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Jensen RO, Schulz F, Roux S, Klingeman DM, Mitchell WP, Udwary D, Moraïs S, Reynoso V, Winkler J, Nagaraju S, De Tissera S, Shapiro N, Ivanova N, Reddy TBK, Mizrahi I, Utturkar SM, Bayer EA, Woyke T, Mouncey NJ, Jewett MC, Simpson SD, Köpke M, Jones DT, Brown SD. Phylogenomics and genetic analysis of solvent-producing Clostridium species. Sci Data 2024; 11:432. [PMID: 38693191 PMCID: PMC11063209 DOI: 10.1038/s41597-024-03210-6] [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: 10/15/2023] [Accepted: 04/02/2024] [Indexed: 05/03/2024] Open
Abstract
The genus Clostridium is a large and diverse group within the Bacillota (formerly Firmicutes), whose members can encode useful complex traits such as solvent production, gas-fermentation, and lignocellulose breakdown. We describe 270 genome sequences of solventogenic clostridia from a comprehensive industrial strain collection assembled by Professor David Jones that includes 194 C. beijerinckii, 57 C. saccharobutylicum, 4 C. saccharoperbutylacetonicum, 5 C. butyricum, 7 C. acetobutylicum, and 3 C. tetanomorphum genomes. We report methods, analyses and characterization for phylogeny, key attributes, core biosynthetic genes, secondary metabolites, plasmids, prophage/CRISPR diversity, cellulosomes and quorum sensing for the 6 species. The expanded genomic data described here will facilitate engineering of solvent-producing clostridia as well as non-model microorganisms with innately desirable traits. Sequences could be applied in conventional platform biocatalysts such as yeast or Escherichia coli for enhanced chemical production. Recently, gene sequences from this collection were used to engineer Clostridium autoethanogenum, a gas-fermenting autotrophic acetogen, for continuous acetone or isopropanol production, as well as butanol, butanoic acid, hexanol and hexanoic acid production.
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Affiliation(s)
| | - Frederik Schulz
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Simon Roux
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | | | | | - Daniel Udwary
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Sarah Moraïs
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva, 84105, Israel
| | | | | | | | | | - Nicole Shapiro
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Natalia Ivanova
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - T B K Reddy
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Itzhak Mizrahi
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva, 84105, Israel
| | - Sagar M Utturkar
- Institute for Cancer Research, Purdue University, West Lafayette, IN, USA
| | - Edward A Bayer
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva, 84105, Israel
- Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Tanja Woyke
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- University of California Merced, Life and Environmental Sciences, Merced, CA, USA
| | - Nigel J Mouncey
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Michael C Jewett
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | | | | | - David T Jones
- Department of Microbiology, University of Otago, Dunedin, New Zealand.
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2
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Takahashi S, Hama T, Nogawa T, Ogawa N, Koshino H. Total Synthesis of Clostrienose. ACS OMEGA 2023; 8:35382-35392. [PMID: 37779990 PMCID: PMC10536848 DOI: 10.1021/acsomega.3c05277] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Accepted: 08/22/2023] [Indexed: 10/03/2023]
Abstract
This paper considers the total synthesis of a cellular differentiation regulator of Clostridium acetobutylicum, clostrienose, which is a unique fatty-acid glycosyl ester consisting of clostrienoic acid, (3R,5E,8E,10E)-3-hydroxy-tetradeca-5,8,10-trienoic acid and α-d-galactofuranosyl-(1 → 2)-α-l-rhamnose. The key features of our synthesis include stereoselective construction of a skipped-triene system in clostrienoic acid and its esterification with a disaccharide residue. The partially protected clostrienoic acid employed for the coupling also served for the preparation of l-rhamnosyl clostrienoate, thus leading to confirmation of the proposed structure unambiguously.
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Affiliation(s)
- Shunya Takahashi
- RIKEN
Center for Sustainable Resource Science, Wako, Saitama 351-0198, Japan
| | - Takenori Hama
- RIKEN
Center for Sustainable Resource Science, Wako, Saitama 351-0198, Japan
- Department
of Applied Chemistry, Meiji University, 1-1-1, Higashimita, Tama-ku, Kawasaki 214-8571, Japan
| | - Toshihiko Nogawa
- RIKEN
Center for Sustainable Resource Science, Wako, Saitama 351-0198, Japan
| | - Narihito Ogawa
- Department
of Applied Chemistry, Meiji University, 1-1-1, Higashimita, Tama-ku, Kawasaki 214-8571, Japan
| | - Hiroyuki Koshino
- RIKEN
Center for Sustainable Resource Science, Wako, Saitama 351-0198, Japan
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3
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Omorotionmwan BB, Wang H, Baker JP, Gizynski K, Yoo M, Akaluka C, Zhang Y, Minton NP. Chromosomal engineering of inducible isopropanol- butanol-ethanol production in Clostridium acetobutylicum. Front Bioeng Biotechnol 2023; 11:1218099. [PMID: 37397966 PMCID: PMC10312008 DOI: 10.3389/fbioe.2023.1218099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2023] [Accepted: 06/05/2023] [Indexed: 07/04/2023] Open
Abstract
The use of environmentally damaging petrochemical feedstocks can be displaced by fermentation processes based on engineered microbial chassis that recycle biomass-derived carbon into chemicals and fuels. The stable retention of introduced genes, designed to extend product range and/or increase productivity, is essential. Accordingly, we have created multiply marked auxotrophic strains of Clostridium acetobutylicum that provide distinct loci (pyrE, argH, purD, pheA) at which heterologous genes can be rapidly integrated using allele-coupled exchange (ACE). For each locus, ACE-mediated insertion is conveniently selected on the basis of the restoration of prototrophy on minimal media. The Clostridioides difficile gene (tcdR) encoding an orthogonal sigma factor (TcdR) was integrated at the pyrE locus under the control of the lactose-inducible, bgaR::PbgaL promoter to allow the simultaneous control of genes/operons inserted at other disparate loci (purD and pheA) that had been placed under the control of the PtcdB promoter. In control experiments, dose-dependent expression of a catP reporter gene was observed with increasing lactose concentration. At the highest doses tested (10 mM) the level of expression was over 10-fold higher than if catP was placed directly under the control of bgaR::PbgaL and over 2-fold greater than achieved using the strong Pfdx promoter of the Clostridium sporogenes ferredoxin gene. The utility of the system was demonstrated in the production of isopropanol by the C. acetobutylicum strain carrying an integrated copy of tcdR following the insertion of a synthetic acetone operon (ctfA/B, adc) at the purD locus and a gene (sadh) encoding a secondary dehydrogenase at pheA. Lactose induction (10 mM) resulted in the production of 4.4 g/L isopropanol and 19.8 g/L Isopropanol-Butanol-Ethanol mixture.
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Affiliation(s)
- Bunmi B. Omorotionmwan
- Clostridia Research Group, BBSRC/EPSRC Synthetic Biology Research Centre (SBRC), Biodiscovery Institute, School of Life Sciences, The University of Nottingham, Nottingham, United Kingdom
| | - Hengzheng Wang
- Clostridia Research Group, BBSRC/EPSRC Synthetic Biology Research Centre (SBRC), Biodiscovery Institute, School of Life Sciences, The University of Nottingham, Nottingham, United Kingdom
| | - Jonathan P. Baker
- Clostridia Research Group, BBSRC/EPSRC Synthetic Biology Research Centre (SBRC), Biodiscovery Institute, School of Life Sciences, The University of Nottingham, Nottingham, United Kingdom
| | - Krzysztof Gizynski
- Clostridia Research Group, BBSRC/EPSRC Synthetic Biology Research Centre (SBRC), Biodiscovery Institute, School of Life Sciences, The University of Nottingham, Nottingham, United Kingdom
| | - Minyeong Yoo
- Clostridia Research Group, BBSRC/EPSRC Synthetic Biology Research Centre (SBRC), Biodiscovery Institute, School of Life Sciences, The University of Nottingham, Nottingham, United Kingdom
| | - Cynthia Akaluka
- Clostridia Research Group, BBSRC/EPSRC Synthetic Biology Research Centre (SBRC), Biodiscovery Institute, School of Life Sciences, The University of Nottingham, Nottingham, United Kingdom
| | - Ying Zhang
- Clostridia Research Group, BBSRC/EPSRC Synthetic Biology Research Centre (SBRC), Biodiscovery Institute, School of Life Sciences, The University of Nottingham, Nottingham, United Kingdom
| | - Nigel P. Minton
- Clostridia Research Group, BBSRC/EPSRC Synthetic Biology Research Centre (SBRC), Biodiscovery Institute, School of Life Sciences, The University of Nottingham, Nottingham, United Kingdom
- NIHR Nottingham Biomedical Research Centre, Nottingham University Hospitals NHS Trust and the University of Nottingham, Nottingham, United Kingdom
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Humphreys JR, Bean Z, Twycross J, Winzer K. The Lanthipeptide Synthetase-like Protein CA_C0082 Is an Effector of Agr Quorum Sensing in Clostridium acetobutylicum. Microorganisms 2023; 11:1460. [PMID: 37374961 DOI: 10.3390/microorganisms11061460] [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: 05/05/2023] [Revised: 05/25/2023] [Accepted: 05/26/2023] [Indexed: 06/29/2023] Open
Abstract
Lanthipeptide synthetases are present in all domains of life. They catalyze a crucial step during lanthipeptide biosynthesis by introducing thioether linkages during posttranslational peptide modification. Lanthipeptides have a wide range of functions, including antimicrobial and morphogenetic activities. Intriguingly, several Clostridium species contain lanthipeptide synthetase-like genes of the class II (lanM) family but lack other components of the lanthipeptide biosynthetic machinery. In all instances, these genes are located immediately downstream of putative agr quorum sensing operons. The physiological role and mode of action of the encoded LanM-like proteins remain uncertain as they lack conserved catalytic residues. Here we show for the industrial organism Clostridium acetobutylicum that the LanM-like protein CA_C0082 is not required for the production of active AgrD-derived signaling peptide but nevertheless acts as an effector of Agr quorum sensing. Expression of CA_C0082 was shown to be controlled by the Agr system and is a prerequisite for granulose (storage polymer) formation. The accumulation of granulose, in turn, was shown to be required for maximal spore formation but also to reduce early solvent formation. CA_C0082 and its putative homologs appear to be closely associated with Agr systems predicted to employ signaling peptides with six-membered ring structures and may represent a new subfamily of LanM-like proteins. This is the first time their contribution to bacterial Agr signaling has been described.
