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Chou KJ, Croft T, Hebdon SD, Magnusson LR, Xiong W, Reyes LH, Chen X, Miller EJ, Riley DM, Dupuis S, Laramore KA, Keller LM, Winkelman D, Maness PC. Engineering the cellulolytic bacterium, Clostridium thermocellum, to co-utilize hemicellulose. Metab Eng 2024; 83:193-205. [PMID: 38631458 DOI: 10.1016/j.ymben.2024.03.008] [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: 12/28/2023] [Revised: 03/15/2024] [Accepted: 03/29/2024] [Indexed: 04/19/2024]
Abstract
Consolidated bioprocessing (CBP) of lignocellulosic biomass holds promise to realize economic production of second-generation biofuels/chemicals, and Clostridium thermocellum is a leading candidate for CBP due to it being one of the fastest degraders of crystalline cellulose and lignocellulosic biomass. However, CBP by C. thermocellum is approached with co-cultures, because C. thermocellum does not utilize hemicellulose. When compared with a single-species fermentation, the co-culture system introduces unnecessary process complexity that may compromise process robustness. In this study, we engineered C. thermocellum to co-utilize hemicellulose without the need for co-culture. By evolving our previously engineered xylose-utilizing strain in xylose, an evolved clonal isolate (KJC19-9) was obtained and showed improved specific growth rate on xylose by ∼3-fold and displayed comparable growth to a minimally engineered strain grown on the bacteria's naturally preferred substrate, cellobiose. To enable full xylan deconstruction to xylose, we recombinantly expressed three different β-xylosidase enzymes originating from Thermoanaerobacterium saccharolyticum into KJC19-9 and demonstrated growth on xylan with one of the enzymes. This recombinant strain was capable of co-utilizing cellulose and xylan simultaneously, and we integrated the β-xylosidase gene into the KJC19-9 genome, creating the KJCBXint strain. The strain, KJC19-9, consumed monomeric xylose but accumulated xylobiose when grown on pretreated corn stover, whereas the final KJCBXint strain showed significantly greater deconstruction of xylan and xylobiose. This is the first reported C. thermocellum strain capable of degrading and assimilating hemicellulose polysaccharide while retaining its cellulolytic capabilities, unlocking significant potential for CBP in advancing the bioeconomy.
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Affiliation(s)
- Katherine J Chou
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO, 80228, USA.
| | - Trevor Croft
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO, 80228, USA
| | - Skyler D Hebdon
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO, 80228, USA
| | - Lauren R Magnusson
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO, 80228, USA
| | - Wei Xiong
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO, 80228, USA
| | - Luis H Reyes
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO, 80228, USA; Grupo de Diseño de Productos y Procesos, Department of Chemical and Food Engineering, Universidad de los Andes, Bogotá, Colombia
| | - Xiaowen Chen
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO, 80228, USA
| | - Emily J Miller
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO, 80228, USA
| | - Danielle M Riley
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO, 80228, USA
| | - Sunnyjoy Dupuis
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO, 80228, USA
| | - Kathrin A Laramore
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO, 80228, USA
| | - Lisa M Keller
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO, 80228, USA
| | - Dirk Winkelman
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO, 80228, USA
| | - Pin-Ching Maness
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO, 80228, USA
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2
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Cowan DA, Albers SV, Antranikian G, Atomi H, Averhoff B, Basen M, Driessen AJM, Jebbar M, Kelman Z, Kerou M, Littlechild J, Müller V, Schönheit P, Siebers B, Vorgias K. Extremophiles in a changing world. Extremophiles 2024; 28:26. [PMID: 38683238 PMCID: PMC11058618 DOI: 10.1007/s00792-024-01341-7] [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: 10/27/2023] [Accepted: 04/02/2024] [Indexed: 05/01/2024]
Abstract
Extremophiles and their products have been a major focus of research interest for over 40 years. Through this period, studies of these organisms have contributed hugely to many aspects of the fundamental and applied sciences, and to wider and more philosophical issues such as the origins of life and astrobiology. Our understanding of the cellular adaptations to extreme conditions (such as acid, temperature, pressure and more), of the mechanisms underpinning the stability of macromolecules, and of the subtleties, complexities and limits of fundamental biochemical processes has been informed by research on extremophiles. Extremophiles have also contributed numerous products and processes to the many fields of biotechnology, from diagnostics to bioremediation. Yet, after 40 years of dedicated research, there remains much to be discovered in this field. Fortunately, extremophiles remain an active and vibrant area of research. In the third decade of the twenty-first century, with decreasing global resources and a steadily increasing human population, the world's attention has turned with increasing urgency to issues of sustainability. These global concerns were encapsulated and formalized by the United Nations with the adoption of the 2030 Agenda for Sustainable Development and the presentation of the seventeen Sustainable Development Goals (SDGs) in 2015. In the run-up to 2030, we consider the contributions that extremophiles have made, and will in the future make, to the SDGs.
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Affiliation(s)
- D A Cowan
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, 0002, South Africa.
| | - S V Albers
- Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - G Antranikian
- Institute of Technical Biocatalysis, Hamburg University of Technology, 21073, Hamburg, Germany
| | - H Atomi
- Graduate School of Engineering, Kyoto University, Kyoto, Japan
| | - B Averhoff
- Department of Molecular Microbiology and Bioenergetics, Institute of Molecular Biosciences, Goethe University Frankfurt, Frankfurt Am Main, Germany
| | - M Basen
- Department of Microbiology, Institute of Biological Sciences, University of Rostock, Rostock, Germany
| | - A J M Driessen
- Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747 AG, Groningen, The Netherlands
| | - M Jebbar
- Univ. Brest, CNRS, Ifremer, Laboratoire de Biologie Et d'Écologie Des Écosystèmes Marins Profonds (BEEP), IUEM, Rue Dumont d'Urville, 29280, Plouzané, France
| | - Z Kelman
- Institute for Bioscience and Biotechnology Research and the National Institute of Standards and Technology, Rockville, MD, USA
| | - M Kerou
- Department of Functional and Evolutionary Ecology, Faculty of Life Sciences, University of Vienna, Vienna, Austria
| | - J Littlechild
- Henry Wellcome Building for Biocatalysis, Faculty of Health and Life Sciences, University of Exeter, Exeter, UK
| | - V Müller
- Department of Molecular Microbiology and Bioenergetics, Institute of Molecular Biosciences, Goethe University Frankfurt, Frankfurt Am Main, Germany
| | - P Schönheit
- Institute of General Microbiology, Christian Albrechts University, Kiel, Germany
| | - B Siebers
- Molecular Enzyme Technology and Biochemistry (MEB), Environmental Microbiology and Biotechnology (EMB), Centre for Water and Environmental Research (CWE), University of Duisburg-Essen, 45117, Essen, Germany
| | - K Vorgias
- Biology Department and RI-Bio3, National and Kapodistrian University of Athens, Athens, Greece
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3
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Alves J, Rand JD, Johnston ABE, Bowen C, Lynskey NN. Methylome-dependent transformation of emm1 group A streptococci. mBio 2023; 14:e0079823. [PMID: 37427929 PMCID: PMC10470502 DOI: 10.1128/mbio.00798-23] [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: 04/06/2023] [Accepted: 05/30/2023] [Indexed: 07/11/2023] Open
Abstract
Genetic intractability presents a fundamental barrier to the manipulation of bacteria, hindering advancements in microbiological research. Group A Streptococcus (GAS), a lethal human pathogen currently associated with an unprecedented surge of infections worldwide, exhibits poor genetic tractability attributed to the activity of a conserved type 1 restriction modification system (RMS). RMS detect and cleave specific target sequences in foreign DNA that are protected in host DNA by sequence-specific methylation. Overcoming this "restriction barrier" thus presents a major technical challenge. Here, we demonstrate for the first time that different RMS variants expressed by GAS give rise to genotype-specific and methylome-dependent variation in transformation efficiency. Furthermore, we show that the magnitude of impact of methylation on transformation efficiency elicited by RMS variant TRDAG, encoded by all sequenced strains of the dominant and upsurge-associated emm1 genotype, is 100-fold greater than for all other TRD tested and is responsible for the poor transformation efficiency associated with this lineage. In dissecting the underlying mechanism, we developed an improved GAS transformation protocol, whereby the restriction barrier is overcome by the addition of the phage anti-restriction protein Ocr. This protocol is highly effective for TRDAG strains including clinical isolates representing all emm1 lineages and will expedite critical research interrogating the genetics of emm1 GAS, negating the need to work in an RMS-negative background. These findings provide a striking example of the impact of RMS target sequence variation on bacterial transformation and the importance of defining lineage-specific mechanisms of genetic recalcitrance. IMPORTANCE Understanding the mechanisms by which bacterial pathogens are able to cause disease is essential to enable the targeted development of novel therapeutics. A key experimental approach to facilitate this research is the generation of bacterial mutants, through either specific gene deletions or sequence manipulation. This process relies on the ability to transform bacteria with exogenous DNA designed to generate the desired sequence changes. Bacteria have naturally developed protective mechanisms to detect and destroy invading DNA, and these systems severely impede the genetic manipulation of many important pathogens, including the lethal human pathogen group A Streptococcus (GAS). Many GAS lineages exist, of which emm1 is dominant among clinical isolates. Based on new experimental evidence, we identify the mechanism by which transformation is impaired in the emm1 lineage and establish an improved and highly efficient transformation protocol to expedite the generation of mutants.
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Affiliation(s)
- Joana Alves
- The Roslin Institute, University of Edinburgh, Easter Bush Campus, Midlothian, Scotland, United Kingdom
| | - Joshua D. Rand
- The Roslin Institute, University of Edinburgh, Easter Bush Campus, Midlothian, Scotland, United Kingdom
| | - Alix B. E. Johnston
- The Roslin Institute, University of Edinburgh, Easter Bush Campus, Midlothian, Scotland, United Kingdom
| | - Connor Bowen
- The Roslin Institute, University of Edinburgh, Easter Bush Campus, Midlothian, Scotland, United Kingdom
| | - Nicola N. Lynskey
- The Roslin Institute, University of Edinburgh, Easter Bush Campus, Midlothian, Scotland, United Kingdom
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Seo H, Singh P, Wyman CE, Cai CM, Trinh CT. Rewiring metabolism of Clostridium thermocellum for consolidated bioprocessing of lignocellulosic biomass poplar to produce short-chain esters. BIORESOURCE TECHNOLOGY 2023:129263. [PMID: 37271458 DOI: 10.1016/j.biortech.2023.129263] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 05/29/2023] [Accepted: 05/30/2023] [Indexed: 06/06/2023]
Abstract
Consolidated bioprocessing (CBP) of lignocellulosic biomass uses cellulolytic microorganisms to enable enzyme production, saccharification, and fermentation to produce biofuels, biochemicals, and biomaterials in a single step. However, understanding and redirecting metabolisms of these microorganisms compatible with CBP are limited. Here, a cellulolytic thermophile Clostridium thermocellum was engineered and demonstrated to be compatible with CBP integrated with a Co-solvent Enhanced Lignocellulosic Fractionation (CELF) pretreatment for conversion of hardwood poplar into short-chain esters with industrial use as solvents, flavors, fragrances, and biofuels. The recombinant C. thermocellum engineered with deletion of carbohydrate esterases and stable overexpression of alcohol acetyltransferases improved ester production without compromised deacetylation activities. These esterases were discovered to exhibit promiscuous thioesterase activities and their deletion enhanced ester production by rerouting the electron and carbon metabolism. Ester production was further improved up to 80-fold and ester composition could be modulated by deleting lactate biosynthesis and using poplar with different pretreatment severity.
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Affiliation(s)
- Hyeongmin Seo
- Department of Chemical and Biomolecular Engineering, The University of Tennessee, Knoxville, TN, USA; Center of Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Priyanka Singh
- Center of Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, USA; Chemical and Environmental Engineering Department, University of California, Riverside, CA 92521, USA
| | - Charles E Wyman
- Center of Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, USA; Chemical and Environmental Engineering Department, University of California, Riverside, CA 92521, USA
| | - Charles M Cai
- Center of Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, USA; Chemical and Environmental Engineering Department, University of California, Riverside, CA 92521, USA
| | - Cong T Trinh
- Department of Chemical and Biomolecular Engineering, The University of Tennessee, Knoxville, TN, USA; Center of Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, USA.
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Simple and Rapid Site-Specific Integration of Multiple Heterologous DNAs into the Escherichia coli Chromosome. J Bacteriol 2023; 205:e0033822. [PMID: 36655997 PMCID: PMC9945576 DOI: 10.1128/jb.00338-22] [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] [Indexed: 01/20/2023] Open
Abstract
Escherichia coli is the most studied and well understood microorganism, but research in this system can still be limited by available genetic tools, including the ability to rapidly integrate multiple DNA constructs efficiently into the chromosome. Site-specific, large serine-recombinases can be useful tools, catalyzing a single, unidirectional recombination event between 2 specific DNA sequences, attB and attP, without requiring host proteins for functionality. Using these recombinases, we have developed a system to integrate up to 12 genetic constructs sequentially and stably into in the E. coli chromosome. A cassette of attB sites was inserted into the chromosome and the corresponding recombinases were cloned onto temperature sensitive plasmids to mediate recombination between a non-replicating, attP-containing "cargo" plasmid and the corresponding attB site on the chromosome. The efficiency of DNA insertion into the E. coli chromosome was approximately 107 CFU/μg DNA for six of the recombinases when the competent cells already contained the recombinase-expressing plasmid and approximately 105 CFU/μg DNA or higher when the recombinase-expressing plasmid and "cargo" plasmid were co-transformed. The "cargo" plasmid contains ΦC31 recombination sites flanking the antibiotic gene, allowing for resistance markers to be removed and reused following transient expression of the ΦC31 recombinase. As an example of the utility of this system, eight DNA methyltransferases from Clostridium clariflavum 4-2a were inserted into the E. coli chromosome to methylate plasmid DNA for evasion of the C. clariflavum restriction systems, enabling the first demonstration of transformation of this cellulose-degrading species. IMPORTANCE More rapid genetic tools can help accelerate strain engineering, even in advanced hosts like Escherichia coli. Here, we adapt a suite of site-specific recombinases to enable simple, rapid, and highly efficient site-specific integration of heterologous DNA into the chromosome. This utility of this system was demonstrated by sequential insertion of eight DNA methyltransferases into the E. coli chromosome, allowing plasmid DNA to be protected from restriction in Clostridium clariflavum and enabling genetic transformation of this organism. This integration system should also be highly portable into non-model organisms.
