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Sang Z, Li X, Yan H, Wang W, Wen Y. Development of a group II intron-based genetic manipulation tool for Streptomyces. Microb Biotechnol 2024; 17:e14472. [PMID: 38683679 PMCID: PMC11057498 DOI: 10.1111/1751-7915.14472] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Revised: 04/07/2024] [Accepted: 04/09/2024] [Indexed: 05/02/2024] Open
Abstract
The availability of an alternative and efficient genetic editing technology is critical for fundamental research and strain improvement engineering of Streptomyces species, which are prolific producers of complex secondary metabolites with significant pharmaceutical activities. The mobile group II introns are retrotransposons that employ activities of catalytic intron RNAs and intron-encoded reverse transcriptase to precisely insert into DNA target sites through a mechanism known as retrohoming. We here developed a group II intron-based gene editing tool to achieve precise chromosomal gene insertion in Streptomyces. Moreover, by repressing the potential competition of RecA-dependent homologous recombination, we enhanced site-specific insertion efficiency of this tool to 2.38%. Subsequently, we demonstrated the application of this tool by screening and characterizing the secondary metabolite biosynthetic gene cluster (BGC) responsible for synthesizing the red pigment in Streptomyces roseosporus. Accompanied with identifying and inactivating this BGC, we observed that the impair of this cluster promoted cell growth and daptomycin production. Additionally, we applied this tool to activate silent jadomycin BGC in Streptomyces venezuelae. Overall, this work demonstrates the potential of this method as an alternative tool for genetic engineering and cryptic natural product mining in Streptomyces species.
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Affiliation(s)
- Ziwei Sang
- State Key Laboratory of Animal Biotech Breeding and College of Biological SciencesChina Agricultural UniversityBeijingChina
| | - Xingwang Li
- State Key Laboratory of Animal Biotech Breeding and College of Biological SciencesChina Agricultural UniversityBeijingChina
| | - Hao Yan
- State Key Laboratory of Microbial Resources, Institute of MicrobiologyChinese Academy of SciencesBeijingChina
| | - Weishan Wang
- State Key Laboratory of Microbial Resources, Institute of MicrobiologyChinese Academy of SciencesBeijingChina
| | - Ying Wen
- State Key Laboratory of Animal Biotech Breeding and College of Biological SciencesChina Agricultural UniversityBeijingChina
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Kwon SW, Paari KA, Malaviya A, Jang YS. Synthetic Biology Tools for Genome and Transcriptome Engineering of Solventogenic Clostridium. Front Bioeng Biotechnol 2020; 8:282. [PMID: 32363182 PMCID: PMC7181999 DOI: 10.3389/fbioe.2020.00282] [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: 01/19/2020] [Accepted: 03/17/2020] [Indexed: 12/18/2022] Open
Abstract
Strains of Clostridium genus are used for production of various value-added products including fuels and chemicals. Development of any commercially viable production process requires a combination of both strain and fermentation process development strategies. The strain development in Clostridium sp. could be achieved by random mutagenesis, and targeted gene alteration methods. However, strain improvement in Clostridium sp. by targeted gene alteration method was challenging due to the lack of efficient tools for genome and transcriptome engineering in this organism. Recently, various synthetic biology tools have been developed to facilitate the strain engineering of solventogenic Clostridium. In this review, we consolidated the recent advancements in toolbox development for genome and transcriptome engineering in solventogenic Clostridium. Here we reviewed the genome-engineering tools employing mobile group II intron, pyrE alleles exchange, and CRISPR/Cas9 with their application for strain development of Clostridium sp. Next, transcriptome engineering tools such as untranslated region (UTR) engineering and synthetic sRNA techniques were also discussed in context of Clostridium strain engineering. Application of any of these discussed techniques will facilitate the metabolic engineering of clostridia for development of improved strains with respect to requisite functional attributes. This might lead to the development of an economically viable butanol production process with improved titer, yield and productivity.
