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Li K, Guo Y, Sun X, Xi X, Wang L, Ren X, Wang C, Liu X. Whole-cell biocatalysis for ε-poly-l-lysine production by a food-grade recombinant Bacillus subtilis. Enzyme Microb Technol 2024; 179:110467. [PMID: 38852284 DOI: 10.1016/j.enzmictec.2024.110467] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2024] [Revised: 05/11/2024] [Accepted: 06/01/2024] [Indexed: 06/11/2024]
Abstract
ε-Poly-l-lysine (ε-PL), a natural food preservative with various advantages, is primarily produced by Streptomyces. It has attracted considerable attentions for the outstanding antibacterial activity, safety, heat stability, water solubility and other remarkable properties. In this study, a food-grade recombinant Bacillus subtilis was constructed for the biocatalysis of ε-PL. Firstly, the d-alanine racemase gene (alrA) was deleted from the genome of Bacillus subtilis 168 to construct an auxotrophic B. subtilis 168 (alrA-). Based on the shuttle plasmid pMA5, a food-grade plasmid pMA5a was constructed by replacing the genes of kanamycin resistance (Kanr) and ampicillin resistance (Ampr) with alrA and the gene encoding α-peptide of β-galactosidase (lacZα), respectively. Subsequently, codon-optimized ε-PL synthase gene (pls) and P-pls were ligated into pMA5a and transformed in E. coli DH5α and expressed in B. subtilis 168 (alrA-). Finally, the whole-cell biocatalysis conditions for ε-PL production by B. subtilis 168 (alrA-)/pMA5a-pls were optimized, and the optimal conditions were 30°C, pH 4, l-lysine concentration of 0.6 g/L, bacterial concentration of 15 % (w/v) and a catalytic time of 7 h. The ε-PL production reached a maximum of 0.33 ± 0.03 g/L. The product was verified to be ε-PL by HPLC and tricine-SDS-PAGE. The information obtained in this study shows critical reference for the food-grade heterologous expression of ε-PL.
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Affiliation(s)
- Kunpeng Li
- State Key Laboratory of Biobased Material and Green Papermaking, Qilu University of Technology, Shandong Academy of Sciences, Jinan 250353, China; Shandong Provincial Key Laboratory of Microbial Engineering, Department of Bioengineering, Qilu University of Technology, Shandong Academy of Sciences, Jinan 250353, China
| | - Yangzi Guo
- State Key Laboratory of Biobased Material and Green Papermaking, Qilu University of Technology, Shandong Academy of Sciences, Jinan 250353, China; Shandong Provincial Key Laboratory of Microbial Engineering, Department of Bioengineering, Qilu University of Technology, Shandong Academy of Sciences, Jinan 250353, China
| | - Xinjie Sun
- State Key Laboratory of Biobased Material and Green Papermaking, Qilu University of Technology, Shandong Academy of Sciences, Jinan 250353, China; Shandong Provincial Key Laboratory of Microbial Engineering, Department of Bioengineering, Qilu University of Technology, Shandong Academy of Sciences, Jinan 250353, China
| | - Xiangheng Xi
- State Key Laboratory of Biobased Material and Green Papermaking, Qilu University of Technology, Shandong Academy of Sciences, Jinan 250353, China; Shandong Provincial Key Laboratory of Microbial Engineering, Department of Bioengineering, Qilu University of Technology, Shandong Academy of Sciences, Jinan 250353, China
| | - Li Wang
- State Key Laboratory of Biobased Material and Green Papermaking, Qilu University of Technology, Shandong Academy of Sciences, Jinan 250353, China; Shandong Provincial Key Laboratory of Microbial Engineering, Department of Bioengineering, Qilu University of Technology, Shandong Academy of Sciences, Jinan 250353, China
| | - Xidong Ren
- State Key Laboratory of Biobased Material and Green Papermaking, Qilu University of Technology, Shandong Academy of Sciences, Jinan 250353, China; Shandong Provincial Key Laboratory of Microbial Engineering, Department of Bioengineering, Qilu University of Technology, Shandong Academy of Sciences, Jinan 250353, China.
| | - Chenying Wang
- State Key Laboratory of Biobased Material and Green Papermaking, Qilu University of Technology, Shandong Academy of Sciences, Jinan 250353, China; School of Food Science and Engineering, Qilu University of Technology, Shandong Academy of Sciences, Jinan 250353, China.
| | - Xinli Liu
- State Key Laboratory of Biobased Material and Green Papermaking, Qilu University of Technology, Shandong Academy of Sciences, Jinan 250353, China; Shandong Provincial Key Laboratory of Microbial Engineering, Department of Bioengineering, Qilu University of Technology, Shandong Academy of Sciences, Jinan 250353, China
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2
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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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Liu Y, Cheng H, Li H, Zhang Y, Wang M. A Programmable CRISPR/Cas9 Toolkit Improves Lycopene Production in Bacillus subtilis. Appl Environ Microbiol 2023; 89:e0023023. [PMID: 37272803 PMCID: PMC10305015 DOI: 10.1128/aem.00230-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Accepted: 05/16/2023] [Indexed: 06/06/2023] Open
Abstract
Bacillus subtilis has been widely used and generally recognized as a safe host for the production of recombinant proteins, high-value chemicals, and pharmaceuticals. Thus, its metabolic engineering attracts significant attention. Nevertheless, the limited availability of selective markers makes this process difficult and time-consuming, especially in the case of multistep biosynthetic pathways. Here, we employ CRISPR/Cas9 technology to build an easy cloning toolkit that addresses commonly encountered obstacles in the metabolic engineering of B. subtilis, including the chromosomal integration locus, promoter, terminator, and guide RNA (gRNA) target. Six promoters were characterized, and the promoter strengths ranged from 0.9- to 23-fold that of the commonly used strong promoter P43. We characterized seven terminators in B. subtilis, and the termination efficiencies (TEs) of the seven terminators are all more than 90%. Six gRNA targets were designed upstream of the promoter and downstream of the terminator. Using a green fluorescent protein (GFP) reporter, we confirmed integration efficiency with the single-locus integration site is up to 100%. We demonstrated the applicability of this toolkit by optimizing the expression of a challenging but industrially important product, lycopene. By heterologous expression of the essential genes for lycopene synthesis on the B. subtilis genome, a total of 13 key genes involved in the lycopene biosynthetic pathway were manipulated. Moreover, our findings showed that the gene cluster ispG-idi-dxs-ispD could positively affect the production of lycopene, while the cluster dxr-ispE-ispF-ispH had a negative effect on lycopene production. Hence, our multilocus integration strategy can facilitate the pathway assembly for production of complex chemicals and pharmaceuticals in B. subtilis. IMPORTANCE We present a toolkit that allows for rapid cloning procedures and one-step subcloning to move from plasmid-based expression to stable chromosome integration and expression in a production strain in less than a week. The utility of the customized tool was demonstrated by integrating the MEP (2C-methyl-d-erythritol-4-phosphate) pathway, part of the pentose phosphate pathway (PPP), and the hetero-lycopene biosynthesis genes by stable expression in the genome. The tool could be useful to engineer B. subtilis strains through diverse recombination events and ultimately improve its potential and scope of industrial application as biological chassis.