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The Roles of Nicotinamide Adenine Dinucleotide Phosphate Reoxidation and Ammonium Assimilation in the Secretion of Amino Acids as Byproducts of Clostridium thermocellum. Appl Environ Microbiol 2023; 89:e0175322. [PMID: 36625594 PMCID: PMC9888227 DOI: 10.1128/aem.01753-22] [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] [Indexed: 01/11/2023] Open
Abstract
Clostridium thermocellum is a cellulolytic thermophile that is considered for the consolidated bioprocessing of lignocellulose to ethanol. Improvements in ethanol yield are required for industrial implementation, but the incompletely understood causes of amino acid secretion impede progress. In this study, amino acid secretion was investigated via gene deletions in ammonium-regulated, nicotinamide adenine dinucleotide phosphate (NADPH)-supplying and NADPH-consuming pathways as well as via physiological characterization in cellobiose-limited or ammonium-limited chemostats. First, the contribution of the NADPH-supplying malate shunt was studied with strains using either the NADPH-yielding malate shunt (Δppdk) or a redox-independent conversion of PEP to pyruvate (Δppdk ΔmalE::Peno-pyk). In the latter, branched-chain amino acids, especially valine, were significantly reduced, whereas the ethanol yield increased from 46 to 60%, suggesting that the secretion of these amino acids balances the NADPH surplus from the malate shunt. The unchanged amino acid secretion in Δppdk falsified a previous hypothesis on an ammonium-regulated PEP-to-pyruvate flux redistribution. The possible involvement of another NADPH-supplier, namely, NADH-dependent reduced ferredoxin:NADP+ oxidoreductase (nfnAB), was also excluded. Finally, the deletion of glutamate synthase (gogat) in ammonium assimilation resulted in the upregulation of NADPH-linked glutamate dehydrogenase activity and decreased amino acid yields. Since gogat in C. thermocellum is putatively annotated as ferredoxin-linked, a claim which is supported by the product redistribution observed in this study, this deletion likely replaced ferredoxin with NADPH in ammonium assimilation. Overall, these findings indicate that a need to reoxidize NADPH is driving the observed amino acid secretion, likely at the expense of the NADH needed for ethanol formation. This suggests that metabolic engineering strategies that simplify the redox metabolism and ammonium assimilation can contribute to increased ethanol yields. IMPORTANCE Improving the ethanol yield of C. thermocellum is important for the industrial implementation of this microorganism in consolidated bioprocessing. A central role of NADPH in driving amino acid byproduct formation was demonstrated by eliminating the NADPH-supplying malate shunt and separately by changing the cofactor specificity in ammonium assimilation. With amino acid secretion diverting carbon and electrons away from ethanol, these insights are important for further metabolic engineering to reach industrial requirements on ethanol yield. This study also provides chemostat data that are relevant for training genome-scale metabolic models and for improving the validity of their predictions, especially considering the reduced degree-of-freedom in the redox metabolism of the strains generated here. In addition, this study advances the fundamental understanding on the mechanisms underlying amino acid secretion in cellulolytic Clostridia as well as on the regulation and cofactor specificity in ammonium assimilation. Together, these efforts aid in the development of C. thermocellum for the sustainable consolidated bioprocessing of lignocellulose to ethanol with minimal pretreatment.
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Increasing the Thermodynamic Driving Force of the Phosphofructokinase Reaction in
Clostridium thermocellum. Appl Environ Microbiol 2022; 88:e0125822. [PMID: 36286488 PMCID: PMC9680637 DOI: 10.1128/aem.01258-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The ability to control the distribution of thermodynamic driving force throughout a metabolic pathway is likely to be an important tool for metabolic engineering. The phosphofructokinase reaction is a key enzyme in Embden-Mayerhof-Parnas glycolysis and therefore improving the thermodynamic driving force of this reaction in
C. thermocellum
is believed to enable higher product titers.
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Ganguly J, Martin-Pascual M, Montiel González D, Bulut A, Vermeulen B, Tjalma I, Vidaki A, van Kranenburg R. Breaking the Restriction Barriers and Applying CRISPRi as a Gene Silencing Tool in Pseudoclostridium thermosuccinogenes. Microorganisms 2022; 10:microorganisms10040698. [PMID: 35456750 PMCID: PMC9044749 DOI: 10.3390/microorganisms10040698] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Revised: 03/15/2022] [Accepted: 03/16/2022] [Indexed: 12/10/2022] Open
Abstract
Pseudoclostridium thermosuccinogenes is a thermophilic bacterium capable of producing succinate from lignocellulosic-derived sugars and has the potential to be exploited as a platform organism. However, exploitation of P. thermosuccinogenes has been limited partly due to the genetic inaccessibility and lack of genome engineering tools. In this study, we established the genetic accessibility for P. thermosuccinogenes DSM 5809. By overcoming restriction barriers, transformation efficiencies of 102 CFU/µg plasmid DNA were achieved. To this end, the plasmid DNA was methylated in vivo when transformed into an engineered E. coli HST04 strain expressing three native methylation systems of the thermophile. This protocol was used to introduce a ThermodCas9-based CRISPRi tool targeting the gene encoding malic enzyme in P. thermosuccinogenes, demonstrating the principle of gene silencing. This resulted in 75% downregulation of its expression and had an impact on the strain’s fermentation profile. Although the details of the functioning of the restriction modification systems require further study, in vivo methylation can already be applied to improve transformation efficiency of P. thermosuccinogenes. Making use of the ThermodCas9-based CRISPRi, this is the first example demonstrating that genetic engineering in P. thermosuccinogenes is feasible and establishing the way for metabolic engineering of this bacterium.
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Affiliation(s)
| | - Maria Martin-Pascual
- Laboratory of Microbiology, Wageningen University and Research, 6708 WE Wageningen, The Netherlands; (M.M.-P.); (B.V.); (I.T.)
| | - Diego Montiel González
- Department of Genetic Identification, Erasmus MC University Medical Center Rotterdam, 3015 GD Rotterdam, The Netherlands; (D.M.G.); (A.V.)
| | - Alkan Bulut
- Fontys University of Applied Sciences, 5612 AR Eindhoven, The Netherlands;
| | - Bram Vermeulen
- Laboratory of Microbiology, Wageningen University and Research, 6708 WE Wageningen, The Netherlands; (M.M.-P.); (B.V.); (I.T.)
| | - Ivo Tjalma
- Laboratory of Microbiology, Wageningen University and Research, 6708 WE Wageningen, The Netherlands; (M.M.-P.); (B.V.); (I.T.)
| | - Athina Vidaki
- Department of Genetic Identification, Erasmus MC University Medical Center Rotterdam, 3015 GD Rotterdam, The Netherlands; (D.M.G.); (A.V.)
| | - Richard van Kranenburg
- Corbion, 4206 AC Gorinchem, The Netherlands;
- Laboratory of Microbiology, Wageningen University and Research, 6708 WE Wageningen, The Netherlands; (M.M.-P.); (B.V.); (I.T.)
- Correspondence:
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Ichikawa S, Ito D, Asaoka S, Abe R, Katsuo N, Ito T, Ito D, Karita S. The expression of alternative sigma-I7 factor induces the transcription of cellulosomal genes in the cellulolytic bacterium Clostridium thermocellum. Enzyme Microb Technol 2022; 156:110002. [DOI: 10.1016/j.enzmictec.2022.110002] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Revised: 01/12/2022] [Accepted: 01/31/2022] [Indexed: 01/07/2023]
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10
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Lee J. Lessons from Clostridial Genetics: Toward Engineering Acetogenic Bacteria. BIOTECHNOL BIOPROC E 2021. [DOI: 10.1007/s12257-021-0062-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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11
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Yan F, Wei R, Cui Q, Bornscheuer UT, Liu Y. Thermophilic whole-cell degradation of polyethylene terephthalate using engineered Clostridium thermocellum. Microb Biotechnol 2021; 14:374-385. [PMID: 32343496 PMCID: PMC7936307 DOI: 10.1111/1751-7915.13580] [Citation(s) in RCA: 66] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Revised: 04/05/2020] [Accepted: 04/07/2020] [Indexed: 12/03/2022] Open
Abstract
Polyethylene terephthalate (PET) is a mass-produced synthetic polyester contributing remarkably to the accumulation of solid plastics waste and plastics pollution in the natural environments. Recently, bioremediation of plastics waste using engineered enzymes has emerged as an eco-friendly alternative approach for the future plastic circular economy. Here we genetically engineered a thermophilic anaerobic bacterium, Clostridium thermocellum, to enable the secretory expression of a thermophilic cutinase (LCC), which was originally isolated from a plant compost metagenome and can degrade PET at up to 70°C. This engineered whole-cell biocatalyst allowed a simultaneous high-level expression of LCC and conspicuous degradation of commercial PET films at 60°C. After 14 days incubation of a batch culture, more than 60% of the initial mass of a PET film (approximately 50 mg) was converted into soluble monomer feedstocks, indicating a markedly higher degradation performance than previously reported whole-cell-based PET biodegradation systems using mesophilic bacteria or microalgae. Our findings provide clear evidence that, compared to mesophilic species, thermophilic microbes are a more promising synthetic microbial chassis for developing future biodegradation processes of PET waste.
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Affiliation(s)
- Fei Yan
- CAS Key Laboratory of BiofuelsShandong Provincial Key Laboratory of Synthetic BiologyQingdao Institute of Bioenergy and Bioprocess TechnologyChinese Academy of SciencesQingdao266101China
- Dalian National Laboratory for Clean EnergyQingdao266101China
- University of Chinese Academy of SciencesChinese Academy of SciencesBeijing100049China
| | - Ren Wei
- Department of Biotechnology and Enzyme CatalysisInstitute of BiochemistryGreifswald UniversityFelix-Hausdorff-Str. 4D-17487GreifswaldGermany
| | - Qiu Cui
- CAS Key Laboratory of BiofuelsShandong Provincial Key Laboratory of Synthetic BiologyQingdao Institute of Bioenergy and Bioprocess TechnologyChinese Academy of SciencesQingdao266101China
- Dalian National Laboratory for Clean EnergyQingdao266101China
- University of Chinese Academy of SciencesChinese Academy of SciencesBeijing100049China
| | - Uwe T. Bornscheuer
- Department of Biotechnology and Enzyme CatalysisInstitute of BiochemistryGreifswald UniversityFelix-Hausdorff-Str. 4D-17487GreifswaldGermany
| | - Ya‐Jun Liu
- CAS Key Laboratory of BiofuelsShandong Provincial Key Laboratory of Synthetic BiologyQingdao Institute of Bioenergy and Bioprocess TechnologyChinese Academy of SciencesQingdao266101China
- Dalian National Laboratory for Clean EnergyQingdao266101China
- University of Chinese Academy of SciencesChinese Academy of SciencesBeijing100049China
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Riley LA, Guss AM. Approaches to genetic tool development for rapid domestication of non-model microorganisms. BIOTECHNOLOGY FOR BIOFUELS 2021; 14:30. [PMID: 33494801 PMCID: PMC7830746 DOI: 10.1186/s13068-020-01872-z] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Accepted: 12/30/2020] [Indexed: 05/04/2023]
Abstract
Non-model microorganisms often possess complex phenotypes that could be important for the future of biofuel and chemical production. They have received significant interest the last several years, but advancement is still slow due to the lack of a robust genetic toolbox in most organisms. Typically, "domestication" of a new non-model microorganism has been done on an ad hoc basis, and historically, it can take years to develop transformation and basic genetic tools. Here, we review the barriers and solutions to rapid development of genetic transformation tools in new hosts, with a major focus on Restriction-Modification systems, which are a well-known and significant barrier to efficient transformation. We further explore the tools and approaches used for efficient gene deletion, DNA insertion, and heterologous gene expression. Finally, more advanced and high-throughput tools are now being developed in diverse non-model microbes, paving the way for rapid and multiplexed genome engineering for biotechnology.
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Affiliation(s)
- Lauren A Riley
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
- Bredesen Center, University of Tennessee, Knoxville, TN, 37996, USA
| | - Adam M Guss
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA.
- Bredesen Center, University of Tennessee, Knoxville, TN, 37996, USA.
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Mazzoli R, Olson DG, Lynd LR. Construction of lactic acid overproducing Clostridium thermocellum through enhancement of lactate dehydrogenase expression. Enzyme Microb Technol 2020; 141:109645. [PMID: 33051021 DOI: 10.1016/j.enzmictec.2020.109645] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Revised: 07/24/2020] [Accepted: 08/05/2020] [Indexed: 12/24/2022]
Abstract
Rapid expansion of global market of lactic acid (LA) has prompted research towards cheaper and more eco-friendly strategies for its production. Nowadays, LA is produced mainly through fermentation of simple sugars or starchy biomass (e.g. corn) and its price is relatively high. Lignocellulose could be an advantageous alternative feedstock for LA production owing to its high abundance and low cost. However, the most effective natural producers of LA cannot directly ferment lignocellulose. So far, metabolic engineering aimed at developing microorganisms combining efficient LA production and cellulose hydrolysis has been generally based on introducing designer cellulase systems in natural LA producers. In the present study, the approach consisted in improving LA production in the natural cellulolytic bacterium Clostridium thermocellum DSM1313. The expression of the native lactate dehydrogenase was enhanced by functional replacement of its original promoter with stronger ones resulting in a 10-fold increase in specific activity, which resulted in a 2-fold increase of LA yield. It is known that eliminating allosteric regulation can also increase lactic acid production in C. thermocellum, however we were unable to insert strong promoters upstream of the de-regulated ldh gene. A strategy combining these regulations and inactivation of parasitic pathways appears essential for developing a homolactic C. thermocellum.