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Affiliation(s)
- Seong Woo Kwon
- Department of Agricultural Chemistry and Food Science Technology, Division of Applied Life Science (BK21 Plus Program), Institute of Agriculture & Life Science (IALS), Gyeongsang National University, Jinju, South Korea
| | | | - Alok Malaviya
- Applied and Industrial Biotechnology Laboratory (AIBL), Department of Life Sciences, CHRIST (Deemed to be University), Bengaluru, India
| | - Yu-Sin Jang
- Department of Agricultural Chemistry and Food Science Technology, Division of Applied Life Science (BK21 Plus Program), Institute of Agriculture & Life Science (IALS), Gyeongsang National University, Jinju, South Korea
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Wen Z, Li Q, Liu J, Jin M, Yang S. Consolidated bioprocessing for butanol production of cellulolytic Clostridia: development and optimization. Microb Biotechnol 2020; 13:410-422. [PMID: 31448546 PMCID: PMC7017829 DOI: 10.1111/1751-7915.13478] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Revised: 08/02/2019] [Accepted: 08/04/2019] [Indexed: 12/20/2022] Open
Abstract
Butanol is an important bulk chemical, as well as a promising renewable gasoline substitute, that is commonly produced by solventogenic Clostridia. The main cost of cellulosic butanol fermentation is caused by cellulases that are required to saccharify lignocellulose, since solventogenic Clostridia cannot efficiently secrete cellulases. However, cellulolytic Clostridia can natively degrade lignocellulose and produce ethanol, acetate, butyrate and even butanol. Therefore, cellulolytic Clostridia offer an alternative to develop consolidated bioprocessing (CBP), which combines cellulase production, lignocellulose hydrolysis and co-fermentation of hexose/pentose into butanol in one step. This review focuses on CBP advances for butanol production of cellulolytic Clostridia and various synthetic biotechnologies that drive these advances. Moreover, the efforts to optimize the CBP-enabling cellulolytic Clostridia chassis are also discussed. These include the development of genetic tools, pentose metabolic engineering and the improvement of butanol tolerance. Designer cellulolytic Clostridia or consortium provide a promising approach and resource to accelerate future CBP for butanol production.
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Affiliation(s)
- Zhiqiang Wen
- School of Environmental and Biological EngineeringNanjing University of Science and TechnologyNanjing210094China
| | - Qi Li
- College of Life SciencesSichuan Normal UniversityLongquan, Chengdu610101China
| | - Jinle Liu
- Key Laboratory of Synthetic BiologyCAS Center for Excellence in Molecular Plant SciencesShanghai Institute of Plant Physiology and EcologyChinese Academy of SciencesShanghai200032China
| | - Mingjie Jin
- School of Environmental and Biological EngineeringNanjing University of Science and TechnologyNanjing210094China
| | - Sheng Yang
- Key Laboratory of Synthetic BiologyCAS Center for Excellence in Molecular Plant SciencesShanghai Institute of Plant Physiology and EcologyChinese Academy of SciencesShanghai200032China
- Huzhou Center of Industrial BiotechnologyShanghai Institutes of Biological SciencesChinese Academy of SciencesShanghai200032China
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Comprehensive analysis of chromosomal mobile genetic elements in the gut microbiome reveals phylum-level niche-adaptive gene pools. PLoS One 2019; 14:e0223680. [PMID: 31830054 PMCID: PMC6907783 DOI: 10.1371/journal.pone.0223680] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2019] [Accepted: 09/25/2019] [Indexed: 12/16/2022] Open
Abstract
Mobile genetic elements (MGEs) drive extensive horizontal transfer in the gut microbiome. This transfer could benefit human health by conferring new metabolic capabilities to commensal microbes, or it could threaten human health by spreading antibiotic resistance genes to pathogens. Despite their biological importance and medical relevance, MGEs from the gut microbiome have not been systematically characterized. Here, we present a comprehensive analysis of chromosomal MGEs in the gut microbiome using a method that enables the identification of the mobilizable unit of MGEs. We curated a database of 5,219 putative MGEs encompassing seven MGE classes called ImmeDB. We observed that many MGEs carry genes that could confer an adaptive advantage to the gut environment including gene families involved in antibiotic resistance, bile salt detoxification, mucus degradation, capsular polysaccharide biosynthesis, polysaccharide utilization, and sporulation. We find that antibiotic resistance genes are more likely to be spread by conjugation via integrative conjugative elements or integrative mobilizable elements than transduction via prophages. Horizontal transfer of MGEs is extensive within phyla but rare across phyla, supporting phylum level niche-adaptive gene pools in the gut microbiome. ImmeDB will be a valuable resource for future studies on the gut microbiome and MGE communities.
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Wen Z, Lu M, Ledesma-Amaro R, Li Q, Jin M, Yang S. TargeTron Technology Applicable in Solventogenic Clostridia: Revisiting 12 Years' Advances. Biotechnol J 2019; 15:e1900284. [PMID: 31475782 DOI: 10.1002/biot.201900284] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2019] [Revised: 08/20/2019] [Indexed: 12/11/2022]
Abstract
Clostridium has great potential in industrial application and medical research. But low DNA repair capacity and plasmids transformation efficiency severely delay development and application of genetic tools based on homologous recombination (HR). TargeTron is a gene editing technique dependent on the mobility of group II introns, rather than homologous recombination, which makes it very suitable for gene disruption of Clostridium. The application of TargeTron technology in solventogenic Clostridium is academically reported in 2007 and this tool has been introduced in various clostridia as it is easy to operate, time saving, and reliable. TargeTron has made great progress in solventogenic Clostridium in the aspects of acetone-butanol-ethanol (ABE) fermentation pathway modification, important functional genes identification, and xylose metabolic pathway analysis and reconstruction. In the review, 12 years' advances of TargeTron technology applicable in solventogenic Clostridium, including its principle, technical characteristics, application, and efforts to expand its capabilities, or to avoid potential drawbacks, are revisisted. Some other technologies as putative competitors or collaborators are also discussed. It is believed that TargeTron combined with CRISPR/Cas-assisted gene/base editing and gene-expression regulation system will make a better future for clostridial genetic modification.