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Affiliation(s)
- Jonathan R Humphreys
- BBSRC/EPSRC Synthetic Biology Research Centre (SBRC), School of Life Sciences, University Park, The University of Nottingham, Nottingham NG7 2RD, UK
| | - Zak Bean
- BBSRC/EPSRC Synthetic Biology Research Centre (SBRC), School of Life Sciences, University Park, The University of Nottingham, Nottingham NG7 2RD, UK
| | - Jamie Twycross
- School of Computer Science, Jubilee Campus, The University of Nottingham, Nottingham NG8 1BB, UK
| | - Klaus Winzer
- BBSRC/EPSRC Synthetic Biology Research Centre (SBRC), School of Life Sciences, University Park, The University of Nottingham, Nottingham NG7 2RD, UK
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5
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Jang YS, Kim WJ, Im JA, Palaniswamy S, Yao Z, Lee HL, Yoon YR, Seong HJ, Papoutsakis ET, Lee SY. Efforts to install a heterologous Wood-Ljungdahl pathway in Clostridium acetobutylicum enable the identification of the native tetrahydrofolate (THF) cycle and result in early induction of solvents. Metab Eng 2023; 77:188-198. [PMID: 37054966 DOI: 10.1016/j.ymben.2023.04.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2022] [Revised: 03/05/2023] [Accepted: 04/10/2023] [Indexed: 04/15/2023]
Abstract
Here, we report the construction of a Clostridium acetobutylicum strain ATCC 824 (pCD07239) by heterologous expression of carbonyl branch genes (CD630_0723∼CD630_0729) from Clostridium difficile, aimed at installing a heterologous Wood-Ljungdahl pathway (WLP). As part of this effort, in order to validate the methyl branch of the WLP in the C. acetobutylicum, we performed 13C-tracing analysis on knockdown mutants of four genes responsible for the formation of 5-methyl-tetrahydrofolate (5-methyl-THF) from formate: CA_C3201, CA_C2310, CA_C2083, and CA_C0291. While C. acetobutylicum 824 (pCD07239) could not grow autotrophically, in heterotrophic fermentation, it began producing butanol at the early growth phase (OD600 of 0.80; 0.162 g/L butanol). In contrast, solvent production in the parent strain did not begin until the early stationary phase (OD600 of 7.40). This study offers valuable insights for future research on biobutanol production during the early growth phase.
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Affiliation(s)
- Yu-Sin Jang
- Division of Applied Life Science (BK21 Four), Department of Applied Life Chemistry, Institute of Agriculture & Life Science (IALS), Gyeongsang National University (GNU), Jinju, 52828, Republic of Korea.
| | - Won Jun Kim
- Metabolic and Biomolecular Engineering National Research Laboratory, Department of Chemical and Biomolecular Engineering (BK21 Four Program), Institute for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea
| | - Jung Ae Im
- Metabolic and Biomolecular Engineering National Research Laboratory, Department of Chemical and Biomolecular Engineering (BK21 Four Program), Institute for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea
| | - Sampathkumar Palaniswamy
- Division of Applied Life Science (BK21 Four), Department of Applied Life Chemistry, Institute of Agriculture & Life Science (IALS), Gyeongsang National University (GNU), Jinju, 52828, Republic of Korea
| | - Zhuang Yao
- Division of Applied Life Science (BK21 Four), Department of Applied Life Chemistry, Institute of Agriculture & Life Science (IALS), Gyeongsang National University (GNU), Jinju, 52828, Republic of Korea
| | - Haeng Lim Lee
- Division of Applied Life Science (BK21 Four), Department of Applied Life Chemistry, Institute of Agriculture & Life Science (IALS), Gyeongsang National University (GNU), Jinju, 52828, Republic of Korea
| | - Ye Rin Yoon
- Division of Applied Life Science (BK21 Four), Department of Applied Life Chemistry, Institute of Agriculture & Life Science (IALS), Gyeongsang National University (GNU), Jinju, 52828, Republic of Korea
| | - Hyeon Jeong Seong
- Division of Applied Life Science (BK21 Four), Department of Applied Life Chemistry, Institute of Agriculture & Life Science (IALS), Gyeongsang National University (GNU), Jinju, 52828, Republic of Korea
| | - Eleftherios T Papoutsakis
- Delaware Biotechnology Institute, University of Delaware, 590 Avenue 1743, Newark, DE, 19713, USA; Department of Biological Sciences, University of Delaware, 118 Wolf Hall, Newark, DE, 19716, USA
| | - Sang Yup Lee
- Metabolic and Biomolecular Engineering National Research Laboratory, Department of Chemical and Biomolecular Engineering (BK21 Four Program), Institute for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea.
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6
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Ghosh D, Ghorai P, Sarkar S, Maiti KS, Hansda SR, Das P. Microbial assemblage for solid waste bioremediation and valorization with an essence of bioengineering. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:16797-16816. [PMID: 36595166 DOI: 10.1007/s11356-022-24849-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Accepted: 12/15/2022] [Indexed: 06/17/2023]
Abstract
Environmental solid waste bioremediation is a method of treating contaminated solid waste that involves changing ecological conditions to foster the growth of a broad spectrum of microorganisms and the destruction of the target contaminants. A wide range of microorganisms creates metabolites that may break down and change solid waste-based pollution to various value-added molecules. Diverse bioremediation technologies, their limitations, and the procedure involve recycling solid waste materials from the environment. The existing environmental solid waste disposal services are insufficient and must be upgraded with more lucrative recovery, recycling, and reuse technologies to decrease the enormous expenditures in treatment procedures. Bioremediation of solid waste eliminates the toxic components. It restores the site with the advent of potential microbial communities towards solid waste valorization utilizing agriculture solid waste, organic food waste, plastic solid waste, and multiple industrial solid wastes.Bioengineering on diverse ranges of microbial regimes has accelerated to provide extra momentum toward solid waste recycling and valorization. This approach increases the activity of bioremediating microbes in the commercial development of waste treatment techniques and increases the cost-effective valuable product generation. This framework facilitates collaboration between solid waste and utilities. It can aid in establishing a long-term management strategy for recycling development with the advent of a broad spectrum of potential microbial assemblages, increasing solid waste contamination tolerance efficiency and solid waste degradability. The current literature survey extensively summarises solid waste remediation valorization using a broad spectrum of microbial assemblages with special emphasis on bioengineering-based acceleration. This approach is to attain sustainable environmental management and value-added biomolecule generation.
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Affiliation(s)
- Dipankar Ghosh
- Microbial Engineering & Algal Biotechnology Laboratory, Department of Biosciences, JIS University, Kolkata, 700109, India.
| | - Palash Ghorai
- Microbial Engineering & Algal Biotechnology Laboratory, Department of Biosciences, JIS University, Kolkata, 700109, India
| | - Soumita Sarkar
- Microbial Engineering & Algal Biotechnology Laboratory, Department of Biosciences, JIS University, Kolkata, 700109, India
| | - Kumar Sagar Maiti
- Microbial Engineering & Algal Biotechnology Laboratory, Department of Biosciences, JIS University, Kolkata, 700109, India
| | - Serma Rimil Hansda
- Microbial Engineering & Algal Biotechnology Laboratory, Department of Biosciences, JIS University, Kolkata, 700109, India
| | - Parna Das
- Microbial Engineering & Algal Biotechnology Laboratory, Department of Biosciences, JIS University, Kolkata, 700109, India
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7
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Identification of serine/threonine kinases that regulate metabolism and sporulation in Clostridium beijerinckii. Appl Microbiol Biotechnol 2022; 106:7563-7575. [DOI: 10.1007/s00253-022-12234-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2022] [Revised: 09/17/2022] [Accepted: 10/07/2022] [Indexed: 11/02/2022]
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8
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De Wannemaeker L, Bervoets I, De Mey M. Unlocking the bacterial domain for industrial biotechnology applications using universal parts and tools. Biotechnol Adv 2022; 60:108028. [PMID: 36031082 DOI: 10.1016/j.biotechadv.2022.108028] [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: 03/10/2022] [Revised: 07/29/2022] [Accepted: 08/16/2022] [Indexed: 11/02/2022]
Abstract
Synthetic biology can play a major role in the development of sustainable industrial biotechnology processes. However, the development of economically viable production processes is currently hampered by the limited availability of host organisms that can be engineered for a specific production process. To date, standard hosts such as Escherichia coli and Saccharomyces cerevisiae are often used as starting points for process development since parts and tools allowing their engineering are readily available. However, their suboptimal metabolic background or impaired performance at industrial scale for a desired production process, can result in increased costs associated with process development and/or disappointing production titres. Building a universal and portable gene expression system allowing genetic engineering of hosts across the bacterial domain would unlock the bacterial domain for industrial biotechnology applications in a highly standardized manner and doing so, render industrial biotechnology processes more competitive compared to the current polluting chemical processes. This review gives an overview of a selection of bacterial hosts highly interesting for industrial biotechnology based on both their metabolic and process optimization properties. Moreover, the requirements and progress made so far to enable universal, standardized, and portable gene expression across the bacterial domain is discussed.