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Affiliation(s)
- R Mazzoli
- Structural and Functional Biochemistry, Laboratory of Proteomics and Metabolic Engineering of Prokaryotes, Department of Life Sciences and Systems Biology, University of Torino, Via Accademia Albertina 13, 10123, Torino, Italy; Thayer School of Engineering, Dartmouth College, 14 Engineering Drive, Hanover, NH, 03755, USA.
| | - D G Olson
- Thayer School of Engineering, Dartmouth College, 14 Engineering Drive, Hanover, NH, 03755, USA
| | - L R Lynd
- Thayer School of Engineering, Dartmouth College, 14 Engineering Drive, Hanover, NH, 03755, USA
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14
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Seo H, Nicely PN, Trinh CT. Endogenous carbohydrate esterases of Clostridium thermocellum are identified and disrupted for enhanced isobutyl acetate production from cellulose. Biotechnol Bioeng 2020; 117:2223-2236. [PMID: 32333614 DOI: 10.1002/bit.27360] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Revised: 04/12/2020] [Accepted: 04/22/2020] [Indexed: 12/18/2022]
Abstract
Medium-chain esters are versatile chemicals with broad applications as flavors, fragrances, solvents, and potential drop-in biofuels. Currently, these esters are largely produced by the conventional chemical process that uses harsh operating conditions and requires high energy input. Alternatively, the microbial conversion route has recently emerged as a promising platform for sustainable and renewable ester production. The ester biosynthesis pathways can utilize either lipases or alcohol acyltransferase (AAT), but the AAT-dependent pathway is more thermodynamically favorable in an aqueous fermentation environment. Even though a cellulolytic thermophile Clostridium thermocellum harboring an AAT-dependent pathway has recently been engineered for direct conversion of lignocellulosic biomass into esters, the production is not efficient. One potential bottleneck is the ester degradation caused by the endogenous carbohydrate esterases (CEs) whose functional roles are poorly understood. The challenge is to identify and disrupt CEs that can alleviate ester degradation while not negatively affecting the efficient and robust capability of C. thermocellum for lignocellulosic biomass deconstruction. In this study, by using bioinformatics, comparative genomics, and enzymatic analysis to screen a library of CEs, we identified and disrupted the two most critical CEs, Clo1313_0613 and Clo1313_0693, that significantly contribute to isobutyl acetate degradation in C. thermocellum. We demonstrated that an engineered esterase-deficient C. thermocellum strain not only reduced ester hydrolysis but also improved isobutyl acetate production while maintaining effective cellulose assimilation.
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Affiliation(s)
- Hyeongmin Seo
- Department of Chemical and Biomolecular Engineering, The University of Tennessee, Knoxville, Tennessee.,Center of Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, Tennessee
| | - Preston N Nicely
- Department of Chemical and Biomolecular Engineering, The University of Tennessee, Knoxville, Tennessee
| | - Cong T Trinh
- Department of Chemical and Biomolecular Engineering, The University of Tennessee, Knoxville, Tennessee.,Center of Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, Tennessee
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15
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Tang S, Xu T, Peng J, Zhou K, Zhu Y, Zhou W, Cheng H, Zhou H. Overexpression of an endogenous raw starch digesting mesophilic α-amylase gene in Bacillus amyloliquefaciens Z3 by in vitro methylation protocol. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2020; 100:3013-3023. [PMID: 32056215 DOI: 10.1002/jsfa.10332] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2019] [Revised: 02/07/2020] [Accepted: 02/13/2020] [Indexed: 06/10/2023]
Abstract
BACKGROUND Mesophilic α-amylases function effectively at low temperatures with high rates of catalysis and require less energy for starch hydrolysis. Bacillus amyloliquefaciens is an essential producer of mesophilic α-amylases. However, because of the existence of the restriction-modification system, introducing exogenous DNAs into wild-type B. amyloliquefaciens is especially tricky. RESULTS α-Amylase producer B. amyloliquefaciens strain Z3 was screened and used as host for endogenous α-amylase gene expression. In vitro methylation was performed in recombinant plasmid pWB980-amyZ3. With the in vitro methylation, the transformation efficiency was increased to 0.96 × 102 colony-forming units μg-1 plasmid DNA. A positive transformant BAZ3-16 with the highest α-amylase secreting capacity was chosen for further experiments. The α-amylase activity of strain BAZ3-16 reached 288.70 ± 16.15 U mL-1 in the flask and 386.03 ± 16.25 U mL-1 in the 5-L stirred-tank fermenter, respectively. The Bacillus amyloliquefaciens Z3 expression system shows excellent genetic stability and high-level extracellular production of the target protein. Moreover, the synergistic interaction of AmyZ3 with amyloglucosidase was determined during the hydrolysis of raw starch. The hydrolysis degree reached 92.34 ± 3.41% for 100 g L-1 raw corn starch and 81.30 ± 2.92% for 100 g L-1 raw cassava starch after 24 h, respectively. CONCLUSION Methylation of the plasmid DNA removes a substantial barrier for transformation of B. amyloliquefaciens strain Z3. Furthermore, the exceptional ability to hydrolyze starch makes α-amylase AmyZ3 and strain BAZ3-16 valuable in the starch industry. © 2020 Society of Chemical Industry.
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Affiliation(s)
- Shizhe Tang
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
| | - Tingliang Xu
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
| | - Jing Peng
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
| | - Kaiyan Zhou
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
| | - Yuling Zhu
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
| | - Wenbo Zhou
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
| | - Haina Cheng
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
- Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, China
| | - Hongbo Zhou
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
- Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, China
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16
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Abstract
Thermophilic microbes are an attractive bioproduction platform due to their inherently lower contamination risk and their ability to perform thermostable enzymatic processes which may be required for biomass processing and other industrial applications. The engineering of microbes for industrial scale processes requires a suite of genetic engineering tools to optimize existing biological systems as well as to design and incorporate new metabolic pathways within strains. Yet, such tools are often lacking and/or inadequate for novel microbes, especially thermophiles. This chapter focuses on genetic tool development and engineering strategies, in addition to challenges, for thermophilic microbes. We provide detailed instructions and techniques for tool development for an anaerobic thermophile, Caldanaerobacter subterraneus subsp. tengcongensis, including culturing, plasmid construction, transformation, and selection. This establishes a foundation for advanced genetic tool development necessary for the metabolic engineering of this microbe and potentially other thermophilic organisms.
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17
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Abstract
Thermophilic organisms hold great potential for industry due to their numerous advantages in biotechnological applications such as higher reaction rate, higher substrate loading, decreased susceptibility to reaction contamination, energy savings in industrial fermentations, and ability to express thermostable proteins that can be utilized in many important industrial processes. Bioprospecting for thermophiles will continue to reveal new enzymatic and metabolic paradigms with industrial applicability. In order to translate these paradigms to production scale, routine methods for microbial genetic engineering are needed, yet remain to be developed in many newly isolated thermophiles. Major challenges and recent developments in the establishment of reliable genetic systems in thermophiles are discussed. Here, we use a hyperthermophilic, cellulolytic bacterium, Caldicellulosiruptor bescii, as a case study to demonstrate the development of a genetic system for an industrially useful thermophile, describing in detail methods for transformation, genetic tool utilization, and chromosomal modification using targeted gene deletion and insertion techniques.
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Affiliation(s)
- Daehwan Chung
- National Renewable Energy Laboratory, Golden, CO, USA.
| | - Nicholas S Sarai
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, USA
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18
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Woods C, Humphreys CM, Rodrigues RM, Ingle P, Rowe P, Henstra AM, Köpke M, Simpson SD, Winzer K, Minton NP. A novel conjugal donor strain for improved DNA transfer into Clostridium spp. Anaerobe 2019; 59:184-191. [PMID: 31269456 PMCID: PMC6866869 DOI: 10.1016/j.anaerobe.2019.06.020] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Revised: 06/27/2019] [Accepted: 06/29/2019] [Indexed: 12/29/2022]
Abstract
Clostridium encompasses species which are relevant to human and animal disease as well as species which have industrial potential, for instance, as producers of chemicals and fuels or as tumour delivery vehicles. Genetic manipulation of these target organisms is critical for advances in these fields. DNA transfer efficiencies, however, vary between species. Low efficiencies can impede the progress of research efforts. A novel conjugal donor strain of Escherichia coli has been created which exhibits a greater than 10-fold increases in conjugation efficiency compared to the traditionally used CA434 strain in the three species tested; C. autoethanogenum DSM 10061, C. sporogenes NCIMB 10696 and C. difficile R20291. The novel strain, designated 'sExpress', does not methylate DNA at Dcm sites (CCWGG) which allows circumvention of cytosine-specific Type IV restriction systems. A robust protocol for conjugation is presented which routinely produces in the order of 105 transconjugants per millilitre of donor cells for C. autoethanogenum, 106 for C. sporogenes and 102 for C. difficile R20291. The novel strain created is predicted to be a superior conjugal donor in a wide range of species which possess Type IV restriction systems.
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Affiliation(s)
- Craig Woods
- Clostridia Research Group, BBSRC/EPSRC Synthetic Biology Research Centre (SBRC), School of Life Sciences, The University of Nottingham, Nottingham, NG7 2RD, UK
| | - Christopher M Humphreys
- Clostridia Research Group, BBSRC/EPSRC Synthetic Biology Research Centre (SBRC), School of Life Sciences, The University of Nottingham, Nottingham, NG7 2RD, UK
| | - Raquel Mesquita Rodrigues
- Clostridia Research Group, BBSRC/EPSRC Synthetic Biology Research Centre (SBRC), School of Life Sciences, The University of Nottingham, Nottingham, NG7 2RD, UK
| | - Patrick Ingle
- Clostridia Research Group, BBSRC/EPSRC Synthetic Biology Research Centre (SBRC), School of Life Sciences, The University of Nottingham, Nottingham, NG7 2RD, UK
| | - Peter Rowe
- Clostridia Research Group, BBSRC/EPSRC Synthetic Biology Research Centre (SBRC), School of Life Sciences, The University of Nottingham, Nottingham, NG7 2RD, UK
| | - Anne M Henstra
- Clostridia Research Group, BBSRC/EPSRC Synthetic Biology Research Centre (SBRC), School of Life Sciences, The University of Nottingham, Nottingham, NG7 2RD, UK
| | - Michael Köpke
- LanzaTech Inc., 8045 Lamon Avenue, Suite 400, Skokie, IL, USA
| | - Sean D Simpson
- LanzaTech Inc., 8045 Lamon Avenue, Suite 400, Skokie, IL, USA
| | - Klaus Winzer
- Clostridia Research Group, BBSRC/EPSRC Synthetic Biology Research Centre (SBRC), School of Life Sciences, The University of Nottingham, Nottingham, NG7 2RD, UK
| | - Nigel P Minton
- Clostridia Research Group, BBSRC/EPSRC Synthetic Biology Research Centre (SBRC), School of Life Sciences, The University of Nottingham, Nottingham, NG7 2RD, UK; NIHR Nottingham Biomedical Research Centre, Nottingham University Hospitals NHS Trust and the University of Nottingham, Nottingham NG7 2RD, UK.
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19
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Rational development of transformation in Clostridium thermocellum ATCC 27405 via complete methylome analysis and evasion of native restriction-modification systems. J Ind Microbiol Biotechnol 2019; 46:1435-1443. [PMID: 31342224 PMCID: PMC6791906 DOI: 10.1007/s10295-019-02218-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2019] [Accepted: 07/11/2019] [Indexed: 12/13/2022]
Abstract
A major barrier to both metabolic engineering and fundamental biological studies is the lack of genetic tools in most microorganisms. One example is Clostridium thermocellum ATCC 27405T, where genetic tools are not available to help validate decades of hypotheses. A significant barrier to DNA transformation is restriction–modification systems, which defend against foreign DNA methylated differently than the host. To determine the active restriction–modification systems in this strain, we performed complete methylome analysis via single-molecule, real-time sequencing to detect 6-methyladenine and 4-methylcytosine and the rarely used whole-genome bisulfite sequencing to detect 5-methylcytosine. Multiple active systems were identified, and corresponding DNA methyltransferases were expressed from the Escherichia coli chromosome to mimic the C. thermocellum methylome. Plasmid methylation was experimentally validated and successfully electroporated into C. thermocellum ATCC 27405. This combined approach enabled genetic modification of the C. thermocellum-type strain and acts as a blueprint for transformation of other non-model microorganisms.
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20
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Development of a shuttle plasmid without host restriction sites for efficient transformation and heterologous gene expression in Clostridium cellulovorans. Appl Microbiol Biotechnol 2019; 103:5391-5400. [DOI: 10.1007/s00253-019-09882-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Revised: 04/16/2019] [Accepted: 04/29/2019] [Indexed: 10/26/2022]
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21
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Liu S, Liu YJ, Feng Y, Li B, Cui Q. Construction of consolidated bio-saccharification biocatalyst and process optimization for highly efficient lignocellulose solubilization. BIOTECHNOLOGY FOR BIOFUELS 2019; 12:35. [PMID: 30820245 PMCID: PMC6378752 DOI: 10.1186/s13068-019-1374-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Accepted: 02/07/2019] [Indexed: 06/09/2023]
Abstract
BACKGROUND The industrial conversion of biomass to high-value biofuels and biochemical is mainly restricted by lignocellulose solubilization. Consolidated bio-saccharification (CBS) is considered a promising process for lignocellulose solubilization depending on whole-cell biocatalysts that simultaneously perform effective cellulase production and hydrolysis. However, it usually takes a long time to reach a high saccharification level using the current CBS biocatalyst and process. RESULTS To promote the saccharification efficiency and reduce the cost, a Clostridium thermocellum recombinant strain ∆pyrF::KBm was constructed as a new CBS biocatalyst in this study. The key CBS factors, including the medium, inoculum size and cultivation, and substrate load, were investigated and optimized. The saccharification process was also stimulated by adding free hemicellulases, suggesting the need to further enhance hemicellulase activity of the whole-cell catalyst. Under the optimal conditions, the CBS process was shortened by 50% with pretreated wheat straw as the substrate. The sugar yield reached 0.795 g/g and the saccharification level was 89.3%. CONCLUSIONS This work provided a new biocatalyst and an optimized process of CBS and confirmed that CBS is a feasible strategy for cost-efficient solubilization of lignocellulose, which will greatly promote the industrial utilization of lignocellulosic biomass.