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Affiliation(s)
- Zhiqiang Wen
- School of Environmental and Biological Engineering, Nanjing University of Science & Technology, Nanjing, 210094, China
| | - Minrui Lu
- School of Environmental and Biological Engineering, Nanjing University of Science & Technology, Nanjing, 210094, China
| | | | - Qi Li
- College of Life Sciences, Sichuan Normal University, Longquan, Chengdu, 610101, China
| | - Mingjie Jin
- School of Environmental and Biological Engineering, Nanjing University of Science & Technology, Nanjing, 210094, China
| | - Sheng Yang
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China.,Huzhou Center of Industrial Biotechnology, Shanghai Institutes of Biological Sciences, Chinese Academy of Sciences, Zhejiang, 313000, China
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Bengelsdorf FR, Poehlein A, Flitsch SK, Linder S, Schiel-Bengelsdorf B, Stegmann BA, Krabben P, Green E, Zhang Y, Minton N, Dürre P. Host Organisms: Clostridium acetobutylicum/ Clostridium beijerinckiiand Related Organisms. Ind Biotechnol (New Rochelle N Y) 2016. [DOI: 10.1002/9783527807796.ch9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Affiliation(s)
- Frank R. Bengelsdorf
- Universität Ulm; Institut für Mikrobiologie und Biotechnologie; Albert-Einstein-Allee 11 89081 Ulm Germany
| | - Anja Poehlein
- Georg-August University; Genomic and Applied Microbiology and Göttingen Genomics Laboratory; Göttingen, Grisebachstr. 8 37077 Göttingen Germany
| | - Stefanie K. Flitsch
- Universität Ulm; Institut für Mikrobiologie und Biotechnologie; Albert-Einstein-Allee 11 89081 Ulm Germany
| | - Sonja Linder
- Universität Ulm; Institut für Mikrobiologie und Biotechnologie; Albert-Einstein-Allee 11 89081 Ulm Germany
| | - Bettina Schiel-Bengelsdorf
- Universität Ulm; Institut für Mikrobiologie und Biotechnologie; Albert-Einstein-Allee 11 89081 Ulm Germany
| | - Benjamin A. Stegmann
- Universität Ulm; Institut für Mikrobiologie und Biotechnologie; Albert-Einstein-Allee 11 89081 Ulm Germany
| | - Preben Krabben
- Green Biologics Limited; 45A Western Avenue, Milton Park Abingdon Oxfordshire OX14 4RU UK
| | - Edward Green
- CHAIN Biotechnology Limited; Imperial College Incubator, Imperial College London; Level 1 Bessemer Building London SW7 2AZ UK
| | - Ying Zhang
- University of Nottingham; BBSRC/EPSRC Synthetic Biology Research Centre (SBRC), School of Life Sciences; University Park Nottingham NG7 2RD UK
| | - Nigel Minton
- University of Nottingham; BBSRC/EPSRC Synthetic Biology Research Centre (SBRC), School of Life Sciences; University Park Nottingham NG7 2RD UK
| | - Peter Dürre
- Universität Ulm; Institut für Mikrobiologie und Biotechnologie; Albert-Einstein-Allee 11 89081 Ulm Germany
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Recent applications of metabolomics to advance microbial biofuel production. Curr Opin Biotechnol 2016; 43:118-126. [PMID: 27883952 DOI: 10.1016/j.copbio.2016.11.006] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2016] [Revised: 10/31/2016] [Accepted: 11/01/2016] [Indexed: 12/26/2022]
Abstract
Biofuel production from plant biomass is a promising source of renewable energy [1]. However, efficient biofuel production involves the complex task of engineering high-performance microorganisms, which requires detailed knowledge of metabolic function and regulation. This review highlights the potential of mass-spectrometry-based metabolomic analysis to guide rational engineering of biofuel-producing microbes. We discuss recent studies that apply knowledge gained from metabolomic analyses to increase the productivity of engineered pathways, characterize the metabolism of emerging biofuel producers, generate novel bioproducts, enable utilization of lignocellulosic feedstock, and improve the stress tolerance of biofuel producers.
