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Daley SR, Kirby S, Sparling R. Adaptive evolution of Clostridium thermocellum ATCC 27405 on alternate carbon sources leads to altered fermentation profiles. Can J Microbiol 2024. [PMID: 38832648 DOI: 10.1139/cjm-2024-0004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/05/2024]
Abstract
Consolidated bioprocessing candidate, Clostridium thermocellum, is a cellulose hydrolysis specialist, with the ability to ferment the released sugars to produce bioethanol. C. thermocellum is generally studied with model substrates Avicel and cellobiose to understand the metabolic pathway leading to ethanol. In the present study, adaptive laboratory evolution, allowing C. thermocellum DSM 1237 to adapt to growth on glucose, fructose, and sorbitol, with the prospect that some strains will adapt their metabolism to yield more ethanol. Adaptive growth on glucose and sorbitol resulted in an approximately 1 mM and 2 mM increase in ethanol yield per millimolar glucose equivalent, respectively, accompanied by a shift in the production of the other expected fermentation end products. The increase in ethanol yield observed for sorbitol adapted cells was due to the carbon source being more reduced compared to cellobiose. Glucose and cellobiose have similar oxidation states thus the increase in ethanol yield is due to the rerouting of electrons from other reduced metabolic products excluding H2 which did not decrease in yield. There was no increase in ethanol yield observed for fructose adapted cells, but there was an unanticipated elimination of formate production, also observed in sorbitol adapted cells suggesting that fructose has regulatory implications on formate production either at the transcription or protein level.
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Affiliation(s)
- Steve R Daley
- Department of Microbiology, University of Manitoba, Winnipeg, MB, Canada
| | - Samantha Kirby
- Department of Microbiology, University of Manitoba, Winnipeg, MB, Canada
| | - Richard Sparling
- Department of Microbiology, University of Manitoba, Winnipeg, MB, Canada
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2
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Wang Y, Hu J, Li Y, Liu Z. Rare earth ion Nd3+ promotes production of cellulose ethanol by Clostridium thermocellum ATCC 27405. Polyhedron 2022. [DOI: 10.1016/j.poly.2021.115555] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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3
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Kazemi Shariat Panahi H, Dehhaghi M, Dehhaghi S, Guillemin GJ, Lam SS, Aghbashlo M, Tabatabaei M. Engineered bacteria for valorizing lignocellulosic biomass into bioethanol. BIORESOURCE TECHNOLOGY 2022; 344:126212. [PMID: 34715341 DOI: 10.1016/j.biortech.2021.126212] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 10/17/2021] [Accepted: 10/20/2021] [Indexed: 06/13/2023]
Abstract
Appropriate bioprocessing of lignocellulosic materials into ethanol could address the world's insatiable appetite for energy while mitigating greenhouse gases. Bioethanol is an ideal gasoline extender and is widely used in many countries in blended form with gasoline at specific ratios to improve fuel characteristics and engine performance. Although the bioethanol production industry has long been operational, finding a suitable microbial agent for the efficient conversion of lignocelluloses is still an active field of study. Among available microbial candidates, engineered bacteria may be promising ethanol producers while may show other desired traits such as thermophilic nature and high ethanol tolerance. This review provides the current knowledge on the introduction, overexpression, and deletion of the genes that have been performed in bacterial hosts to achieve higher ethanol yield, production rate and titer, and tolerance. The constraints and possible solutions and economic feasibility of the processes utilizing such engineered strains are also discussed.