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Affiliation(s)
- Shiyue Liu
- CAS Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
- Dalian National Laboratory for Clean Energy, Chinese Academy of Sciences, Dalian, China
- University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing, China
| | - Ya-Jun Liu
- CAS Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
- Dalian National Laboratory for Clean Energy, Chinese Academy of Sciences, Dalian, China
| | - Yingang Feng
- CAS Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
- Dalian National Laboratory for Clean Energy, Chinese Academy of Sciences, Dalian, China
| | - Bin Li
- CAS Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
- Dalian National Laboratory for Clean Energy, Chinese Academy of Sciences, Dalian, China
| | - Qiu Cui
- CAS Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
- Dalian National Laboratory for Clean Energy, Chinese Academy of Sciences, Dalian, China
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22
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Seo H, Lee JW, Garcia S, Trinh CT. Single mutation at a highly conserved region of chloramphenicol acetyltransferase enables isobutyl acetate production directly from cellulose by Clostridium thermocellum at elevated temperatures. BIOTECHNOLOGY FOR BIOFUELS 2019; 12:245. [PMID: 31636704 PMCID: PMC6792240 DOI: 10.1186/s13068-019-1583-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Accepted: 10/01/2019] [Indexed: 05/03/2023]
Abstract
BACKGROUND Esters are versatile chemicals and potential drop-in biofuels. To develop a sustainable production platform, microbial ester biosynthesis using alcohol acetyltransferases (AATs) has been studied for decades. Volatility of esters endows high-temperature fermentation with advantageous downstream product separation. However, due to the limited thermostability of AATs known, the ester biosynthesis has largely relied on use of mesophilic microbes. Therefore, developing thermostable AATs is important for ester production directly from lignocellulosic biomass by the thermophilic consolidated bioprocessing (CBP) microbes, e.g., Clostridium thermocellum. RESULTS In this study, we engineered a thermostable chloramphenicol acetyltransferase from Staphylococcus aureus (CATSa) for enhanced isobutyl acetate production at elevated temperatures. We first analyzed the broad alcohol substrate range of CATSa. Then, we targeted a highly conserved region in the binding pocket of CATSa for mutagenesis. The mutagenesis revealed that F97W significantly increased conversion of isobutanol to isobutyl acetate. Using CATSa F97W, we demonstrated direct conversion of cellulose into isobutyl acetate by an engineered C. thermocellum at elevated temperatures. CONCLUSIONS This study highlights that CAT is a potential thermostable AAT that can be harnessed to develop the thermophilic CBP microbial platform for biosynthesis of designer bioesters directly from lignocellulosic biomass.
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Affiliation(s)
- Hyeongmin Seo
- Department of Chemical and Biomolecular Engineering, The University of Tennessee, Knoxville, TN USA
- Center for Bioenergy Innovation (CBI), Oak Ridge National Laboratory, Oak Ridge, TN USA
| | - Jong-Won Lee
- Bredesen Center for Interdisciplinary Research and Graduate Education, The University of Tennessee, Knoxville, TN USA
- Center for Bioenergy Innovation (CBI), Oak Ridge National Laboratory, Oak Ridge, TN USA
| | - Sergio Garcia
- Department of Chemical and Biomolecular Engineering, The University of Tennessee, Knoxville, TN USA
- Center for Bioenergy Innovation (CBI), Oak Ridge National Laboratory, Oak Ridge, TN USA
| | - Cong T. Trinh
- Department of Chemical and Biomolecular Engineering, The University of Tennessee, Knoxville, TN USA
- Bredesen Center for Interdisciplinary Research and Graduate Education, The University of Tennessee, Knoxville, TN USA
- Center for Bioenergy Innovation (CBI), Oak Ridge National Laboratory, Oak Ridge, TN USA
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23
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Philipps G, de Vries S, Jennewein S. Development of a metabolic pathway transfer and genomic integration system for the syngas-fermenting bacterium Clostridium ljungdahlii. BIOTECHNOLOGY FOR BIOFUELS 2019; 12:112. [PMID: 31086564 PMCID: PMC6507227 DOI: 10.1186/s13068-019-1448-1] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Accepted: 04/22/2019] [Indexed: 05/15/2023]
Abstract
BACKGROUND Clostridium spp. can synthesize valuable chemicals and fuels by utilizing diverse waste-stream substrates, including starchy biomass, lignocellulose, and industrial waste gases. However, metabolic engineering in Clostridium spp. is challenging due to the low efficiency of gene transfer and genomic integration of entire biosynthetic pathways. RESULTS We have developed a reliable gene transfer and genomic integration system for the syngas-fermenting bacterium Clostridium ljungdahlii based on the conjugal transfer of donor plasmids containing large transgene cassettes (> 5 kb) followed by the inducible activation of Himar1 transposase to promote integration. We established a conjugation protocol for the efficient generation of transconjugants using the Gram-positive origins of replication repL and repH. We also investigated the impact of DNA methylation on conjugation efficiency by testing donor constructs with all possible combinations of Dam and Dcm methylation patterns, and used bisulfite conversion and PacBio sequencing to determine the DNA methylation profile of the C. ljungdahlii genome, resulting in the detection of four sequence motifs with N6-methyladenosine. As proof of concept, we demonstrated the transfer and genomic integration of a heterologous acetone biosynthesis pathway using a Himar1 transposase system regulated by a xylose-inducible promoter. The functionality of the integrated pathway was confirmed by detecting enzyme proteotypic peptides and the formation of acetone and isopropanol by C. ljungdahlii cultures utilizing syngas as a carbon and energy source. CONCLUSIONS The developed multi-gene delivery system offers a versatile tool to integrate and stably express large biosynthetic pathways in the industrial promising syngas-fermenting microorganism C. ljungdahlii. The simple transfer and stable integration of large gene clusters (like entire biosynthetic pathways) is expanding the range of possible fermentation products of heterologously expressing recombinant strains. We also believe that the developed gene delivery system can be adapted to other clostridial strains as well.
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Affiliation(s)
- Gabriele Philipps
- Department for Industrial Biotechnology, Fraunhofer IME, Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Forckenbeckstr. 6, 52074 Aachen, Germany
| | - Sebastian de Vries
- Department for Industrial Biotechnology, Fraunhofer IME, Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Forckenbeckstr. 6, 52074 Aachen, Germany
- Present Address: Department of Intensive Care Medicine, University Hospital, RWTH Aachen University, Pauwelsstr. 30, 52074 Aachen, Germany
| | - Stefan Jennewein
- Department for Industrial Biotechnology, Fraunhofer IME, Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Forckenbeckstr. 6, 52074 Aachen, Germany
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24
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Hon S, Holwerda EK, Worthen RS, Maloney MI, Tian L, Cui J, Lin PP, Lynd LR, Olson DG. Expressing the Thermoanaerobacterium saccharolyticum pforA in engineered Clostridium thermocellum improves ethanol production. BIOTECHNOLOGY FOR BIOFUELS 2018; 11:242. [PMID: 30202437 PMCID: PMC6125887 DOI: 10.1186/s13068-018-1245-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Accepted: 08/27/2018] [Indexed: 05/12/2023]
Abstract
BACKGROUND Clostridium thermocellum has been the subject of multiple metabolic engineering strategies to improve its ability to ferment cellulose to ethanol, with varying degrees of success. For ethanol production in C. thermocellum, the conversion of pyruvate to acetyl-CoA is catalyzed primarily by the pyruvate ferredoxin oxidoreductase (PFOR) pathway. Thermoanaerobacterium saccharolyticum, which was previously engineered to produce ethanol of high yield (> 80%) and titer (70 g/L), also uses a pyruvate ferredoxin oxidoreductase, pforA, for ethanol production. RESULTS Here, we introduced the T. saccharolyticum pforA and ferredoxin into C. thermocellum. The introduction of pforA resulted in significant improvements to ethanol yield and titer in C. thermocellum grown on 50 g/L of cellobiose, but only when four other T. saccharolyticum genes (adhA, nfnA, nfnB, and adhEG544D ) were also present. T. saccharolyticum ferredoxin did not have any observable impact on ethanol production. The improvement to ethanol production was sustained even when all annotated native C. thermocellum pfor genes were deleted. On high cellulose concentrations, the maximum ethanol titer achieved by this engineered C. thermocellum strain from 100 g/L Avicel was 25 g/L, compared to 22 g/L for the reference strain, LL1319 (adhA(Tsc)-nfnAB(Tsc)-adhEG544D (Tsc)) under similar conditions. In addition, we also observed that deletion of the C. thermocellum pfor4 results in a significant decrease in isobutanol production. CONCLUSIONS Here, we demonstrate that the pforA gene can improve ethanol production in C. thermocellum as part of the T. saccharolyticum pyruvate-to-ethanol pathway. In our previous strain, high-yield (~ 75% of theoretical) ethanol production could be achieved with at most 20 g/L substrate. In this strain, high-yield ethanol production can be achieved up to 50 g/L substrate. Furthermore, the introduction of pforA increased the maximum titer by 14%.
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Affiliation(s)
- Shuen Hon
- Thayer School of Engineering, Dartmouth College, 14 Engineering Drive, Hanover, NH 03755 USA
- Bioenergy Science Center, Oak Ridge National Laboratories, Oak Ridge, TN 37830 USA
- Center for Bioenergy Innovation, Oak Ridge National Laboratories, Oak Ridge, TN 37830 USA
| | - Evert K. Holwerda
- Thayer School of Engineering, Dartmouth College, 14 Engineering Drive, Hanover, NH 03755 USA
- Bioenergy Science Center, Oak Ridge National Laboratories, Oak Ridge, TN 37830 USA
- Center for Bioenergy Innovation, Oak Ridge National Laboratories, Oak Ridge, TN 37830 USA
| | - Robert S. Worthen
- Thayer School of Engineering, Dartmouth College, 14 Engineering Drive, Hanover, NH 03755 USA
- Bioenergy Science Center, Oak Ridge National Laboratories, Oak Ridge, TN 37830 USA
- Center for Bioenergy Innovation, Oak Ridge National Laboratories, Oak Ridge, TN 37830 USA
| | - Marybeth I. Maloney
- Thayer School of Engineering, Dartmouth College, 14 Engineering Drive, Hanover, NH 03755 USA
- Bioenergy Science Center, Oak Ridge National Laboratories, Oak Ridge, TN 37830 USA
- Center for Bioenergy Innovation, Oak Ridge National Laboratories, Oak Ridge, TN 37830 USA
| | - Liang Tian
- Thayer School of Engineering, Dartmouth College, 14 Engineering Drive, Hanover, NH 03755 USA
- Bioenergy Science Center, Oak Ridge National Laboratories, Oak Ridge, TN 37830 USA
- Center for Bioenergy Innovation, Oak Ridge National Laboratories, Oak Ridge, TN 37830 USA
| | - Jingxuan Cui
- Bioenergy Science Center, Oak Ridge National Laboratories, Oak Ridge, TN 37830 USA
- Center for Bioenergy Innovation, Oak Ridge National Laboratories, Oak Ridge, TN 37830 USA
- Department of Biological Sciences, Dartmouth College, Hanover, NH 03755 USA
| | - Paul P. Lin
- Bioenergy Science Center, Oak Ridge National Laboratories, Oak Ridge, TN 37830 USA
- University of California, Los Angeles, Los Angeles, CA 90095 USA
| | - Lee R. Lynd
- Thayer School of Engineering, Dartmouth College, 14 Engineering Drive, Hanover, NH 03755 USA
- Bioenergy Science Center, Oak Ridge National Laboratories, Oak Ridge, TN 37830 USA
- Center for Bioenergy Innovation, Oak Ridge National Laboratories, Oak Ridge, TN 37830 USA
- Department of Biological Sciences, Dartmouth College, Hanover, NH 03755 USA
| | - Daniel G. Olson
- Thayer School of Engineering, Dartmouth College, 14 Engineering Drive, Hanover, NH 03755 USA
- Bioenergy Science Center, Oak Ridge National Laboratories, Oak Ridge, TN 37830 USA
- Center for Bioenergy Innovation, Oak Ridge National Laboratories, Oak Ridge, TN 37830 USA
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Groom J, Chung D, Kim SK, Guss A, Westpheling J. Deletion of the Clostridium thermocellum recA gene reveals that it is required for thermophilic plasmid replication but not plasmid integration at homologous DNA sequences. J Ind Microbiol Biotechnol 2018; 45:753-763. [PMID: 29808293 PMCID: PMC6483729 DOI: 10.1007/s10295-018-2049-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Accepted: 05/19/2018] [Indexed: 12/30/2022]
Abstract
A limitation to the engineering of cellulolytic thermophiles is the availability of functional, thermostable (≥ 60 °C) replicating plasmid vectors for rapid expression and testing of genes that provide improved or novel fuel molecule production pathways. A series of plasmid vectors for genetic manipulation of the cellulolytic thermophile Caldicellulosiruptor bescii has recently been extended to Clostridium thermocellum, another cellulolytic thermophile that very efficiently solubilizes plant biomass and produces ethanol. While the C. bescii pBAS2 replicon on these plasmids is thermostable, the use of homologous promoters, signal sequences and genes led to undesired integration into the bacterial chromosome, a result also observed with less thermostable replicating vectors. In an attempt to overcome undesired plasmid integration in C. thermocellum, a deletion of recA was constructed. As expected, C. thermocellum ∆recA showed impaired growth in chemically defined medium and an increased susceptibility to UV damage. Interestingly, we also found that recA is required for replication of the C. bescii thermophilic plasmid pBAS2 in C. thermocellum, but it is not required for replication of plasmid pNW33N. In addition, the C. thermocellum recA mutant retained the ability to integrate homologous DNA into the C. thermocellum chromosome. These data indicate that recA can be required for replication of certain plasmids, and that a recA-independent mechanism exists for the integration of homologous DNA into the C. thermocellum chromosome. Understanding thermophilic plasmid replication is not only important for engineering of these cellulolytic thermophiles, but also for developing genetic systems in similar new potentially useful non-model organisms.
