can be used for high-level protein expression in B. subtilis.
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Morabbi Heravi K, Rigi G, Rezaei Arjomand M, Rostami A, Ahmadian G. An Alternative Bacterial Expression System Using Bacillus pumilus SG2 Chitinase Promoter. IRANIAN JOURNAL OF BIOTECHNOLOGY 2015; 13:17-24. [PMID: 28959305 DOI: 10.15171/ijb.1175] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
BACKGROUND Chitin is an abundant natural polysaccharide found in fungi, algae, and exoskeleton of insects. Several bacterial species are capable of utilizing chitin as their carbon source. These bacteria produce chitinases for degradation of chitin into N-acetyl-D-glucosamine. So far, regulation of the chitinase encoding genes has been studied in different bacterial species. Among Bacillus species, B. pumilus strain SG2 encodes two chitinases, ChiS and ChiL. The promoter region of chiSL genes (P chiS ) is mainly regulated by the general carbon catabolite repression (CCR) system in B. subtilis due to the presence of a catabolite responsive element (cre). OBJECTIVES Use of P chiS in constructing an inducible expression system in B. subtilis was investigated. MATERIALS AND METHODS In the first step, complete and shortened versions of P chiS were inserted upstream of the lacZ on a pBS72/pUC18 shuttle plasmid. The β-galactosidase activity of B. subtilis carrying one of the relevant plasmids was measured in the presence of different carbon sources. RESULTS An expression system based on the chitinase promoter of B. pumilus SG2 was established. Modification of P chiS and the culture medium resulted in production of β-galactosidase in B. subtilis up to 1,800 Miller unit (MU) activity. CONCLUSIONS The chitinase promoter developed in this study, has potential to be used in an expression vector that could be induced by chitin. In addition, compared to the other inducers like IPTG and lactose, chitin is definitely cheaper and more available as an inducer.
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Affiliation(s)
- Kambiz Morabbi Heravi
- Institut für Industrielle Genetik, Universität Stuttgart, Allmandring 31, 70569 Stuttgart, Germany
| | - Garshasb Rigi
- Department of Biology, Faculty of Science, Behbahan Khatam Alanbia University of Technology, Behbahan, Iran
| | - Maryam Rezaei Arjomand
- Department of Industrial and Environmental Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran, Iran
| | - Amin Rostami
- Department of Industrial and Environmental Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran, Iran
| | - Gholamreza Ahmadian
- Department of Industrial and Environmental Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran, Iran
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Bacillus amyloliquefaciens AG1 biosurfactant: Putative receptor diversity and histopathological effects on Tuta absoluta midgut. J Invertebr Pathol 2015; 132:42-47. [DOI: 10.1016/j.jip.2015.08.010] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2015] [Revised: 08/15/2015] [Accepted: 08/20/2015] [Indexed: 11/22/2022]
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Prediction and identification of an acid-inducible promoter from Lactococcus lactis ssp. cremoris MG1363. Food Sci Biotechnol 2015. [DOI: 10.1007/s10068-015-0227-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
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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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Chen J, Chen X, Dai J, Xie G, Yan L, Lu L, Chen J. Cloning, enhanced expression and characterization of an α-amylase gene from a wild strain in B. subtilis WB800. Int J Biol Macromol 2015; 80:200-7. [PMID: 26092061 DOI: 10.1016/j.ijbiomac.2015.06.018] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2015] [Revised: 06/10/2015] [Accepted: 06/11/2015] [Indexed: 11/30/2022]
Abstract
A Bacillus strain with high productivity of α-amylase isolated from a starch farm was identified as Bacillus amyloliquefaciens. The α-amylase encoding gene amy1 was cloned into pMD18-T vector and amplified in E. coli DH5α. Shuttle vector pP43MNX was reconstructed to obtain vector pP43X for heterologous expression of the α-amylase in B. subtilis WB800. Recombinant enzyme was sufficiently purified by precipitation, gel filtration and anion exchange with a specific activity of 5566 U/mg. The α-amylase sequence contains an open reading frame of 1545 bp, which encodes a protein of 514 amino acid residues with a predicted molecular mass of 58.4 kDa. The enzyme exhibited maximal activity at pH 6.0 and 60 °C. Catalytic efficiency of the recombinant α-amylase was inhibited by Hg(2+), Pb(2+) and Cu(2+), but stimulated by Li(+), Mn(2+) and Ca(2+). The purified enzyme showed decreased activity toward detergents (SDS, Tween 20 and Triton X-100). Compared with production by the wild strain, there was a 1.48-fold increase in the productivity of α-amylase in recombinant B. subtilis WB800.