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Affiliation(s)
- Hamed Kazemi Shariat Panahi
- Henan Province Engineering Research Center for Forest Biomass Value-added Products, School of Forestry, Henan Agricultural University, Zhengzhou, Henan, 450002, China; Neuroinflammation Group, Department of Biomedical Sciences, Faculty of Medicine, Health and Human Sciences, Macquarie University, NSW, Australia; Biofuel Research Team (BRTeam), Terengganu, Malaysia
| | - Mona Dehhaghi
- Neuroinflammation Group, Department of Biomedical Sciences, Faculty of Medicine, Health and Human Sciences, Macquarie University, NSW, Australia; Biofuel Research Team (BRTeam), Terengganu, Malaysia; PANDIS.org, Australia
| | - Somayeh Dehhaghi
- Department of Agricultural Extension and Education, Tarbiat Modares University, Tehran 14115-336, Iran
| | - Gilles J Guillemin
- Neuroinflammation Group, Department of Biomedical Sciences, Faculty of Medicine, Health and Human Sciences, Macquarie University, NSW, Australia; PANDIS.org, Australia
| | - Su Shiung Lam
- Henan Province Engineering Research Center for Forest Biomass Value-added Products, School of Forestry, Henan Agricultural University, Zhengzhou, Henan, 450002, China; Higher Institution Centre of Excellence (HICoE), Institute of Tropical Aquaculture and Fisheries (AKUATROP), Universiti Malaysia Terengganu, 21030 Kuala Nerus, Terengganu, Malaysia.
| | - Mortaza Aghbashlo
- Department of Mechanical Engineering of Agricultural Machinery, Faculty of Agricultural Engineering and Technology, College of Agriculture and Natural Resources, University of Tehran, Karaj, Iran
| | - Meisam Tabatabaei
- Henan Province Engineering Research Center for Forest Biomass Value-added Products, School of Forestry, Henan Agricultural University, Zhengzhou, Henan, 450002, China; Biofuel Research Team (BRTeam), Terengganu, Malaysia; Higher Institution Centre of Excellence (HICoE), Institute of Tropical Aquaculture and Fisheries (AKUATROP), Universiti Malaysia Terengganu, 21030 Kuala Nerus, Terengganu, Malaysia; Microbial Biotechnology Department, Agricultural Biotechnology Research Institute of Iran (ABRII), Agricultural Research, Education and Extension Organization (AREEO), Karaj, Iran
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4
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Biorefinery Gets Hot: Thermophilic Enzymes and Microorganisms for Second-Generation Bioethanol Production. Processes (Basel) 2021. [DOI: 10.3390/pr9091583] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
To mitigate the current global energy and the environmental crisis, biofuels such as bioethanol have progressively gained attention from both scientific and industrial perspectives. However, at present, commercialized bioethanol is mainly derived from edible crops, thus raising serious concerns given its competition with feed production. For this reason, lignocellulosic biomasses (LCBs) have been recognized as important alternatives for bioethanol production. Because LCBs supply is sustainable, abundant, widespread, and cheap, LCBs-derived bioethanol currently represents one of the most viable solutions to meet the global demand for liquid fuel. However, the cost-effective conversion of LCBs into ethanol remains a challenge and its implementation has been hampered by several bottlenecks that must still be tackled. Among other factors related to the challenging and variable nature of LCBs, we highlight: (i) energy-demanding pretreatments, (ii) expensive hydrolytic enzyme blends, and (iii) the need for microorganisms that can ferment mixed sugars. In this regard, thermophiles represent valuable tools to overcome some of these limitations. Thus, the aim of this review is to provide an overview of the state-of-the-art technologies involved, such as the use of thermophilic enzymes and microorganisms in industrial-relevant conditions, and to propose possible means to implement thermophiles into second-generation ethanol biorefineries that are already in operation.
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Bai SK, Hong Y, Wu YR. Emerging technologies for genetic modification of solventogenic clostridia: From tool to strategy development. BIORESOURCE TECHNOLOGY 2021; 334:125222. [PMID: 33951568 DOI: 10.1016/j.biortech.2021.125222] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Revised: 04/20/2021] [Accepted: 04/21/2021] [Indexed: 06/12/2023]
Abstract
Solventogenic clostridia has been considered as one of the most potential microbial cell factories for biofuel production in the biorefinery industry. However, the inherent shortcomings of clostridia strains such as low productivity, by-products formation and toxic tolerance still strongly restrict the large-scale application. Therefore, concerns regarding the genetic modification of solventogenic clostridia have spurred interests into the development of modern gene-editing tools. In this review, we summarize the latest advances of genetic tools involved in modifying solventogenic clostridia. Following a systematic comparison on their respective characteristics, we then review the corresponding strategies for overcoming the obstacles to the enhanced production. Discussing the progress of other microbial cell factories for solventogenesis, we finally describe the key challenges and trends with valuable recommendations for future large-scale biosolvent industrial application.