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Affiliation(s)
- Lien De Wannemaeker
- Centre for Synthetic Biology (CSB), Ghent University, Coupure links 653, 9000 Ghent, Belgium
| | - Indra Bervoets
- Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium
| | - Marjan De Mey
- Centre for Synthetic Biology (CSB), Ghent University, Coupure links 653, 9000 Ghent, Belgium.
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9
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Liu D, Ge S, Wang Z, Li M, Zhuang W, Yang P, Chen Y, Ying H. Identification of a sensor histidine kinase (BfcK) controlling biofilm formation in Clostridium acetobutylicum. Chin J Chem Eng 2022. [DOI: 10.1016/j.cjche.2021.04.024] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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10
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Oh HJ, Ko JK, Gong G, Lee SM, Um Y. Production of Hexanol as the Main Product Through Syngas Fermentation by Clostridium carboxidivorans P7. Front Bioeng Biotechnol 2022; 10:850370. [PMID: 35547160 PMCID: PMC9081523 DOI: 10.3389/fbioe.2022.850370] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Accepted: 04/04/2022] [Indexed: 11/24/2022] Open
Abstract
The production of hexanol from syngas by acetogens has gained attention as a replacement for petroleum-derived hexanol, which is widely used in the chemical synthesis and plastic industries. However, acetogenic bacteria generally produce C2 compounds (e.g., acetate and ethanol) as the main products. In this study, the gas fermentation conditions favorable for hexanol production were investigated at different temperatures (30-37°C) and CO gas contents (30-70%) in batch gas fermentation. Hexanol production increased from 0.02 to 0.09 g/L when the cultivation temperature was lowered from 37 to 30°C. As the CO content increased from 30 to 70%, the CO consumption rate and hexanol production (yield, titer, and ratio of C6 compound to total products) increased with the CO content. When 70% CO gas was repeatedly provided by flushing the headspace of the bottles at 30°C, the total alcohol production increased to 4.32 g/L at the expense of acids. Notably, hexanol production (1.90 g/L) was higher than that of ethanol (1.20 g/L) and butanol (1.20 g/L); this is the highest level of hexanol produced in gas fermentation to date and the first report of hexanol as the main product. Hexanol production was further enhanced to 2.34 g/L when 2 g/L ethanol was supplemented at the beginning of 70% CO gas refeeding fermentation. Particularly, hexanol productivity was significantly enhanced to 0.18 g/L/day while the supplemented ethanol was consumed, indicating that the conversion of ethanol to acetyl-CoA and reducing equivalents positively affected hexanol production. These optimized culture conditions (gas fermentation at 30°C and refeeding with 70% CO gas) and ethanol supplementation provide an effective and sustainable approach for bio-hexanol production.
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Affiliation(s)
- Hyun Ju Oh
- Clean Energy Research Center, Korea Institute of Science and Technology, Seoul, South Korea
| | - Ja Kyong Ko
- Clean Energy Research Center, Korea Institute of Science and Technology, Seoul, South Korea
- Division of Energy and Environment Technology, KIST School, University of Science and Technology (UST), Daejeon, South Korea
| | - Gyeongtaek Gong
- Clean Energy Research Center, Korea Institute of Science and Technology, Seoul, South Korea
- Division of Energy and Environment Technology, KIST School, University of Science and Technology (UST), Daejeon, South Korea
| | - Sun-Mi Lee
- Clean Energy Research Center, Korea Institute of Science and Technology, Seoul, South Korea
- Division of Energy and Environment Technology, KIST School, University of Science and Technology (UST), Daejeon, South Korea
| | - Youngsoon Um
- Clean Energy Research Center, Korea Institute of Science and Technology, Seoul, South Korea
- Division of Energy and Environment Technology, KIST School, University of Science and Technology (UST), Daejeon, South Korea
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11
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Chen A, Jiang Z, Burkart MD. Enzymology of standalone elongating ketosynthases. Chem Sci 2022; 13:4225-4238. [PMID: 35509474 PMCID: PMC9006962 DOI: 10.1039/d1sc07256k] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Accepted: 03/09/2022] [Indexed: 12/16/2022] Open
Abstract
The β-ketoacyl-acyl carrier protein synthase, or ketosynthase (KS), catalyses carbon-carbon bond formation in fatty acid and polyketide biosynthesis via a decarboxylative Claisen-like condensation. In prokaryotes, standalone elongating KSs interact with the acyl carrier protein (ACP) which shuttles substrates to each partner enzyme in the elongation cycle for catalysis. Despite ongoing research for more than 50 years since KS was first identified in E. coli, the complex mechanism of KSs continues to be unravelled, including recent understanding of gating motifs, KS-ACP interactions, substrate recognition and delivery, and roles in unsaturated fatty acid biosynthesis. In this review, we summarize the latest studies, primarily conducted through structural biology and molecular probe design, that shed light on the emerging enzymology of standalone elongating KSs.
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Affiliation(s)
- Aochiu Chen
- Department of Chemistry and Biochemistry, University of California, San Diego 9500 Gilman Drive La Jolla CA 92093-0358 USA
| | - Ziran Jiang
- Department of Chemistry and Biochemistry, University of California, San Diego 9500 Gilman Drive La Jolla CA 92093-0358 USA
| | - Michael D Burkart
- Department of Chemistry and Biochemistry, University of California, San Diego 9500 Gilman Drive La Jolla CA 92093-0358 USA
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12
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Patidar P, Prakash T. Decoding the roles of extremophilic microbes in the anaerobic environments: Past, Present, and Future. CURRENT RESEARCH IN MICROBIAL SCIENCES 2022; 3:100146. [PMID: 35909618 PMCID: PMC9325894 DOI: 10.1016/j.crmicr.2022.100146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Revised: 06/11/2022] [Accepted: 06/13/2022] [Indexed: 12/03/2022] Open
Abstract
The inaccessible extreme environments harbor a large majority of anaerobic microbes which remain unknown. Anaerobic microbes are used in a variety of industrial applications. In the future, metagenomic-assisted techniques can be used to identify novel anaerobic microbes from the unexplored extreme environments. Genetic engineering can be used to enhance the efficiency of anaerobic microbes for various processes.
The genome of an organism is directly or indirectly correlated with its environment. Consequently, different microbes have evolved to survive and sustain themselves in a variety of environments, including unusual anaerobic environments. It is believed that their genetic material could have played an important role in the early evolution of their existence in the past. Presently, out of the uncountable number of microbes found in different ecosystems we have been able to discover only one percent of the total communities. A large majority of the microbial populations exists in the most unusual and extreme environments. For instance, many anaerobic bacteria are found in the gastrointestinal tract of humans, soil, and hydrothermal vents. The recent advancements in Metagenomics and Next Generation Sequencing technologies have improved the understanding of their roles in these environments. Presently, anaerobic bacteria are used in various industries associated with biofuels, fermentation, production of enzymes, vaccines, vitamins, and dairy products. This broad applicability brings focus to the significant contribution of their genomes in these functions. Although the anaerobic microbes have become an irreplaceable component of our lives, a major and important section of such anaerobic microbes still remain unexplored. Therefore, it can be said that unlocking the role of the microbial genomes of the anaerobes can be a noteworthy discovery not just for mankind but for the entire biosystem as well.
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Affiliation(s)
- Pratyusha Patidar
- School of Basic Sciences, Indian Institute of Technology (IIT) Mandi, HP, India
| | - Tulika Prakash
- School of Basic Sciences, Indian Institute of Technology (IIT) Mandi, HP, India
- Corresponding author.
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13
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Patakova P, Branska B, Vasylkivska M, Jureckova K, Musilova J, Provaznik I, Sedlar K. Transcriptomic studies of solventogenic clostridia, Clostridium acetobutylicum and Clostridium beijerinckii. Biotechnol Adv 2021; 58:107889. [PMID: 34929313 DOI: 10.1016/j.biotechadv.2021.107889] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Revised: 12/10/2021] [Accepted: 12/14/2021] [Indexed: 12/13/2022]
Abstract
Solventogenic clostridia are not a strictly defined group within the genus Clostridium but its representatives share some common features, i.e. they are anaerobic, non-pathogenic, non-toxinogenic and endospore forming bacteria. Their main metabolite is typically 1-butanol but depending on species and culture conditions, they can form other metabolites such as acetone, isopropanol, ethanol, butyric, lactic and acetic acids, and hydrogen. Although these organisms were previously used for the industrial production of solvents, they later fell into disuse, being replaced by more efficient chemical production. A return to a more biological production of solvents therefore requires a thorough understanding of clostridial metabolism. Transcriptome analysis, which reflects the involvement of individual genes in all cellular processes within a population, at any given (sampling) moment, is a valuable tool for gaining a deeper insight into clostridial life. In this review, we describe techniques to study transcription, summarize the evolution of these techniques and compare methods for data processing and visualization of solventogenic clostridia, particularly the species Clostridium acetobutylicum and Clostridium beijerinckii. Individual approaches for evaluating transcriptomic data are compared and their contributions to advancements in the field are assessed. Moreover, utilization of transcriptomic data for reconstruction of computational clostridial metabolic models is considered and particular models are described. Transcriptional changes in glucose transport, central carbon metabolism, the sporulation cycle, butanol and butyrate stress responses, the influence of lignocellulose-derived inhibitors on growth and solvent production, and other respective topics, are addressed and common trends are highlighted.