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Affiliation(s)
- Joseph Groom
- Department of Genetics, Davison Life Sciences Building, University of Georgia, Athens, GA, 30602, USA
- Department of Chemical Engineering, University of Washington, Seattle, WA, 98105, USA
- Oak Ridge National Laboratory, The Center for BioEnergy Innovation, Oak Ridge, TN, 37831, USA
| | - Daehwan Chung
- National Renewable Energy Laboratory, Biosciences Center, Golden, CO, 80401, USA
- Oak Ridge National Laboratory, The BioEnergy Science Center, Oak Ridge, TN, 37831, USA
- Oak Ridge National Laboratory, The Center for BioEnergy Innovation, Oak Ridge, TN, 37831, USA
| | - Sun-Ki Kim
- Department of Genetics, Davison Life Sciences Building, University of Georgia, Athens, GA, 30602, USA
- Oak Ridge National Laboratory, The BioEnergy Science Center, Oak Ridge, TN, 37831, USA
- Oak Ridge National Laboratory, The Center for BioEnergy Innovation, Oak Ridge, TN, 37831, USA
| | - Adam Guss
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
- Oak Ridge National Laboratory, The BioEnergy Science Center, Oak Ridge, TN, 37831, USA
- Oak Ridge National Laboratory, The Center for BioEnergy Innovation, Oak Ridge, TN, 37831, USA
| | - Janet Westpheling
- Department of Genetics, Davison Life Sciences Building, University of Georgia, Athens, GA, 30602, USA.
- Oak Ridge National Laboratory, The BioEnergy Science Center, Oak Ridge, TN, 37831, USA.
- Oak Ridge National Laboratory, The Center for BioEnergy Innovation, Oak Ridge, TN, 37831, USA.
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Ortiz de Ora L, Lamed R, Liu YJ, Xu J, Cui Q, Feng Y, Shoham Y, Bayer EA, Muñoz-Gutiérrez I. Regulation of biomass degradation by alternative σ factors in cellulolytic clostridia. Sci Rep 2018; 8:11036. [PMID: 30038431 PMCID: PMC6056542 DOI: 10.1038/s41598-018-29245-5] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Accepted: 07/04/2018] [Indexed: 11/28/2022] Open
Abstract
Bacteria can adjust their genetic programs via alternative σ factors to face new environmental pressures. Here, we analyzed a unique set of paralogous alternative σ factors, termed σIs, which fine-tune the regulation of one of the most intricate cellulolytic systems in nature, the bacterial cellulosome, that is involved in degradation of environmental polysaccharides. We combined bioinformatics with experiments to decipher the regulatory networks of five σIs in Clostridium thermocellum, the epitome of cellulolytic microorganisms, and one σI in Pseudobacteroides cellulosolvens which produces the cellulosomal system with the greatest known complexity. Despite high homology between different σIs, our data suggest limited cross-talk among them. Remarkably, the major cross-talk occurs within the main cellulosomal genes which harbor the same σI-dependent promoter elements, suggesting a promoter-based mechanism to guarantee the expression of relevant genes. Our findings provide insights into the mechanisms used by σIs to differentiate among their corresponding regulons, representing a comprehensive overview of the regulation of the cellulosome to date. Finally, we show the advantage of using a heterologous host system for analysis of multiple σIs, since information generated by their analysis in their natural host can be misinterpreted owing to a cascade of interactions among the different σIs.
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Affiliation(s)
- Lizett Ortiz de Ora
- Department of Molecular Microbiology and Biotechnology, Tel Aviv University, Tel Aviv, Israel
| | - Raphael Lamed
- Department of Molecular Microbiology and Biotechnology, Tel Aviv University, Tel Aviv, Israel
| | - Ya-Jun Liu
- CAS Key Laboratory of Biofuels and Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, China
| | - Jian Xu
- CAS Key Laboratory of Biofuels and Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, China
| | - Qiu Cui
- CAS Key Laboratory of Biofuels and Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, China
| | - Yingang Feng
- CAS Key Laboratory of Biofuels and Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, China
| | - Yuval Shoham
- Department of Biotechnology and Food Engineering, Technion-IIT, Haifa, Israel
| | - Edward A Bayer
- Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot, Israel
| | - Iván Muñoz-Gutiérrez
- Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot, Israel. .,Outreach Research Training and Minority Science Programs, Francisco Ayala School of Biological Sciences, University of California, Irvine, California, USA.
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27
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Freed E, Fenster J, Smolinski SL, Walker J, Henard CA, Gill R, Eckert CA. Building a genome engineering toolbox in nonmodel prokaryotic microbes. Biotechnol Bioeng 2018; 115:2120-2138. [PMID: 29750332 DOI: 10.1002/bit.26727] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Revised: 04/02/2018] [Accepted: 03/10/2018] [Indexed: 12/26/2022]
Abstract
The realization of a sustainable bioeconomy requires our ability to understand and engineer complex design principles for the development of platform organisms capable of efficient conversion of cheap and sustainable feedstocks (e.g., sunlight, CO2 , and nonfood biomass) into biofuels and bioproducts at sufficient titers and costs. For model microbes, such as Escherichia coli, advances in DNA reading and writing technologies are driving the adoption of new paradigms for engineering biological systems. Unfortunately, microbes with properties of interest for the utilization of cheap and renewable feedstocks, such as photosynthesis, autotrophic growth, and cellulose degradation, have very few, if any, genetic tools for metabolic engineering. Therefore, it is important to develop "design rules" for building a genetic toolbox for novel microbes. Here, we present an overview of our current understanding of these rules for the genetic manipulation of prokaryotic microbes and the available genetic tools to expand our ability to genetically engineer nonmodel systems.
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Affiliation(s)
- Emily Freed
- National Renewable Energy Laboratory, Biosciences Center, Golden, CO.,Renewable and Sustainable Energy Institute, University of Colorado, Boulder, CO
| | - Jacob Fenster
- Renewable and Sustainable Energy Institute, University of Colorado, Boulder, CO.,Chemical and Biological Engineering, University of Colorado, Boulder, CO
| | | | - Julie Walker
- Renewable and Sustainable Energy Institute, University of Colorado, Boulder, CO
| | - Calvin A Henard
- National Renewable Energy Laboratory, National Bioenergy Center, Golden, CO
| | - Ryan Gill
- National Renewable Energy Laboratory, Biosciences Center, Golden, CO.,Renewable and Sustainable Energy Institute, University of Colorado, Boulder, CO.,Chemical and Biological Engineering, University of Colorado, Boulder, CO
| | - Carrie A Eckert
- National Renewable Energy Laboratory, Biosciences Center, Golden, CO.,Renewable and Sustainable Energy Institute, University of Colorado, Boulder, CO
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Zou X, Ren Z, Wang N, Cheng Y, Jiang Y, Wang Y, Xu C. Function analysis of 5'-UTR of the cellulosomal xyl- doc cluster in Clostridium papyrosolvens. BIOTECHNOLOGY FOR BIOFUELS 2018; 11:43. [PMID: 29467821 PMCID: PMC5815224 DOI: 10.1186/s13068-018-1040-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Accepted: 02/02/2018] [Indexed: 05/04/2023]
Abstract
BACKGROUND Anaerobic, mesophilic, and cellulolytic Clostridium papyrosolvens produces an efficient cellulolytic extracellular complex named cellulosome that hydrolyzes plant cell wall polysaccharides into simple sugars. Its genome harbors two long cellulosomal clusters: cip-cel operon encoding major cellulosome components (including scaffolding) and xyl-doc gene cluster encoding hemicellulases. Compared with works on cip-cel operon, there are much fewer studies on xyl-doc mainly due to its rare location in cellulolytic clostridia. Sequence analysis of xyl-doc revealed that it harbors a 5' untranslated region (5'-UTR) which potentially plays a role in the regulation of downstream gene expression. Here, we analyzed the function of 5'-UTR of xyl-doc cluster in C. papyrosolvens in vivo via transformation technology developed in this study. RESULTS In this study, we firstly developed an electrotransformation method for C. papyrosolvens DSM 2782 before the analysis of 5'-UTR of xyl-doc cluster. In the optimized condition, a field with an intensity of 7.5-9.0 kV/cm was applied to a cuvette (0.2 cm gap) containing a mixture of plasmid and late cell suspended in exponential phase to form a 5 ms pulse in a sucrose-containing buffer. Afterwards, the putative promoter and the 5'-UTR of xyl-doc cluster were determined by sequence alignment. It is indicated that xyl-doc possesses a long conservative 5'-UTR with a complex secondary structure encompassing at least two perfect stem-loops which are potential candidates for controlling the transcriptional termination. In the last step, we employed an oxygen-independent flavin-based fluorescent protein (FbFP) as a quantitative reporter to analyze promoter activity and 5'-UTR function in vivo. It revealed that 5'-UTR significantly blocked transcription of downstream genes, but corn stover can relieve its suppression. CONCLUSIONS In the present study, our results demonstrated that 5'-UTR of the cellulosomal xyl-doc cluster blocks the transcriptional activity of promoter. However, some substrates, such as corn stover, can relieve the effect of depression of 5'-UTR. Thus, it is speculated that 5'-UTR of xyl-doc was a putative riboswitch to regulate the expression of downstream cellulosomal genes, which is helpful to understand the complex regulation of cellulosome.
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Affiliation(s)
- Xia Zou
- Research Center for Harmful Algae and Marine Biology, College of Life Science and Technology, Jinan University, Guangzhou, 510632 Guangdong Province China
| | - Zhenxing Ren
- Institute of Applied Chemistry, Shanxi University, Taiyuan, 030006 Shanxi Province China
| | - Na Wang
- Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Institute of Biotechnology, Shanxi University, Taiyuan, 030006 Shanxi Province China
| | - Yin Cheng
- Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Institute of Biotechnology, Shanxi University, Taiyuan, 030006 Shanxi Province China
| | - Yuanyuan Jiang
- Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Institute of Biotechnology, Shanxi University, Taiyuan, 030006 Shanxi Province China
| | - Yan Wang
- Research Center for Harmful Algae and Marine Biology, College of Life Science and Technology, Jinan University, Guangzhou, 510632 Guangdong Province China
| | - Chenggang Xu
- Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Institute of Biotechnology, Shanxi University, Taiyuan, 030006 Shanxi Province China
- Single-Cell Center, CAS Key Laboratory of Biofuels and Shandong Key Laboratory of Energy Genetics, Qingdao Institute of BioEnergy and BioProcess Technology, Chinese Academy of Sciences, Qingdao, 266101 Shandong Province China
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Wang Y, Okugawa K, Kunitake E, Sakka M, Kimura T, Sakka K. Development of an efficient host-vector system of Ruminiclostridium josui. J Basic Microbiol 2018; 58:448-458. [PMID: 29388680 DOI: 10.1002/jobm.201700620] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2017] [Revised: 12/23/2017] [Accepted: 12/30/2017] [Indexed: 01/22/2023]
Abstract
Although Ruminiclostridium josui (formerly Clostridium josui), a strictly anaerobic mesophilic cellulolytic bacterium, is a promising candidate for biomass utilization via consolidated bioprocessing, its host-vector system has not yet been established. The existence of a restriction and modification system is a significant barrier to the transformation of R. josui. Here, we partially purified restriction endonuclease RjoI from R. josui cell extract using column chromatography. Further characterization showed that RjoI is an isoschizomer of DpnI, recognizing the sequence 5'-Gmet ATC-3', where the A nucleotide is Dam-methylated. RjoI cleaved the recognition sequence between the A and T nucleotides, producing blunt ends. We then successfully introduced plasmids prepared from Escherichia coli C2925 (dam- /dcm- ) into R. josui by electroporation. The highest transformation efficiency of 6.6 × 103 transformants/μg of DNA was obtained using a square-wave pulse (750 V, 1 ms). When the R. josui cel48A gene, devoid of the dockerin-encoding region, cloned into newly developed plasmid pKKM801 was introduced into R. josui, a truncated form of RjCel48A, RjCel48AΔdoc, was detected in the culture supernatant but not in the intracellular fraction. This is the first report on the establishment of fundamental technology for molecular breeding of R. josui.