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Affiliation(s)
- Sheng-Kai Bai
- Department of Biology, Shantou University, Shantou, Guangdong 515063, China
| | - Ying Hong
- Department of Biology, Shantou University, Shantou, Guangdong 515063, China
| | - Yi-Rui Wu
- Department of Biology, Shantou University, Shantou, Guangdong 515063, China; Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou, Guangdong 515063, China; Institute of Marine Sciences, Shantou University, Shantou, Guangdong 515063, China.
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6
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Joseph RC, Kelley SQ, Kim NM, Sandoval NR. Metabolic Engineering and the Synthetic Biology Toolbox for
Clostridium. Metab Eng 2021. [DOI: 10.1002/9783527823468.ch16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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7
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Fu H, Luo S, Dai K, Qu C, Wang J. Engineering Thermoanaerobacterium aotearoense SCUT27/Δldh with pyruvate formate lyase-activating protein (PflA) knockout for enhanced ethanol tolerance and production. Process Biochem 2021. [DOI: 10.1016/j.procbio.2021.04.014] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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8
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Bing RG, Sulis DB, Wang JP, Adams MW, Kelly RM. Thermophilic microbial deconstruction and conversion of natural and transgenic lignocellulose. ENVIRONMENTAL MICROBIOLOGY REPORTS 2021; 13:272-293. [PMID: 33684253 PMCID: PMC10519370 DOI: 10.1111/1758-2229.12943] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 02/25/2021] [Accepted: 02/28/2021] [Indexed: 06/12/2023]
Abstract
The potential to convert renewable plant biomasses into fuels and chemicals by microbial processes presents an attractive, less environmentally intense alternative to conventional routes based on fossil fuels. This would best be done with microbes that natively deconstruct lignocellulose and concomitantly form industrially relevant products, but these two physiological and metabolic features are rarely and simultaneously observed in nature. Genetic modification of both plant feedstocks and microbes can be used to increase lignocellulose deconstruction capability and generate industrially relevant products. Separate efforts on plants and microbes are ongoing, but these studies lack a focus on optimal, complementary combinations of these disparate biological systems to obtain a convergent technology. Improving genetic tools for plants have given rise to the generation of low-lignin lines that are more readily solubilized by microorganisms. Most focus on the microbiological front has involved thermophilic bacteria from the genera Caldicellulosiruptor and Clostridium, given their capacity to degrade lignocellulose and to form bio-products through metabolic engineering strategies enabled by ever-improving molecular genetics tools. Bioengineering plant properties to better fit the deconstruction capabilities of candidate consolidated bioprocessing microorganisms has potential to achieve the efficient lignocellulose deconstruction needed for industrial relevance.
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Affiliation(s)
- Ryan G. Bing
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC 27695
| | - Daniel B. Sulis
- Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, NC 27695
| | - Jack P. Wang
- Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, NC 27695
| | - Michael W.W. Adams
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia 30602
| | - Robert M. Kelly
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC 27695
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9
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Poudel S, Cope AL, O'Dell KB, Guss AM, Seo H, Trinh CT, Hettich RL. Identification and characterization of proteins of unknown function (PUFs) in Clostridium thermocellum DSM 1313 strains as potential genetic engineering targets. BIOTECHNOLOGY FOR BIOFUELS 2021; 14:116. [PMID: 33971924 PMCID: PMC8112048 DOI: 10.1186/s13068-021-01964-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Accepted: 04/26/2021] [Indexed: 05/13/2023]
Abstract
BACKGROUND Mass spectrometry-based proteomics can identify and quantify thousands of proteins from individual microbial species, but a significant percentage of these proteins are unannotated and hence classified as proteins of unknown function (PUFs). Due to the difficulty in extracting meaningful metabolic information, PUFs are often overlooked or discarded during data analysis, even though they might be critically important in functional activities, in particular for metabolic engineering research. RESULTS We optimized and employed a pipeline integrating various "guilt-by-association" (GBA) metrics, including differential expression and co-expression analyses of high-throughput mass spectrometry proteome data and phylogenetic coevolution analysis, and sequence homology-based approaches to determine putative functions for PUFs in Clostridium thermocellum. Our various analyses provided putative functional information for over 95% of the PUFs detected by mass spectrometry in a wild-type and/or an engineered strain of C. thermocellum. In particular, we validated a predicted acyltransferase PUF (WP_003519433.1) with functional activity towards 2-phenylethyl alcohol, consistent with our GBA and sequence homology-based predictions. CONCLUSIONS This work demonstrates the value of leveraging sequence homology-based annotations with empirical evidence based on the concept of GBA to broadly predict putative functions for PUFs, opening avenues to further interrogation via targeted experiments.