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Affiliation(s)
- Petra Patakova
- University of Chemistry and Technology Prague, Technicka 5, 16628 Prague 6, Czech Republic.
| | - Barbora Branska
- University of Chemistry and Technology Prague, Technicka 5, 16628 Prague 6, Czech Republic
| | - Maryna Vasylkivska
- University of Chemistry and Technology Prague, Technicka 5, 16628 Prague 6, Czech Republic
| | | | - Jana Musilova
- Brno University of Technology, Technicka 10, 61600 Brno, Czech Republic
| | - Ivo Provaznik
- Brno University of Technology, Technicka 10, 61600 Brno, Czech Republic
| | - Karel Sedlar
- Brno University of Technology, Technicka 10, 61600 Brno, Czech Republic
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14
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Rivas-Astroza M, Paredes I, Guerrero K, Mau S, Quintero J, Gentina JC, Conejeros R, Aroca G. Kinetic model of Clostridium beijerinckii's Acetone-Butanol-Ethanol fermentation considering metabolically diverse cell types. J Biotechnol 2021; 342:1-12. [PMID: 34648892 DOI: 10.1016/j.jbiotec.2021.09.021] [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: 05/23/2021] [Revised: 09/26/2021] [Accepted: 09/29/2021] [Indexed: 11/16/2022]
Abstract
Clostridium beijerinckii population branches into metabolically diverse cell types in batch cultures. Here, we present a new kinetic model of C. beijerinckii's Acetone-Butanol-Ethanol fermentation that considers three cell types: producers of acids (acidogenic), consumer of acids and producers of solvents (solventogenic), and spores cells. The model accurately recapitulates batch culture data. Also, the model estimates cell type-specific kinetic parameters, which can be helpful to improve the operation of the ABE fermentation and give a framework to study acidogenic and solventogenic metabolic pathways. To exemplify the latter, we used a constraint-based model to study how the ABE pathways are used among acidogenic and solventogenic cell types. We found that among both cell types, glycolytic production of ATP and consumption of NAD+ varies widely during the fermentation, with their maximum production/consumption rates happening when acidogenic and solventogenic growth rates were at their highest. However, acidogenic cells use the ABE pathway to contribute with an extra 12.5% of the total production of ATP, whereas solventogenic cell types use the ABE pathway to supply more than 75% of the demand for NAD+, alternating between the production of lactate and butyrate, being both coupled to the production of NAD+.
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Affiliation(s)
- Marcelo Rivas-Astroza
- Escuela de Ingeniería Bioquímica, Pontificia Universidad Católica de Valparaíso, Av. Brasil 2085, Valparaíso, Chile.
| | - Iván Paredes
- Escuela de Ingeniería Bioquímica, Pontificia Universidad Católica de Valparaíso, Av. Brasil 2085, Valparaíso, Chile
| | - Karlo Guerrero
- Escuela de Ingeniería Bioquímica, Pontificia Universidad Católica de Valparaíso, Av. Brasil 2085, Valparaíso, Chile
| | - Silvia Mau
- Escuela de Ingeniería Bioquímica, Pontificia Universidad Católica de Valparaíso, Av. Brasil 2085, Valparaíso, Chile
| | - Julián Quintero
- Escuela de Ingeniería Bioquímica, Pontificia Universidad Católica de Valparaíso, Av. Brasil 2085, Valparaíso, Chile
| | - Juan Carlos Gentina
- Escuela de Ingeniería Bioquímica, Pontificia Universidad Católica de Valparaíso, Av. Brasil 2085, Valparaíso, Chile
| | - Raúl Conejeros
- Escuela de Ingeniería Bioquímica, Pontificia Universidad Católica de Valparaíso, Av. Brasil 2085, Valparaíso, Chile
| | - Germán Aroca
- Escuela de Ingeniería Bioquímica, Pontificia Universidad Católica de Valparaíso, Av. Brasil 2085, Valparaíso, Chile
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15
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Scherlach K, Hertweck C. Mining and unearthing hidden biosynthetic potential. Nat Commun 2021; 12:3864. [PMID: 34162873 PMCID: PMC8222398 DOI: 10.1038/s41467-021-24133-5] [Citation(s) in RCA: 107] [Impact Index Per Article: 35.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Accepted: 06/04/2021] [Indexed: 12/11/2022] Open
Abstract
Genetically encoded small molecules (secondary metabolites) play eminent roles in ecological interactions, as pathogenicity factors and as drug leads. Yet, these chemical mediators often evade detection, and the discovery of novel entities is hampered by low production and high rediscovery rates. These limitations may be addressed by genome mining for biosynthetic gene clusters, thereby unveiling cryptic metabolic potential. The development of sophisticated data mining methods and genetic and analytical tools has enabled the discovery of an impressive array of previously overlooked natural products. This review shows the newest developments in the field, highlighting compound discovery from unconventional sources and microbiomes. Natural products are an important source of bioactive compounds and have versatile applications in different fields, but their discovery is challenging. Here, the authors review the recent developments in genome mining for discovery of natural products, focusing on compounds from unconventional microorganisms and microbiomes.
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Affiliation(s)
- Kirstin Scherlach
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology, HKI, Jena, Germany
| | - Christian Hertweck
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology, HKI, Jena, Germany. .,Faculty of Biological Sciences, Friedrich Schiller University Jena, Jena, Germany.
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16
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Diallo M, Kengen SWM, López-Contreras AM. Sporulation in solventogenic and acetogenic clostridia. Appl Microbiol Biotechnol 2021; 105:3533-3557. [PMID: 33900426 PMCID: PMC8102284 DOI: 10.1007/s00253-021-11289-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 04/03/2021] [Accepted: 04/07/2021] [Indexed: 02/07/2023]
Abstract
The Clostridium genus harbors compelling organisms for biotechnological production processes; while acetogenic clostridia can fix C1-compounds to produce acetate and ethanol, solventogenic clostridia can utilize a wide range of carbon sources to produce commercially valuable carboxylic acids, alcohols, and ketones by fermentation. Despite their potential, the conversion by these bacteria of carbohydrates or C1 compounds to alcohols is not cost-effective enough to result in economically viable processes. Engineering solventogenic clostridia by impairing sporulation is one of the investigated approaches to improve solvent productivity. Sporulation is a cell differentiation process triggered in bacteria in response to exposure to environmental stressors. The generated spores are metabolically inactive but resistant to harsh conditions (UV, chemicals, heat, oxygen). In Firmicutes, sporulation has been mainly studied in bacilli and pathogenic clostridia, and our knowledge of sporulation in solvent-producing or acetogenic clostridia is limited. Still, sporulation is an integral part of the cellular physiology of clostridia; thus, understanding the regulation of sporulation and its connection to solvent production may give clues to improve the performance of solventogenic clostridia. This review aims to provide an overview of the triggers, characteristics, and regulatory mechanism of sporulation in solventogenic clostridia. Those are further compared to the current knowledge on sporulation in the industrially relevant acetogenic clostridia. Finally, the potential applications of spores for process improvement are discussed.Key Points• The regulatory network governing sporulation initiation varies in solventogenic clostridia.• Media composition and cell density are the main triggers of sporulation.• Spores can be used to improve the fermentation process.
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Affiliation(s)
- Mamou Diallo
- Wageningen Food and Biobased Research, Wageningen, The Netherlands.
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, The Netherlands.
| | - Servé W M Kengen
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, The Netherlands
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17
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Zheng Z, Cai Y, Zhang Y, Zhao Y, Gao Y, Cui Z, Hu Y, Wang X. The effects of C/N (10-25) on the relationship of substrates, metabolites, and microorganisms in "inhibited steady-state" of anaerobic digestion. WATER RESEARCH 2021; 188:116466. [PMID: 33027695 DOI: 10.1016/j.watres.2020.116466] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Revised: 09/04/2020] [Accepted: 09/24/2020] [Indexed: 06/11/2023]
Abstract
The carbon/nitrogen ratio (C/N) is a key parameter that affects the performance of anaerobic digestion (AD). Recent AD research has focused on optimizing the C/N of feedstock. The so-called "inhibited steady-state" refers to a special state of ammonia inhibition of AD that often occurs at low-C/N (below 25) when degradable nitrogen-rich substrates, such as livestock manure, are used as feedstock. However, the mechanism behind the "inhibited steady-state" is still unknown. In the current study, co-digestion and recirculation were used to create a C/N gradient in the influent to explore the relationship between substrates, metabolites, and microorganisms in the "inhibited steady-state." Data were collected at the macro, microbial, and genetic levels. Three CSTRs were successfully made run into the "inhibited steady-state" using influent C/Ns of 10-12. Digestion performance levels of R10-R12 were low and stable, transitioning from an aceticlastic methane-producing pathway to a hydrogenotrophic pathway as the C/N gradually decreased. As the abundance of the hydrogenophilic methanogens increased, the abundance of syntrophic acetate-oxidizing bacteria (SAOB) also increased. The succession between populations of Methanosaeta and Methanosarcina may be used as a microbiological indicator of ammonia inhibition. Under high-C/Ns, cooperation among bacteria was high, while under low-C/Ns, competition among bacteria was high. These results clarify the processes underlying the "inhibited steady-state," which is a condition often faced in actual large-scale biogas facilities that use degradable nitrogen-rich substrates. Moreover, practical guidelines for evaluating ammonia inhibition are provided, and strategies to alleviate ammonia suppression are developed.
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Affiliation(s)
- Zehui Zheng
- College of Agronomy and Biotechnology/Biomass Engineering Center, China Agricultural University, Beijing 100193, China
| | - Yafan Cai
- Department of Biochemical conversion, Deutsches Biomassforschungszentrum gemeinnütziges GmbH, Torgauer Straße116, 04347 Leipzig, Germany.
| | - Yue Zhang
- College of Agronomy and Biotechnology/Biomass Engineering Center, China Agricultural University, Beijing 100193, China
| | - Yubin Zhao
- College of Agronomy and Biotechnology/Biomass Engineering Center, China Agricultural University, Beijing 100193, China
| | - Youhui Gao
- College of Agronomy and Biotechnology/Biomass Engineering Center, China Agricultural University, Beijing 100193, China
| | - Zongjun Cui
- College of Agronomy and Biotechnology/Biomass Engineering Center, China Agricultural University, Beijing 100193, China
| | - Yuegao Hu
- College of Agronomy and Biotechnology/Biomass Engineering Center, China Agricultural University, Beijing 100193, China
| | - Xiaofen Wang
- College of Agronomy and Biotechnology/Biomass Engineering Center, China Agricultural University, Beijing 100193, China.