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Ehsaan M, Kuit W, Zhang Y, Cartman ST, Heap JT, Winzer K, Minton NP. Mutant generation by allelic exchange and genome resequencing of the biobutanol organism Clostridium acetobutylicum ATCC 824. BIOTECHNOLOGY FOR BIOFUELS 2016; 9:4. [PMID: 26732067 PMCID: PMC4700727 DOI: 10.1186/s13068-015-0410-0] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2015] [Accepted: 12/04/2015] [Indexed: 05/28/2023]
Abstract
BACKGROUND Clostridium acetobutylicum represents a paradigm chassis for the industrial production of the biofuel biobutanol and a focus for metabolic engineering. We have previously developed procedures for the creation of in-frame, marker-less deletion mutants in the pathogen Clostridium difficile based on the use of pyrE and codA genes as counter selection markers. In the current study we sought to test their suitability for use in C. acetobutylicum. RESULTS Both systems readily allowed the isolation of in-frame deletions of the C. acetobutylicum ATCC 824 spo0A and the cac824I genes, leading to a sporulation minus phenotype and improved transformation, respectively. The pyrE-based system was additionally used to inactivate a putative glycogen synthase (CA_C2239, glgA) and the pSOL1 amylase gene (CA_P0168, amyP), leading to lack of production of granulose and amylase, respectively. Their isolation provided the opportunity to make use of one of the key pyrE system advantages, the ability to rapidly complement mutations at appropriate gene dosages in the genome. In both cases, their phenotypes were restored in terms of production of granulose (glgA) and amylase (amyP). Genome re-sequencing of the ATCC 824 COSMIC consortium laboratory strain used revealed the presence of 177 SNVs and 49 Indels, including a 4916-bp deletion in the pSOL1 megaplasmid. A total of 175 SNVs and 48 Indels were subsequently shown to be present in an 824 strain re-acquired (Nov 2011) from the ATCC and are, therefore, most likely errors in the published genome sequence, NC_003030 (chromosome) and NC_001988 (pSOL1). CONCLUSIONS The codA or pyrE counter selection markers appear equally effective in isolating deletion mutants, but there is considerable merit in using a pyrE mutant as the host as, through the use of ACE (Allele-Coupled Exchange) vectors, mutants created (by whatever means) can be rapidly complemented concomitant with restoration of the pyrE allele. This avoids the phenotypic effects frequently observed with high copy number plasmids and dispenses with the need to add antibiotic to ensure plasmid retention. Our study also revealed a surprising number of errors in the ATCC 824 genome sequence, while at the same time emphasising the need to re-sequence commonly used laboratory strains.
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Affiliation(s)
- Muhammad Ehsaan
- />Clostridia Research Group, BBSRC/EPSRC Synthetic Biology Research Centre (SBRC), University of Nottingham, University Park, Nottingham, NG7 2RD UK
| | - Wouter Kuit
- />Clostridia Research Group, BBSRC/EPSRC Synthetic Biology Research Centre (SBRC), University of Nottingham, University Park, Nottingham, NG7 2RD UK
- />MicCell Bioservices B.V., Edisonstraat 101, 7006 RB Doetinchem, The Netherlands
| | - Ying Zhang
- />Clostridia Research Group, BBSRC/EPSRC Synthetic Biology Research Centre (SBRC), University of Nottingham, University Park, Nottingham, NG7 2RD UK
| | - Stephen T. Cartman
- />Clostridia Research Group, BBSRC/EPSRC Synthetic Biology Research Centre (SBRC), University of Nottingham, University Park, Nottingham, NG7 2RD UK
- />Intermediates Sustainability, INVISTA Intermediates, Wilton Centre, Redcar, TS10 4RF UK
| | - John T. Heap
- />Clostridia Research Group, BBSRC/EPSRC Synthetic Biology Research Centre (SBRC), University of Nottingham, University Park, Nottingham, NG7 2RD UK
- />Department of Life Sciences, Centre for Synthetic Biology and Innovation, Imperial College London, South Kensington Campus, London, SW7 2AZ UK
| | - Klaus Winzer
- />Clostridia Research Group, BBSRC/EPSRC Synthetic Biology Research Centre (SBRC), University of Nottingham, University Park, Nottingham, NG7 2RD UK
| | - Nigel P. Minton
- />Clostridia Research Group, BBSRC/EPSRC Synthetic Biology Research Centre (SBRC), University of Nottingham, University Park, Nottingham, NG7 2RD UK
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Qu Y, Wu WT. Editorial: bioenergy and biorefinery - biological solution for sustainable development of human society. Biotechnol J 2015; 10:823-4. [PMID: 26047136 DOI: 10.1002/biot.201500291] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Yinbo Qu
- State Key Laboratory of Microbial Technology, Shandong University, China.
| | - Wen-Teng Wu
- Department of Chemical Engineering, National Cheng-Kung University, Taiwan.
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