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Affiliation(s)
- Yayun Wang
- Graduate School of Bioresources, Mie University, Mie, Japan
| | - Kei Okugawa
- Graduate School of Bioresources, Mie University, Mie, Japan
| | - Emi Kunitake
- Graduate School of Bioresources, Mie University, Mie, Japan
| | - Makiko Sakka
- Graduate School of Bioresources, Mie University, Mie, Japan
| | - Tetsuya Kimura
- Graduate School of Bioresources, Mie University, Mie, Japan
| | - Kazuo Sakka
- Graduate School of Bioresources, Mie University, Mie, Japan
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30
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Whitham JM, Moon JW, Rodriguez M, Engle NL, Klingeman DM, Rydzak T, Abel MM, Tschaplinski TJ, Guss AM, Brown SD. Clostridium thermocellum LL1210 pH homeostasis mechanisms informed by transcriptomics and metabolomics. BIOTECHNOLOGY FOR BIOFUELS 2018; 11:98. [PMID: 29632556 PMCID: PMC5887222 DOI: 10.1186/s13068-018-1095-y] [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: 11/11/2017] [Accepted: 03/24/2018] [Indexed: 05/21/2023]
Abstract
BACKGROUND Clostridium (Ruminiclostridium) thermocellum is a model fermentative anaerobic thermophile being studied and engineered for consolidated bioprocessing of lignocellulosic feedstocks into fuels and chemicals. Engineering efforts have resulted in significant improvements in ethanol yields and titers although further advances are required to make the bacterium industry-ready. For instance, fermentations at lower pH could enable co-culturing with microbes that have lower pH optima, augment productivity, and reduce buffering cost. C. thermocellum is typically grown at neutral pH, and little is known about its pH limits or pH homeostasis mechanisms. To better understand C. thermocellum pH homeostasis we grew strain LL1210 (C. thermocellum DSM1313 Δhpt ΔhydG Δldh Δpfl Δpta-ack), currently the highest ethanol producing strain of C. thermocellum, at different pH values in chemostat culture and applied systems biology tools. RESULTS Clostridium thermocellum LL1210 was found to be growth-limited below pH 6.24 at a dilution rate of 0.1 h-1. F1F0-ATPase gene expression was upregulated while many ATP-utilizing enzymes and pathways were downregulated at pH 6.24. These included most flagella biosynthesis genes, genes for chemotaxis, and other motility-related genes (> 50) as well as sulfate transport and reduction, nitrate transport and nitrogen fixation, and fatty acid biosynthesis genes. Clustering and enrichment of differentially expressed genes at pH values 6.48, pH 6.24 and pH 6.12 (washout conditions) compared to pH 6.98 showed inverse differential expression patterns between the F1F0-ATPase and genes for other ATP-utilizing enzymes. At and below pH 6.24, amino acids including glutamate and valine; long-chain fatty acids, their iso-counterparts and glycerol conjugates; glycolysis intermediates 3-phosphoglycerate, glucose 6-phosphate, and glucose accumulated intracellularly. Glutamate was 267 times more abundant in cells at pH 6.24 compared to pH 6.98, and intercellular concentration reached 1.8 μmol/g pellet at pH 5.80 (stopped flow). CONCLUSIONS Clostridium thermocellum LL1210 can grow under slightly acidic conditions, similar to limits reported for other strains. This foundational study provides a detailed characterization of a relatively acid-intolerant bacterium and provides genetic targets for strain improvement. Future studies should examine adding gene functions used by more acid-tolerant bacteria for improved pH homeostasis at acidic pH values.
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Affiliation(s)
- Jason M. Whitham
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN USA
- BioEnergy Science Center, National Laboratory, Oak Ridge, TN USA
| | - Ji-Won Moon
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN USA
| | - Miguel Rodriguez
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN USA
- BioEnergy Science Center, National Laboratory, Oak Ridge, TN USA
| | - Nancy L. Engle
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN USA
- BioEnergy Science Center, National Laboratory, Oak Ridge, TN USA
| | - Dawn M. Klingeman
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN USA
- BioEnergy Science Center, National Laboratory, Oak Ridge, TN USA
| | - Thomas Rydzak
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN USA
- BioEnergy Science Center, National Laboratory, Oak Ridge, TN USA
- Present Address: Department of Biological Science, University of Calgary, Calgary, AB T2N 1N4 Canada
| | - Malaney M. Abel
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN USA
- BioEnergy Science Center, National Laboratory, Oak Ridge, TN USA
| | - Timothy J. Tschaplinski
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN USA
- BioEnergy Science Center, National Laboratory, Oak Ridge, TN USA
| | - Adam M. Guss
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN USA
- BioEnergy Science Center, National Laboratory, Oak Ridge, TN USA
| | - Steven D. Brown
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN USA
- BioEnergy Science Center, National Laboratory, Oak Ridge, TN USA
- Present Address: LanzaTech, Inc., Skokie, IL USA
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31
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Eminoğlu A, Murphy SJL, Maloney M, Lanahan A, Giannone RJ, Hettich RL, Tripathi SA, Beldüz AO, Lynd LR, Olson DG. Deletion of the hfsB gene increases ethanol production in Thermoanaerobacterium saccharolyticum and several other thermophilic anaerobic bacteria. BIOTECHNOLOGY FOR BIOFUELS 2017; 10:282. [PMID: 29213322 PMCID: PMC5707799 DOI: 10.1186/s13068-017-0968-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Accepted: 11/13/2017] [Indexed: 05/22/2023]
Abstract
BACKGROUND With the discovery of interspecies hydrogen transfer in the late 1960s (Bryant et al. in Arch Microbiol 59:20-31, 1967), it was shown that reducing the partial pressure of hydrogen could cause mixed acid fermenting organisms to produce acetate at the expense of ethanol. Hydrogen and ethanol are both more reduced than glucose. Thus there is a tradeoff between production of these compounds imposed by electron balancing requirements; however, the mechanism is not fully known. RESULTS Deletion of the hfsA or B subunits resulted in a roughly 1.8-fold increase in ethanol yield. The increase in ethanol production appears to be associated with an increase in alcohol dehydrogenase activity, which appears to be due, at least in part, to increased expression of the adhE gene, and may suggest a regulatory linkage between hfsB and adhE. We studied this system most intensively in the organism Thermoanaerobacterium saccharolyticum; however, deletion of hfsB also increases ethanol production in other thermophilic bacteria suggesting that this could be used as a general technique for engineering thermophilic bacteria for improved ethanol production in organisms with hfs-type hydrogenases. CONCLUSION Since its discovery by Shaw et al. (JAMA 191:6457-64, 2009), the hfs hydrogenase has been suspected to act as a regulator due to the presence of a PAS domain. We provide additional support for the presence of a regulatory phenomenon. In addition, we find a practical application for this scientific insight, namely increasing ethanol yield in strains that are of interest for ethanol production from cellulose or hemicellulose. In two of these organisms (T. xylanolyticum and T. thermosaccharolyticum), the ethanol yields are the highest reported to date.
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Affiliation(s)
- Ayşenur Eminoğlu
- Department of Biology, Molecular Biology Research Laboratories, Faculty of Art and Science, Recep Tayyip Erdogan University, Rize, Turkey
| | - Sean Jean-Loup Murphy
- Thayer School of Engineering, Dartmouth College, 14 Engineering Drive, Hanover, NH 03755 USA
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN USA
| | - Marybeth Maloney
- Thayer School of Engineering, Dartmouth College, 14 Engineering Drive, Hanover, NH 03755 USA
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN USA
| | - Anthony Lanahan
- Thayer School of Engineering, Dartmouth College, 14 Engineering Drive, Hanover, NH 03755 USA
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN USA
| | - Richard J. Giannone
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN USA
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN USA
| | - Robert L. Hettich
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN USA
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN USA
| | | | - Ali Osman Beldüz
- Department of Biology, Faculty of Science, Karadeniz Technical University, Trabzon, Turkey
| | - Lee R. Lynd
- Thayer School of Engineering, Dartmouth College, 14 Engineering Drive, Hanover, NH 03755 USA
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN USA
- Department of Biological Sciences, Dartmouth College, Hanover, NH USA
| | - Daniel G. Olson
- Thayer School of Engineering, Dartmouth College, 14 Engineering Drive, Hanover, NH 03755 USA
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN USA
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Gilna P, Lynd LR, Mohnen D, Davis MF, Davison BH. Progress in understanding and overcoming biomass recalcitrance: a BioEnergy Science Center (BESC) perspective. BIOTECHNOLOGY FOR BIOFUELS 2017; 10:285. [PMID: 29213324 PMCID: PMC5707806 DOI: 10.1186/s13068-017-0971-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Accepted: 11/15/2017] [Indexed: 06/07/2023]
Abstract
The DOE BioEnergy Science Center has operated as a virtual center with multiple partners for a decade targeting overcoming biomass recalcitrance. BESC has redefined biomass recalcitrance from an observable phenotype to a better understood and manipulatable fundamental and operational property. These manipulations are the result of deeper biological understanding and can be combined with other advanced biotechnology improvements in biomass conversion to improve bioenergy processes and markets. This article provides an overview of key accomplishments in overcoming recalcitrance via better plants, better microbes, and better tools and combinations. A perspective on the aspects of successful center operation is presented.
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Affiliation(s)
- Paul Gilna
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
- Biosciences Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, Bldg. 1505, Rm. 100A, Oak Ridge, TN 37831-6037 USA
| | - Lee R. Lynd
- Biosciences Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, Bldg. 1505, Rm. 100A, Oak Ridge, TN 37831-6037 USA
- Thayer School of Engineering, Dartmouth College, Hanover, NH 03755 USA
| | - Debra Mohnen
- Biosciences Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, Bldg. 1505, Rm. 100A, Oak Ridge, TN 37831-6037 USA
- Complex Carbohydrate Research Center and Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602 USA
| | - Mark F. Davis
- Biosciences Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, Bldg. 1505, Rm. 100A, Oak Ridge, TN 37831-6037 USA
- National Bioenergy Center, National Renewable Energy Laboratory, Golden, CO 80401 USA
| | - Brian H. Davison
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
- Biosciences Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, Bldg. 1505, Rm. 100A, Oak Ridge, TN 37831-6037 USA
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Yan Q, Fong SS. Challenges and Advances for Genetic Engineering of Non-model Bacteria and Uses in Consolidated Bioprocessing. Front Microbiol 2017; 8:2060. [PMID: 29123506 PMCID: PMC5662904 DOI: 10.3389/fmicb.2017.02060] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2017] [Accepted: 10/09/2017] [Indexed: 12/26/2022] Open
Abstract
Metabolic diversity in microorganisms can provide the basis for creating novel biochemical products. However, most metabolic engineering projects utilize a handful of established model organisms and thus, a challenge for harnessing the potential of novel microbial functions is the ability to either heterologously express novel genes or directly utilize non-model organisms. Genetic manipulation of non-model microorganisms is still challenging due to organism-specific nuances that hinder universal molecular genetic tools and translatable knowledge of intracellular biochemical pathways and regulatory mechanisms. However, in the past several years, unprecedented progress has been made in synthetic biology, molecular genetics tools development, applications of omics data techniques, and computational tools that can aid in developing non-model hosts in a systematic manner. In this review, we focus on concerns and approaches related to working with non-model microorganisms including developing molecular genetics tools such as shuttle vectors, selectable markers, and expression systems. In addition, we will discuss: (1) current techniques in controlling gene expression (transcriptional/translational level), (2) advances in site-specific genome engineering tools [homologous recombination (HR) and clustered regularly interspaced short palindromic repeats (CRISPR)], and (3) advances in genome-scale metabolic models (GSMMs) in guiding design of non-model species. Application of these principles to metabolic engineering strategies for consolidated bioprocessing (CBP) will be discussed along with some brief comments on foreseeable future prospects.
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Affiliation(s)
- Qiang Yan
- Department of Chemical and Life Science Engineering, Virginia Commonwealth University, Richmond, VA, United States
| | - Stephen S. Fong
- Department of Chemical and Life Science Engineering, Virginia Commonwealth University, Richmond, VA, United States
- Center for the Study of Biological Complexity, Virginia Commonwealth University, Richmond, VA, United States
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Enhanced ethanol formation by Clostridium thermocellum via pyruvate decarboxylase. Microb Cell Fact 2017; 16:171. [PMID: 28978312 PMCID: PMC5628457 DOI: 10.1186/s12934-017-0783-9] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Accepted: 09/26/2017] [Indexed: 12/31/2022] Open
Abstract
Background Pyruvate decarboxylase (PDC) is a well-known pathway for ethanol production, but has not been demonstrated for high titer ethanol production at temperatures above 50 °C. Result Here we examined the thermostability of eight PDCs. The purified bacterial enzymes retained 20% of activity after incubation for 30 min at 55 °C. Expression of these PDC genes, except the one from Zymomonas mobilis, improved ethanol production by Clostridium thermocellum. Ethanol production was further improved by expression of the heterologous alcohol dehydrogenase gene adhA from Thermoanaerobacterium saccharolyticum. Conclusion The best PDC enzyme was from Acetobactor pasteurianus. A strain of C. thermocellum expressing the pdc gene from A. pasteurianus and the adhA gene from T. saccharolyticum was able to produce 21.3 g/L ethanol from 60 g/L cellulose, which is 70% of the theoretical maximum yield. Electronic supplementary material The online version of this article (doi:10.1186/s12934-017-0783-9) contains supplementary material, which is available to authorized users.
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Hon S, Olson DG, Holwerda EK, Lanahan AA, Murphy SJL, Maloney MI, Zheng T, Papanek B, Guss AM, Lynd LR. The ethanol pathway from Thermoanaerobacterium saccharolyticum improves ethanol production in Clostridium thermocellum. Metab Eng 2017; 42:175-184. [PMID: 28663138 DOI: 10.1016/j.ymben.2017.06.011] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2017] [Revised: 05/27/2017] [Accepted: 06/23/2017] [Indexed: 12/31/2022]
Abstract
Clostridium thermocellum ferments cellulose, is a promising candidate for ethanol production from cellulosic biomass, and has been the focus of studies aimed at improving ethanol yield. Thermoanaerobacterium saccharolyticum ferments hemicellulose, but not cellulose, and has been engineered to produce ethanol at high yield and titer. Recent research has led to the identification of four genes in T. saccharolyticum involved in ethanol production: adhE, nfnA, nfnB and adhA. We introduced these genes into C. thermocellum and observed significant improvements to ethanol yield, titer, and productivity. The four genes alone, however, were insufficient to achieve in C. thermocellum the ethanol yields and titers observed in engineered T. saccharolyticum strains, even when combined with gene deletions targeting hydrogen production. This suggests that other parts of T. saccharolyticum metabolism may also be necessary to reproduce the high ethanol yield and titer phenotype in C. thermocellum.
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Affiliation(s)
- Shuen Hon
- Thayer School of Engineering, Dartmouth College, Hanover, NH 03755, USA; Bioenergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37830, USA
| | - Daniel G Olson
- Thayer School of Engineering, Dartmouth College, Hanover, NH 03755, USA; Bioenergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37830, USA.
| | - Evert K Holwerda
- Thayer School of Engineering, Dartmouth College, Hanover, NH 03755, USA; Bioenergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37830, USA
| | - Anthony A Lanahan
- Thayer School of Engineering, Dartmouth College, Hanover, NH 03755, USA; Bioenergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37830, USA
| | - Sean J L Murphy
- Thayer School of Engineering, Dartmouth College, Hanover, NH 03755, USA; Bioenergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37830, USA
| | - Marybeth I Maloney
- Thayer School of Engineering, Dartmouth College, Hanover, NH 03755, USA; Bioenergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37830, USA
| | - Tianyong Zheng
- Department of Biological Sciences, Dartmouth College, Hanover, NH 03755, USA; Bioenergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37830, USA
| | - Beth Papanek
- Bioenergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37830, USA; Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37830, USA
| | - Adam M Guss
- Bioenergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37830, USA; Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37830, USA
| | - Lee R Lynd
- Thayer School of Engineering, Dartmouth College, Hanover, NH 03755, USA; Department of Biological Sciences, Dartmouth College, Hanover, NH 03755, USA; Bioenergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37830, USA.