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18
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Patakova P, Kolek J, Jureckova K, Branska B, Sedlar K, Vasylkivska M, Provaznik I. Deeper below the surface-transcriptional changes in selected genes of Clostridium beijerinckii in response to butanol shock. Microbiologyopen 2020; 10:e1146. [PMID: 33319506 PMCID: PMC7884928 DOI: 10.1002/mbo3.1146] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 11/27/2020] [Accepted: 11/30/2020] [Indexed: 01/04/2023] Open
Abstract
The main bottleneck in the return of industrial butanol production from renewable feedstock through acetone–butanol–ethanol (ABE) fermentation by clostridia, such as Clostridium beijerinckii, is the low final butanol concentration. The problem is caused by the high toxicity of butanol to the production cells, and therefore, understanding the mechanisms by which clostridia react to butanol shock is of key importance. Detailed analyses of transcriptome data that were obtained after butanol shock and their comparison with data from standard ABE fermentation have resulted in new findings, while confirmed expected population responses. Although butanol shock resulted in upregulation of heat shock protein genes, their regulation is different than was assumed based on standard ABE fermentation transcriptome data. While glucose uptake, glycolysis, and acidogenesis genes were downregulated after butanol shock, solventogenesis genes were upregulated. Cyclopropanation of fatty acids and formation of plasmalogens seem to be significant processes involved in cell membrane stabilization in the presence of butanol. Surprisingly, one of the three identified Agr quorum‐sensing system genes was upregulated. Upregulation of several putative butanol efflux pumps was described after butanol addition and a large putative polyketide gene cluster was found, the transcription of which seemed to depend on the concentration of butanol.
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Affiliation(s)
- Petra Patakova
- Department of Biotechnology, University of Chemistry and Technology Prague, Prague, Czech Republic
| | - Jan Kolek
- Department of Biotechnology, University of Chemistry and Technology Prague, Prague, Czech Republic
| | - Katerina Jureckova
- Department of Biomedical Engineering, Brno University of Technology, Brno, Czech Republic
| | - Barbora Branska
- Department of Biotechnology, University of Chemistry and Technology Prague, Prague, Czech Republic
| | - Karel Sedlar
- Department of Biomedical Engineering, Brno University of Technology, Brno, Czech Republic
| | - Maryna Vasylkivska
- Department of Biotechnology, University of Chemistry and Technology Prague, Prague, Czech Republic
| | - Ivo Provaznik
- Department of Biomedical Engineering, Brno University of Technology, Brno, Czech Republic
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19
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Neuwirth T, Letzel AC, Tank C, Ishida K, Cyrulies M, Schmölz L, Lorkowski S, Hertweck C. Induced Production, Synthesis, and Immunomodulatory Action of Clostrisulfone, a Diarylsulfone from Clostridium acetobutylicum. Chemistry 2020; 26:15855-15858. [PMID: 32996646 PMCID: PMC7756337 DOI: 10.1002/chem.202003500] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Revised: 09/29/2020] [Indexed: 01/25/2023]
Abstract
The anaerobe Clostridium acetobutylicum belongs to the most important industrially used bacteria. Whereas genome mining points to a high potential for secondary metabolism in C. acetobutylicum, the functions of most biosynthetic gene clusters are cryptic. We report that the addition of supra‐physiological concentrations of cysteine triggered the formation of a novel natural product, clostrisulfone (1). Its structure was fully elucidated by NMR, MS and the chemical synthesis of a reference compound. Clostrisulfone is the first reported natural product with a diphenylsulfone scaffold. A biomimetic synthesis suggests that pentamethylchromanol‐derived radicals capture sulfur dioxide to form 1. In a cell‐based assay using murine macrophages a biphasic and dose‐dependent regulation of the LPS‐induced release of nitric oxide was observed in the presence of 1.
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Affiliation(s)
- Toni Neuwirth
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Chemistry and Infection Biology (HKI), Beutenbergstr. 11a, 07745, Jena, Germany
| | - Anne-Catrin Letzel
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Chemistry and Infection Biology (HKI), Beutenbergstr. 11a, 07745, Jena, Germany
| | - Cedric Tank
- BioPilotPlant, Leibniz Institute for Natural Product Chemistry and Infection Biology (HKI), Beutenbergstr. 11a, 07745, Jena, Germany
| | - Keishi Ishida
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Chemistry and Infection Biology (HKI), Beutenbergstr. 11a, 07745, Jena, Germany
| | - Michael Cyrulies
- BioPilotPlant, Leibniz Institute for Natural Product Chemistry and Infection Biology (HKI), Beutenbergstr. 11a, 07745, Jena, Germany
| | - Lisa Schmölz
- Institute of Nutritional Sciences, Friedrich Schiller University Jena, Dornburger Straße 25, 07743, Jena, Germany
| | - Stefan Lorkowski
- Institute of Nutritional Sciences, Friedrich Schiller University Jena, Dornburger Straße 25, 07743, Jena, Germany
| | - Christian Hertweck
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Chemistry and Infection Biology (HKI), Beutenbergstr. 11a, 07745, Jena, Germany.,Faculty of Biological Sciences, Friedrich Schiller University Jena, 07743, Jena, Germany
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20
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Li JS, Du Y, Gu D, Cai W, Green A, Ng S, Leung A, Del Rio Flores A, Zhang W. Discovery and Biosynthesis of Clostyrylpyrones from the Obligate Anaerobe Clostridium roseum. Org Lett 2020; 22:8204-8209. [PMID: 33052676 DOI: 10.1021/acs.orglett.0c02656] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Anaerobic bacteria are a promising new source for natural product discovery. Examination of extracts from the obligate anaerobe Clostridium roseum led to the discovery of a new family of natural products, the clostyrylpyrones. The polyketide synthase-based biosynthetic mechanism of clostyrylpyrones is further proposed on the basis of bioinformatic, gene knockout, biochemical analysis, and heterologous expression studies.
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Affiliation(s)
- Jeffrey S Li
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, California 94720, United States
| | - Yongle Du
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, California 94720, United States
| | - Di Gu
- Department of Chemistry, University of California, Berkeley, California 94720, United States
| | - Wenlong Cai
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, California 94720, United States
| | - Allison Green
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, California 94720, United States
| | - Samuel Ng
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, California 94720, United States
| | - Alexander Leung
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, California 94720, United States
| | - Antonio Del Rio Flores
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, California 94720, United States
| | - Wenjun Zhang
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, California 94720, United States.,Chan Zuckerberg Biohub, San Francisco, California 94158, United States
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21
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Diallo M, Kint N, Monot M, Collas F, Martin-Verstraete I, van der Oost J, Kengen SWM, López-Contreras AM. Transcriptomic and Phenotypic Analysis of a spoIIE Mutant in Clostridium beijerinckii. Front Microbiol 2020; 11:556064. [PMID: 33042064 PMCID: PMC7522474 DOI: 10.3389/fmicb.2020.556064] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Accepted: 08/20/2020] [Indexed: 11/26/2022] Open
Abstract
SpoIIE is a phosphatase involved in the activation of the first sigma factor of the forespore, σ F , during sporulation. A ΔspoIIE mutant of Clostridium beijerinckii NCIMB 8052, previously generated by CRISPR-Cas9, did not sporulate but still produced granulose and solvents. Microscopy analysis also showed that the cells of the ΔspoIIE mutant are elongated with the presence of multiple septa. This observation suggests that in C. beijerinckii, SpoIIE is necessary for the completion of the sporulation process, as seen in Bacillus and Clostridium acetobutylicum. Moreover, when grown in reactors, the spoIIE mutant produced higher levels of solvents than the wild type strain. The impact of the spoIIE inactivation on gene transcription was assessed by comparative transcriptome analysis at three time points (4 h, 11 h and 23 h). Approximately 5% of the genes were differentially expressed in the mutant compared to the wild type strain at all time points. Out of those only 12% were known sporulation genes. As expected, the genes belonging to the regulon of the sporulation specific transcription factors (σ F , σ E , σ G , σ K ) were strongly down-regulated in the mutant. Inactivation of spoIIE also caused differential expression of genes involved in various cell processes at each time point. Moreover, at 23 h, genes involved in butanol formation and tolerance, as well as in cell motility, were up-regulated in the mutant. In contrast, several genes involved in cell wall composition, oxidative stress and amino acid transport were down-regulated. These results indicate an intricate interdependence of sporulation and stationary phase cellular events in C. beijerinckii.