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Affiliation(s)
- Yang Liu
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Haijiao Cheng
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Haoni Li
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China
| | - Yingzhe Zhang
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Meng Wang
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
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Filluelo O, Ferrando J, Picart P. Metabolic engineering of Bacillus subtilis toward the efficient and stable production of C 30-carotenoids. AMB Express 2023; 13:38. [PMID: 37119332 PMCID: PMC10148934 DOI: 10.1186/s13568-023-01542-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2023] [Accepted: 04/05/2023] [Indexed: 05/01/2023] Open
Abstract
Commercial carotenoid production is dominated by chemical synthesis and plant extraction, both of which are unsustainable and can be detrimental to the environment. A promising alternative for the mass production of carotenoids from both an ecological and commercial perspective is microbial synthesis. To date, C30 carotenoid production in Bacillus subtilis has been achieved using plasmid systems for the overexpression of biosynthetic enzymes. In the present study, we employed a clustered regularly interspaced short palindromic repeat-Cas9 (CRISPR-Cas9) system to develop an efficient, safe, and stable C30 carotenoid-producing B. subtilis strain, devoid of plasmids and antibiotic selection markers. To this end, the expression levels of crtM (dehydrosqualene synthase) and crtN (dehydrosqualene desaturase) genes from Staphylococcus aureus were upregulated by the insertion of three gene copies into the chromosome of B. subtilis. Subsequently, the supply of the C30 carotenoid precursor farnesyl diphosphate (FPP), which is the substrate for CrtMN enzymes, was enhanced by expressing chromosomally integrated Bacillus megaterium-derived farnesyl diphosphate synthase (FPPS), a key enzyme in the FPP pathway, and abolishing the expression of farnesyl diphosphate phosphatase (YisP), an enzyme responsible for the undesired conversion of FPP to farnesol. The consecutive combination of these features resulted in a stepwise increased production of C30 carotenoids. For the first time, a B. subtilis strain that can endogenously produce C30 carotenoids has been constructed, which we anticipate will serve as a chassis for further metabolic engineering and fermentation optimization aimed at developing a commercial scale bioproduction process.
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Affiliation(s)
- Oriana Filluelo
- Faculty of Pharmacy and Food Science Technology, Department of Biology, Healthcare and the Environment, Microbiology Section, University of Barcelona, Avinguda Joan XXIII, 27-31, Barcelona, 08028, Spain
| | - Jordi Ferrando
- Faculty of Pharmacy and Food Science Technology, Department of Biology, Healthcare and the Environment, Microbiology Section, University of Barcelona, Avinguda Joan XXIII, 27-31, Barcelona, 08028, Spain
| | - Pere Picart
- Faculty of Pharmacy and Food Science Technology, Department of Biology, Healthcare and the Environment, Microbiology Section, University of Barcelona, Avinguda Joan XXIII, 27-31, Barcelona, 08028, Spain.
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Manina AS, Forlani F. Biotechnologies in Perfume Manufacturing: Metabolic Engineering of Terpenoid Biosynthesis. Int J Mol Sci 2023; 24:ijms24097874. [PMID: 37175581 PMCID: PMC10178209 DOI: 10.3390/ijms24097874] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Revised: 04/22/2023] [Accepted: 04/24/2023] [Indexed: 05/15/2023] Open
Abstract
The fragrance industry is increasingly turning to biotechnology to produce sustainable and high-quality fragrance ingredients. Microbial-based approaches have been found to be particularly promising, as they offer a more practical, economical and sustainable alternative to plant-based biotechnological methods for producing terpene derivatives of perfumery interest. Among the evaluated works, the heterologous expression of both terpene synthase and mevalonate pathway into Escherichia coli has shown the highest yields. Biotechnology solutions have the potential to help address the growing demand for sustainable and high-quality fragrance ingredients in an economically viable and responsible manner. These approaches can help compensate for supply issues of rare or impermanent raw materials, while also meeting the increasing demand for sustainable ingredients and processes. Although scaling up biotransformation processes can present challenges, they also offer advantages in terms of safety and energy savings. Exploring microbial cell factories for the production of natural fragrance compounds is a promising solution to both supply difficulties and the demand for sustainable ingredients and processes in the fragrance industry.
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Affiliation(s)
- Alessia Shelby Manina
- Department of Food Environmental and Nutritional Science (DeFENS), University of Milan, 20133 Milan, Italy
| | - Fabio Forlani
- Department of Food Environmental and Nutritional Science (DeFENS), University of Milan, 20133 Milan, Italy
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Wiles D, Shanbhag BK, O'Brien M, Doblin MS, Bacic A, Beddoe T. Heterologous production of Cannabis sativa-derived specialised metabolites of medicinal significance - Insights into engineering strategies. PHYTOCHEMISTRY 2022; 203:113380. [PMID: 36049526 DOI: 10.1016/j.phytochem.2022.113380] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Revised: 08/08/2022] [Accepted: 08/14/2022] [Indexed: 06/15/2023]
Abstract
Cannabis sativa L. has been known for at least 2000 years as a source of important, medically significant specialised metabolites and several bio-active molecules have been enriched from multiple chemotypes. However, due to the many levels of complexity in both the commercial cultivation of cannabis and extraction of its specialised metabolites, several heterologous production approaches are being pursued in parallel. In this review, we outline the recent achievements in engineering strategies used for heterologous production of cannabinoids, terpenes and flavonoids along with their strength and weakness. We provide an overview of the specialised metabolism pathway in C. sativa and a comprehensive list of the specialised metabolites produced along with their medicinal significance. We highlight cannabinoid-like molecules produced by other species. We discuss the key biosynthetic enzymes and their heterologous production using various hosts such as microbial and eukaryotic systems. A brief discussion on complementary production strategies using co-culturing and cell-free systems is described. Various approaches to optimise specialised metabolite production through co-expression, enzyme engineering and pathway engineering are discussed. We derive insights from recent advances in metabolic engineering of hosts with improved precursor supply and suggest their application for the production of C. sativa speciality metabolites. We present a collation of non-conventional hosts with speciality traits that can improve the feasibility of commercial heterologous production of cannabis-based specialised metabolites. We provide a perspective of emerging research in synthetic biology, allied analytical techniques and plant heterologous platforms as focus areas for heterologous production of cannabis specialised metabolites in the future.