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Affiliation(s)
- Suresh Poudel
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
- The Center for Bioenergy Innovation at Oak Ridge National Laboratory, Oak Ridge, TN, USA
- The Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, TN, USA
| | - Alexander L Cope
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
- The Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, TN, USA
| | - Kaela B O'Dell
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
- The Center for Bioenergy Innovation at Oak Ridge National Laboratory, Oak Ridge, TN, USA
- The Bredesen Center, University of Tennessee, Knoxville, TN, USA
| | - Adam M Guss
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
- The Bredesen Center, University of Tennessee, Knoxville, TN, USA
| | - Hyeongmin Seo
- The Center for Bioenergy Innovation at Oak Ridge National Laboratory, Oak Ridge, TN, USA
- Department of Chemical and Biomolecular Engineering, University of Tennessee, Knoxville, TN, USA
| | - Cong T Trinh
- The Center for Bioenergy Innovation at Oak Ridge National Laboratory, Oak Ridge, TN, USA
- The Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, TN, USA
- The Bredesen Center, University of Tennessee, Knoxville, TN, USA
- Department of Chemical and Biomolecular Engineering, University of Tennessee, Knoxville, TN, USA
| | - Robert L Hettich
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA.
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10
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Froese AG, Sparling R. Cross-feeding and wheat straw extractives enhance growth of Clostridium thermocellum-containing co-cultures for consolidated bioprocessing. Bioprocess Biosyst Eng 2021; 44:819-830. [PMID: 33392746 DOI: 10.1007/s00449-020-02490-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Accepted: 11/24/2020] [Indexed: 01/19/2023]
Abstract
Co-cultures consisting of three thermophilic and lignocellulolytic bacteria, namely Clostridium thermocellum, C. stercorarium, and Thermoanaerobacter thermohydrosulfuricus, degrade lignocellulosic material in a synergistic manner. When cultured in a defined minimal medium two of the members appeared to be auxotrophic and unable to grow, but the growth of all species was observed in all co-culture combinations, indicating cross-feeding of unidentified growth factors between the members. Growth factors also appeared to be present in water-soluble extractives obtained from wheat straw, allowing for the growth of the auxotrophic monocultures in the defined minimal medium. Cell enumeration during growth on wheat straw in this medium revealed different growth profiles of the members that varied between the co-cultures. End-product profiles also varied substantially between the cultures, with significantly higher ethanol production in all co-cultures compared to the mono-cultures. Understanding interactions between co-culture members, and the additional nutrients provided by lignocellulosic substrates, will aid us in consolidated bioprocessing design.
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Affiliation(s)
- Alan G Froese
- Department of Microbiology, University of Manitoba, 213 Buller Building, Winnipeg, MB, R3T 2N2, Canada
| | - Richard Sparling
- Department of Microbiology, University of Manitoba, 213 Buller Building, Winnipeg, MB, R3T 2N2, Canada.