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Affiliation(s)
- Mamou Diallo
- Wageningen Food and Biobased Research, Wageningen, Netherlands
- Laboratory of Microbiology, Wageningen University, Wageningen, Netherlands
| | - Nicolas Kint
- Laboratoire Pathogènese des Bactéries Anaérobies, Institut Pasteur, UMR CNRS 2001, Université de Paris, Paris, France
| | - Marc Monot
- Biomics platform, C2RT, Institut Pasteur, Paris, France
| | - Florent Collas
- Wageningen Food and Biobased Research, Wageningen, Netherlands
| | - Isabelle Martin-Verstraete
- Laboratoire Pathogènese des Bactéries Anaérobies, Institut Pasteur, UMR CNRS 2001, Université de Paris, Paris, France
- Institut Universitaire de France, Paris, France
| | - John van der Oost
- Laboratory of Microbiology, Wageningen University, Wageningen, Netherlands
| | - Servé W. M. Kengen
- Laboratory of Microbiology, Wageningen University, Wageningen, Netherlands
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22
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Abdelrazig S, Safo L, Rance GA, Fay MW, Theodosiou E, Topham PD, Kim DH, Fernández-Castané A. Metabolic characterisation of Magnetospirillum gryphiswaldense MSR-1 using LC-MS-based metabolite profiling. RSC Adv 2020; 10:32548-32560. [PMID: 35516490 PMCID: PMC9056635 DOI: 10.1039/d0ra05326k] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Accepted: 08/23/2020] [Indexed: 12/21/2022] Open
Abstract
Magnetosomes are nano-sized magnetic nanoparticles with exquisite properties that can be used in a wide range of healthcare and biotechnological applications. They are biosynthesised by magnetotactic bacteria (MTB), such as Magnetospirillum gryphiswaldense MSR-1 (Mgryph). However, magnetosome bioprocessing yields low quantities compared to chemical synthesis of magnetic nanoparticles. Therefore, an understanding of the intracellular metabolites and metabolic networks related to Mgryph growth and magnetosome formation are vital to unlock the potential of this organism to develop improved bioprocesses. In this work, we investigated the metabolism of Mgryph using untargeted metabolomics. Liquid chromatography-mass spectrometry (LC-MS) was performed to profile spent medium samples of Mgryph cells grown under O2-limited (n = 6) and O2-rich conditions (n = 6) corresponding to magnetosome- and non-magnetosome producing cells, respectively. Multivariate, univariate and pathway enrichment analyses were conducted to identify significantly altered metabolites and pathways. Rigorous metabolite identification was carried out using authentic standards, the Mgryph-specific metabolite database and MS/MS mzCloud database. PCA and OPLS-DA showed clear separation and clustering of sample groups with cross-validation values of R2X = 0.76, R2Y = 0.99 and Q2 = 0.98 in OPLS-DA. As a result, 50 metabolites linked to 45 metabolic pathways were found to be significantly altered in the tested conditions, including: glycine, serine and threonine; butanoate; alanine, aspartate and glutamate metabolism; aminoacyl-tRNA biosynthesis and; pyruvate and citric acid cycle (TCA) metabolisms. Our findings demonstrate the potential of LC-MS to characterise key metabolites in Mgryph and will contribute to further understanding the metabolic mechanisms that affect Mgryph growth and magnetosome formation. Metabolic pathways in Magnetospirillum gryphiswaldense MSR-1 are significantly altered under microaerobic (O2-limited) growth conditions enabling magnetosome formation.![]()
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Affiliation(s)
- Salah Abdelrazig
- Centre for Analytical Bioscience, Advanced Materials and Healthcare Technologies Division, School of Pharmacy, University of Nottingham Nottingham NG7 2RD UK +44 (0)115 74 84697
| | - Laudina Safo
- Centre for Analytical Bioscience, Advanced Materials and Healthcare Technologies Division, School of Pharmacy, University of Nottingham Nottingham NG7 2RD UK +44 (0)115 74 84697
| | - Graham A Rance
- Nanoscale and Microscale Research Centre, University of Nottingham Nottingham NG7 2RD UK
| | - Michael W Fay
- Nanoscale and Microscale Research Centre, University of Nottingham Nottingham NG7 2RD UK
| | - Eirini Theodosiou
- Aston Institute of Materials Research, Aston University Birmingham B4 7ET UK +44 (0)121 204 4870
| | - Paul D Topham
- Aston Institute of Materials Research, Aston University Birmingham B4 7ET UK +44 (0)121 204 4870
| | - Dong-Hyun Kim
- Centre for Analytical Bioscience, Advanced Materials and Healthcare Technologies Division, School of Pharmacy, University of Nottingham Nottingham NG7 2RD UK +44 (0)115 74 84697
| | - Alfred Fernández-Castané
- Aston Institute of Materials Research, Aston University Birmingham B4 7ET UK +44 (0)121 204 4870.,Energy and Bioproducts Research Institute, Aston University Birmingham B4 7ET UK
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23
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Chen Y, Yang Y, Ji X, Zhao R, Li G, Gu Y, Shi A, Jiang W, Zhang Q. The SCIFF-Derived Ranthipeptides Participate in Quorum Sensing in Solventogenic Clostridia. Biotechnol J 2020; 15:e2000136. [PMID: 32713052 DOI: 10.1002/biot.202000136] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Revised: 06/25/2020] [Indexed: 12/29/2022]
Abstract
Ranthipeptides, defined as radical non-α thioether-containing peptides, are a newly emerging class of natural products belonging to the ribosomally synthesized and post-translationally modified peptide (RiPP) superfamily. Ranthipeptides are shown to be widespread in the bacterial kingdom, whereas heretofore their biological functions remain completely elusive. In this work, putative ranthipeptides are investigated from two solventogenic clostridia, Clostridium beijerinckii and Clostridium ljungdahlii, which are derived from the so-called six Cys in forty-five residues (SCIFF) family of precursor peptides. A series of analysis show that these two ranthipeptides participate in quorum sensing and controlling cellular metabolism. These results highlight the diverse biological functions of the ever-increasing family of RiPP natural products and showcase the potential to engineer industrially interesting organisms by manipulating their RiPP biosynthetic pathways.
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Affiliation(s)
- Yunliang Chen
- School of Agricultural Equipment Engineering, Jiangsu University, Zhenjiang, 212013, China.,Department of Chemistry, Fudan University, Shanghai, 200433, China
| | - Yunpeng Yang
- Chinese Academy of Sciences (CAS) Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai Institute of Plant Physiology and Ecology, Shanghai, 200032, China.,Institute of Neuroscience, Chinese Academy of Sciences (CAS) Key Laboratory of Primate Neurobiology, CAS Center for Excellence in Brain Science and Intelligence Technology, CAS, Shanghai Institutes for Biological Sciences, Shanghai, 200031, China
| | - Xinjian Ji
- Department of Chemistry, Fudan University, Shanghai, 200433, China
| | - Ran Zhao
- Chinese Academy of Sciences (CAS) Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai Institute of Plant Physiology and Ecology, Shanghai, 200032, China
| | - Guoquan Li
- School of Agricultural Equipment Engineering, Jiangsu University, Zhenjiang, 212013, China
| | - Yang Gu
- Chinese Academy of Sciences (CAS) Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai Institute of Plant Physiology and Ecology, Shanghai, 200032, China
| | - Aiping Shi
- School of Agricultural Equipment Engineering, Jiangsu University, Zhenjiang, 212013, China
| | - Weihong Jiang
- Chinese Academy of Sciences (CAS) Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai Institute of Plant Physiology and Ecology, Shanghai, 200032, China
| | - Qi Zhang
- Department of Chemistry, Fudan University, Shanghai, 200433, China
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Kotte AK, Severn O, Bean Z, Schwarz K, Minton NP, Winzer K. RRNPP-type quorum sensing affects solvent formation and sporulation in Clostridium acetobutylicum. MICROBIOLOGY (READING, ENGLAND) 2020; 166:579-592. [PMID: 32375981 PMCID: PMC7376267 DOI: 10.1099/mic.0.000916] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Accepted: 03/27/2020] [Indexed: 12/14/2022]
Abstract
The strictly anaerobic bacterium Clostridium acetobutylicum is well known for its ability to convert sugars into organic acids and solvents, most notably the potential biofuel butanol. However, the regulation of its fermentation metabolism, in particular the shift from acid to solvent production, remains poorly understood. The aim of this study was to investigate whether cell-cell communication plays a role in controlling the timing of this shift or the extent of solvent formation. Analysis of the available C. acetobutylicum genome sequences revealed the presence of eight putative RRNPP-type quorum-sensing systems, here designated qssA to qssH, each consisting of an RRNPP-type regulator gene followed by a small open reading frame encoding a putative signalling peptide precursor. The identified regulator and signal peptide precursor genes were designated qsrA to qsrH and qspA to qspH, respectively. Triplicate regulator mutants were generated in strain ATCC 824 for each of the eight systems and screened for phenotypic changes. The qsrB mutants showed increased solvent formation during early solventogenesis and hence the QssB system was selected for further characterization. Overexpression of qsrB severely reduced solvent and endospore formation and this effect could be overcome by adding short synthetic peptides to the culture medium representing a specific region of the QspB signalling peptide precursor. In addition, overexpression of qspB increased the production of acetone and butanol and the initial (48 h) titre of heat-resistant endospores. Together, these findings establish a role for QssB quorum sensing in the regulation of early solventogenesis and sporulation in C. acetobutylicum.