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Affiliation(s)
- Danielle Wiles
- Department of Animal, Plant and Soil Sciences and AgriBio Centre for AgriBioscience, School of Agriculture, Biomedicine and Environment, La Trobe University, Bundoora, Victoria, 3083, Australia; Australian Research Council Research Hub for Medicinal Agriculture, AgriBio Centre for AgriBioscience, La Trobe University, Bundoora, VIC, 3086, Australia
| | - Bhuvana K Shanbhag
- Department of Animal, Plant and Soil Sciences and AgriBio Centre for AgriBioscience, School of Agriculture, Biomedicine and Environment, La Trobe University, Bundoora, Victoria, 3083, Australia; Australian Research Council Research Hub for Medicinal Agriculture, AgriBio Centre for AgriBioscience, La Trobe University, Bundoora, VIC, 3086, Australia
| | - Martin O'Brien
- Department of Animal, Plant and Soil Sciences and AgriBio Centre for AgriBioscience, School of Agriculture, Biomedicine and Environment, La Trobe University, Bundoora, Victoria, 3083, Australia; Australian Research Council Research Hub for Medicinal Agriculture, AgriBio Centre for AgriBioscience, La Trobe University, Bundoora, VIC, 3086, Australia
| | - Monika S Doblin
- Department of Animal, Plant and Soil Sciences and AgriBio Centre for AgriBioscience, School of Agriculture, Biomedicine and Environment, La Trobe University, Bundoora, Victoria, 3083, Australia; Australian Research Council Research Hub for Medicinal Agriculture, AgriBio Centre for AgriBioscience, La Trobe University, Bundoora, VIC, 3086, Australia; La Trobe Institute for Agriculture & Food, Department of Animal, Plant and Soil Science, AgriBio Centre for AgriBioscience, La Trobe University, Bundoora, VIC, Australia
| | - Antony Bacic
- Department of Animal, Plant and Soil Sciences and AgriBio Centre for AgriBioscience, School of Agriculture, Biomedicine and Environment, La Trobe University, Bundoora, Victoria, 3083, Australia; Australian Research Council Research Hub for Medicinal Agriculture, AgriBio Centre for AgriBioscience, La Trobe University, Bundoora, VIC, 3086, Australia; La Trobe Institute for Agriculture & Food, Department of Animal, Plant and Soil Science, AgriBio Centre for AgriBioscience, La Trobe University, Bundoora, VIC, Australia
| | - Travis Beddoe
- Department of Animal, Plant and Soil Sciences and AgriBio Centre for AgriBioscience, School of Agriculture, Biomedicine and Environment, La Trobe University, Bundoora, Victoria, 3083, Australia; Australian Research Council Research Hub for Medicinal Agriculture, AgriBio Centre for AgriBioscience, La Trobe University, Bundoora, VIC, 3086, Australia.
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Shukla V, Runthala A, Rajput VS, Chandrasai PD, Tripathi A, Phulara SC. Computational and synthetic biology approaches for the biosynthesis of antiviral and anticancer terpenoids from Bacillus subtilis. Med Chem 2021; 18:307-322. [PMID: 34254925 DOI: 10.2174/1573406417666210712211557] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Revised: 04/18/2021] [Accepted: 04/25/2021] [Indexed: 11/22/2022]
Abstract
Recent advancements in medicinal research have identified several antiviral and anticancer terpenoids that are usually deployed as a source of flavor, fragrances and pharmaceuticals. Under the current COVID-19 pandemic conditions, natural therapeutics with least side effects are the need of the hour to save the patients, especially, which are pre-affected with other medical complications. Although, plants are the major sources of terpenoids; however, for the environmental concerns, the global interest has shifted to the biocatalytic production of molecules from microbial sources. The gram-positive bacterium Bacillus subtilis is a suitable host in this regard due to its GRAS (generally regarded as safe) status, ease in genetic manipulations and wide industrial acceptability. The B. subtilis synthesizes its terpenoid molecules from 1-deoxy-d-xylulose-5-phosphate (DXP) pathway, a common route in almost all microbial strains. Here, we summarize the computational and synthetic biology approaches to improve the production of terpenoid-based therapeutics from B. subtilis by utilizing DXP pathway. We focus on the in-silico approaches for screening the functionally improved enzyme-variants of the two crucial enzymes namely, the DXP synthase (DXS) and farnesyl pyrophosphate synthase (FPPS). The approaches for engineering the active sites are subsequently explained. It will be helpful to construct the functionally improved enzymes for the high-yield production of terpenoid-based anticancer and antiviral metabolites, which would help to reduce the cost and improve the availability of such therapeutics for the humankind.
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Affiliation(s)
- Vibha Shukla
- Food, Drug and Chemical Toxicology Group, CSIR-Indian Institute of Toxicology Research, Vishvigyan Bhawan, 31 Mahatma Gandhi Marg, Lucknow-226001, India
| | - Ashish Runthala
- Department of Biotechnology, Koneru Lakshmaiah Education Foundation, Vaddeswaram, Guntur-522502, Andhra Pradesh, India
| | | | - Potla Durthi Chandrasai
- Department of Biotechnology, National Institute of Technology Warangal, Warangal-506004, Telangana, India
| | - Anurag Tripathi
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad- 201002, India
| | - Suresh Chandra Phulara
- Department of Biotechnology, Koneru Lakshmaiah Education Foundation, Vaddeswaram, Guntur-522502, Andhra Pradesh, India
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Yang J, Zhu Q, Xu F, Yang M, Du H, Bian X, Lu Z, Lu Y, Lu F. Genome Mining, Heterologous Expression, Antibacterial and Antioxidant Activities of Lipoamides and Amicoumacins from Compost-Associated Bacillus subtilis fmb60. Molecules 2021; 26:molecules26071892. [PMID: 33810551 PMCID: PMC8036425 DOI: 10.3390/molecules26071892] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 03/18/2021] [Accepted: 03/23/2021] [Indexed: 11/25/2022] Open
Abstract
Bacillus subtilis fmb60, which has broad-spectrum antimicrobial activities, was isolated from plant straw compost. A hybrid NRPS/PKS cluster was screened from the genome. Sixteen secondary metabolites produced by the gene cluster were isolated and identified using LC-HRMS and NMR. Three lipoamides D–F (1–3) and two amicoumacin derivatives, amicoumacins D, E (4, 5), were identified, and are reported here for the first time. Lipoamides D–F exhibited strong antibacterial activities against harmful foodborne bacteria, with the MIC ranging from 6.25 to 25 µg/mL. Amicoumacin E scavenged 38.8% of ABTS+ radicals at 1 mg/mL. Direct cloning and heterologous expression of the NRPS/PKS and ace gene cluster identified its importance for the biosynthesis of amicoumacins. This study demonstrated that there is a high potential for biocontrol utilization of B. subtilis fmb60, and genome mining for clusters of secondary metabolites of B. subtilis fmb60 has revealed a greater biosynthetic potential for the production of novel natural products than previously anticipated.
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Affiliation(s)
- Jie Yang
- Jiangsu Key Laboratory of Marine Bioresources and Environment, Jiangsu Ocean University, Lianyungang 222005, China; (J.Y.); (Q.Z.); (F.X.)
