1
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Delarouzée A, Lopes Ferreira N, Baum C, Wasels F. Gene essentiality in the solventogenic Clostridium acetobutylicum DSM 792. Appl Environ Microbiol 2024; 90:e0028224. [PMID: 38864631 PMCID: PMC11267918 DOI: 10.1128/aem.00282-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2024] [Accepted: 05/20/2024] [Indexed: 06/13/2024] Open
Abstract
Clostridium acetobutylicum is a solventogenic, anaerobic, gram-positive bacterium that is commonly considered the model organism for studying acetone-butanol-ethanol fermentation. The need to produce these chemicals sustainably and with a minimal impact on the environment has revived the interest in research on this bacterium. The recent development of efficient genetic tools allows to better understand the physiology of this micro-organism, aiming at improving its fermentation capacities. Knowledge about gene essentiality would guide the future genetic editing strategies and support the understanding of crucial cellular functions in this bacterium. In this work, we applied a transposon insertion site sequencing method to generate large mutant libraries containing millions of independent mutants that allowed us to identify a core group of 418 essential genes needed for in vitro development. Future research on this significant biocatalyst will be guided by the data provided in this work, which will serve as a valuable resource for the community. IMPORTANCE Clostridium acetobutylicum is a leading candidate to synthesize valuable compounds like three and four carbons alcohols. Its ability to convert carbohydrates into a mixture of acetone, butanol, and ethanol as well as other chemicals of interest upon genetic engineering makes it an advantageous organism for the valorization of lignocellulose-derived sugar mixtures. Since, genetic optimization depends on the fundamental insights supplied by accurate gene function assignment, gene essentiality analysis is of great interest as it can shed light on the function of many genes whose functions are still to be confirmed. The data obtained in this study will be of great value for the research community aiming to develop C. acetobutylicum as a platform organism for the production of chemicals of interest.
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Affiliation(s)
| | | | - Chloé Baum
- Institut Pasteur, Université Paris Cité, Plate-forme Technologique Biomics, Paris, France
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2
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Ehsaan M, Yoo M, Kuit W, Foulquier C, Soucaille P, Minton NP. Chromosomal integration of the pSOL1 megaplasmid of Clostridium acetobutylicum for continuous and stable advanced biofuels production. Nat Microbiol 2024; 9:1655-1660. [PMID: 38877224 PMCID: PMC11222136 DOI: 10.1038/s41564-024-01714-w] [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: 05/30/2023] [Accepted: 04/24/2024] [Indexed: 06/16/2024]
Abstract
Biofuel production by Clostridium acetobutylicum is compromised by strain degeneration due to loss of its pSOL1 megaplasmid. Here we used engineering biology to stably integrate pSOL1 into the chromosome together with a synthetic isopropanol pathway. In a membrane bioreactor continuously fed with glucose mineral medium, the final strain produced advanced biofuels, n-butanol and isopropanol, at high yield (0.31 g g-1), titre (15.4 g l-1) and productivity (15.5 g l-1 h-1) without degeneration.
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Affiliation(s)
- Muhammad Ehsaan
- BBSRC/EPSRC Synthetic Biology Research Centre, School of Life Sciences, Biodiscovery Institute, University of Nottingham, Nottingham, UK
| | - Minyeong Yoo
- BBSRC/EPSRC Synthetic Biology Research Centre, School of Life Sciences, Biodiscovery Institute, University of Nottingham, Nottingham, UK
| | - Wouter Kuit
- BBSRC/EPSRC Synthetic Biology Research Centre, School of Life Sciences, Biodiscovery Institute, University of Nottingham, Nottingham, UK
| | - Céline Foulquier
- TBI, Université de Toulouse, CNRS, INRAE, INSA, Toulouse, France
| | - Philippe Soucaille
- BBSRC/EPSRC Synthetic Biology Research Centre, School of Life Sciences, Biodiscovery Institute, University of Nottingham, Nottingham, UK.
- TBI, Université de Toulouse, CNRS, INRAE, INSA, Toulouse, France.
| | - Nigel P Minton
- BBSRC/EPSRC Synthetic Biology Research Centre, School of Life Sciences, Biodiscovery Institute, University of Nottingham, Nottingham, UK
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3
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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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4
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Charubin K, Hill JD, Papoutsakis ET. DNA transfer between two different species mediated by heterologous cell fusion in Clostridium coculture. mBio 2024; 15:e0313323. [PMID: 38214507 PMCID: PMC10865971 DOI: 10.1128/mbio.03133-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Accepted: 12/01/2023] [Indexed: 01/13/2024] Open
Abstract
Prokaryotic evolution is driven by random mutations and horizontal gene transfer (HGT). HGT occurs via transformation, transduction, or conjugation. We have previously shown that in syntrophic cocultures of Clostridium acetobutylicum and Clostridium ljungdahlii, heterologous cell fusion leads to a large-scale exchange of proteins and RNA between the two organisms. Here, we present evidence that heterologous cell fusion facilitates the exchange of DNA between the two organisms. Using selective subculturing, we isolated C. acetobutylicum cells which acquired and integrated into their genome portions of plasmid DNA from a plasmid-carrying C. ljungdahlii strain. Limiting-dilution plating and DNA methylation data based on PacBio Single-Molecule Real Time (SMRT) sequencing support the existence of hybrid C. acetobutylicum/C. ljungdahlii cells. These findings expand our understanding of multi-species microbiomes, their survival strategies, and evolution.IMPORTANCEInvestigations of natural multispecies microbiomes and synthetic microbial cocultures are attracting renewed interest for their potential application in biotechnology, ecology, and medical fields. Previously, we have shown the syntrophic coculture of C. acetobutylicum and C. ljungdahlii undergoes heterologous cell-to-cell fusion, which facilitates the exchange of cytoplasmic protein and RNA between the two organisms. We now show that heterologous cell fusion between the two Clostridium organisms can facilitate the exchange of DNA. By applying selective pressures to this coculture system, we isolated clones of wild-type C. acetobutylicum which acquired the erythromycin resistance (erm) gene from the C. ljungdahlii strain carrying a plasmid with the erm gene. Single-molecule real-time sequencing revealed that the erm gene was integrated into the genome in a mosaic fashion. Our data also support the persistence of hybrid C. acetobutylicum/C. ljungdahlii cells displaying hybrid DNA-methylation patterns.
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Affiliation(s)
- Kamil Charubin
- Department of Chemical and Biomolecular Engineering, The Delaware Biotechnology Institute, University of Delaware, Newark, Delaware, USA
| | - John D. Hill
- Department of Chemical and Biomolecular Engineering, The Delaware Biotechnology Institute, University of Delaware, Newark, Delaware, USA
| | - Eleftherios Terry Papoutsakis
- Department of Chemical and Biomolecular Engineering, The Delaware Biotechnology Institute, University of Delaware, Newark, Delaware, USA
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5
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Roe JM, Seely K, Bussard CJ, Eischen Martin E, Mouw EG, Bayles KW, Hollingsworth MA, Brooks AE, Dailey KM. Hacking the Immune Response to Solid Tumors: Harnessing the Anti-Cancer Capacities of Oncolytic Bacteria. Pharmaceutics 2023; 15:2004. [PMID: 37514190 PMCID: PMC10384176 DOI: 10.3390/pharmaceutics15072004] [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: 06/26/2023] [Revised: 07/13/2023] [Accepted: 07/18/2023] [Indexed: 07/30/2023] Open
Abstract
Oncolytic bacteria are a classification of bacteria with a natural ability to specifically target solid tumors and, in the process, stimulate a potent immune response. Currently, these include species of Klebsiella, Listeria, Mycobacteria, Streptococcus/Serratia (Coley's Toxin), Proteus, Salmonella, and Clostridium. Advancements in techniques and methodology, including genetic engineering, create opportunities to "hijack" typical host-pathogen interactions and subsequently harness oncolytic capacities. Engineering, sometimes termed "domestication", of oncolytic bacterial species is especially beneficial when solid tumors are inaccessible or metastasize early in development. This review examines reported oncolytic bacteria-host immune interactions and details the known mechanisms of these interactions to the protein level. A synopsis of the presented membrane surface molecules that elicit particularly promising oncolytic capacities is paired with the stimulated localized and systemic immunogenic effects. In addition, oncolytic bacterial progression toward clinical translation through engineering efforts are discussed, with thorough attention given to strains that have accomplished Phase III clinical trial initiation. In addition to therapeutic mitigation after the tumor has formed, some bacterial species, referred to as "prophylactic", may even be able to prevent or "derail" tumor formation through anti-inflammatory capabilities. These promising species and their particularly favorable characteristics are summarized as well. A complete understanding of the bacteria-host interaction will likely be necessary to assess anti-cancer capacities and unlock the full cancer therapeutic potential of oncolytic bacteria.
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Affiliation(s)
- Jason M Roe
- College of Osteopathic Medicine, Rocky Vista University, Ivins, UT 84738, USA
| | - Kevin Seely
- College of Osteopathic Medicine, Rocky Vista University, Ivins, UT 84738, USA
| | - Caleb J Bussard
- College of Osteopathic Medicine, Rocky Vista University, Parker, CO 80130, USA
| | | | - Elizabeth G Mouw
- College of Osteopathic Medicine, Rocky Vista University, Ivins, UT 84738, USA
| | - Kenneth W Bayles
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Michael A Hollingsworth
- Eppley Institute for Cancer Research, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Amanda E Brooks
- College of Osteopathic Medicine, Rocky Vista University, Ivins, UT 84738, USA
- College of Osteopathic Medicine, Rocky Vista University, Parker, CO 80130, USA
- Office of Research & Scholarly Activity, Rocky Vista University, Ivins, UT 84738, USA
| | - Kaitlin M Dailey
- Eppley Institute for Cancer Research, University of Nebraska Medical Center, Omaha, NE 68198, USA
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6
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Humphreys JR, Debebe BJ, Diggle SP, Winzer K. Clostridium beijerinckii strain degeneration is driven by the loss of Spo0A activity. Front Microbiol 2023; 13:1075609. [PMID: 36704551 PMCID: PMC9871927 DOI: 10.3389/fmicb.2022.1075609] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Accepted: 12/12/2022] [Indexed: 01/12/2023] Open
Abstract
Solventogenic clostridia represent a diverse group of anaerobic, spore-forming bacteria capable of producing acetone, butanol and ethanol through their unique biphasic metabolism. An intrinsic problem with these organisms however is their tendency to degenerate when repeatedly subcultured or when grown continuously. This phenomenon sees cells lose their ability to produce solvents and spores, posing a significant problem for industrial applications. To investigate the mechanistic and evolutionary basis of degeneration we combined comparative genomics, ultra-deep sequencing, and concepts of sociomicrobiology using Clostridium beijerinckii NCIMB 8052 as our model organism. These approaches revealed spo0A, the master regulator gene involved in spore and solvent formation, to be key to the degeneration process in this strain. Comparative genomics of 71 degenerate variants revealed four distinct hotspot regions that contained considerably more mutations than the rest of the genome. These included spo0A as well as genes suspected to regulate its expression and activity. Ultra-deep sequencing of populations during the subculturing process showed transient increases in mutations we believe linked to the spo0A network, however, these were ultimately dominated by mutations in the master regulator itself. Through frequency-dependent fitness assays, we found that spo0A mutants gained a fitness advantage, relative to the wild type, presumably allowing for propagation throughout the culture. Combined, our data provides new insights into the phenomenon of clostridial strain degeneration and the C. beijerinckii NCIMB 8052 solvent and spore regulation network.