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Affiliation(s)
- Ann-Kathrin Kotte
- BBSRC/EPSRC Synthetic Biology Research Centre (SBRC), School of Life Sciences, University Park, The University of Nottingham, Nottingham, UK
- Present address: Independent Commodity Intelligence Service, Bishopsgate, London, UK
| | - Oliver Severn
- BBSRC/EPSRC Synthetic Biology Research Centre (SBRC), School of Life Sciences, University Park, The University of Nottingham, Nottingham, UK
- Present address: Singer Instruments, Roadwater, Watchet, UK
| | - Zak Bean
- BBSRC/EPSRC Synthetic Biology Research Centre (SBRC), School of Life Sciences, University Park, The University of Nottingham, Nottingham, UK
- Present address: CHAIN Biotechnology Ltd, MediCity, Nottingham, UK
| | - Katrin Schwarz
- BBSRC/EPSRC Synthetic Biology Research Centre (SBRC), School of Life Sciences, University Park, The University of Nottingham, Nottingham, UK
- Present address: Azotic Technologies Ltd, BioCity, Nottingham, UK
| | - Nigel P. Minton
- BBSRC/EPSRC Synthetic Biology Research Centre (SBRC), School of Life Sciences, University Park, The University of Nottingham, Nottingham, UK
| | - Klaus Winzer
- BBSRC/EPSRC Synthetic Biology Research Centre (SBRC), School of Life Sciences, University Park, The University of Nottingham, Nottingham, UK
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25
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Thomas GH. Microbial Musings – June 2020. Microbiology (Reading) 2020; 166:498-500. [PMID: 32633711 PMCID: PMC7376269 DOI: 10.1099/mic.0.000951] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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26
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Xin X, Cheng C, Du G, Chen L, Xue C. Metabolic Engineering of Histidine Kinases in Clostridium beijerinckii for Enhanced Butanol Production. Front Bioeng Biotechnol 2020; 8:214. [PMID: 32266241 PMCID: PMC7098912 DOI: 10.3389/fbioe.2020.00214] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Accepted: 03/03/2020] [Indexed: 12/31/2022] Open
Abstract
Clostridium beijerinckii, a promising industrial microorganism for butanol production, suffers from low butanol titer and lack of high-efficiency genetical engineering toolkit. A few histidine kinases (HKs) responsible for Spo0A phosphorylation have been demonstrated as functionally important components in regulating butanol biosynthesis in solventogenic clostridia such as C. acetobutylicum, but no study about HKs has been conducted in C. beijerinckii. In this study, six annotated but uncharacterized candidate HK genes sharing partial homologies (no less than 30%) with those in C. acetobutylicum were selected based on sequence alignment. The encoding region of these HK genes were deleted with CRISPR-Cas9n-based genome editing technology. The deletion of cbei2073 and cbei4484 resulted in significant change in butanol biosynthesis, with butanol production increased by 40.8 and 17.3% (13.8 g/L and 11.5 g/L vs. 9.8 g/L), respectively, compared to the wild-type. Faster butanol production rates were observed, with butanol productivity greatly increased by 40.0 and 20.0%, respectively, indicating these two HKs are important in regulating cellular metabolism in C. beijerinckii. In addition, the sporulation frequencies of two HKs inactivated strains decreased by 96.9 and 77.4%, respectively. The other four HK-deletion (including cbei2087, cbei2435, cbei4925, and cbei1553) mutant strains showed few phenotypic changes compared with the wild-type. This study demonstrated the role of HKs on sporulation and solventogenesis in C. beijerinckii, and provided a novel engineering strategy of HKs for improving metabolite production. The hyper-butanol-producing strains generated in this study have great potentials in industrial biobutanol production.
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Affiliation(s)
- Xin Xin
- School of Bioengineering, Dalian University of Technology, Dalian, China
| | - Chi Cheng
- School of Bioengineering, Dalian University of Technology, Dalian, China
| | - Guangqing Du
- School of Bioengineering, Dalian University of Technology, Dalian, China
| | - Lijie Chen
- School of Bioengineering, Dalian University of Technology, Dalian, China
| | - Chuang Xue
- School of Bioengineering, Dalian University of Technology, Dalian, China
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27
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Investigation of secondary metabolism in the industrial butanol hyper-producer Clostridium saccharoperbutylacetonicum N1-4. J Ind Microbiol Biotechnol 2020; 47:319-328. [PMID: 32103460 DOI: 10.1007/s10295-020-02266-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Accepted: 02/12/2020] [Indexed: 12/15/2022]
Abstract
Clostridium saccharoperbutylacetonicum N1-4 (Csa) is a historically significant anaerobic bacterium which can perform saccharolytic fermentations to produce acetone, butanol, and ethanol (ABE). Recent genomic analyses have highlighted this organism's potential to produce polyketide and nonribosomal peptide secondary metabolites, but little is known regarding the identity and function of these metabolites. This study provides a detailed bioinformatic analysis of seven biosynthetic gene clusters (BGCs) present in the Csa genome that are predicted to produce polyketides/nonribosomal peptides. An RNA-seq-based untargeted transcriptomic approach revealed that five of seven BGCs were expressed during ABE fermentation. Additional characterization of a highly expressed nonribosomal peptide synthetase gene led to the discovery of its associated metabolite and its biosynthetic pathway. Transcriptomic analysis suggested an association of this nonribosomal peptide synthetase gene with butanol tolerance, which was supported by butanol challenge assays.
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28
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Yoo M, Nguyen NPT, Soucaille P. Trends in Systems Biology for the Analysis and Engineering of Clostridium acetobutylicum Metabolism. Trends Microbiol 2020; 28:118-140. [DOI: 10.1016/j.tim.2019.09.003] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Revised: 09/04/2019] [Accepted: 09/06/2019] [Indexed: 11/25/2022]
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29
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Meyer A, Saaem I, Silverman A, Varaljay VA, Mickol R, Blum S, Tobias AV, Schwalm ND, Mojadedi W, Onderko E, Bristol C, Liu S, Pratt K, Casini A, Eluere R, Moser F, Drake C, Gupta M, Kelley-Loughnane N, Lucks JP, Akingbade KL, Lux MP, Glaven S, Crookes-Goodson W, Jewett MC, Gordon DB, Voigt CA. Organism Engineering for the Bioproduction of the Triaminotrinitrobenzene (TATB) Precursor Phloroglucinol (PG). ACS Synth Biol 2019; 8:2746-2755. [PMID: 31750651 DOI: 10.1021/acssynbio.9b00393] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Organism engineering requires the selection of an appropriate chassis, editing its genome, combining traits from different source species, and controlling genes with synthetic circuits. When a strain is needed for a new target objective, for example, to produce a chemical-of-need, the best strains, genes, techniques, software, and expertise may be distributed across laboratories. Here, we report a project where we were assigned phloroglucinol (PG) as a target, and then combined unique capabilities across the United States Army, Navy, and Air Force service laboratories with the shared goal of designing an organism to produce this molecule. In addition to the laboratory strain Escherichia coli, organisms were screened from soil and seawater. Putative PG-producing enzymes were mined from a strain bank of bacteria isolated from aircraft and fuel depots. The best enzyme was introduced into the ocean strain Marinobacter atlanticus CP1 with its genome edited to redirect carbon flux from natural fatty acid ester (FAE) production. PG production was also attempted in Bacillus subtilis and Clostridium acetobutylicum. A genetic circuit was constructed in E. coli that responds to PG accumulation, which was then ported to an in vitro paper-based system that could serve as a platform for future low-cost strain screening or for in-field sensing. Collectively, these efforts show how distributed biotechnology laboratories with domain-specific expertise can be marshalled to quickly provide a solution for a targeted organism engineering project, and highlights data and material sharing protocols needed to accelerate future efforts.
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Affiliation(s)
- Adam Meyer
- Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Ishtiaq Saaem
- Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- The Foundry, 75 Ames Street, Cambridge Massachusetts 02142, United States
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, United States
| | - Adam Silverman
- Center for Synthetic Biology, Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois 60208, United States
| | - Vanessa A. Varaljay
- Soft Matter Materials Branch, Materials and Manufacturing Directorate, Air Force Research Laboratory, Wright-Patterson AFB, Ohio 45433, United States
| | - Rebecca Mickol
- American Society for Engineering Education, 1818 N Street NW Suite 600, Washington, D.C. 20036, United States
| | - Steven Blum
- U.S. Army Combat Capabilities Development Command Chemical Biological Center, 8198 Blackhawk Road, Aberdeen Proving Ground, Maryland 21010, United States
| | - Alexander V. Tobias
- U.S. Army Research Laboratory, FCDD-RLS-EB, 2800 Powder Mill Road, Adelphi, Maryland 20783, United States
| | - Nathan D. Schwalm
- U.S. Army Research Laboratory, FCDD-RLS-EB, 2800 Powder Mill Road, Adelphi, Maryland 20783, United States
| | - Wais Mojadedi
- Oak Ridge Associate Universities, P.O.