- Co-Innovation Center of Jiangsu Marine Bio-industry Technology, Jiangsu Ocean University, Lianyungang 222005, China
- Jiangsu Marine Resources Development Research Institute, Lianyungang 222000, China
| | - Qingzheng Zhu
- Jiangsu Key Laboratory of Marine Bioresources and Environment, Jiangsu Ocean University, Lianyungang 222005, China; (J.Y.); (Q.Z.); (F.X.)
| | - Feng Xu
- Jiangsu Key Laboratory of Marine Bioresources and Environment, Jiangsu Ocean University, Lianyungang 222005, China; (J.Y.); (Q.Z.); (F.X.)
| | - Ming Yang
- Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China; (M.Y.); (X.B.)
| | - Hechao Du
- College of Food Science and Technology, Nanjing Agricultural University, 1 Weigang, Nanjing 210095, China; (H.D.); (Z.L.)
| | - Xiaoying Bian
- Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China; (M.Y.); (X.B.)
| | - Zhaoxin Lu
- College of Food Science and Technology, Nanjing Agricultural University, 1 Weigang, Nanjing 210095, China; (H.D.); (Z.L.)
| | - Yingjian Lu
- College of Food Science and Engineering, Nanjing University of Finance and Economics, Nanjing 210003, China
- Correspondence: (Y.L.); (F.L.); Tel./Fax: +86-258-439-5155 (Y.L.); +86-258-439-5963 (F.L.)
| | - Fengxia Lu
- College of Food Science and Technology, Nanjing Agricultural University, 1 Weigang, Nanjing 210095, China; (H.D.); (Z.L.)
- Correspondence: (Y.L.); (F.L.); Tel./Fax: +86-258-439-5155 (Y.L.); +86-258-439-5963 (F.L.)
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9
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Shukla V, Phulara SC. Impact of culture condition modulation on the high-yield, high-specificity and cost-effective production of terpenoids from microbial sources: A review. Appl Environ Microbiol 2021; 87:AEM.02369-20. [PMID: 33257314 PMCID: PMC7851692 DOI: 10.1128/aem.02369-20] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Recent years have seen a remarkable increase in the non-natural production of terpenoids from microbial route. This is due to the advancements in synthetic biology tools and techniques, which have overcome the challenges associated with the non-native production of terpenoids from microbial hosts. Although, microbes in their native form have ability to grow in wide range of physicochemical parameters such as, pH, temperature, agitation, aeration etc; however, after genetic modifications, culture conditions need to be optimized in order to achieve improved titers of desired terpenoids from engineered microbes. The physicochemical parameters together with medium supplements, such as, inducer, carbon and nitrogen source, and cofactor supply not only play an important role in high-yield production of target terpenoids from engineered host, but also reduce the accumulation of undesired metabolites in fermentation medium, thus facilitate product recovery. Further, for the economic production of terpenoids, the biomass derived sugars can be utilized together with the optimized culture conditions. In the present mini-review, we have highlighted the impact of culture conditions modulation on the high-yield and high-specificity production of terpenoids from engineered microbes. Lastly, utilization of economic feedstock has also been discussed for the cost-effective and sustainable production of terpenoids.
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Affiliation(s)
- Vibha Shukla
- Food, Drug and Chemical Toxicology Group, CSIR-Indian Institute of Toxicology Research, Vishvigyan Bhawan, 31 Mahatma Gandhi Marg, Lucknow-226001, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad-201002, India
| | - Suresh Chandra Phulara
- Department of Biotechnology, Koneru Lakshmaiah Education Foundation, Vaddeswaram, Guntur-522502, Andhra Pradesh, India
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10
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Sun C, Dong X, Zhang R, Xie C. Effectiveness of recombinant Escherichia coli on the production of (R)-(+)-perillyl alcohol. BMC Biotechnol 2021; 21:3. [PMID: 33419424 PMCID: PMC7791655 DOI: 10.1186/s12896-020-00662-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 12/08/2020] [Indexed: 01/11/2023] Open
Abstract
Background (R)-(+)-perillyl alcohol is a naturally oxygenated monoterpene widely used as the natural flavor additives, insecticides, jet fuels and anti-cancer therapies. It was also readily available monoterpene precursors. However, this natural product is present at low concentrations from plant sources which are not economically viable. Therefore, alternative microbial production methods are rapidly emerging as an attractive alternative to make (R)-(+)-perillyl alcohol production more sustainable and environmentally friendly. Results We engineered Escherichia coli to possess a heterologous mevalonate (MVA) pathway, including limonene synthase, P-cymene monoxygenase hydroxylase and P-cymene monoxygenase reductase for the production of (R)-(+)-perillyl alcohol. The concentration of (R)-(+)-limonene (the monoterpene precursor to (R)-(+)-perillyl alcohol) reached 45 mg/L from glucose. Enhanced (R)-(+)-perillyl alcohol production was therefore achieved. The strain produced (R)-(+)-perillyl alcohol at a titer of 87 mg/L and a yield of 1.5 mg/g glucose in a 5 L bioreactor fed batch system. Conclusions These datas highlight the efficient production of (R)-(+)-perillyl alcohol through the mevalonate pathway from glucose. This method serves as a platform for the future production of other monoterpenes.
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Affiliation(s)
- Chao Sun
- A State Key Laboratory Base of Eco-Chemical Engineering, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, 53 Zhengzhou Rd., Qingdao, 266042, China.,CAS Key Laboratory of Bio-based Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, 189 Songling Rd., Qingdao, 266101, China
| | - Xianjuan Dong
- CAS Key Laboratory of Bio-based Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, 189 Songling Rd., Qingdao, 266101, China
| | - Rubing Zhang
- CAS Key Laboratory of Bio-based Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, 189 Songling Rd., Qingdao, 266101, China.
| | - Congxia Xie
- A State Key Laboratory Base of Eco-Chemical Engineering, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, 53 Zhengzhou Rd., Qingdao, 266042, China.
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11
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Pramastya H, Song Y, Elfahmi EY, Sukrasno S, Quax WJ. Positioning Bacillus subtilis as terpenoid cell factory. J Appl Microbiol 2020; 130:1839-1856. [PMID: 33098223 PMCID: PMC8247319 DOI: 10.1111/jam.14904] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Revised: 09/29/2020] [Accepted: 10/09/2020] [Indexed: 12/16/2022]
Abstract
Increasing demands for bioactive compounds have motivated researchers to employ micro‐organisms to produce complex natural products. Currently, Bacillus subtilis has been attracting lots of attention to be developed into terpenoids cell factories due to its generally recognized safe status and high isoprene precursor biosynthesis capacity by endogenous methylerythritol phosphate (MEP) pathway. In this review, we describe the up‐to‐date knowledge of each enzyme in MEP pathway and the subsequent steps of isomerization and condensation of C5 isoprene precursors. In addition, several representative terpene synthases expressed in B. subtilis and the engineering steps to improve corresponding terpenoids production are systematically discussed. Furthermore, the current available genetic tools are mentioned as along with promising strategies to improve terpenoids in B. subtilis, hoping to inspire future directions in metabolic engineering of B. subtilis for further terpenoid cell factory development.