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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, United Kingdom
| | - Bisrat J. Debebe
- DeepSeq, Centre for Genetics and Genomics, The University of Nottingham, Nottingham, United Kingdom
| | - Stephen P. Diggle
- Center for Microbial Dynamics and Infection, School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, United States
| | - Klaus Winzer
- BBSRC/EPSRC Synthetic Biology Research Centre (SBRC), School of Life Sciences, University Park, The University of Nottingham, Nottingham, United Kingdom,*Correspondence: Klaus Winzer, ✉
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7
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Increased Butyrate Production in Clostridium saccharoperbutylacetonicum from Lignocellulose-Derived Sugars. Appl Environ Microbiol 2022; 88:e0241921. [PMID: 35311509 DOI: 10.1128/aem.02419-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Butyrate is produced by chemical synthesis based on crude oil, produced by microbial fermentation, or extracted from animal fats (M. Dwidar, J.-Y. Park, R. J. Mitchell, and B.-I. Sang, The Scientific World Journal, 2012:471417, 2012, https://doi.org/10.1100/2012/471417). Butyrate production by anaerobic bacteria is highly favorable since waste or sustainable resources can be used as the substrates. For this purpose, the native hyper-butanol producer Clostridium saccharoperbutylacetonicum N1-4(HMT) was used as a chassis strain due to its broad substrate spectrum. BLASTp analysis of the predicted proteome of C. saccharoperbutylacetonicum N1-4(HMT) resulted in the identification of gene products potentially involved in acetone-butanol-ethanol (ABE) fermentation. Their participation in ABE fermentation was either confirmed or disproven by the parallel production of acids or solvents and the respective transcript levels obtained by transcriptome analysis of this strain. The genes encoding phosphotransacetylase (pta) and butyraldehyde dehydrogenase (bld) were deleted to reduce acetate and alcohol formation. The genes located in the butyryl-CoA synthesis (bcs) operon encoding crotonase, butyryl-CoA dehydrogenase with electron-transferring protein subunits α and β, and 3-hydroxybutyryl-CoA dehydrogenase were overexpressed to channel the flux further towards butyrate formation. Thereby, the native hyper-butanol producer C. saccharoperbutylacetonicum N1-4(HMT) was converted into the hyper-butyrate producer C. saccharoperbutylacetonicum ΔbldΔpta [pMTL83151_BCS_PbgaL]. The transcription pattern following deletion and overexpression was characterized by a second transcriptomic study, revealing partial compensation for the deletion. Furthermore, this strain was characterized in pH-controlled fermentations with either glucose or Excello, a substrate yielded from spruce biomass. Butyrate was the main product, with maximum butyrate concentrations of 11.7 g·L-1 and 14.3 g·L-1, respectively. Minimal amounts of by-products were detected. IMPORTANCE Platform chemicals such as butyrate are usually produced chemically from crude oil, resulting in the carry-over of harmful compounds. The selective production of butyrate using sustainable resources or waste without harmful by-products can be achieved by bacteria such as clostridia. The hyper-butanol producer Clostridium saccharoperbutylacetonicum N1-4(HMT) was converted into a hyper-butyrate producer. Butyrate production with very small amounts of by-products was established with glucose and the sustainable lignocellulosic sugar substrate Excello extracted from spruce biomass by the biorefinery Borregaard (Sarpsborg, Norway).
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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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9
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Li Q, Zhang J, Yang J, Jiang Y, Yang S. Recent progress on n-butanol production by lactic acid bacteria. World J Microbiol Biotechnol 2021; 37:205. [PMID: 34698975 DOI: 10.1007/s11274-021-03173-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2021] [Accepted: 10/13/2021] [Indexed: 11/26/2022]
Abstract
n-Butanol is an essential chemical intermediate produced through microbial fermentation. However, its toxicity to microbial cells has limited its production to a great extent. The anaerobe lactic acid bacteria (LAB) are the most resistant to n-butanol, so it should be the first choice for improving n-butanol production. The present article aims to review the following aspects of n-butanol production by LAB: (1) the tolerance of LAB to n-butanol, including its tolerance level and potential tolerance mechanisms; (2) genome editing tools in the n-butanol-resistant LAB; (3) methods of LAB modification for n-butanol production and the production levels after modification. This review will provide a theoretical basis for further research on n-butanol production by LAB.
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Affiliation(s)
- Qi Li
- College of Life Sciences, Sichuan Normal University, Chengdu, 610101, China
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai, 200032, China
| | - Jieze Zhang
- Department of Chemistry, University of Southern California, Los Angeles, CA, 90089, USA
| | - Junjie Yang
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai, 200032, China
| | - Yu Jiang
- Huzhou Center of Industrial Biotechnology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Huzhou, 313000, China
- Shanghai Taoyusheng Biotechnology Company Ltd, Shanghai, 200032, China
| | - Sheng Yang
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai, 200032, China.
- Huzhou Center of Industrial Biotechnology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Huzhou, 313000, China.
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10
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Diversity and Evolution of Clostridium beijerinckii and Complete Genome of the Type Strain DSM 791T. Processes (Basel) 2021. [DOI: 10.3390/pr9071196] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Clostridium beijerinckii is a relatively widely studied, yet non-model, bacterium. While 246 genome assemblies of its various strains are available currently, the diversity of the whole species has not been studied, and it has only been analyzed in part for a missing genome of the type strain. Here, we sequenced and assembled the complete genome of the type strain Clostridium beijerinckii DSM 791T, composed of a circular chromosome and a circular megaplasmid, and used it for a comparison with other genomes to evaluate diversity and capture the evolution of the whole species. We found that strains WB53 and HUN142 were misidentified and did not belong to the Clostridium beijerinckii species. Additionally, we filtered possibly misassembled genomes, and we used the remaining 237 high-quality genomes to define the pangenome of the whole species. By its functional annotation, we showed that the core genome contains genes responsible for basic metabolism, while the accessory genome has genes affecting final phenotype that may vary among different strains. We used the core genome to reconstruct the phylogeny of the species and showed its great diversity, which complicates the identification of particular strains, yet hides possibilities to reveal hitherto unreported phenotypic features and processes utilizable in biotechnology.
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11
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Flaiz M, Ludwig G, Bengelsdorf FR, Dürre P. Production of the biocommodities butanol and acetone from methanol with fluorescent FAST-tagged proteins using metabolically engineered strains of Eubacterium limosum. BIOTECHNOLOGY FOR BIOFUELS 2021; 14:117. [PMID: 33971948 PMCID: PMC8111989 DOI: 10.1186/s13068-021-01966-2] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Accepted: 04/29/2021] [Indexed: 05/12/2023]
Abstract
BACKGROUND The interest in using methanol as a substrate to cultivate acetogens increased in recent years since it can be sustainably produced from syngas and has the additional benefit of reducing greenhouse gas emissions. Eubacterium limosum is one of the few acetogens that can utilize methanol, is genetically accessible and, therefore, a promising candidate for the recombinant production of biocommodities from this C1 carbon source. Although several genetic tools are already available for certain acetogens including E. limosum, the use of brightly fluorescent reporter proteins is still limited. RESULTS In this study, we expanded the genetic toolbox of E. limosum by implementing the fluorescence-activating and absorption shifting tag (FAST) as a fluorescent reporter protein. Recombinant E. limosum strains that expressed the gene encoding FAST in an inducible and constitutive manner were constructed. Cultivation of these recombinant strains resulted in brightly fluorescent cells even under anaerobic conditions. Moreover, we produced the biocommodities butanol and acetone from methanol with recombinant E. limosum strains. Therefore, we used E. limosum cultures that produced FAST-tagged fusion proteins of the bifunctional acetaldehyde/alcohol dehydrogenase or the acetoacetate decarboxylase, respectively, and determined the fluorescence intensity and product concentrations during growth. CONCLUSIONS The addition of FAST as an oxygen-independent fluorescent reporter protein expands the genetic toolbox of E. limosum. Moreover, our results show that FAST-tagged fusion proteins can be constructed without negatively impacting the stability, functionality, and productivity of the resulting enzyme. Finally, butanol and acetone can be produced from methanol using recombinant E. limosum strains expressing genes encoding fluorescent FAST-tagged fusion proteins.
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Affiliation(s)
- Maximilian Flaiz
- Institute of Microbiology and Biotechnology, Ulm University, Albert-Einstein-Allee 11, 89081, Ulm, Germany.
| | - Gideon Ludwig
- Institute of Microbiology and Biotechnology, Ulm University, Albert-Einstein-Allee 11, 89081, Ulm, Germany
| | - Frank R Bengelsdorf
- Institute of Microbiology and Biotechnology, Ulm University, Albert-Einstein-Allee 11, 89081, Ulm, Germany
| | - Peter Dürre
- Institute of Microbiology and Biotechnology, Ulm University, Albert-Einstein-Allee 11, 89081, Ulm, Germany
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12
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Rückel A, Hannemann J, Maierhofer C, Fuchs A, Weuster-Botz D. Studies on Syngas Fermentation With Clostridium carboxidivorans in Stirred-Tank Reactors With Defined Gas Impurities. Front Microbiol 2021; 12:655390. [PMID: 33936011 PMCID: PMC8081853 DOI: 10.3389/fmicb.2021.655390] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Accepted: 03/22/2021] [Indexed: 11/13/2022] Open
Abstract
Syngas fermentation processes with acetogenic bacteria like Clostridium carboxidivorans have been proven to be a promising approach for the conversion of CO-rich waste gases into short- and medium-chain alcohols. The challenge of synthesis gas impurities, on the other hand, has always been a major concern for establishing an industrial-scale process, since some of the trace components in waste gases, such as NH3, H2S, and NOx, can have inhibiting or even toxic effects on microbial growth and product formation. Thus, this study aims to identify the effects of the main trace impurities in syngas from gasification of biogenic residues by the supply of defined concentrations of trace impurities to the cultivation medium. Autotrophic gas fermentation studies were performed with C. carboxidivorans in batch-operated fully-controlled stirred-tank bioreactors with continuous gas supply (80% CO and 20% CO2). The syngas components NH3 and H2S had a positive effect on both growth and alcohol formation (ethanol, 1-butanol, and 1-hexanol). The maximum biomass concentration was increased by more than 50%, and the maximum ethanol concentration was more than doubled with 5.0 g L−1 NH4Cl or 1.0 g L−1 H2S provided by the addition of 2.2 g L−1 thioacetamide. The addition of the nitrogen oxide species nitrate and nitrite, on the other hand, reduced biomass growth as well as alcohol concentrations. Already, the supply of 0.1 g L−1 NaNO3 resulted in reduced growth and 25% reduction of the maximum ethanol concentration. The production of the longer chain alcohols 1-butanol and 1-hexanol was reduced as well. All NaNO2 concentrations tested showed a strong toxic effect on the metabolism of C. carboxidivorans, and neither CO consumption nor product formation was observed after addition. As a consequence, NOx components in syngas from the gasification of biogenic residues should be reduced by the gasification process and/or selectively removed from the syngas after gasification.