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11
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Garcia S, Thompson RA, Giannone RJ, Dash S, Maranas CD, Trinh CT. Development of a Genome-Scale Metabolic Model of Clostridium thermocellum and Its Applications for Integration of Multi-Omics Datasets and Computational Strain Design. Front Bioeng Biotechnol 2020; 8:772. [PMID: 32974289 PMCID: PMC7471609 DOI: 10.3389/fbioe.2020.00772] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Accepted: 06/18/2020] [Indexed: 01/29/2023] Open
Abstract
Solving environmental and social challenges such as climate change requires a shift from our current non-renewable manufacturing model to a sustainable bioeconomy. To lower carbon emissions in the production of fuels and chemicals, plant biomass feedstocks can replace petroleum using microorganisms as biocatalysts. The anaerobic thermophile Clostridium thermocellum is a promising bacterium for bioconversion due to its capability to efficiently degrade lignocellulosic biomass. However, the complex metabolism of C. thermocellum is not fully understood, hindering metabolic engineering to achieve high titers, rates, and yields of targeted molecules. In this study, we developed an updated genome-scale metabolic model of C. thermocellum that accounts for recent metabolic findings, has improved prediction accuracy, and is standard-conformant to ensure easy reproducibility. We illustrated two applications of the developed model. We first formulated a multi-omics integration protocol and used it to understand redox metabolism and potential bottlenecks in biofuel (e.g., ethanol) production in C. thermocellum. Second, we used the metabolic model to design modular cells for efficient production of alcohols and esters with broad applications as flavors, fragrances, solvents, and fuels. The proposed designs not only feature intuitive push-and-pull metabolic engineering strategies, but also present novel manipulations around important central metabolic branch-points. We anticipate the developed genome-scale metabolic model will provide a useful tool for system analysis of C. thermocellum metabolism to fundamentally understand its physiology and guide metabolic engineering strategies to rapidly generate modular production strains for effective biosynthesis of biofuels and biochemicals from lignocellulosic biomass.
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Affiliation(s)
- Sergio Garcia
- Department of Chemical and Biomolecular Engineering, The University of Tennessee, Knoxville, TN, United States.,Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - R Adam Thompson
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, United States.,Bredesen Center for Interdisciplinary Research and Graduate Education, The University of Tennessee, Knoxville, TN, United States.,Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Richard J Giannone
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, United States.,Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Satyakam Dash
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, United States.,Department of Chemical Engineering, The Pennsylvania State University, University Park, PA, United States
| | - Costas D Maranas
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, United States.,Department of Chemical Engineering, The Pennsylvania State University, University Park, PA, United States
| | - Cong T Trinh
- Department of Chemical and Biomolecular Engineering, The University of Tennessee, Knoxville, TN, United States.,Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, United States.,Bredesen Center for Interdisciplinary Research and Graduate Education, The University of Tennessee, Knoxville, TN, United States.,Oak Ridge National Laboratory, Oak Ridge, TN, United States
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12
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Ganguly J, Martin‐Pascual M, van Kranenburg R. CRISPR interference (CRISPRi) as transcriptional repression tool for Hungateiclostridium thermocellum DSM 1313. Microb Biotechnol 2020; 13:339-349. [PMID: 31802632 PMCID: PMC7017836 DOI: 10.1111/1751-7915.13516] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Revised: 11/06/2019] [Accepted: 11/12/2019] [Indexed: 01/13/2023] Open
Abstract
Hungateiclostridium thermocellum DSM 1313 has biotechnological potential as a whole-cell biocatalyst for ethanol production using lignocellulosic renewable sources. The full exploitation of H. thermocellum has been hampered due to the lack of simple and high-throughput genome engineering tools. Recently in our research group, a thermophilic bacterial CRISPR-Cas9-based system has been developed as a transcriptional suppression tool for regulation of gene expression. We applied ThermoCas9-based CRISPR interference (CRISPRi) to repress the H. thermocellum central metabolic lactate dehydrogenase (ldh) and phosphotransacetylase (pta) genes. The effects of repression on target genes were studied based on transcriptional expression and product formation. Single-guide RNA (sgRNA) under the control of native intergenic 16S/23S rRNA promoter from H. thermocellum directing the ThermodCas9 to the promoter region of both pta and ldh silencing transformants reduced expression up to 67% and 62% respectively. This resulted in 24% and 17% decrease in lactate and acetate production, correspondingly. Hence, the CRISPRi approach for H. thermocellum to downregulate metabolic genes can be used for remodelling of metabolic pathways without the requisite for genome engineering. These data established for the first time the feasibility of employing CRISPRi-mediated gene repression of metabolic genes in H. thermocellum DSM 1313.