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Affiliation(s)
- H Pramastya
- University of Groningen, Groningen, The Netherlands.,Pharmaceutical Biology Research Group, School of Pharmacy, Institut Teknologi Bandung, Bandung, Indonesia
| | - Y Song
- University of Groningen, Groningen, The Netherlands
| | - E Y Elfahmi
- Pharmaceutical Biology Research Group, School of Pharmacy, Institut Teknologi Bandung, Bandung, Indonesia
| | - S Sukrasno
- Pharmaceutical Biology Research Group, School of Pharmacy, Institut Teknologi Bandung, Bandung, Indonesia
| | - W J Quax
- University of Groningen, Groningen, The Netherlands
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12
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Pramastya H, Xue D, Abdallah II, Setroikromo R, Quax WJ. High level production of amorphadiene using Bacillus subtilis as an optimized terpenoid cell factory. N Biotechnol 2020; 60:159-167. [PMID: 33148534 DOI: 10.1016/j.nbt.2020.10.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Revised: 10/15/2020] [Accepted: 10/16/2020] [Indexed: 02/09/2023]
Abstract
The anti-malarial drug artemisinin, produced naturally in the plant Artemisia annua, experiences unstable and insufficient supply as its production relies heavily on the plant source. To meet the massive demand for this compound, metabolic engineering of microbes has been studied extensively. In this study, we focus on improving the production of amorphadiene, a crucial artemisinin precursor, in Bacillus subtilis. The expression level of the plant-derived amorphadiene synthase (ADS) was upregulated by fusion with green fluorescent protein (GFP). Furthermore, a co-expression system of ADS and a synthetic operon carrying the 2-C-methyl-D-erythritol-4-phosphate (MEP) pathway genes was established. Subsequently, farnesyl pyrophosphate synthase (FPPS), a key enzyme in formation of the sesquiterpene precursor farnesyl pyrophosphate (FPP), was expressed to supply sufficient substrate for ADS. The consecutive combination of these features yielded a B. subtilis strain expressing chromosomally integrated GFP-ADS followed by FPPS and a plasmid encoded synthetic operon showing a stepwise increased production of amorphadiene. An experimental design-aided systematic medium optimization was used to maximize the production level for the most promising engineered B. subtilis strain, resulting in an amorphadiene yield of 416 ± 15 mg/L, which is 20-fold higher than that previously reported in B. subtilis and more than double the production in Escherichia coli or Saccharomyces cerevisiae on a shake flask fermentation level.
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Affiliation(s)
- Hegar Pramastya
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, 9713 AV, Groningen, the Netherlands; Pharmaceutical Biology Research Group, School of Pharmacy, Institut Teknologi Bandung, 40132, Bandung, Indonesia
| | - Dan Xue
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, 9713 AV, Groningen, the Netherlands
| | - Ingy I Abdallah
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, 9713 AV, Groningen, the Netherlands; Department of Pharmacognosy, Faculty of Pharmacy, Alexandria University, Egypt
| | - Rita Setroikromo
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, 9713 AV, Groningen, the Netherlands
| | - Wim J Quax
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, 9713 AV, Groningen, the Netherlands.
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13
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Song Y, Guan Z, van Merkerk R, Pramastya H, Abdallah II, Setroikromo R, Quax WJ. Production of Squalene in Bacillus subtilis by Squalene Synthase Screening and Metabolic Engineering. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2020; 68:4447-4455. [PMID: 32208656 PMCID: PMC7168599 DOI: 10.1021/acs.jafc.0c00375] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Squalene synthase (SQS) catalyzes the conversion of two farnesyl pyrophosphates to squalene, an important intermediate in between isoprene and valuable triterpenoids. In this study, we have constructed a novel biosynthesis pathway for squalene in Bacillus subtilis and performed metabolic engineering aiming at facilitating further exploitation and production of squalene-derived triterpenoids. Therefore, systematic studies and analysis were performed including selection of multiple SQS candidates from various organisms, comparison of expression vectors, optimization of cultivation temperatures, and examination of rate-limiting factors within the synthetic pathway. We were, for the first time, able to obtain squalene synthesis in B. subtilis. Furthermore, we achieved a 29-fold increase of squalene yield (0.26-7.5 mg/L) by expressing SQS from Bacillus megaterium and eliminating bottlenecks within the upstream methylerythritol-phosphate pathway. Moreover, our findings showed that also ispA could positively affect the production of squalene.
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Affiliation(s)
- Yafeng Song
- Department
of Chemical and Pharmaceutical Biology, Groningen Research Institute
of Pharmacy, University of Groningen, Antonius Deusinglaan 1, 9713 AV Groningen, The Netherlands
| | - Zheng Guan
- Department
of Chemical and Pharmaceutical Biology, Groningen Research Institute
of Pharmacy, University of Groningen, Antonius Deusinglaan 1, 9713 AV Groningen, The Netherlands
| | - Ronald van Merkerk
- Department
of Chemical and Pharmaceutical Biology, Groningen Research Institute
of Pharmacy, University of Groningen, Antonius Deusinglaan 1, 9713 AV Groningen, The Netherlands
| | - Hegar Pramastya
- Department
of Chemical and Pharmaceutical Biology, Groningen Research Institute
of Pharmacy, University of Groningen, Antonius Deusinglaan 1, 9713 AV Groningen, The Netherlands
- Pharmaceutical
Biology Research Group, School of Pharmacy, Institut Teknologi Bandung, 40132 Bandung, Indonesia
| | - Ingy I. Abdallah
- Department
of Chemical and Pharmaceutical Biology, Groningen Research Institute
of Pharmacy, University of Groningen, Antonius Deusinglaan 1, 9713 AV Groningen, The Netherlands
- Department
of Pharmacognosy, Faculty of Pharmacy, Alexandria
University, Alexandria 21521, Egypt
| | - Rita Setroikromo
- Department
of Chemical and Pharmaceutical Biology, Groningen Research Institute
of Pharmacy, University of Groningen, Antonius Deusinglaan 1, 9713 AV Groningen, The Netherlands
| | - Wim J. Quax
- Department
of Chemical and Pharmaceutical Biology, Groningen Research Institute
of Pharmacy, University of Groningen, Antonius Deusinglaan 1, 9713 AV Groningen, The Netherlands
- . Phone: +31 (0) 50 363 2558, (0) 50 363 8174. Fax: +31 (0) 50 363 3000
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14
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Abdallah II, Xue D, Pramastya H, van Merkerk R, Setroikromo R, Quax WJ. A regulated synthetic operon facilitates stable overexpression of multigene terpenoid pathway in Bacillus subtilis. ACTA ACUST UNITED AC 2020; 47:243-249. [DOI: 10.1007/s10295-019-02257-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Accepted: 12/14/2019] [Indexed: 01/17/2023]
Abstract
Abstract
The creation of microbial cell factories for sustainable production of natural products is important for medical and industrial applications. This requires stable expression of biosynthetic pathways in a host organism with favorable fermentation properties such as Bacillus subtilis. The aim of this study is to construct B. subtilis strains that produce valuable terpenoid compounds by overexpressing the innate methylerythritol phosphate (MEP) pathway. A synthetic operon allowing the concerted and regulated expression of multiple genes was developed. Up to 8 genes have been combined in this operon and a stably inherited plasmid-based vector was constructed resulting in a high production of C30 carotenoids. For this, two vectors were examined, one with rolling circle replication and another with theta replication. Theta-replication constructs were clearly superior in structural and segregational stability compared to rolling circle constructs. A strain overexpressing all eight genes of the MEP pathway on a theta-replicating plasmid clearly produced the highest level of carotenoids. The level of transcription for each gene in the operon was similar as RT-qPCR analysis indicated. Hence, that corresponding strain can be used as a stable cell factory for production of terpenoids. This is the first report of merging and stably expressing this large-size operon (eight genes) from a plasmid-based system in B. subtilis enabling high C30 carotenoid production.