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Affiliation(s)
- Anton Rückel
- Institute of Biochemical Engineering, Technical University of Munich, Garching, Germany
| | - Jens Hannemann
- Institute of Biochemical Engineering, Technical University of Munich, Garching, Germany
| | - Carolin Maierhofer
- Institute of Biochemical Engineering, Technical University of Munich, Garching, Germany
| | - Alexander Fuchs
- Institute of Biochemical Engineering, Technical University of Munich, Garching, Germany
| | - Dirk Weuster-Botz
- Institute of Biochemical Engineering, Technical University of Munich, Garching, Germany
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13
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Zhu C, Du G, Zhang J, Xue C. A high-efficient strategy for combinatorial engineering paralogous gene family: A case study on histidine kinases in Clostridium. Biotechnol Bioeng 2021; 118:2770-2780. [PMID: 33871069 DOI: 10.1002/bit.27796] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 04/08/2021] [Accepted: 04/17/2021] [Indexed: 11/10/2022]
Abstract
Microorganisms harbor bulks of functionally similar or undefined genes, which belong to paralogous gene family. There is a necessity of exploring combinatorial or interactive functions of these genes, but conventional loss-of-function strategy with one-by-one rounds suffers extremely low efficiency for generating mutant libraries with all gene permutations. Here, taking histidine kinases (HKs) in Clostridium acetobutylicum as a proof-of-concept, we developed a multi-plasmid cotransformation strategy for generating all theoretical HKs combinations in one round. For five HKs with 31 theoretical combinations, the library containing 22 mutants within all the possible HKs-inactivated combinations was constructed with 11 days compared to 242 days by conventional strategy, while the other 9 combinations cannot survive. Six mutants with the enhanced butanol production and tolerance were obtained with changes of cell development during fermentation, one of which could produce 54.2% more butanol (56.4% more solvents), while the butanol production of other mutants was unchanged or decreased. The cotransformation strategy demonstrated potentials for fast exploring pleiotropic function of paralogous family genes in cell survival, cell development, and target product metabolism.
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Affiliation(s)
- Chao Zhu
- School of Bioengineering, Engineering Research Center of Application and Transformation for Synthetic Biology, Dalian University of Technology, Dalian, China.,Ningbo Institute of Dalian University of Technology, Ningbo, China
| | - Guangqing Du
- School of Bioengineering, Engineering Research Center of Application and Transformation for Synthetic Biology, Dalian University of Technology, Dalian, China.,Ningbo Institute of Dalian University of Technology, Ningbo, China
| | - Jie Zhang
- School of Bioengineering, Engineering Research Center of Application and Transformation for Synthetic Biology, Dalian University of Technology, Dalian, China
| | - Chuang Xue
- School of Bioengineering, Engineering Research Center of Application and Transformation for Synthetic Biology, Dalian University of Technology, Dalian, China.,Ningbo Institute of Dalian University of Technology, Ningbo, China
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14
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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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15
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Vees CA, Neuendorf CS, Pflügl S. Towards continuous industrial bioprocessing with solventogenic and acetogenic clostridia: challenges, progress and perspectives. J Ind Microbiol Biotechnol 2020; 47:753-787. [PMID: 32894379 PMCID: PMC7658081 DOI: 10.1007/s10295-020-02296-2] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Accepted: 07/20/2020] [Indexed: 12/11/2022]
Abstract
The sustainable production of solvents from above ground carbon is highly desired. Several clostridia naturally produce solvents and use a variety of renewable and waste-derived substrates such as lignocellulosic biomass and gas mixtures containing H2/CO2 or CO. To enable economically viable production of solvents and biofuels such as ethanol and butanol, the high productivity of continuous bioprocesses is needed. While the first industrial-scale gas fermentation facility operates continuously, the acetone-butanol-ethanol (ABE) fermentation is traditionally operated in batch mode. This review highlights the benefits of continuous bioprocessing for solvent production and underlines the progress made towards its establishment. Based on metabolic capabilities of solvent producing clostridia, we discuss recent advances in systems-level understanding and genome engineering. On the process side, we focus on innovative fermentation methods and integrated product recovery to overcome the limitations of the classical one-stage chemostat and give an overview of the current industrial bioproduction of solvents.
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Affiliation(s)
- Charlotte Anne Vees
- Institute of Chemical, Environmental and Bioscience Engineering, Research Area Biochemical Engineering, Technische Universität Wien, Gumpendorfer Straße 1a, 1060 Vienna, Austria
| | - Christian Simon Neuendorf
- Institute of Chemical, Environmental and Bioscience Engineering, Research Area Biochemical Engineering, Technische Universität Wien, Gumpendorfer Straße 1a, 1060 Vienna, Austria
| | - Stefan Pflügl
- Institute of Chemical, Environmental and Bioscience Engineering, Research Area Biochemical Engineering, Technische Universität Wien, Gumpendorfer Straße 1a, 1060 Vienna, Austria
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16
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Degeneration of industrial bacteria caused by genetic instability. World J Microbiol Biotechnol 2020; 36:119. [DOI: 10.1007/s11274-020-02901-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Accepted: 07/14/2020] [Indexed: 12/11/2022]
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17
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Zhang J, Hong W, Guo L, Wang Y, Wang Y. Enhancing plasmid transformation efficiency and enabling CRISPR-Cas9/Cpf1-based genome editing in Clostridium tyrobutyricum. Biotechnol Bioeng 2020; 117:2911-2917. [PMID: 32437010 DOI: 10.1002/bit.27435] [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: 04/03/2020] [Revised: 04/30/2020] [Accepted: 05/19/2020] [Indexed: 12/16/2022]
Abstract
Clostridium tyrobutyricum ATCC 25755 is known as a natural hyper-butyrate producer with great potentials as an excellent platform to be engineered for valuable biochemical production from renewable resources. However, limited transformation efficiency and the lack of genetic manipulation tools have hampered the broader applications of this micro-organism. In this study, the effects of Type I restriction-modification system and native plasmid on conjugation efficiency of C. tyrobutyricum were investigated through gene deletion. The deletion of Type I restriction endonuclease resulted in a 3.7-fold increase in conjugation efficiency, while the additional elimination of the native plasmid further enhanced conjugation efficiency to 6.05 ± 0.75 × 103 CFU/ml-donor, which was 15.3-fold higher than the wild-type strain. Fermentation results indicated that the deletion of those two genetic elements did not significantly influence the end-products production in the resultant mutant ΔRMIΔNP. Thanks to the increased conjugation efficiency, the CRISPR-Cas9/Cpf1 systems, which previously could not be implemented in C. tyrobutyricum, were successfully employed for genome editing in ΔRMIΔNP with an efficiency of 12.5-25%. Altogether, approaches we developed herein offer valuable guidance for establishing efficient DNA transformation methods in nonmodel micro-organisms. The ΔRMIΔNP mutant can serve as a great chassis to be engineered for diverse valuable biofuel and biochemical production.
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Affiliation(s)
- Jie Zhang
- Department of Biosystems Engineering, Auburn University, Auburn, Alabama.,Key Laboratory for Feed Biotechnology of the Ministry of Agriculture and Rural Affairs, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Wei Hong
- Department of Biosystems Engineering, Auburn University, Auburn, Alabama.,Key Laboratory of Endemic and Ethnic Diseases, Guizhou Medical University, Ministry of Education, Guiyang, China
| | - Liang Guo
- College of Environmental Science and Engineering, Ocean University of China, Qingdao, China
| | - Yifen Wang
- Department of Biosystems Engineering, Auburn University, Auburn, Alabama.,Center for Bioenergy and Bioproducts, Auburn University, Auburn, Alabama
| | - Yi Wang
- Department of Biosystems Engineering, Auburn University, Auburn, Alabama.,Center for Bioenergy and Bioproducts, Auburn University, Auburn, Alabama
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18
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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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19
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COMPUTER RECOGNITION OF CHEMICAL SUBSTANCES BASED ON THEIR ELECTROPHYSIOLOGICAL CHARACTERISTICS. BIOTECHNOLOGIA ACTA 2019. [DOI: 10.15407/biotech12.05.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
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20
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21
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A Strongly Fluorescing Anaerobic Reporter and Protein-Tagging System for Clostridium Organisms Based on the Fluorescence-Activating and Absorption-Shifting Tag Protein (FAST). Appl Environ Microbiol 2019; 85:AEM.00622-19. [PMID: 31076434 DOI: 10.1128/aem.00622-19] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Accepted: 05/07/2019] [Indexed: 01/03/2023] Open
Abstract
Visualizing protein localization and characterizing gene expression activity in live Clostridium cells is limited for lack of a real-time, highly fluorescent, oxygen-independent reporter system. Enzymatic reporter systems have been used successfully for many years with Clostridium spp.; however, these assays do not allow for real-time analysis of gene expression activity with flow cytometry or for visualizing protein localization through fusion proteins. Commonly used fluorescent reporter proteins require oxygen for chromophore maturation and cannot be used for most strictly anaerobic Clostridium organisms. Here we show that the fluorescence-activating and absorption-shifting tag protein (FAST), when associated with the fluorogenic ligand 4-hydroxy-3-methylbenzylidene-rhodanine (HMBR; now commercially available) and other commercially available ligands, is highly fluorescent in Clostridium acetobutylicum under anaerobic conditions. Using flow cytometry and a fluorescence microplate reader, we demonstrated FAST as a reporter system by employing the promoters of the C. acetobutylicum thiolase (thl), acetoacetate decarboxylase (adc), and phosphotransbutyrylase (ptb) metabolic genes, as well as a mutant Pthl and modified ribosome binding site (RBS) versions of Padc and Pptb Flow cytometry-based sorting was efficient and fast in sorting FAST-expressing cells, and positively and negatively sorted cells could be effectively recultured. FAST was also used to tag and examine protein localization of the predicted cell division FtsZ partner protein, ZapA, to visualize the divisome localization in live C. acetobutylicum cells. Our findings suggest that FAST can be used to further investigate Clostridium divisomes and more broadly the localization and expression levels of other proteins in Clostridium organisms, thus enabling cell biology studies with these organisms.IMPORTANCE FAST in association with the fluorogenic ligand HMBR is characterized as a successful, highly fluorescent reporter system in C. acetobutylicum FAST can be used to distinguish between promoters in live cells using flow cytometry or a fluorescence microplate reader and can be used to tag and examine protein localization in live, anaerobically grown cells. Given that FAST is highly fluorescent under anaerobic conditions, it can be used in several applications of this and likely many Clostridium organisms and other strict anaerobes, including studies involving cell sorting, sporulation dynamics, and population characterization in pure as well as mixed cultures, such as those in various native or synthetic microbiomes and syntrophic cultures.