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Affiliation(s)
- Jing Chen
- School of Life Science and Technology, China Pharmaceutical University, Nanjing 210009, PR China
| | - Xianghua Chen
- School of Life Science and Technology, China Pharmaceutical University, Nanjing 210009, PR China
| | - Jun Dai
- School of Life Science and Technology, China Pharmaceutical University, Nanjing 210009, PR China
| | - Guangrong Xie
- School of Life Science and Technology, China Pharmaceutical University, Nanjing 210009, PR China
| | - Luying Yan
- School of Life Science and Technology, China Pharmaceutical University, Nanjing 210009, PR China
| | - Lina Lu
- School of Life Science and Technology, China Pharmaceutical University, Nanjing 210009, PR China
| | - Jianhua Chen
- School of Life Science and Technology, China Pharmaceutical University, Nanjing 210009, PR China.
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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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50
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Patel R, Vasilev C, Beck D, Monteferrante CG, van Dijl JM, Hunter CN, Smith C, Robinson C. A mutation leading to super-assembly of twin-arginine translocase (Tat) protein complexes. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2014; 1843:1978-86. [PMID: 24875903 DOI: 10.1016/j.bbamcr.2014.05.009] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2014] [Revised: 05/16/2014] [Accepted: 05/19/2014] [Indexed: 10/25/2022]
Abstract
The Tat system transports folded proteins across the bacterial plasma membrane. The mechanism is believed to involve coalescence of a TatC-containing unit with a separate TatA complex, but the full translocation complex has never been visualised and the assembly process is poorly defined. We report the analysis of the Bacillus subtilis TatAyCy system, which occurs as separate TatAyCy and TatAy complexes at steady state, using single-particle electron microscopy (EM) and advanced atomic force microscopy (AFM) approaches. We show that a P2A mutation in the TatAy subunit leads to apparent super-assembly of Tat complexes. Purification of TatCy-containing complexes leads to a large increase in the TatA:TatC ratio, suggesting that TatAy(P2A) complexes may have attached to the TatAyCy complex. EM and AFM analyses show that the wild-type TatAyCy complex purifies as roughly spherical complexes of 9-16nm diameter, whereas the P2A mutation leads to accumulation of large (up to 500nm long) fibrils that are chains of numerous complexes. Time lapsed AFM imaging, recorded on fibrils under liquid, shows that they adopt a variety of tightly curved conformations, with radii of curvature of 10-12nm comparable to the size of single TatAy(P2A) complexes. The combined data indicate that the mutation leads to super-assembly of TatAy(P2A) complexes and we propose that an individual TatAy(P2A) complex assembles initially with a TatAy(P2A)Cy complex, after which further TatAy(P2A) complexes attach to each other. The data further suggest that the N-terminal extracytoplasmic domain of TatAy plays an essential role in Tat complex interactions.
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Affiliation(s)
- Roshani Patel
- School of Life Sciences, Gibbet Hill Campus, The University of Warwick, Coventry CV4 7AL, UK
| | - Cvetelin Vasilev
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield S10 2TN, UK
| | - Daniel Beck
- School of Life Sciences, Gibbet Hill Campus, The University of Warwick, Coventry CV4 7AL, UK
| | - Carmine G Monteferrante
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Jan Maarten van Dijl
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - C Neil Hunter
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield S10 2TN, UK
| | - Corinne Smith
- School of Life Sciences, Gibbet Hill Campus, The University of Warwick, Coventry CV4 7AL, UK
| | - Colin Robinson
- Centre for Molecular Processing, School of Biosciences, University of Kent, Canterbury CT2 7NJ, UK.
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