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Affiliation(s)
- Ingy I Abdallah
- grid.4830.f 0000 0004 0407 1981 Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy University of Groningen Antonius Deusinglaan 1 9713 AV Groningen The Netherlands
| | - Dan Xue
- grid.4830.f 0000 0004 0407 1981 Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy University of Groningen Antonius Deusinglaan 1 9713 AV Groningen The Netherlands
| | - Hegar Pramastya
- grid.4830.f 0000 0004 0407 1981 Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy University of Groningen Antonius Deusinglaan 1 9713 AV Groningen The Netherlands
- grid.434933.a 0000 0004 1808 0563 Pharmaceutical Biology Research Group, School of Pharmacy Institut Teknologi Bandung 40132 Bandung Indonesia
| | - Ronald van Merkerk
- grid.4830.f 0000 0004 0407 1981 Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy University of Groningen Antonius Deusinglaan 1 9713 AV Groningen The Netherlands
| | - Rita Setroikromo
- grid.4830.f 0000 0004 0407 1981 Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy University of Groningen Antonius Deusinglaan 1 9713 AV Groningen The Netherlands
| | - Wim J Quax
- grid.4830.f 0000 0004 0407 1981 Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy University of Groningen Antonius Deusinglaan 1 9713 AV Groningen The Netherlands
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15
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Cui S, Lv X, Wu Y, Li J, Du G, Ledesma-Amaro R, Liu L. Engineering a Bifunctional Phr60-Rap60-Spo0A Quorum-Sensing Molecular Switch for Dynamic Fine-Tuning of Menaquinone-7 Synthesis in Bacillus subtilis. ACS Synth Biol 2019; 8:1826-1837. [PMID: 31257862 DOI: 10.1021/acssynbio.9b00140] [Citation(s) in RCA: 67] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Quorum sensing (QS)-based dynamic regulation has been widely used as basic tool for fine-tuning gene expression in response to cell density changes without adding expensive inducers. However, most reported QS systems primarily relied on down-regulation rather than up-regulation of gene expression, significantly limiting its potential as a molecular switch to control metabolic flux. To solve this challenge, we developed a bifunctional and modular Phr60-Rap60-Spo0A QS system, based on two native promoters, PabrB (down-regulation by Spo0A-P) and PspoiiA (up-regulation by Spo0A-P). We constructed a library of promoters with different capacities to implement down-regulation and up-regulation by changing the location, number, and sequences of the binding sites for Spo0A-P. The QS system can dynamically balance the relationship between efficient synthesis of the target product and cell growth. Finally, we validated the usefulness of this strategy by dynamic control of menaquinone-7 (MK-7) synthesis in Bacillus subtilis 168, a model Gram-positive bacterium, with the bifunctional Phr60-Rap60-Spo0A quorum sensing system. Our dynamic pathway regulation led to a 40-fold improvement of MK-7 production from 9 to 360 mg/L in shake flasks and 200 mg/L in 15-L bioreactor. Taken together, our bilayer QS system has been successfully integrated with biocatalytic functions to achieve dynamic pathway regulation in B. subtilis 168, which may be extended for use in other microbes to fine-tune gene expression and improve metabolites production.
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Affiliation(s)
- Shixiu Cui
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
- Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Xueqin Lv
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
- Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Yaokang Wu
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
- Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Jianghua Li
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
- Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Guocheng Du
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
- Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
| | | | - Long Liu
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
- Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
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16
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Caulier S, Nannan C, Gillis A, Licciardi F, Bragard C, Mahillon J. Overview of the Antimicrobial Compounds Produced by Members of the Bacillus subtilis Group. Front Microbiol 2019; 10:302. [PMID: 30873135 PMCID: PMC6401651 DOI: 10.3389/fmicb.2019.00302] [Citation(s) in RCA: 299] [Impact Index Per Article: 59.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Accepted: 02/05/2019] [Indexed: 12/19/2022] Open
Abstract
Over the last seven decades, applications using members of the Bacillus subtilis group have emerged in both food processes and crop protection industries. Their ability to form survival endospores and the plethora of antimicrobial compounds they produce has generated an increased industrial interest as food preservatives, therapeutic agents and biopesticides. In the growing context of food biopreservation and biological crop protection, this review suggests a comprehensive way to visualize the antimicrobial spectrum described within the B. subtilis group, including volatile compounds. This classification distinguishes the bioactive metabolites based on their biosynthetic pathways and chemical nature: i.e., ribosomal peptides (RPs), volatile compounds, polyketides (PKs), non-ribosomal peptides (NRPs), and hybrids between PKs and NRPs. For each clade, the chemical structure, biosynthesis and antimicrobial activity are described and exemplified. This review aims at constituting a convenient and updated classification of antimicrobial metabolites from the B. subtilis group, whose complex phylogeny is prone to further development.