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22
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Okonkwo CC, Ujor V, Ezeji TC. Chromosomal integration of aldo-keto-reductase and short-chain dehydrogenase/reductase genes in Clostridium beijerinckii NCIMB 8052 enhanced tolerance to lignocellulose-derived microbial inhibitory compounds. Sci Rep 2019; 9:7634. [PMID: 31114009 PMCID: PMC6529405 DOI: 10.1038/s41598-019-44061-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2019] [Accepted: 05/08/2019] [Indexed: 12/23/2022] Open
Abstract
In situ detoxification of lignocellulose-derived microbial inhibitory compounds is an economical strategy for the fermentation of lignocellulose-derived sugars to fuels and chemicals. In this study, we investigated homologous integration and constitutive expression of Cbei_3974 and Cbei_3904, which encode aldo-keto reductase and previously annotated short chain dehydrogenase/reductase, respectively, in Clostridium beijerinckii NCIMB 8052 (Cb), resulting in two strains: Cb_3974 and Cb_3904. Expression of Cbei_3974 led to 2-fold increase in furfural detoxification relative to Cb_3904 and Cb_wild type. Correspondingly, butanol production was up to 1.2-fold greater in furfural-challenged cultures of Cb_3974 relative to Cb_3904 and Cb_wild type. With 4-hydroxybezaldehyde and syringaldehyde supplementation, Cb_3974 showed up to 2.4-fold increase in butanol concentration when compared to Cb_3904 and Cb_wild type. Syringic and vanillic acids were considerably less deleterious to all three strains of Cb tested. Overall, Cb_3974 showed greater tolerance to furfural, 4-hydroxybezaldehyde, and syringaldehyde with improved capacity for butanol production. Hence, development of Cb_3974 represents a significant progress towards engineering solventogenic Clostridium species that are tolerant to lignocellulosic biomass hydrolysates as substrates for ABE fermentation.
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Affiliation(s)
- Christopher Chukwudi Okonkwo
- Department of Animal Sciences, The Ohio State University, and Ohio State Agricultural Research and Development Center (OARDC), 305 Gerlaugh Hall, 1680 Madison Avenue, Wooster, OH, 44691, USA
| | - Victor Ujor
- Bioenergy and Biological Waste Management Program, Agricultural Technical Institute, The Ohio State University, 1328 Dover Road, Wooster, OH, 44691, USA
| | - Thaddeus Chukwuemeka Ezeji
- Department of Animal Sciences, The Ohio State University, and Ohio State Agricultural Research and Development Center (OARDC), 305 Gerlaugh Hall, 1680 Madison Avenue, Wooster, OH, 44691, USA.
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23
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σ 54 (σ L) plays a central role in carbon metabolism in the industrially relevant Clostridium beijerinckii. Sci Rep 2019; 9:7228. [PMID: 31076628 PMCID: PMC6510779 DOI: 10.1038/s41598-019-43822-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Accepted: 04/23/2019] [Indexed: 11/09/2022] Open
Abstract
The solventogenic C. beijerinckii DSM 6423, a microorganism that naturally produces isopropanol and butanol, was previously modified by random mutagenesis. In this work, one of the resulting mutants was characterized. This strain, selected with allyl alcohol and designated as the AA mutant, shows a dominant production of acids, a severely diminished butanol synthesis capacity, and produces acetone instead of isopropanol. Interestingly, this solvent-deficient strain was also found to have a limited consumption of two carbohydrates and to be still able to form spores, highlighting its particular phenotype. Sequencing of the AA mutant revealed point mutations in several genes including CIBE_0767 (sigL), which encodes the σ54 sigma factor. Complementation with wild-type sigL fully restored solvent production and sugar assimilation and RT-qPCR analyses revealed its transcriptional control of several genes related to solventogensis, demonstrating the central role of σ54 in C. beijerinckii DSM 6423. Comparative genomics analysis suggested that this function is conserved at the species level, and this hypothesis was further confirmed through the deletion of sigL in the model strain C. beijerinckii NCIMB 8052.
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Kolesinska B, Fraczyk J, Binczarski M, Modelska M, Berlowska J, Dziugan P, Antolak H, Kaminski ZJ, Witonska IA, Kregiel D. Butanol Synthesis Routes for Biofuel Production: Trends and Perspectives. MATERIALS (BASEL, SWITZERLAND) 2019; 12:E350. [PMID: 30678076 PMCID: PMC6384976 DOI: 10.3390/ma12030350] [Citation(s) in RCA: 66] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Revised: 01/18/2019] [Accepted: 01/21/2019] [Indexed: 12/05/2022]
Abstract
Butanol has similar characteristics to gasoline, and could provide an alternative oxygenate to ethanol in blended fuels. Butanol can be produced either via the biotechnological route, using microorganisms such as clostridia, or by the chemical route, using petroleum. Recently, interest has grown in the possibility of catalytic coupling of bioethanol into butanol over various heterogenic systems. This reaction has great potential, and could be a step towards overcoming the disadvantages of bioethanol as a sustainable transportation fuel. This paper summarizes the latest research on butanol synthesis for the production of biofuels in different biotechnological and chemical ways; it also compares potentialities and limitations of these strategies.
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Affiliation(s)
- Beata Kolesinska
- Institute of Organic Chemistry, Faculty of Chemistry, Lodz University of Technology, Zeromskiego 116, 90-924 Lodz, Poland.
| | - Justyna Fraczyk
- Institute of Organic Chemistry, Faculty of Chemistry, Lodz University of Technology, Zeromskiego 116, 90-924 Lodz, Poland.
| | - Michal Binczarski
- Institute of General and Ecological Chemistry, Faculty of Chemistry, Lodz University of Technology, Zeromskiego 116, 90-924 Lodz, Poland.
| | - Magdalena Modelska
- Institute of General and Ecological Chemistry, Faculty of Chemistry, Lodz University of Technology, Zeromskiego 116, 90-924 Lodz, Poland.
| | - Joanna Berlowska
- Institute of Fermentation Technology and Microbiology, Faculty of Biochemistry and Food Sciences, Lodz University of Technology, Wolczanska 171/173, 90-924 Lodz, Poland.
| | - Piotr Dziugan
- Institute of Fermentation Technology and Microbiology, Faculty of Biochemistry and Food Sciences, Lodz University of Technology, Wolczanska 171/173, 90-924 Lodz, Poland.
| | - Hubert Antolak
- Institute of Fermentation Technology and Microbiology, Faculty of Biochemistry and Food Sciences, Lodz University of Technology, Wolczanska 171/173, 90-924 Lodz, Poland.
| | - Zbigniew J Kaminski
- Institute of Organic Chemistry, Faculty of Chemistry, Lodz University of Technology, Zeromskiego 116, 90-924 Lodz, Poland.
| | - Izabela A Witonska
- Institute of General and Ecological Chemistry, Faculty of Chemistry, Lodz University of Technology, Zeromskiego 116, 90-924 Lodz, Poland.
| | - Dorota Kregiel
- Institute of Fermentation Technology and Microbiology, Faculty of Biochemistry and Food Sciences, Lodz University of Technology, Wolczanska 171/173, 90-924 Lodz, Poland.
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25
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Charubin K, Bennett RK, Fast AG, Papoutsakis ET. Engineering Clostridium organisms as microbial cell-factories: challenges & opportunities. Metab Eng 2018; 50:173-191. [DOI: 10.1016/j.ymben.2018.07.012] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Revised: 07/18/2018] [Accepted: 07/19/2018] [Indexed: 11/25/2022]
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26
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Ralston MT, Papoutsakis ET. RNAseq‐based transcriptome assembly of
Clostridium acetobutylicum
for functional genome annotation and discovery. AIChE J 2018. [DOI: 10.1002/aic.16396] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Matthew T. Ralston
- Molecular Biotechnology Laboratory, Delaware Biotechnology Institute University of Delaware Newark DE 19711
- Center for Bioinformatics and Computational Biology University of Delaware Newark DE 19711
| | - Eleftherios T. Papoutsakis
- Dept. of Chemical and Biomolecular Engineering University of Delaware Newark DE 19711
- Molecular Biotechnology Laboratory, Delaware Biotechnology Institute University of Delaware Newark DE 19711
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27
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Reviving the Weizmann process for commercial n-butanol production. Nat Commun 2018; 9:3682. [PMID: 30206218 PMCID: PMC6134114 DOI: 10.1038/s41467-018-05661-z] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2017] [Accepted: 07/11/2018] [Indexed: 12/25/2022] Open
Abstract
Developing a commercial process for the biological production of n-butanol is challenging as it needs to combine high titer, yield, and productivities. Here we engineer Clostridium acetobutylicum to stably and continuously produce n-butanol on a mineral media with glucose as sole carbon source. We further design a continuous process for fermentation of high concentration glucose syrup using in situ extraction of alcohols by distillation under low pressure and high cell density cultures to increase the titer, yield, and productivity of n-butanol production to the level of 550 g/L, 0.35 g/g, and 14 g/L/hr, respectively. This process provides a mean to produce n-butanol at performance levels comparable to that of corn wet milling ethanol plants using yeast as a biocatalyst. It may hold the potential to be scaled-up at pilot and industrial levels for the commercial production of n-butanol. Organic solvent n-butanol is produced mainly by petrochemical method. Here, the authors revive the historical Weizmann process by engineering Clostridium acetobutylicum strain and developing low pressure distillation and high cell density cultures for n-butanol continuous production at high-yield titer and productivity.