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Rydzak T, Garcia D, Stevenson DM, Sladek M, Klingeman DM, Holwerda EK, Amador-Noguez D, Brown SD, Guss AM. Deletion of Type I glutamine synthetase deregulates nitrogen metabolism and increases ethanol production in Clostridium thermocellum. Metab Eng 2017; 41:182-191. [PMID: 28400329 DOI: 10.1016/j.ymben.2017.04.002] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2016] [Revised: 03/27/2017] [Accepted: 04/07/2017] [Indexed: 12/25/2022]
Abstract
Clostridium thermocellum rapidly deconstructs cellulose and ferments resulting hydrolysis products into ethanol and other products, and is thus a promising platform organism for the development of cellulosic biofuel production via consolidated bioprocessing. While recent metabolic engineering strategies have targeted eliminating canonical fermentation products (acetate, lactate, formate, and H2), C. thermocellum also secretes amino acids, which has limited ethanol yields in engineered strains to approximately 70% of the theoretical maximum. To investigate approaches to decrease amino acid secretion, we attempted to reduce ammonium assimilation by deleting the Type I glutamine synthetase (glnA) in an essentially wild type strain of C. thermocellum. Deletion of glnA reduced levels of secreted valine and total amino acids by 53% and 44% respectively, and increased ethanol yields by 53%. RNA-seq analysis revealed that genes encoding the RNF-complex were more highly expressed in ΔglnA and may have a role in improving NADH-availability for ethanol production. While a significant up-regulation of genes involved in nitrogen assimilation and urea uptake suggested that deletion of glnA induces a nitrogen starvation response, metabolomic analysis showed an increase in intracellular glutamine levels indicative of nitrogen-rich conditions. We propose that deletion of glnA causes deregulation of nitrogen metabolism, leading to overexpression of nitrogen metabolism genes and, in turn, elevated glutamine levels. Here we demonstrate that perturbation of nitrogen assimilation is a promising strategy to redirect flux from the production of nitrogenous compounds toward biofuels in C. thermocellum.
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Affiliation(s)
- Thomas Rydzak
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States; BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - David Garcia
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States; BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - David M Stevenson
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, United States
| | - Margaret Sladek
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States; BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Dawn M Klingeman
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States; BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Evert K Holwerda
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States; Thayer School of Engineering at Dartmouth College, Hanover, NH, United States
| | - Daniel Amador-Noguez
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, United States
| | - Steven D Brown
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States; BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Adam M Guss
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States; BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN, United States.
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LacI Transcriptional Regulatory Networks in Clostridium thermocellum DSM1313. Appl Environ Microbiol 2017; 83:AEM.02751-16. [PMID: 28003194 DOI: 10.1128/aem.02751-16] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2016] [Accepted: 12/14/2016] [Indexed: 12/30/2022] Open
Abstract
Organisms regulate gene expression in response to the environment to coordinate metabolic reactions. Clostridium thermocellum expresses enzymes for both lignocellulose solubilization and its fermentation to produce ethanol. One LacI regulator termed GlyR3 in C. thermocellum ATCC 27405 was previously identified as a repressor of neighboring genes with repression relieved by laminaribiose (a β-1,3 disaccharide). To better understand the three C. thermocellum LacI regulons, deletion mutants were constructed using the genetically tractable DSM1313 strain. DSM1313 lacI genes Clo1313_2023, Clo1313_0089, and Clo1313_0396 encode homologs of GlyR1, GlyR2, and GlyR3 from strain ATCC 27405, respectively. Growth on cellobiose or pretreated switchgrass was unaffected by any of the gene deletions under controlled-pH fermentations. Global gene expression patterns from time course analyses identified glycoside hydrolase genes encoding hemicellulases, including cellulosomal enzymes, that were highly upregulated (5- to 100-fold) in the absence of each LacI regulator, suggesting that these were repressed under wild-type conditions and that relatively few genes were controlled by each regulator under the conditions tested. Clo1313_2022, encoding lichenase enzyme LicB, was derepressed in a ΔglyR1 strain. Higher expression of Clo1313_1398, which encodes the Man5A mannanase, was observed in a ΔglyR2 strain, and α-mannobiose was identified as a probable inducer for GlyR2-regulated genes. For the ΔglyR3 strain, upregulation of the two genes adjacent to glyR3 in the celC-glyR3-licA operon was consistent with earlier studies. Electrophoretic mobility shift assays have confirmed LacI transcription factor binding to specific regions of gene promoters.IMPORTANCE Understanding C. thermocellum gene regulation is of importance for improved fundamental knowledge of this industrially relevant bacterium. Most LacI transcription factors regulate local genomic regions; however, a small number of those genes encode global regulatory proteins with extensive regulons. This study indicates that there are small specific C. thermocellum LacI regulons. The identification of LacI repressor activity for hemicellulase gene expression is a key result of this work and will add to the small body of existing literature on the area of gene regulation in C. thermocellum.
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Biswas R, Wilson CM, Giannone RJ, Klingeman DM, Rydzak T, Shah MB, Hettich RL, Brown SD, Guss AM. Improved growth rate in Clostridium thermocellum hydrogenase mutant via perturbed sulfur metabolism. BIOTECHNOLOGY FOR BIOFUELS 2017; 10:6. [PMID: 28053665 PMCID: PMC5209896 DOI: 10.1186/s13068-016-0684-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2016] [Accepted: 12/08/2016] [Indexed: 05/16/2023]
Abstract
BACKGROUND Metabolic engineering is a commonly used approach to develop organisms for an industrial function, but engineering aimed at improving one phenotype can negatively impact other phenotypes. This lack of robustness can prove problematic. Cellulolytic bacterium Clostridium thermocellum is able to rapidly ferment cellulose to ethanol and other products. Recently, genes involved in H2 production, including the hydrogenase maturase hydG and NiFe hydrogenase ech, were deleted from the chromosome of C. thermocellum. While ethanol yield increased, the growth rate of ΔhydG decreased substantially compared to wild type. RESULTS Addition of 5 mM acetate to the growth medium improved the growth rate in C. thermocellum ∆hydG, whereas wild type remained unaffected. Transcriptomic analysis of the wild type showed essentially no response to the addition of acetate. However, in C. thermocellum ΔhydG, 204 and 56 genes were significantly differentially regulated relative to wild type in the absence and presence of acetate, respectively. Genes, Clo1313_0108-0125, which are predicted to encode a sulfate transport system and sulfate assimilatory pathway, were drastically upregulated in C. thermocellum ΔhydG in the presence of added acetate. A similar pattern was seen with proteomics. Further physiological characterization demonstrated an increase in sulfide synthesis and elimination of cysteine consumption in C. thermocellum ΔhydG. Clostridium thermocellum ΔhydGΔech had a higher growth rate than ΔhydG in the absence of added acetate, and a similar but less pronounced transcriptional and physiological effect was seen in this strain upon addition of acetate. CONCLUSIONS Sulfur metabolism is perturbed in C. thermocellum ΔhydG strains, likely to increase flux through sulfate reduction to act either as an electron sink to balance redox reactions or to offset an unknown deficiency in sulfur assimilation.
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Affiliation(s)
- Ranjita Biswas
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37830 USA
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37830 USA
- Centre for Rural Development and Technology, Indian Institute of Technology Delhi, Hauz Khas, New Delhi, 110016 India
| | - Charlotte M. Wilson
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37830 USA
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37830 USA
| | - Richard J. Giannone
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37830 USA
- Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37830 USA
| | - Dawn M. Klingeman
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37830 USA
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37830 USA
| | - Thomas Rydzak
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37830 USA
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37830 USA
| | - Manesh B. Shah
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37830 USA
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37830 USA
| | - Robert L. Hettich
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37830 USA
- Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37830 USA
| | - Steven D. Brown
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37830 USA
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37830 USA
| | - Adam M. Guss
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37830 USA
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37830 USA
- One Bethel Valley Road, Oak Ridge, TN 37831-6038 USA
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Groom J, Chung D, Olson DG, Lynd LR, Guss AM, Westpheling J. Promiscuous plasmid replication in thermophiles: Use of a novel hyperthermophilic replicon for genetic manipulation of Clostridium thermocellum at its optimum growth temperature. Metab Eng Commun 2016; 3:30-38. [PMID: 29468112 PMCID: PMC5779722 DOI: 10.1016/j.meteno.2016.01.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2015] [Revised: 01/15/2016] [Accepted: 01/28/2016] [Indexed: 12/22/2022] Open
Abstract
Clostridium thermocellum is a leading candidate for the consolidated bioprocessing of lignocellulosic biomass for the production of fuels and chemicals. A limitation to the engineering of this strain is the availability of stable replicating plasmid vectors for homologous and heterologous expression of genes that provide improved and/or novel pathways for fuel production. Current vectors relay on replicons from mesophilic bacteria and are not stable at the optimum growth temperature of C. thermocellum. To develop more thermostable genetic tools for C. thermocellum, we constructed vectors based on the hyperthermophilic Caldicellulosiruptor bescii replicon pBAS2. Autonomously replicating shuttle vectors based on pBAS2 reproducibly transformed C. thermocellum at 60 °C and were maintained in multiple copy. Promoters, selectable markers and plasmid replication proteins from C. bescii were functional in C. thermocellum. Phylogenetic analyses of the proteins contained on pBAS2 revealed that the replication initiation protein RepL is unique among thermophiles. These results suggest that pBAS2 may be a broadly useful replicon for other thermophilic Firmicutes.
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Affiliation(s)
- Joseph Groom
- Department of Genetics, University of Georgia, Athens, GA, USA
- The BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Daehwan Chung
- Department of Genetics, University of Georgia, Athens, GA, USA
- The BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN, USA
- National Renewable Energy Laboratory, Biosciences Center, Golden, CO, USA
| | - Daniel G. Olson
- The BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN, USA
- Thayer School of Engineering at Dartmouth College, Hanover, NH, USA
| | - Lee R. Lynd
- The BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN, USA
- Thayer School of Engineering at Dartmouth College, Hanover, NH, USA
| | - Adam M. Guss
- The BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN, USA
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Janet Westpheling
- Department of Genetics, University of Georgia, Athens, GA, USA
- The BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN, USA
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Hon S, Lanahan AA, Tian L, Giannone RJ, Hettich RL, Olson DG, Lynd LR. Development of a plasmid-based expression system in Clostridium thermocellum and its use to screen heterologous expression of bifunctional alcohol dehydrogenases ( adhEs). Metab Eng Commun 2016; 3:120-129. [PMID: 29142822 PMCID: PMC5678826 DOI: 10.1016/j.meteno.2016.04.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2015] [Revised: 03/15/2016] [Accepted: 04/21/2016] [Indexed: 12/27/2022] Open
Abstract
Clostridium thermocellum is a promising candidate for ethanol production from cellulosic biomass, but requires metabolic engineering to improve ethanol yield. A key gene in the ethanol production pathway is the bifunctional aldehyde and alcohol dehydrogenase, adhE. To explore the effects of overexpressing wild-type, mutant, and exogenous adhEs, we developed a new expression plasmid, pDGO144, that exhibited improved transformation efficiency and better gene expression than its predecessor, pDGO-66. This new expression plasmid will allow for many other metabolic engineering and basic research efforts in C. thermocellum. As proof of concept, we used this plasmid to express 12 different adhE genes (both wild type and mutant) from several organisms. Ethanol production varied between clones immediately after transformation, but tended to converge to a single value after several rounds of serial transfer. The previously described mutant C. thermocellum D494G adhE gave the best ethanol production, which is consistent with previously published results.
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Affiliation(s)
- Shuen Hon
- Thayer School of Engineering, Dartmouth College, Hanover, NH, USA
- BioEnergy Science Center, Oak Ridge, TN, USA
| | - Anthony A. Lanahan
- Thayer School of Engineering, Dartmouth College, Hanover, NH, USA
- BioEnergy Science Center, Oak Ridge, TN, USA
| | - Liang Tian
- Thayer School of Engineering, Dartmouth College, Hanover, NH, USA
- BioEnergy Science Center, Oak Ridge, TN, USA
| | - Richard J. Giannone
- BioEnergy Science Center, Oak Ridge, TN, USA
- Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Robert L. Hettich
- BioEnergy Science Center, Oak Ridge, TN, USA
- Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Daniel G. Olson
- Thayer School of Engineering, Dartmouth College, Hanover, NH, USA
- BioEnergy Science Center, Oak Ridge, TN, USA
| | - Lee R. Lynd
- Thayer School of Engineering, Dartmouth College, Hanover, NH, USA
- BioEnergy Science Center, Oak Ridge, TN, USA
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Advances in Consolidated Bioprocessing Using Clostridium thermocellumand Thermoanaerobacter saccharolyticum. Ind Biotechnol (New Rochelle N Y) 2016. [DOI: 10.1002/9783527807796.ch10] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
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Lo J, Olson DG, Murphy SJL, Tian L, Hon S, Lanahan A, Guss AM, Lynd LR. Engineering electron metabolism to increase ethanol production in Clostridium thermocellum. Metab Eng 2016; 39:71-79. [PMID: 27989806 DOI: 10.1016/j.ymben.2016.10.018] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2016] [Revised: 10/17/2016] [Accepted: 10/25/2016] [Indexed: 11/28/2022]
Abstract
The NfnAB (NADH-dependent reduced ferredoxin: NADP+ oxidoreductase) and Rnf (ion-translocating reduced ferredoxin: NAD+ oxidoreductase) complexes are thought to catalyze electron transfer between reduced ferredoxin and NAD(P)+. Efficient electron flux is critical for engineering fuel production pathways, but little is known about the relative importance of these enzymes in vivo. In this study we investigate the importance of the NfnAB and Rnf complexes in Clostridium thermocellum for growth on cellobiose and Avicel using gene deletion, enzyme assays, and fermentation product analysis. The NfnAB complex does not seem to play a major role in metabolism, since deletion of nfnAB genes had little effect on the distribution of fermentation products. By contrast, the Rnf complex appears to play an important role in ethanol formation. Deletion of rnf genes resulted in a decrease in ethanol formation. Overexpression of rnf genes resulted in an increase in ethanol production of about 30%, but only in strains where the hydG hydrogenase maturation gene was also deleted.