Box 117, MS-29, Oak Ridge, Tennessee 37831, United States
| | - Elizabeth Onderko
- National Research Council, 500 5th Street NW, Washington, D.C. 20001, United States
| | - Cassandra Bristol
- The Foundry, 75 Ames Street, Cambridge Massachusetts 02142, United States
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, United States
| | - Shangtao Liu
- Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- The Foundry, 75 Ames Street, Cambridge Massachusetts 02142, United States
| | - Katelin Pratt
- The Foundry, 75 Ames Street, Cambridge Massachusetts 02142, United States
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, United States
| | - Arturo Casini
- The Foundry, 75 Ames Street, Cambridge Massachusetts 02142, United States
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, United States
| | - Raissa Eluere
- The Foundry, 75 Ames Street, Cambridge Massachusetts 02142, United States
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, United States
| | - Felix Moser
- Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Carrie Drake
- UES, Inc., 4401 Dayton-Xenia Road, Dayton, Ohio 45432, United States
| | - Maneesh Gupta
- Soft Matter Materials Branch, Materials and Manufacturing Directorate, Air Force Research Laboratory, Wright-Patterson AFB, Ohio 45433, United States
| | - Nancy Kelley-Loughnane
- Soft Matter Materials Branch, Materials and Manufacturing Directorate, Air Force Research Laboratory, Wright-Patterson AFB, Ohio 45433, United States
| | - Julius P. Lucks
- Center for Synthetic Biology, Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois 60208, United States
| | - Katherine L. Akingbade
- U.S. Army Research Laboratory, FCDD-RLS-EB, 2800 Powder Mill Road, Adelphi, Maryland 20783, United States
| | - Matthew P. Lux
- U.S. Army Combat Capabilities Development Command Chemical Biological Center, 8198 Blackhawk Road, Aberdeen Proving Ground, Maryland 21010, United States
| | - Sarah Glaven
- Center for Bio/Molecular Science and Engineering, Naval Research Laboratory, Washington, D.C. 20375, United States
| | - Wendy Crookes-Goodson
- Soft Matter Materials Branch, Materials and Manufacturing Directorate, Air Force Research Laboratory, Wright-Patterson AFB, Ohio 45433, United States
| | - Michael C. Jewett
- Center for Synthetic Biology, Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois 60208, United States
| | - D. Benjamin Gordon
- Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- The Foundry, 75 Ames Street, Cambridge Massachusetts 02142, United States
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, United States
| | - Christopher A. Voigt
- Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- The Foundry, 75 Ames Street, Cambridge Massachusetts 02142, United States
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30
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Zunyimycin C inhibits the proliferation of lung cancer cells by inducing apoptosis through an AKT-related mechanism. Med Chem Res 2019. [DOI: 10.1007/s00044-019-02417-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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31
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Grammbitter GLC, Schmalhofer M, Karimi K, Shi YM, Schöner TA, Tobias NJ, Morgner N, Groll M, Bode HB. An Uncommon Type II PKS Catalyzes Biosynthesis of Aryl Polyene Pigments. J Am Chem Soc 2019; 141:16615-16623. [DOI: 10.1021/jacs.8b10776] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- Gina L. C. Grammbitter
- Molekulare Biotechnologie, Fachbereich Biowissenschaften, Goethe-Universität Frankfurt am Main and Buchmann Institute for Molecular Life Sciences (BMLS), Goethe-Universität Frankfurt, Max-von-Laue-Straße 9 and 15, 60438 Frankfurt am Main, Germany
| | - Maximilian Schmalhofer
- Center for Integrated Protein Science at the Department Chemie, Lehrstuhl für Biochemie, Technische Universität München, Lichtenbergstraße 4, 85748 Garching, Germany
| | - Kudratullah Karimi
- Institut für Physikalische und Theoretische Chemie, Goethe-Universität Frankfurt, Max-von-Laue-Straße 7, 60438 Frankfurt am Main, Germany
| | - Yi-Ming Shi
- Molekulare Biotechnologie, Fachbereich Biowissenschaften, Goethe-Universität Frankfurt am Main and Buchmann Institute for Molecular Life Sciences (BMLS), Goethe-Universität Frankfurt, Max-von-Laue-Straße 9 and 15, 60438 Frankfurt am Main, Germany
| | - Tim A. Schöner
- Molekulare Biotechnologie, Fachbereich Biowissenschaften, Goethe-Universität Frankfurt am Main and Buchmann Institute for Molecular Life Sciences (BMLS), Goethe-Universität Frankfurt, Max-von-Laue-Straße 9 and 15, 60438 Frankfurt am Main, Germany
| | - Nicholas J. Tobias
- Molekulare Biotechnologie, Fachbereich Biowissenschaften, Goethe-Universität Frankfurt am Main and Buchmann Institute for Molecular Life Sciences (BMLS), Goethe-Universität Frankfurt, Max-von-Laue-Straße 9 and 15, 60438 Frankfurt am Main, Germany
| | - Nina Morgner
- Institut für Physikalische und Theoretische Chemie, Goethe-Universität Frankfurt, Max-von-Laue-Straße 7, 60438 Frankfurt am Main, Germany
| | - Michael Groll
- Center for Integrated Protein Science at the Department Chemie, Lehrstuhl für Biochemie, Technische Universität München, Lichtenbergstraße 4, 85748 Garching, Germany
| | - Helge B. Bode
- Molekulare Biotechnologie, Fachbereich Biowissenschaften, Goethe-Universität Frankfurt am Main and Buchmann Institute for Molecular Life Sciences (BMLS), Goethe-Universität Frankfurt, Max-von-Laue-Straße 9 and 15, 60438 Frankfurt am Main, Germany
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32
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Acidogenesis, solventogenesis, metabolic stress response and life cycle changes in Clostridium beijerinckii NRRL B-598 at the transcriptomic level. Sci Rep 2019; 9:1371. [PMID: 30718562 PMCID: PMC6362236 DOI: 10.1038/s41598-018-37679-0] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2018] [Accepted: 12/13/2018] [Indexed: 01/16/2023] Open
Abstract
Clostridium beijerinckii NRRL B-598 is a sporulating, butanol and hydrogen producing strain that utilizes carbohydrates by the acetone-butanol-ethanol (ABE) fermentative pathway. The pathway consists of two metabolic phases, acidogenesis and solventogenesis, from which the latter one can be coupled with sporulation. Thorough transcriptomic profiling during a complete life cycle and both metabolic phases completed with flow cytometry, microscopy and a metabolites analysis helped to find out key genes involved in particular cellular events. The description of genes/operons that are closely involved in metabolism or the cell cycle is a necessary condition for metabolic engineering of the strain and will be valuable for all C. beijerinckii strains and other Clostridial species. The study focused on glucose transport and catabolism, hydrogen formation, metabolic stress response, binary fission, motility/chemotaxis and sporulation, which resulted in the composition of the unique image reflecting clostridial population changes. Surprisingly, the main change in expression of individual genes was coupled with the sporulation start and not with the transition from acidogenic to solventogenic metabolism. As expected, solvents formation started at pH decrease and the accumulation of butyric and acetic acids in the cultivation medium.
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33
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Dunbar KL, Büttner H, Molloy EM, Dell M, Kumpfmüller J, Hertweck C. Genome Editing Reveals Novel Thiotemplated Assembly of Polythioamide Antibiotics in Anaerobic Bacteria. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201807970] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Kyle L. Dunbar
- Dept. of Biomolecular Chemistry; Leibniz Institute for Natural Product Research and Infection Biology, HKI; Beutenbergstrasse 11a 07745 Jena Germany
| | - Hannah Büttner
- Dept. of Biomolecular Chemistry; Leibniz Institute for Natural Product Research and Infection Biology, HKI; Beutenbergstrasse 11a 07745 Jena Germany
| | - Evelyn M. Molloy
- Dept. of Biomolecular Chemistry; Leibniz Institute for Natural Product Research and Infection Biology, HKI; Beutenbergstrasse 11a 07745 Jena Germany
| | - Maria Dell
- Dept. of Biomolecular Chemistry; Leibniz Institute for Natural Product Research and Infection Biology, HKI; Beutenbergstrasse 11a 07745 Jena Germany
| | - Jana Kumpfmüller
- Dept. of Biomolecular Chemistry; Leibniz Institute for Natural Product Research and Infection Biology, HKI; Beutenbergstrasse 11a 07745 Jena Germany
| | - Christian Hertweck
- Dept. of Biomolecular Chemistry; Leibniz Institute for Natural Product Research and Infection Biology, HKI; Beutenbergstrasse 11a 07745 Jena Germany
- Natural Product Chemistry; Friedrich Schiller University; 07743 Jena Germany
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34
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Dunbar KL, Büttner H, Molloy EM, Dell M, Kumpfmüller J, Hertweck C. Genome Editing Reveals Novel Thiotemplated Assembly of Polythioamide Antibiotics in Anaerobic Bacteria. Angew Chem Int Ed Engl 2018; 57:14080-14084. [PMID: 30193003 DOI: 10.1002/anie.201807970] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Revised: 08/23/2018] [Indexed: 12/18/2022]
Abstract
Closthioamide (CTA) is a unique symmetric nonribosomal peptide with six thioamide moieties that is produced by the Gram-positive obligate anaerobe Ruminiclostridium cellulolyticum. CTA displays potent inhibitory activity against important clinical pathogens, making it a promising drug candidate. Yet, the biosynthesis of this DNA gyrase-targeting antibiotic has remained enigmatic. Using a combination of genome mining, genome editing (targeted group II intron, CRISPR/Cas9), and heterologous expression, we show that CTA biosynthesis involves specialized enzymes for starter unit biosynthesis, amide bond formation, thionation, and dimerization. Surprisingly, CTA biosynthesis involves a novel thiotemplated peptide assembly line that markedly differs from known nonribosomal peptide synthetases. These findings provide the first insights into the biosynthesis of thioamide-containing nonribosomal peptides and offer a starting point for the discovery of related natural products.
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Affiliation(s)
- Kyle L Dunbar
- Dept. of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology, HKI, Beutenbergstrasse 11a, 07745, Jena, Germany
| | - Hannah Büttner
- Dept. of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology, HKI, Beutenbergstrasse 11a, 07745, Jena, Germany
| | - Evelyn M Molloy
- Dept. of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology, HKI, Beutenbergstrasse 11a, 07745, Jena, Germany
| | - Maria Dell
- Dept. of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology, HKI, Beutenbergstrasse 11a, 07745, Jena, Germany
| | - Jana Kumpfmüller
- Dept. of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology, HKI, Beutenbergstrasse 11a, 07745, Jena, Germany
| | - Christian Hertweck
- Dept. of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology, HKI, Beutenbergstrasse 11a, 07745, Jena, Germany.,Natural Product Chemistry, Friedrich Schiller University, 07743, Jena, Germany
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35
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Li JS, Barber CC, Zhang W. Natural products from anaerobes. J Ind Microbiol Biotechnol 2018; 46:375-383. [PMID: 30284140 DOI: 10.1007/s10295-018-2086-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Accepted: 09/25/2018] [Indexed: 12/27/2022]
Abstract
Natural product discovery in the microbial world has historically been biased toward aerobes. Recent in silico analysis demonstrates that genomes of anaerobes encode unexpected biosynthetic potential for natural products, however, chemical data on natural products from the anaerobic world are extremely limited. Here, we review the current body of work on natural products isolated from strictly anaerobic microbes, including recent genome mining efforts to discover polyketides and non-ribosomal peptides from anaerobes. These known natural products of anaerobes have demonstrated interesting molecular scaffolds, biosynthetic logic, and/or biological activities, making anaerobes a promising reservoir for future natural product discovery.
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Affiliation(s)
- Jeffrey S Li
- Department of Chemical and Biomolecular Engineering, University of California Berkeley, Berkeley, CA, USA
| | - Colin Charles Barber
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA, USA
| | - Wenjun Zhang
- Department of Chemical and Biomolecular Engineering, University of California Berkeley, Berkeley, CA, USA. .,Chan Zuckerberg Biohub, San Francisco, CA, USA.
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