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28
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Small and Low but Potent: the Complex Regulatory Role of the Small RNA SolB in Solventogenesis in Clostridium acetobutylicum. Appl Environ Microbiol 2018; 84:AEM.00597-18. [PMID: 29728392 DOI: 10.1128/aem.00597-18] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Accepted: 05/01/2018] [Indexed: 12/15/2022] Open
Abstract
The recently revived Clostridium acetobutylicum-based acetone-butanol-ethanol (ABE) fermentation is widely celebrated and studied for its impact on industrial biotechnology. C. acetobutylicum has been studied and engineered extensively, yet critical areas of the molecular basis for how solvent formation is regulated remain unresolved. The core solventogenic genes (adhE1/aad, ctfA, ctfB, and adc) are carried on the sol locus of the pSOL1 megaplasmid, whose loss leads to asporogenous, "degenerate" cells. The sol locus includes a noncoding small RNA (sRNA), SolB, whose role is presumed to be critical for solventogenesis but has eluded resolution. In the present study, SolB overexpression downregulated the sol-locus genes at the transcript level, resulting in attenuated protein expression and a solvent-deficient phenotype, thus suggesting that SolB affects expression of all sol-locus transcripts and seemingly validating its hypothesized role as a repressor. However, deletion of solB resulted in a total loss of acetone production and severe attenuation of butanol formation, with complex effects on sol-locus genes and proteins: it had a small impact on adc mRNA or its corresponding protein (acetoacetate decarboxylase) expression level, somewhat reduced adhE1 and ctfA-ctfB mRNA levels, and abolished the ctfA-ctfB-encoded coenzyme A transferase (CoAT) activity. Computational predictions support a model whereby SolB expressed at low levels enables the stabilization and translation of sol-locus transcripts to facilitate tuning of the production of various solvents depending on the prevailing culture conditions. A key predicted SolB target is the ribosome binding site (RBS) of the ctfA transcript, and this was verified by expressing variants of the ctfA-ctfB genes to demonstrate the importance of SolB for acetone formation.IMPORTANCE Small noncoding RNAs regulate many important metabolic and developmental programs in prokaryotes, but their role in anaerobes has been explored minimally. Regulation of solvent formation in the important industrial organism C. acetobutylicum remains incompletely understood. While the genes for solvent formation and their promoters are known, the means by which this organism tunes the ratios of key solvents, notably the butanol/acetone ratio to balance its electron resources, remains unknown. Significantly, the roles of several coding and noncoding genes in the sol locus in tuning the solvent formation ratios have not been explored. Here we show that the small RNA SolB fine-tunes the expression of solvents, with acetone formation being a key target, by regulating the translation of the acetone formation rate-limiting enzyme, the coenzyme A transferase (CoAT). It is notable that SolB expressed at very low levels enables CoAT translation, while at high, nonphysiological expression levels, it leads to degradation of the corresponding transcript.
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A plasmid borne, functionally novel glycoside hydrolase family 30 subfamily 8 endoxylanase from solventogenic Clostridium. Biochem J 2018; 475:1533-1551. [PMID: 29626157 PMCID: PMC5934979 DOI: 10.1042/bcj20180050] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2018] [Revised: 03/28/2018] [Accepted: 04/03/2018] [Indexed: 11/24/2022]
Abstract
Glycoside hydrolase family 30 subfamily 8 (GH30-8) β-1,4-endoxylanases are known for their appendage-dependent function requiring recognition of an α-1,2-linked glucuronic acid (GlcA) common to glucuronoxylans for hydrolysis. Structural studies have indicated that the GlcA moiety of glucuronoxylans is coordinated through six hydrogen bonds and a salt bridge. These GlcA-dependent endoxylanases do not have significant activity on xylans that do not bear GlcA substitutions such as unsubstituted linear xylooligosaccharides or cereal bran arabinoxylans. In the present study, we present the structural and biochemical characteristics of xylanase 30A from Clostridium acetobutylicum (CaXyn30A) which was originally selected for study due to predicted structural differences within the GlcA coordination loops. Amino acid sequence comparisons indicated that this Gram-positive-derived GH30-8 more closely resembles Gram-negative derived forms of these endoxylanases: a hypothesis borne out in the developed crystallographic structure model of the CaXyn30A catalytic domain (CaXyn30A-CD). CaXyn30A-CD hydrolyzes xylans to linear and substituted oligoxylosides showing the greatest rate with the highly arabinofuranose (Araf)-substituted cereal arabinoxylans. CaXyn30A-CD hydrolyzes xylooligosaccharides larger than xylotriose and shows an increased relative rate of hydrolysis for xylooligosaccharides containing α-1,2-linked arabinofuranose substitutions. Biochemical analysis confirms that CaXyn30A benefits from five xylose-binding subsites which extend from the −3 subsite to the +2 subsite of the binding cleft. These studies indicate that CaXyn30A is a GlcA-independent endoxylanase that may have evolved for the preferential recognition of α-1,2-Araf substitutions on xylan chains.
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Máté de Gérando H, Wasels F, Bisson A, Clement B, Bidard F, Jourdier E, López-Contreras AM, Lopes Ferreira N. Genome and transcriptome of the natural isopropanol producer Clostridium beijerinckii DSM6423. BMC Genomics 2018; 19:242. [PMID: 29636009 PMCID: PMC5894183 DOI: 10.1186/s12864-018-4636-7] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2017] [Accepted: 03/28/2018] [Indexed: 12/23/2022] Open
Abstract
Background There is a worldwide interest for sustainable and environmentally-friendly ways to produce fuels and chemicals from renewable resources. Among them, the production of acetone, butanol and ethanol (ABE) or Isopropanol, Butanol and Ethanol (IBE) by anaerobic fermentation has already a long industrial history. Isopropanol has recently received a specific interest and the best studied natural isopropanol producer is C. beijerinckii DSM 6423 (NRRL B-593). This strain metabolizes sugars into a mix of IBE with only low concentrations of ethanol produced (< 1 g/L). However, despite its relative ancient discovery, few genomic details have been described for this strain. Research efforts including omics and genetic engineering approaches are therefore needed to enable the use of C. beijerinckii as a microbial cell factory for production of isopropanol. Results The complete genome sequence and a first transcriptome analysis of C. beijerinckii DSM 6423 are described in this manuscript. The combination of MiSeq and de novo PacBio sequencing revealed a 6.38 Mbp chromosome containing 6254 genomic objects. Three Mobile Genetic Elements (MGE) were also detected: a linear double stranded DNA bacteriophage (ϕ6423) and two plasmids (pNF1 and pNF2) highlighting the genomic complexity of this strain. A first RNA-seq transcriptomic study was then performed on 3 independent glucose fermentations. Clustering analysis allowed us to detect some key gene clusters involved in the main life cycle steps (acidogenesis, solvantogenesis and sporulation) and differentially regulated among the fermentation. These putative clusters included some putative metabolic operons comparable to those found in other reference strains such as C. beijerinckii NCIMB 8052 or C. acetobutylicum ATCC 824. Interestingly, only one gene was encoding for an alcohol dehydrogenase converting acetone into isopropanol, suggesting a single genomic event occurred on this strain to produce isopropanol. Conclusions We present the full genome sequence of Clostridium beijerinckii DSM 6423, providing a complete genetic background of this strain. This offer a great opportunity for the development of dedicated genetic tools currently lacking for this strain. Moreover, a first RNA-seq analysis allow us to better understand the global metabolism of this natural isopropanol producer, opening the door to future targeted engineering approaches. Electronic supplementary material The online version of this article (10.1186/s12864-018-4636-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Hadrien Máté de Gérando
- Wageningen Food and Biobased Research, Bornse Weilanden 9, 6709WG, Wageningen, The Netherlands.,IFP Energies Nouvelles, 1 et 4 avenue de Bois-Préau, 92852, Rueil-Malmaison, France
| | - François Wasels
- IFP Energies Nouvelles, 1 et 4 avenue de Bois-Préau, 92852, Rueil-Malmaison, France
| | - Angélique Bisson
- IFP Energies Nouvelles, 1 et 4 avenue de Bois-Préau, 92852, Rueil-Malmaison, France
| | - Benjamin Clement
- IFP Energies Nouvelles, 1 et 4 avenue de Bois-Préau, 92852, Rueil-Malmaison, France
| | - Frédérique Bidard
- IFP Energies Nouvelles, 1 et 4 avenue de Bois-Préau, 92852, Rueil-Malmaison, France
| | - Etienne Jourdier
- IFP Energies Nouvelles, 1 et 4 avenue de Bois-Préau, 92852, Rueil-Malmaison, France
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Identification of large cryptic plasmids in Clostridioides (Clostridium) difficile. Plasmid 2018; 96-97:25-38. [DOI: 10.1016/j.plasmid.2018.04.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Revised: 04/12/2018] [Accepted: 04/23/2018] [Indexed: 12/17/2022]
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Sun C, Zhang S, Xin F, Shanmugam S, Wu YR. Genomic comparison of Clostridium species with the potential of utilizing red algal biomass for biobutanol production. BIOTECHNOLOGY FOR BIOFUELS 2018; 11:42. [PMID: 29467820 PMCID: PMC5815214 DOI: 10.1186/s13068-018-1044-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Accepted: 02/05/2018] [Indexed: 05/17/2023]
Abstract
BACKGROUND Sustainable biofuels, which are widely considered as an attractive alternative to fossil fuels, can be generated by utilizing various biomass from the environment. Marine biomass, such as red algal biomass, is regarded as one potential renewable substrate source for biofuels conversion due to its abundance of fermentable sugars (e.g., galactose). Previous studies focused on the enhancement of biofuels production from different Clostridium species; however, there has been limited investigation into their metabolic pathways, especially on the conversion of biofuels from galactose, via whole genomic comparison and evolutionary analysis. RESULTS Two galactose-utilizing Clostridial strains were examined and identified as Clostridium acetobutylicum strain WA and C. beijerinckii strain WB. Via the genomic sequencing of both strains, the comparison of the whole genome together with the relevant protein prediction of 33 other Clostridium species was established to reveal a clear genome profile based upon various genomic features. Among them, five representative strains, including C. beijerinckii NCIMB14988, C. diolis DSM 15410, C. pasteurianum BC1, strain WA and WB, were further discussed to demonstrate the main differences among their respective metabolic pathways, especially in their carbohydrate metabolism. The metabolic pathways involved in the generation of biofuels and other potential products (e.g., riboflavin) were also reconstructed based on the utilization of marine biomass. Finally, a batch fermentation process was performed to verify the fermentative products from strains WA and WB using 60 g/L of galactose, which is the main hydrolysate from algal biomass. It was observed that strain WA and WB could produce up to 16.98 and 12.47 g/L of biobutanol, together with 21,560 and 10,140 mL/L biohydrogen, respectively. CONCLUSIONS The determination of the production of various biofuels by both strains WA and WB and their genomic comparisons with other typical Clostridium species on the analysis of various metabolic pathways was presented. Through the identification of their metabolic pathways, which are involved in the conversion of galactose into various potential products, such as biobutanol, the obtained results extend the current insight into the potential capability of utilizing marine red algal biomass and provide a systematic investigation into the relationship between this genus and the generation of sustainable bioenergy.