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Affiliation(s)
- Simon Caulier
- Laboratory of Food and Environmental Microbiology, Earth and Life Institute, Université catholique de Louvain, Louvain-la-Neuve, Belgium.,Laboratory of Phytopathology-Applied Microbiology, Earth and Life Institute, Université catholique de Louvain, Louvain-la-Neuve, Belgium
| | - Catherine Nannan
- Laboratory of Food and Environmental Microbiology, Earth and Life Institute, Université catholique de Louvain, Louvain-la-Neuve, Belgium
| | - Annika Gillis
- Laboratory of Food and Environmental Microbiology, Earth and Life Institute, Université catholique de Louvain, Louvain-la-Neuve, Belgium
| | - Florent Licciardi
- Laboratory of Food and Environmental Microbiology, Earth and Life Institute, Université catholique de Louvain, Louvain-la-Neuve, Belgium
| | - Claude Bragard
- Laboratory of Phytopathology-Applied Microbiology, Earth and Life Institute, Université catholique de Louvain, Louvain-la-Neuve, Belgium
| | - Jacques Mahillon
- Laboratory of Food and Environmental Microbiology, Earth and Life Institute, Université catholique de Louvain, Louvain-la-Neuve, Belgium
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17
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Abdallah II, Pramastya H, van Merkerk R, Sukrasno, Quax WJ. Metabolic Engineering of Bacillus subtilis Toward Taxadiene Biosynthesis as the First Committed Step for Taxol Production. Front Microbiol 2019; 10:218. [PMID: 30842758 PMCID: PMC6391936 DOI: 10.3389/fmicb.2019.00218] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Accepted: 01/28/2019] [Indexed: 11/13/2022] Open
Abstract
Terpenoids are natural products known for their medicinal and commercial applications. Metabolic engineering of microbial hosts for the production of valuable compounds, such as artemisinin and Taxol, has gained vast interest in the last few decades. The Generally Regarded As Safe (GRAS) Bacillus subtilis 168 with its broad metabolic potential is considered one of these interesting microbial hosts. In the effort toward engineering B. subtilis as a cell factory for the production of the chemotherapeutic Taxol, we expressed the plant-derived taxadiene synthase (TXS) enzyme. TXS is responsible for the conversion of the precursor geranylgeranyl pyrophosphate (GGPP) to taxa-4,11-diene, which is the first committed intermediate in Taxol biosynthesis. Furthermore, overexpression of eight enzymes in the biosynthesis pathway was performed to increase the flux of the GGPP precursor. This was achieved by creating a synthetic operon harboring the B. subtilis genes encoding the 2-C-methyl-D-erythritol-4-phosphate (MEP) pathway (dxs, ispD, ispF, ispH, ispC, ispE, ispG) together with ispA (encoding geranyl and farnesyl pyrophosphate synthases) responsible for providing farnesyl pyrophosphate (FPP). In addition, a vector harboring the crtE gene (encoding geranylgeranyl pyrophosphate synthase, GGPPS, of Pantoea ananatis) to increase the supply of GGPP was introduced. The overexpression of the MEP pathway enzymes along with IspA and GGPPS caused an 83-fold increase in the amount of taxadiene produced compared to the strain only expressing TXS and relying on the innate pathway of B. subtilis. The total amount of taxadiene produced by that strain was 17.8 mg/l. This is the first account of the successful expression of taxadiene synthase in B. subtilis. We determined that the expression of GGPPS through the crtE gene is essential for the formation of sufficient precursor, GGPP, in B. subtilis as its innate metabolism is not efficient in producing it. Finally, the extracellular localization of taxadiene production by overexpressing the complete MEP pathway along with IspA and GGPPS presents the prospect for further engineering aiming for semisynthesis of Taxol.
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Affiliation(s)
- Ingy I Abdallah
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, Groningen, Netherlands
| | - Hegar Pramastya
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, Groningen, Netherlands.,Pharmaceutical Biology Research Group, School of Pharmacy, Institut Teknologi Bandung, Bandung, Indonesia
| | - Ronald van Merkerk
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, Groningen, Netherlands
| | - Sukrasno
- Pharmaceutical Biology Research Group, School of Pharmacy, Institut Teknologi Bandung, Bandung, Indonesia
| | - Wim J Quax
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, Groningen, Netherlands
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18
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Cao Y, Zhang R, Liu W, Zhao G, Niu W, Guo J, Xian M, Liu H. Manipulation of the precursor supply for high-level production of longifolene by metabolically engineered Escherichia coli. Sci Rep 2019; 9:95. [PMID: 30643175 PMCID: PMC6331559 DOI: 10.1038/s41598-018-36495-w] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Accepted: 04/16/2018] [Indexed: 01/26/2023] Open
Abstract
Longifolene is a naturally occurring tricyclic sesquiterpene widely used in many different fields. Up to now, this valuable terpene was mainly manufactured from the high-boiling fraction of certain pine resins. Microbial production can be a promising alternative to the extraction from natural plant sources. Here, we present the metabolic engineering strategy to assemble biosynthetic pathway for longifolene production in Escherichia coli. E. coli was rendered to produce longifolene by heterologously expressing a codon optimized longifolene synthase from Picea abies. Augmentation of the metabolic flux to farnesyl pyrophosphate (FPP) by different FPP synthases conferred a 1.8-fold increase in longifolene production. An additional enhancement of longifolene production (up to 2.64 mg/L) was achieved by introducing an exogenous mevalonate pathway. Under fed-batch conditions, the best-performing strain was able to produce 382 mg/L of longifolene in a 5 L bioreactor. These results demonstrated the feasibility of producing longifolene by microbial fermentation and could serve as the basis for the construction of more robust strains in the future.
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Affiliation(s)
- Yujin Cao
- CAS Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China.
| | - Rubing Zhang
- CAS Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
| | - Wei Liu
- CAS Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
| | - Guang Zhao
- CAS Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
| | - Wei Niu
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, Nebraska, United States
| | - Jiantao Guo
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, Nebraska, United States
| | - Mo Xian
- CAS Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China.
| | - Huizhou Liu
- CAS Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China.
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19
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Xiao H, Zhang Y, Wang M. Discovery and Engineering of Cytochrome P450s for Terpenoid Biosynthesis. Trends Biotechnol 2018; 37:618-631. [PMID: 30528904 DOI: 10.1016/j.tibtech.2018.11.008] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2018] [Revised: 10/28/2018] [Accepted: 11/15/2018] [Indexed: 01/29/2023]
Abstract
Terpenoids represent 60% of known natural products, including many drugs and drug candidates, and their biosynthesis is attracting great interest. However, the unknown cytochrome P450s (CYPs) in terpenoid biosynthetic pathways make the heterologous production of related terpenoids impossible, while the slow kinetics of some known CYPs greatly limit the efficiency of terpenoid biosynthesis. Thus, there is a compelling need to discover and engineer CYPs for terpenoid biosynthesis to fully realize their great potential for industrial application. This review article summarizes the current state of CYP discovery and engineering in terpenoid biosynthesis, focusing on recent synthetic biology approaches toward prototyping CYPs in heterologous hosts. We also propose several strategies for further accelerating CYP discovery and engineering.
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Affiliation(s)
- Han Xiao
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, and Laboratory of Molecular Biochemical Engineering, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dong-chuan Road, Shanghai, 200240, China; Co-first author with equal contribution.
| | - Yue Zhang
- Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China; Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China; Co-first author with equal contribution
| | - Meng Wang
- Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China; Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China.