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Affiliation(s)
- Jonathan Lo
- Thayer School of Engineering, Dartmouth College, Hanover, NH 03755, USA; BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge TN 37830, USA
| | - Daniel G Olson
- Thayer School of Engineering, Dartmouth College, Hanover, NH 03755, USA; BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge TN 37830, USA
| | - Sean Jean-Loup Murphy
- Thayer School of Engineering, Dartmouth College, Hanover, NH 03755, USA; BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge TN 37830, USA
| | - Liang Tian
- Thayer School of Engineering, Dartmouth College, Hanover, NH 03755, USA; BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge TN 37830, USA
| | - Shuen Hon
- Thayer School of Engineering, Dartmouth College, Hanover, NH 03755, USA; BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge TN 37830, USA
| | - Anthony Lanahan
- Thayer School of Engineering, Dartmouth College, Hanover, NH 03755, USA; BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge TN 37830, USA
| | - Adam M Guss
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge TN 37830, USA; Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37830, USA
| | - Lee R Lynd
- Thayer School of Engineering, Dartmouth College, Hanover, NH 03755, USA; BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge TN 37830, USA.
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Kolek J, Sedlar K, Provaznik I, Patakova P. Dam and Dcm methylations prevent gene transfer into Clostridium pasteurianum NRRL B-598: development of methods for electrotransformation, conjugation, and sonoporation. BIOTECHNOLOGY FOR BIOFUELS 2016; 9:14. [PMID: 26793273 PMCID: PMC4719659 DOI: 10.1186/s13068-016-0436-y] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2015] [Accepted: 01/08/2016] [Indexed: 05/15/2023]
Abstract
BACKGROUND Butanol is currently one of the most discussed biofuels. Its use provides many benefits in comparison to bio-ethanol, but the price of its fermentative production is still high. Genetic improvements could help solve many problems associated with butanol production during ABE fermentation, such as its toxicity, low concentration achievable in the cultivation medium, the need for a relatively expensive substrate, and many more. Clostridium pasteurianum NRRL B-598 is non-type strain producing butanol, acetone, and a negligible amount of ethanol. Its main benefits are high oxygen tolerance, utilization of a wide range of carbon and nitrogen sources, and the availability of its whole genome sequence. However, there is no established method for the transfer of foreign DNA into this strain; this is the next step necessary for progress in its use for butanol production. RESULTS We have described functional protocols for conjugation and transformation of the bio-butanol producer C. pasteurianum NRRL B-598 by foreign plasmid DNA. We show that the use of unmethylated plasmid DNA is necessary for efficient transformation or successful conjugation. Genes encoding DNA methylation and those for restriction-modification systems and antibiotic resistance were searched for in the whole genome sequence and their homologies with other clostridial bacteria were determined. Furthermore, activity of described novel type I restriction system was proved experimentally. The described electrotransformation protocol achieved an efficiency 1.2 × 10(2) cfu/μg DNA after step-by-step optimization and an efficiency of 1.6 × 10(2) cfu/μg DNA was achieved by the sonoporation technique using a standard laboratory ultrasound bath. The highest transformation efficiency was achieved using a combination of these approaches; sono/electroporation led to an increase in transformation efficiency, to 5.3 × 10(2) cfu/μg DNA. CONCLUSIONS Both Dam and Dcm methylations are detrimental for transformation of C. pasteurianum NRRL B-598. Methods for conjugation, electroporation, sonoporation, and a combined method for sono/electroporation were established for this strain. The methods described could be used for genetic improvement of this strain, which is suitable for bio-butanol production.
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Affiliation(s)
- Jan Kolek
- />Department of Biotechnology, University of Chemistry and Technology Prague, Technicka 5, 166 28 Prague, Czech Republic
| | - Karel Sedlar
- />Department of Biomedical Engineering, Brno University of Technology, Technicka 12, 616 00 Brno, Czech Republic
| | - Ivo Provaznik
- />Department of Biomedical Engineering, Brno University of Technology, Technicka 12, 616 00 Brno, Czech Republic
| | - Petra Patakova
- />Department of Biotechnology, University of Chemistry and Technology Prague, Technicka 5, 166 28 Prague, Czech Republic
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Restriction modification system analysis and development of in vivo methylation for the transformation of Clostridium cellulovorans. Appl Microbiol Biotechnol 2015; 100:2289-99. [PMID: 26590584 DOI: 10.1007/s00253-015-7141-9] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2015] [Revised: 10/28/2015] [Accepted: 11/02/2015] [Indexed: 12/11/2022]
Abstract
Clostridium cellulovorans, a cellulolytic bacterium producing butyric and acetic acids as main fermentation products, is a promising host for biofuel production from cellulose. However, the transformation method of C. cellulovorans was not available, hindering its genetic engineering. To overcome this problem, its restriction modification (RM) systems were analyzed and a novel in vivo methylation was established for its successful transformation in the present study. Specifically, two RM systems, Cce743I and Cce743II, were determined. R. Cce743I has the same specificity as LlaJI, recognizing 5'-GACGC-3' and 5'-GCGTC-3', while M. Cce743I methylates the external cytosine in the strand (5'-GACG(m)C-3'). R. Cce743II, has the same specificity as LlaI, recognizing 5'-CCAGG-3' and 5'-CCTGG-3', while M. Cce743II methylates the external cytosine of both strands. An in vivo methylation system, expressing M. Cce743I and M. Cce743II from C. cellulovorans in Escherichia coli, was then established to protect plasmids used in electrotransformation. Transformants expressing an aldehyde/alcohol dehydrogenase (adhE2), which converted butyryl-CoA to n-butanol and acetyl-CoA to ethanol, were obtained. For the first time, an effective transformation method was developed for metabolic engineering of C. cellulovorans for biofuel production directly from cellulose.
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Thompson RA, Layton DS, Guss AM, Olson DG, Lynd LR, Trinh CT. Elucidating central metabolic redox obstacles hindering ethanol production in Clostridium thermocellum. Metab Eng 2015; 32:207-219. [PMID: 26497628 DOI: 10.1016/j.ymben.2015.10.004] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2015] [Revised: 10/08/2015] [Accepted: 10/12/2015] [Indexed: 01/24/2023]
Abstract
Clostridium thermocellum is an anaerobic, Gram-positive, thermophilic bacterium that has generated great interest due to its ability to ferment lignocellulosic biomass to ethanol. However, ethanol production is low due to the complex and poorly understood branched metabolism of C. thermocellum, and in some cases overflow metabolism as well. In this work, we developed a predictive stoichiometric metabolic model for C. thermocellum which incorporates the current state of understanding, with particular attention to cofactor specificity in the atypical glycolytic enzymes and the complex energy, redox, and fermentative pathways with the goal of aiding metabolic engineering efforts. We validated the model's capability to encompass experimentally observed phenotypes for the parent strain and derived mutants designed for significant perturbation of redox and energy pathways. Metabolic flux distributions revealed significant alterations in key metabolic branch points (e.g., phosphoenol pyruvate, pyruvate, acetyl-CoA, and cofactor nodes) in engineered strains for channeling electron and carbon fluxes for enhanced ethanol synthesis, with the best performing strain doubling ethanol yield and titer compared to the parent strain. In silico predictions of a redox-imbalanced genotype incapable of growth were confirmed in vivo, and a mutant strain was used as a platform to probe redox bottlenecks in the central metabolism that hinder efficient ethanol production. The results highlight the robustness of the redox metabolism of C. thermocellum and the necessity of streamlined electron flux from reduced ferredoxin to NAD(P)H for high ethanol production. The model was further used to design a metabolic engineering strategy to phenotypically constrain C. thermocellum to achieve high ethanol yields while requiring minimal genetic manipulations. The model can be applied to design C. thermocellum as a platform microbe for consolidated bioprocessing to produce ethanol and other reduced metabolites.
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Affiliation(s)
- R Adam Thompson
- Bredesen Center for Interdisciplinary Research and Graduate Education, The University of Tennessee, Knoxville and Oak Ridge National Laboratory, Oak Ridge, TN, USA; BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Donovan S Layton
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN, USA; Department of Chemical and Biomolecular Engineering, The University of Tennessee, Knoxville, TN, USA
| | - Adam M Guss
- Bredesen Center for Interdisciplinary Research and Graduate Education, The University of Tennessee, Knoxville and Oak Ridge National Laboratory, Oak Ridge, TN, USA; BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN, USA; Biosciecnes Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Daniel G Olson
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN, USA; Thayer School of Engineering, Dartmouth College, Hanover, NH, USA
| | - Lee R Lynd
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN, USA; Thayer School of Engineering, Dartmouth College, Hanover, NH, USA
| | - Cong T Trinh
- Bredesen Center for Interdisciplinary Research and Graduate Education, The University of Tennessee, Knoxville and Oak Ridge National Laboratory, Oak Ridge, TN, USA; BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN, USA; Department of Chemical and Biomolecular Engineering, The University of Tennessee, Knoxville, TN, USA.
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Ichikawa S, Karita S. Bacterial production and secretion of water-insoluble fuel compounds from cellulose without the supplementation of cellulases. FEMS Microbiol Lett 2015; 362:fnv202. [DOI: 10.1093/femsle/fnv202] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/18/2015] [Indexed: 01/15/2023] Open
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47
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Elimination of metabolic pathways to all traditional fermentation products increases ethanol yields in Clostridium thermocellum. Metab Eng 2015; 32:49-54. [PMID: 26369438 DOI: 10.1016/j.ymben.2015.09.002] [Citation(s) in RCA: 65] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2015] [Revised: 08/27/2015] [Accepted: 09/02/2015] [Indexed: 01/01/2023]
Abstract
Clostridium thermocellum has the natural ability to convert cellulose to ethanol, making it a promising candidate for consolidated bioprocessing (CBP) of cellulosic biomass to biofuels. To further improve its CBP capabilities, a mutant strain of C. thermocellum was constructed (strain AG553; C. thermocellum Δhpt ΔhydG Δldh Δpfl Δpta-ack) to increase flux to ethanol by removing side product formation. Strain AG553 showed a two- to threefold increase in ethanol yield relative to the wild type on all substrates tested. On defined medium, strain AG553 exceeded 70% of theoretical ethanol yield on lower loadings of the model crystalline cellulose Avicel, effectively eliminating formate, acetate, and lactate production and reducing H2 production by fivefold. On 5 g/L Avicel, strain AG553 reached an ethanol yield of 63.5% of the theoretical maximum compared with 19.9% by the wild type, and it showed similar yields on pretreated switchgrass and poplar. The elimination of organic acid production suggested that the strain might be capable of growth under higher substrate loadings in the absence of pH control. Final ethanol titer peaked at 73.4mM in mutant AG553 on 20 g/L Avicel, at which point the pH decreased to a level that does not allow growth of C. thermocellum, likely due to CO2 accumulation. In comparison, the maximum titer of wild type C. thermocellum was 14.1mM ethanol on 10 g/L Avicel. With the elimination of the metabolic pathways to all traditional fermentation products other than ethanol, AG553 is the best ethanol-yielding CBP strain to date and will serve as a platform strain for further metabolic engineering for the bioconversion of lignocellulosic biomass.
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48
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Lin PP, Mi L, Morioka AH, Yoshino KM, Konishi S, Xu SC, Papanek BA, Riley LA, Guss AM, Liao JC. Consolidated bioprocessing of cellulose to isobutanol using Clostridium thermocellum. Metab Eng 2015; 31:44-52. [DOI: 10.1016/j.ymben.2015.07.001] [Citation(s) in RCA: 92] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2015] [Revised: 06/06/2015] [Accepted: 07/01/2015] [Indexed: 10/23/2022]
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49
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Elimination of formate production in Clostridium thermocellum. J Ind Microbiol Biotechnol 2015; 42:1263-72. [PMID: 26162629 PMCID: PMC4536278 DOI: 10.1007/s10295-015-1644-3] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2015] [Accepted: 06/15/2015] [Indexed: 02/05/2023]
Abstract
The ability of Clostridium thermocellum to rapidly degrade cellulose and ferment resulting hydrolysis products into ethanol makes it a promising platform organism for cellulosic biofuel production via consolidated bioprocessing. Currently, however, ethanol yield is far below theoretical maximum due to branched product pathways that divert carbon and electrons towards formate, H2, lactate, acetate, and secreted amino acids. To redirect carbon and electron flux away from formate, genes encoding pyruvate:formate lyase (pflB) and PFL-activating enzyme (pflA) were deleted. Formate production in the resulting Δpfl strain was eliminated and acetate production decreased by 50 % on both complex and defined medium. The growth rate of the Δpfl strain decreased by 2.9-fold on defined medium and biphasic growth was observed on complex medium. Supplementation of defined medium with 2 mM formate restored Δpfl growth rate to 80 % of the parent strain. The role of pfl in metabolic engineering strategies and C1 metabolism is discussed.
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50
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Development of a regulatable plasmid-based gene expression system for Clostridium thermocellum. Appl Microbiol Biotechnol 2015; 99:7589-99. [DOI: 10.1007/s00253-015-6610-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2014] [Revised: 04/07/2015] [Accepted: 04/15/2015] [Indexed: 01/31/2023]
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