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Affiliation(s)
- Chongran Sun
- Department of Biology, Shantou University, Shantou, 515063 Guangdong China
| | - Shuangfei Zhang
- Department of Biology, Shantou University, Shantou, 515063 Guangdong China
| | - Fengxue Xin
- Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou, 515063 Guangdong China
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 211816 Jiangsu China
| | | | - Yi-Rui Wu
- Department of Biology, Shantou University, Shantou, 515063 Guangdong China
- Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou, 515063 Guangdong China
- STU-UNIVPM Joint Algal Research Center, Shantou University, Shantou, 515063 Guangdong China
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A systematically chromosomally engineered Escherichia coli efficiently produces butanol. Metab Eng 2017; 44:284-292. [PMID: 29102594 DOI: 10.1016/j.ymben.2017.10.014] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Revised: 10/27/2017] [Accepted: 10/30/2017] [Indexed: 11/22/2022]
Abstract
Biotechnological production of butanol in heterologous hosts has recently attracted many interests. Of the heterologous hosts investigated to date, engineered Escherichia coli has shown a superior butanol yield than the natural butanol-producing clostridial strains. However, all reported butanol-producing E. coli strains contain vectors and inducible promoters, which means antibiotics and inducers are required in the fermentation. The aim of this study was to develop a completely chromosomally engineered E. coli strain capable of producing butanol efficiently in the absence of vectors, antibiotics, and inducers. The challenges are the expression strength of chromosomally engineered genes under constitutive promoters is much weaker than the vector engineered genes under inducible promoters. To address these challenges, the butanol pathway was engineered into the chromosome in the first place, then the host and the butanol pathway was iteratively engineered through rational and non-rational strategies to develop an efficient butanol producer where the heterologous butanol pathway fits the host well. Finally, a systematically chromosomally engineered E. coli strain EB243, in which 33 native genes were deleted and 5 heterologous genes were introduced, was developed. Strain EB243 could produce 20g/L butanol with a yield of 34% (w/w, 83% of theoretical yield) in batch fermentation without any antibiotics and inducers, thus showed great potential for industrial application. This work also demonstrated a procedure on how to integrate the existing knowledge to engineer a strain with industrial application potential.
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Wasels F, Jean-Marie J, Collas F, López-Contreras AM, Lopes Ferreira N. A two-plasmid inducible CRISPR/Cas9 genome editing tool for Clostridium acetobutylicum. J Microbiol Methods 2017; 140:5-11. [PMID: 28610973 DOI: 10.1016/j.mimet.2017.06.010] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2017] [Revised: 06/09/2017] [Accepted: 06/09/2017] [Indexed: 01/18/2023]
Abstract
CRISPR/Cas-based genetic engineering has revolutionised molecular biology in both eukaryotes and prokaryotes. Several tools dedicated to the genomic transformation of the Clostridium genus of Gram-positive bacteria have been described in the literature; however, the integration of large DNA fragments still remains relatively limited. In this study, a CRISPR/Cas9 genome editing tool using a two-plasmid strategy was developed for the solventogenic strain Clostridium acetobutylicum ATCC 824. Codon-optimised cas9 from Streptococcus pyogenes was placed under the control of an anhydrotetracycline-inducible promoter on one plasmid, while the gRNA expression cassettes and editing templates were located on a second plasmid. Through the sequential introduction of these vectors into the cell, we achieved highly accurate genome modifications, including nucleotide substitution, gene deletion and cassette insertion up to 3.6kb. To demonstrate its potential, this genome editing tool was used to generate a marker-free mutant of ATCC 824 that produced an isopropanol-butanol-ethanol mixture. Whole-genome sequencing confirmed that no off-target modifications were present in the mutants. Such a tool is a prerequisite for efficient metabolic engineering in this solventogenic strain and provides an alternative editing strategy that might be applicable to other Clostridium strains.
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Affiliation(s)
- François Wasels
- IFP Energies nouvelles, Biotechnology Department, 1 et 4 avenue de Bois-Préau, 92852 Rueil-Malmaison, France.
| | - Jennifer Jean-Marie
- IFP Energies nouvelles, Biotechnology Department, 1 et 4 avenue de Bois-Préau, 92852 Rueil-Malmaison, France
| | - Florent Collas
- Wageningen Food and Biobased Research, Bornse Weilanden 9, 6709WG Wageningen, The Netherlands
| | - Ana M López-Contreras
- Wageningen Food and Biobased Research, Bornse Weilanden 9, 6709WG Wageningen, The Netherlands
| | - Nicolas Lopes Ferreira
- IFP Energies nouvelles, Biotechnology Department, 1 et 4 avenue de Bois-Préau, 92852 Rueil-Malmaison, France
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Genome Editing in Clostridium saccharoperbutylacetonicum N1-4 with the CRISPR-Cas9 System. Appl Environ Microbiol 2017; 83:AEM.00233-17. [PMID: 28258147 DOI: 10.1128/aem.00233-17] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2017] [Accepted: 02/26/2017] [Indexed: 12/12/2022] Open
Abstract
Clostridium saccharoperbutylacetonicum N1-4 is well known as a hyper-butanol-producing strain. However, the lack of genetic engineering tools hinders further elucidation of its solvent production mechanism and development of more robust strains. In this study, we set out to develop an efficient genome engineering system for this microorganism based on the clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated 9 (CRISPR-Cas9) system. First, the functionality of the CRISPR-Cas9 system previously customized for Clostridium beijerinckii was evaluated in C. saccharoperbutylacetonicum by targeting pta and buk, two essential genes for acetate and butyrate production, respectively. pta and buk single and double deletion mutants were successfully obtained based on this system. However, the genome engineering efficiency was rather low (the mutation rate is <20%). Therefore, the efficiency was further optimized by evaluating various promoters for guide RNA (gRNA) expression. With promoter P J23119 , we achieved a mutation rate of 75% for pta deletion without serial subculturing as suggested previously for C. beijerinckii Thus, this developed CRISPR-Cas9 system is highly desirable for efficient genome editing in C. saccharoperbutylacetonicum Batch fermentation results revealed that both the acid and solvent production profiles were altered due to the disruption of acid production pathways; however, neither acetate nor butyrate production was eliminated with the deletion of the corresponding gene. The butanol production, yield, and selectivity were improved in mutants, depending on the fermentation medium. In the pta buk double deletion mutant, the butanol production in P2 medium reached 19.0 g/liter, which is one of the highest levels ever reported from batch fermentations.IMPORTANCE An efficient CRISPR-Cas9 genome engineering system was developed for C. saccharoperbutylacetonicum N1-4. This paves the way for elucidating the solvent production mechanism in this hyper-butanol-producing microorganism and developing strains with desirable butanol-producing features. This tool can be easily adapted for use in closely related microorganisms. As also reported by others, here we demonstrated with solid data that the highly efficient expression of gRNA is the key factor determining the efficiency of CRISPR-Cas9 for genome editing. The protocol developed in this study can provide essential references for other researchers who work in the areas of metabolic engineering and synthetic biology. The developed mutants can be used as excellent starting strains for development of more robust ones for desirable solvent production.
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Poehlein A, Solano JDM, Flitsch SK, Krabben P, Winzer K, Reid SJ, Jones DT, Green E, Minton NP, Daniel R, Dürre P. Microbial solvent formation revisited by comparative genome analysis. BIOTECHNOLOGY FOR BIOFUELS 2017; 10:58. [PMID: 28286553 PMCID: PMC5343299 DOI: 10.1186/s13068-017-0742-z] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2016] [Accepted: 02/28/2017] [Indexed: 05/04/2023]
Abstract
BACKGROUND Microbial formation of acetone, isopropanol, and butanol is largely restricted to bacteria belonging to the genus Clostridium. This ability has been industrially exploited over the last 100 years. The solvents are important feedstocks for the chemical and biofuel industry. However, biological synthesis suffers from high substrate costs and competition from chemical synthesis supported by the low price of crude oil. To render the biotechnological production economically viable again, improvements in microbial and fermentation performance are necessary. However, no comprehensive comparisons of respective species and strains used and their specific abilities exist today. RESULTS The genomes of a total 30 saccharolytic Clostridium strains, representative of the species Clostridium acetobutylicum, C. aurantibutyricum, C. beijerinckii, C. diolis, C. felsineum, C. pasteurianum, C. puniceum, C. roseum, C. saccharobutylicum, and C. saccharoperbutylacetonicum, have been determined; 10 of them completely, and compared to 14 published genomes of other solvent-forming clostridia. Two major groups could be differentiated and several misclassified species were detected. CONCLUSIONS Our findings represent a comprehensive study of phylogeny and taxonomy of clostridial solvent producers that highlights differences in energy conservation mechanisms and substrate utilization between strains, and allow for the first time a direct comparison of sequentially selected industrial strains at the genetic level. Detailed data mining is now possible, supporting the identification of new engineering targets for improved solvent production.