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20
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Draft Genome Sequence of " Candidatus Spirobacillus cienkowskii," a Pathogen of Freshwater Daphnia Species, Reconstructed from Hemolymph Metagenomic Reads. Microbiol Resour Announc 2018; 7:MRA01175-18. [PMID: 30533855 PMCID: PMC6284087 DOI: 10.1128/mra.01175-18] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Accepted: 11/05/2018] [Indexed: 11/25/2022] Open
Abstract
We report here the near-complete genome sequence of “Candidatus Spirobacillus cienkowskii,” a spiral-shaped, red-pigmented uncultivated bacterial pathogen of Daphnia spp. The genome is 2.74 Mbp in size, has a GC content of 32.1%, and contains genes associated with bacterial motility and the production of carotenoids, which could explain the distinctive red color of hosts infected with this pathogen. We report here the near-complete genome sequence of “Candidatus Spirobacillus cienkowskii,” a spiral-shaped, red-pigmented uncultivated bacterial pathogen of Daphnia spp. The genome is 2.74 Mbp in size, has a GC content of 32.1%, and contains genes associated with bacterial motility and the production of carotenoids, which could explain the distinctive red color of hosts infected with this pathogen.
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Dong Z, Chen X, Cai K, Shen P, Tian K, Jin P, Liu X, Wang Z. Overexpression of the Bacillus licheniformis GroES enhances thermotolerance of Bacillus subtilis WB600. BIOTECHNOL BIOTEC EQ 2018. [DOI: 10.1080/13102818.2018.1517029] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022] Open
Affiliation(s)
- Zixing Dong
- Department of Biochemical Engineering, College of Chemical Engineering and Materials Science, Tianjin University of Science & Technology, Tianjin, PR China
| | - Xiaoling Chen
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, College of Biotechnology, Tianjin University of Science & Technology, Tianjin, PR China
| | - Ke Cai
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, College of Biotechnology, Tianjin University of Science & Technology, Tianjin, PR China
| | - Peili Shen
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, College of Biotechnology, Tianjin University of Science & Technology, Tianjin, PR China
| | - Kangming Tian
- Department of Biochemical Engineering, College of Chemical Engineering and Materials Science, Tianjin University of Science & Technology, Tianjin, PR China
| | - Peng Jin
- Department of Biochemical Engineering, College of Chemical Engineering and Materials Science, Tianjin University of Science & Technology, Tianjin, PR China
| | - Xiaoguang Liu
- Department of Biochemical Engineering, College of Chemical Engineering and Materials Science, Tianjin University of Science & Technology, Tianjin, PR China
| | - Zhengxiang Wang
- Department of Biochemical Engineering, College of Chemical Engineering and Materials Science, Tianjin University of Science & Technology, Tianjin, PR China
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, College of Biotechnology, Tianjin University of Science & Technology, Tianjin, PR China
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Schempp FM, Drummond L, Buchhaupt M, Schrader J. Microbial Cell Factories for the Production of Terpenoid Flavor and Fragrance Compounds. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2018; 66:2247-2258. [PMID: 28418659 DOI: 10.1021/acs.jafc.7b00473] [Citation(s) in RCA: 110] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Terpenoid flavor and fragrance compounds are of high interest to the aroma industry. Microbial production offers an alternative sustainable access to the desired terpenoids independent of natural sources. Genetically engineered microorganisms can be used to synthesize terpenoids from cheap and renewable resources. Due to its modular architecture, terpenoid biosynthesis is especially well suited for the microbial cell factory concept: a platform host engineered for a high flux toward the central C5 prenyl diphosphate precursors enables the production of a broad range of target terpenoids just by varying the pathway modules converting the C5 intermediates to the product of interest. In this review typical terpenoid flavor and fragrance compounds marketed or under development by biotech and aroma companies are given, and the specificities of the aroma market are discussed. The main part of this work focuses on key strategies and recent advances to engineer microbes to become efficient terpenoid producers.
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Affiliation(s)
- Florence M Schempp
- DECHEMA-Forschungsinstitut, Industrial Biotechnology , Theodor-Heuss-Allee 25 , 60486 Frankfurt am Main , Germany
| | - Laura Drummond
- DECHEMA-Forschungsinstitut, Industrial Biotechnology , Theodor-Heuss-Allee 25 , 60486 Frankfurt am Main , Germany
| | - Markus Buchhaupt
- DECHEMA-Forschungsinstitut, Industrial Biotechnology , Theodor-Heuss-Allee 25 , 60486 Frankfurt am Main , Germany
| | - Jens Schrader
- DECHEMA-Forschungsinstitut, Industrial Biotechnology , Theodor-Heuss-Allee 25 , 60486 Frankfurt am Main , Germany
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Biosynthesis and production of sabinene: current state and perspectives. Appl Microbiol Biotechnol 2017; 102:1535-1544. [DOI: 10.1007/s00253-017-8695-5] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2017] [Revised: 12/03/2017] [Accepted: 12/04/2017] [Indexed: 01/10/2023]
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Abdallah II, Czepnik M, van Merkerk R, Quax WJ. Insights into the Three-Dimensional Structure of Amorpha-4,11-diene Synthase and Probing of Plasticity Residues. JOURNAL OF NATURAL PRODUCTS 2016; 79:2455-2463. [PMID: 27673334 DOI: 10.1021/acs.jnatprod.6b00236] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Amorphadiene synthase (ADS) is known for its vital role as a key enzyme in the biosynthesis of the antimalarial drug artemisinin. Despite the vast research targeting this enzyme, an X-ray crystal structure of the enzyme has not yet been reported. In spite of the remarkable difference in product profile among various sesquiterpene synthases, they all share a common α-helical fold with many highly conserved regions especially the bivalent metal ion binding motifs. Hence, to better understand the structural basis of the mechanism of ADS, a reliable 3D homology model representing the conformation of the ADS enzyme and the position of its substrate, farnesyl diphosphate, in the active site was constructed. The model was generated using the reported crystal structure of α-bisabolol synthase mutant, an enzyme with high sequence identity with ADS, as a template. Site-directed mutagenesis was used to probe the active site residues. Seven residues were probed showing their vital role in the ADS mechanism and/or their effect on product profile. The generated variants confirmed the validity of the ADS model. This model will serve as a basis for exploring structure-function relationships of all residues in the active site to obtain further insight into the ADS mechanism.
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Affiliation(s)
- Ingy I Abdallah
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen , 9713 AV, Groningen, The Netherlands
| | - Magdalena Czepnik
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen , 9713 AV, Groningen, The Netherlands
| | - Ronald van Merkerk
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen , 9713 AV, Groningen, The Netherlands
| | - Wim J Quax
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen , 9713 AV, Groningen, The Netherlands
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Zebec Z, Wilkes J, Jervis AJ, Scrutton NS, Takano E, Breitling R. Towards synthesis of monoterpenes and derivatives using synthetic biology. Curr Opin Chem Biol 2016; 34:37-43. [DOI: 10.1016/j.cbpa.2016.06.002] [Citation(s) in RCA: 73] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2016] [Revised: 05/31/2016] [Accepted: 06/01/2016] [Indexed: 12/16/2022]
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