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Affiliation(s)
- Anja Poehlein
- Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Georg-August University Göttingen, Grisebachstr. 8, 37077 Göttingen, Germany
| | - José David Montoya Solano
- Institut für Mikrobiologie und Biotechnologie, Universität Ulm, Albert-Einstein-Allee 11, 89081 Ulm, Germany
| | - Stefanie K. Flitsch
- Institut für Mikrobiologie und Biotechnologie, Universität Ulm, Albert-Einstein-Allee 11, 89081 Ulm, Germany
| | - Preben Krabben
- Green Biologics Ltd., 45A Western Avenue, Milton Park, Abingdon, Oxfordshire OX14 4RU UK
| | - Klaus Winzer
- Clostridia Research Group, BBSRC/EPSRC Synthetic Biology Research Centre (SBRC), School of Life Sciences, University of Nottingham, Nottingham, NG7 2RD UK
| | - Sharon J. Reid
- Department of Molecular and Cell Biology, University of Cape Town, Rondebosch, Cape Town, 7701 South Africa
| | - David T. Jones
- Department of Microbiology and Immunology, University of Otago, Dunedin, 9010 New Zealand
| | - Edward Green
- CHAIN Biotechnology Ltd., Imperial College Incubator, Level 1 Bessemer Building, Imperial College London, London, SW7 2AZ UK
| | - Nigel P. Minton
- Clostridia Research Group, BBSRC/EPSRC Synthetic Biology Research Centre (SBRC), School of Life Sciences, University of Nottingham, Nottingham, NG7 2RD UK
| | - Rolf Daniel
- Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Georg-August University Göttingen, Grisebachstr. 8, 37077 Göttingen, Germany
| | - Peter Dürre
- Institut für Mikrobiologie und Biotechnologie, Universität Ulm, Albert-Einstein-Allee 11, 89081 Ulm, Germany
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Zhang Y, Jiao S, Lv J, Du R, Yan X, Wan C, Zhang R, Han B. Sigma Factor Regulated Cellular Response in a Non-solvent Producing Clostridium beijerinckii Degenerated Strain: A Comparative Transcriptome Analysis. Front Microbiol 2017; 8:23. [PMID: 28194137 PMCID: PMC5276810 DOI: 10.3389/fmicb.2017.00023] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2016] [Accepted: 01/04/2017] [Indexed: 01/11/2023] Open
Abstract
Clostridium beijerinckii DG-8052, derived from NCIMB 8052, cannot produce solvent or form spores, a phenomenon known as degeneration. To explore the mechanisms of degeneration at the gene level, transcriptomic profiles of the wild-type 8052 and DG-8052 strains were compared. Expression of 5168 genes comprising 98.6% of the genome was assessed. Interestingly, 548 and 702 genes were significantly up-regulated in the acidogenesis and solventogenesis phases of DG-8052, respectively, and mainly responsible for the phosphotransferase system, sugar metabolic pathways, and chemotaxis; meanwhile, 699 and 797 genes were significantly down-regulated, respectively, and mainly responsible for sporulation, oxidoreduction, and solventogenesis. The functions of some altered genes, including 286 and 333 at the acidogenesis and solventogenesis phases, respectively, remain unknown. Dysregulation of the fermentation machinery was accompanied by lower transcription levels of glycolysis rate-limiting enzymes (pfk and pyk), and higher transcription of cell chemotaxis genes (cheA, cheB, cheR, cheW, and cheY), controlled mainly by σ54 at acidogenesis. Meanwhile, abnormal spore formation was associated with repressed spo0A, sigE, sigF, sigG, and sigK which are positively regulated by σ70, and correspondingly inhibited expression of CoA-transferase at the solventogenesis phase. These findings indicated that morphological and physiological changes in the degenerated Clostridium strain may be related to altered expression of sigma factors, providing valuable targets for strain development of Clostridium species.
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Affiliation(s)
- Yan Zhang
- School of Medicine, Institute for Genome Sciences, University of Maryland, Baltimore MD, USA
| | - Shengyin Jiao
- School of Public Health, Health Science Center, Xi'an Jiaotong University Xi'an, China
| | - Jia Lv
- School of Public Health, Health Science Center, Xi'an Jiaotong University Xi'an, China
| | - Renjia Du
- School of Public Health, Health Science Center, Xi'an Jiaotong University Xi'an, China
| | - Xiaoni Yan
- School of Public Health, Health Science Center, Xi'an Jiaotong University Xi'an, China
| | - Caixia Wan
- Department of Bioengineering, University of Missouri, Columbia MO, USA
| | - Ruijuan Zhang
- School of Public Health, Health Science Center, Xi'an Jiaotong University Xi'an, China
| | - Bei Han
- School of Public Health, Health Science Center, Xi'an Jiaotong University Xi'an, China
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Transcriptional analysis of degenerate strain Clostridium beijerinckii DG-8052 reveals a pleiotropic response to CaCO 3-associated recovery of solvent production. Sci Rep 2016; 6:38818. [PMID: 27966599 PMCID: PMC5155275 DOI: 10.1038/srep38818] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2016] [Accepted: 11/14/2016] [Indexed: 12/22/2022] Open
Abstract
Degenerate Clostridium beijerinckii strain (DG-8052) can be partially recovered by supplementing CaCO3 to fermentation media. Genome resequencing of DG-8052 showed no general regulator mutated. This study focused on transcriptional analysis of DG-8052 and its response to CaCO3 treatment via microarray. The expressions of 5168 genes capturing 98.6% of C. beijerinckii NCIMB 8052 genome were examed. The results revealed that with addition of CaCO3 565 and 916 genes were significantly up-regulated, and 704 and 1044 genes significantly down-regulated at acidogenic and solventogenic phase of DG-8052, respectively. These genes are primarily responsible for glycolysis to solvent/acid production (poR, pfo), solventogensis (buk, ctf, aldh, adh, bcd) and sporulation (spo0A, sigE, sigma-70, bofA), cell motility and division (ftsA, ftsK, ftsY, ftsH, ftsE, mreB, mreC, mreD, rodA), and molecular chaperones (grpE, dnaK, dnaJ, hsp20, hsp90), etc. The functions of some altered genes in DG-8052, totalling 5.7% at acidogenisis and 8.0% at sovlentogenisis, remain unknown. The response of the degenerate strain to CaCO3 was suggested significantly pleiotropic. This study reveals the multitude of regulatory function that CaCO3 has in clostridia and provides detailed insights into degeneration mechanisms at gene regulation level. It also enables us to develop effective strategies to prevent strain degeneration in future.
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Wong SS, Mi L, Liao JC. Microbial Production of Butanols. Ind Biotechnol (New Rochelle N Y) 2016. [DOI: 10.1002/9783527807833.ch19] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Affiliation(s)
- Sio Si Wong
- University of California; Department of Chemical and Biomolecular Engineering; 420 Westwood Plaza, 5531Boelter Hall Los Angeles CA 90095 USA
| | - Luo Mi
- University of California; Department of Chemical and Biomolecular Engineering; 420 Westwood Plaza, 5531Boelter Hall Los Angeles CA 90095 USA
| | - James C. Liao
- University of California; Department of Chemical and Biomolecular Engineering; 420 Westwood Plaza, 5531Boelter Hall Los Angeles CA 90095 USA
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Wang Y, Zhang ZT, Seo SO, Lynn P, Lu T, Jin YS, Blaschek HP. Gene transcription repression in Clostridium beijerinckii using CRISPR-dCas9. Biotechnol Bioeng 2016; 113:2739-2743. [PMID: 27240718 DOI: 10.1002/bit.26020] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2016] [Revised: 05/17/2016] [Accepted: 05/22/2016] [Indexed: 11/06/2022]
Abstract
CRISPR-Cas9 has been explored as a powerful tool for genome engineering for many organisms. Meanwhile, dCas9 which lacks endonuclease activity but can still bind to target loci has been engineered for efficient gene transcription repression. Clostridium beijerinckii, an industrially significant species capable of biosolvent production, is generally difficult to metabolically engineer. Recently, we reported our work in developing customized CRISPR-Cas9 system for genome engineering in C. beijerinckii. However, in many cases, gene expression repression (rather than actual DNA mutation) is more desirable for various biotechnological applications. Here, we further demonstrated gene transcription repression in C. beijerinckii using CRISPR-dCas9. A small RNA promoter was employed to drive the expression of the single chimeric guide RNA targeting on the promoter region of amylase gene, while a constitutive thiolase promoter was used to drive Streptococcus pyogenes dCas9 expression. The growth assay on starch agar plates showed qualitatively significant repression of amylase activity in C. beijerinckii transformant with CRISPR-dCas9 compared to the control strain. Further amylase activity quantification demonstrated consistent repression (65-97% through the fermentation process) on the activity in the transformant with CRISPR-dCas9 versus in the control. Our results provided essential references for engineering CRISPR-dCas9 as an effective tool for tunable gene transcription repression in diverse microorganisms. Biotechnol. Bioeng. 2016;113: 2739-2743. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Yi Wang
- Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, Illinois.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois
| | - Zhong-Tian Zhang
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois
| | - Seung-Oh Seo
- Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, Illinois.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois
| | - Patrick Lynn
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois
| | - Ting Lu
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois.,Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, Illinois
| | - Yong-Su Jin
- Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, Illinois.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois
| | - Hans P Blaschek
- Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, Illinois. .,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois. .,The Integrated Bioprocessing Research Laboratory (IBRL), University of Illinois at Urbana-Champaign, 1207 W Gregory Drive, Urbana, 61801, Illinois.
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Yoo M, Croux C, Meynial-Salles I, Soucaille P. Elucidation of the roles of adhE1 and adhE2 in the primary metabolism of Clostridium acetobutylicum by combining in-frame gene deletion and a quantitative system-scale approach. BIOTECHNOLOGY FOR BIOFUELS 2016; 9:92. [PMID: 27118994 PMCID: PMC4845359 DOI: 10.1186/s13068-016-0507-0] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2016] [Accepted: 04/12/2016] [Indexed: 05/26/2023]
Abstract
BACKGROUND Clostridium acetobutylicum possesses two homologous adhE genes, adhE1 and adhE2, which have been proposed to be responsible for butanol production in solventogenic and alcohologenic cultures, respectively. To investigate their contributions in detail, in-frame deletion mutants of each gene were constructed and subjected to quantitative transcriptomic (mRNA molecules/cell) and fluxomic analyses in acidogenic, solventogenic, and alcohologenic chemostat cultures. RESULTS Under solventogenesis, compared to the control strain, only ΔadhE1 mutant exhibited significant changes showing decreased butanol production and transcriptional expression changes in numerous genes. In particular, adhE2 was over expressed (126-fold); thus, AdhE2 can partially replace AdhE1 for butanol production (more than 30 % of the in vivo butanol flux) under solventogenesis. Under alcohologenesis, only ΔadhE2 mutant exhibited striking changes in gene expression and metabolic fluxes, and butanol production was completely lost. Therefore, it was demonstrated that AdhE2 is essential for butanol production and thus metabolic fluxes were redirected toward butyrate formation. Under acidogenesis, metabolic fluxes were not significantly changed in both mutants except the complete loss of butanol formation in ΔadhE2, but numerous changes in gene expression were observed. Furthermore, most of the significantly up- or down-regulated genes under this condition showed the same pattern of change in both mutants. CONCLUSIONS This quantitative system-scale analysis confirms the proposed roles of AdhE1 and AdhE2 in butanol formation that AdhE1 is the key enzyme under solventogenesis, whereas AdhE2 is the key enzyme for butanol formation under acidogenesis and alcohologenesis. Our study also highlights the metabolic flexibility of C. acetobutylicum to genetic alterations of its primary metabolism.
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Affiliation(s)
- Minyeong Yoo
- />INSA, UPS, INP, LISBP, Université de Toulouse, Toulouse, France
- />INRA, UMR792, Toulouse, France
- />CNRS, UMR5504, Toulouse, France
| | - Christian Croux
- />INSA, UPS, INP, LISBP, Université de Toulouse, Toulouse, France
- />INRA, UMR792, Toulouse, France
- />CNRS, UMR5504, Toulouse, France
| | - Isabelle Meynial-Salles
- />INSA, UPS, INP, LISBP, Université de Toulouse, Toulouse, France
- />INRA, UMR792, Toulouse, France
- />CNRS, UMR5504, Toulouse, France
| | - Philippe Soucaille
- />INSA, UPS, INP, LISBP, Université de Toulouse, Toulouse, France
- />INRA, UMR792, Toulouse, France
- />CNRS, UMR5504, Toulouse, France
- />Metabolic Explorer, Biopôle Clermont-Limagne, Saint Beauzire, France
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Li SY, Chiang CJ, Tseng IT, He CR, Chao YP. Bioreactors andin situproduct recovery techniques for acetone–butanol–ethanol fermentation. FEMS Microbiol Lett 2016; 363:fnw107. [DOI: 10.1093/femsle/fnw107] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/13/2016] [Indexed: 11/12/2022] Open
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43
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Liao JC, Mi L, Pontrelli S, Luo S. Fuelling the future: microbial engineering for the production of sustainable biofuels. Nat Rev Microbiol 2016; 14:288-304. [DOI: 10.1038/nrmicro.2016.32] [Citation(s) in RCA: 386] [Impact Index Per Article: 48.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
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Yan Y, Basu A, Li T, He J. Direct conversion of xylan to butanol by a wild-typeClostridiumspecies strain G117. Biotechnol Bioeng 2016; 113:1702-10. [DOI: 10.1002/bit.25940] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2015] [Revised: 01/15/2016] [Accepted: 01/18/2016] [Indexed: 11/09/2022]
Affiliation(s)
- Yu Yan
- Department of Civil and Environmental Engineering; National University of Singapore; Block E2-02-13, 1 Engineering Drive 3 117576 Singapore
| | - Anindya Basu
- Department of Civil and Environmental Engineering; National University of Singapore; Block E2-02-13, 1 Engineering Drive 3 117576 Singapore
| | - Tinggang Li
- Department of Civil and Environmental Engineering; National University of Singapore; Block E2-02-13, 1 Engineering Drive 3 117576 Singapore
| | - Jianzhong He
- Department of Civil and Environmental Engineering; National University of Singapore; Block E2-02-13, 1 Engineering Drive 3 117576 Singapore
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Oh YH, Eom GT, Kang KH, Joo JC, Jang YA, Choi JW, Song BK, Lee SH, Park SJ. Construction of heterologous gene expression cassettes for the development of recombinant Clostridium beijerinckii. Bioprocess Biosyst Eng 2016; 39:555-63. [DOI: 10.1007/s00449-016-1537-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2015] [Accepted: 01/05/2016] [Indexed: 02/08/2023]
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Jin Y, Fang Y, Huang M, Sun J, Huang Y, Gao X, Li R, He K, Zhao H. Combination of RNA sequencing and metabolite data to elucidate improved toxic compound tolerance and butanol fermentation of Clostridium acetobutylicum from wheat straw hydrolysate by supplying sodium sulfide. BIORESOURCE TECHNOLOGY 2015; 198:77-86. [PMID: 26364231 DOI: 10.1016/j.biortech.2015.08.139] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2015] [Revised: 08/21/2015] [Accepted: 08/22/2015] [Indexed: 06/05/2023]
Abstract
Sodium sulfide (SS) was added to the non-detoxified wheat straw hydrolysate for ABE fermentation by Clostridium acetobutylicum CICC8012. Biochemical measurements demonstrated that supplementation with SS promoted earlier and enhanced conversion of acid to ABE and led to a 27.48% improvement in sugar consumption, a 20.48% improvement in the sugar-based ABE yield, a 47.63% improvement in the butanol titer, and a 53.50% improvement in the ABE concentration. The response of C. acetobutylicum CICC8012 at the mRNA level was examined by a transcriptional analysis performed with RNA sequencing. The expression of genes involved in the membrane transport of carbohydrates, glycolysis, and ABE formation increased following SS-supplemented fermentation, whereas the expression of genes encoding enzymes involved in acid formation decreased, which indicates that supplemental SS affected the central fermentative pathway, down-regulated the metabolic flux toward the acid formation branches, and up-regulated the metabolic flux toward the ABE formation branches.
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Affiliation(s)
- Yanling Jin
- Key Laboratory of Environmental and Applied Microbiology, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China; Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu 610041, China
| | - Yang Fang
- Key Laboratory of Environmental and Applied Microbiology, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China; Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu 610041, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Mengjun Huang
- Key Laboratory of Environmental and Applied Microbiology, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China; Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu 610041, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jiaolong Sun
- Key Laboratory of Environmental and Applied Microbiology, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China; Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu 610041, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yuhong Huang
- Key Laboratory of Environmental and Applied Microbiology, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China; Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu 610041, China
| | - Xiaofeng Gao
- Key Laboratory of Environmental and Applied Microbiology, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China; Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu 610041, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Renqiang Li
- Key Laboratory of Environmental and Applied Microbiology, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China; Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu 610041, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Kaize He
- Key Laboratory of Environmental and Applied Microbiology, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China; Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu 610041, China
| | - Hai Zhao
- Key Laboratory of Environmental and Applied Microbiology, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China; Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu 610041, China.
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Abstract
Engineering industrial microorganisms for ambitious applications, for example, the production of second-generation biofuels such as butanol, is impeded by a lack of knowledge of primary metabolism and its regulation. A quantitative system-scale analysis was applied to the biofuel-producing bacterium Clostridium acetobutylicum, a microorganism used for the industrial production of solvent. An improved genome-scale model, iCac967, was first developed based on thorough biochemical characterizations of 15 key metabolic enzymes and on extensive literature analysis to acquire accurate fluxomic data. In parallel, quantitative transcriptomic and proteomic analyses were performed to assess the number of mRNA molecules per cell for all genes under acidogenic, solventogenic, and alcohologenic steady-state conditions as well as the number of cytosolic protein molecules per cell for approximately 700 genes under at least one of the three steady-state conditions. A complete fluxomic, transcriptomic, and proteomic analysis applied to different metabolic states allowed us to better understand the regulation of primary metabolism. Moreover, this analysis enabled the functional characterization of numerous enzymes involved in primary metabolism, including (i) the enzymes involved in the two different butanol pathways and their cofactor specificities, (ii) the primary hydrogenase and its redox partner, (iii) the major butyryl coenzyme A (butyryl-CoA) dehydrogenase, and (iv) the major glyceraldehyde-3-phosphate dehydrogenase. This study provides important information for further metabolic engineering of C. acetobutylicum to develop a commercial process for the production of n-butanol. Currently, there is a resurgence of interest in Clostridium acetobutylicum, the biocatalyst of the historical Weizmann process, to produce n-butanol for use both as a bulk chemical and as a renewable alternative transportation fuel. To develop a commercial process for the production of n-butanol via a metabolic engineering approach, it is necessary to better characterize both the primary metabolism of C. acetobutylicum and its regulation. Here, we apply a quantitative system-scale analysis to acidogenic, solventogenic, and alcohologenic steady-state C. acetobutylicum cells and report for the first time quantitative transcriptomic, proteomic, and fluxomic data. This approach allows for a better understanding of the regulation of primary metabolism and for the functional characterization of numerous enzymes involved in primary metabolism.
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The Clostridium sporulation programs: diversity and preservation of endospore differentiation. Microbiol Mol Biol Rev 2015; 79:19-37. [PMID: 25631287 DOI: 10.1128/mmbr.00025-14] [Citation(s) in RCA: 122] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
SUMMARY Bacillus and Clostridium organisms initiate the sporulation process when unfavorable conditions are detected. The sporulation process is a carefully orchestrated cascade of events at both the transcriptional and posttranslational levels involving a multitude of sigma factors, transcription factors, proteases, and phosphatases. Like Bacillus genomes, sequenced Clostridium genomes contain genes for all major sporulation-specific transcription and sigma factors (spo0A, sigH, sigF, sigE, sigG, and sigK) that orchestrate the sporulation program. However, recent studies have shown that there are substantial differences in the sporulation programs between the two genera as well as among different Clostridium species. First, in the absence of a Bacillus-like phosphorelay system, activation of Spo0A in Clostridium organisms is carried out by a number of orphan histidine kinases. Second, downstream of Spo0A, the transcriptional and posttranslational regulation of the canonical set of four sporulation-specific sigma factors (σ(F), σ(E), σ(G), and σ(K)) display different patterns, not only compared to Bacillus but also among Clostridium organisms. Finally, recent studies demonstrated that σ(K), the last sigma factor to be activated according to the Bacillus subtilis model, is involved in the very early stages of sporulation in Clostridium acetobutylicum, C. perfringens, and C. botulinum as well as in the very late stages of spore maturation in C. acetobutylicum. Despite profound differences in initiation, propagation, and orchestration of expression of spore morphogenetic components, these findings demonstrate not only the robustness of the endospore sporulation program but also the plasticity of the program to generate different complex phenotypes, some apparently regulated at the epigenetic level.
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Optimized Transformation of Newly Constructed Escherichia coli-Clostridia Shuttle Vectors into Clostridium beijerinckii. Appl Biochem Biotechnol 2015; 177:226-36. [DOI: 10.1007/s12010-015-1740-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Accepted: 06/30/2015] [Indexed: 10/23/2022]
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50
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Yu L, Zhao J, Xu M, Dong J, Varghese S, Yu M, Tang IC, Yang ST. Metabolic engineering of Clostridium tyrobutyricum for n-butanol production: effects of CoA transferase. Appl Microbiol Biotechnol 2015; 99:4917-30. [DOI: 10.1007/s00253-015-6566-5] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2015] [Revised: 03/18/2015] [Accepted: 03/20/2015] [Indexed: 01/31/2023]
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