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Affiliation(s)
| | - Maria Martin‐Pascual
- Laboratory of MicrobiologyWageningen UniversityStippeneng 46708WE WageningenThe Netherlands
| | - Richard van Kranenburg
- CorbionArkelsedijk 464206AC GorinchemThe Netherlands
- Laboratory of MicrobiologyWageningen UniversityStippeneng 46708WE WageningenThe Netherlands
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13
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Mazzoli R, Olson D. Clostridium thermocellum: A microbial platform for high-value chemical production from lignocellulose. ADVANCES IN APPLIED MICROBIOLOGY 2020; 113:111-161. [PMID: 32948265 DOI: 10.1016/bs.aambs.2020.07.004] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Second generation biorefining, namely fermentation processes based on lignocellulosic feedstocks, has attracted tremendous interest (owing to the large availability and low cost of this biomass) as a strategy to produce biofuels and commodity chemicals that is an alternative to oil refining. However, the innate recalcitrance of lignocellulose has slowed progress toward economically viable processes. Consolidated bioprocessing (CBP), i.e., single-step fermentation of lignocellulose may dramatically reduce the current costs of 2nd generation biorefining. Metabolic engineering has been used as a tool to develop improved microbial strains supporting CBP. Clostridium thermocellum is among the most efficient cellulose degraders isolated so far and one of the most promising host organisms for application of CBP. The development of efficient and reliable genetic tools has allowed significant progress in metabolic engineering of this strain aimed at expanding the panel of growth substrates and improving the production of a number of commodity chemicals of industrial interest such as ethanol, butanol, isobutanol, isobutyl acetate and lactic acid. The present review aims to summarize recent developments in metabolic engineering of this organism which currently represents a reference model for the development of biocatalysts for 2nd generation biorefining.
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14
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Holwerda EK, Olson DG, Ruppertsberger NM, Stevenson DM, Murphy SJL, Maloney MI, Lanahan AA, Amador-Noguez D, Lynd LR. Metabolic and evolutionary responses of Clostridium thermocellum to genetic interventions aimed at improving ethanol production. BIOTECHNOLOGY FOR BIOFUELS 2020; 13:40. [PMID: 32175007 PMCID: PMC7063780 DOI: 10.1186/s13068-020-01680-5] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Accepted: 02/10/2020] [Indexed: 05/06/2023]
Abstract
BACKGROUND Engineering efforts targeted at increasing ethanol by modifying the central fermentative metabolism of Clostridium thermocellum have been variably successful. Here, we aim to understand this variation by a multifaceted approach including genomic and transcriptomic analysis combined with chemostat cultivation and high solids cellulose fermentation. Three strain lineages comprising 16 strains total were examined. Two strain lineages in which genes involved in pathways leading to organic acids and/or sporulation had been knocked out resulted in four end-strains after adaptive laboratory evolution (ALE). A third strain lineage recapitulated mutations involving adhE that occurred spontaneously in some of the engineered strains. RESULTS Contrary to lactate dehydrogenase, deleting phosphotransacetylase (pta, acetate) negatively affected steady-state biomass concentration and caused increased extracellular levels of free amino acids and pyruvate, while no increase in ethanol was detected. Adaptive laboratory evolution (ALE) improved growth and shifted elevated levels of amino acids and pyruvate towards ethanol, but not for all strain lineages. Three out of four end-strains produced ethanol at higher yield, and one did not. The occurrence of a mutation in the adhE gene, expanding its nicotinamide-cofactor compatibility, enabled two end-strains to produce more ethanol. A disruption in the hfsB hydrogenase is likely the reason why a third end-strain was able to make more ethanol. RNAseq analysis showed that the distribution of fermentation products was generally not regulated at the transcript level. At 120 g/L cellulose loadings, deletions of spo0A, ldh and pta and adaptive evolution did not negatively influence cellulose solubilization and utilization capabilities. Strains with a disruption in hfsB or a mutation in adhE produced more ethanol, isobutanol and 2,3-butanediol under these conditions and the highest isobutanol and ethanol titers reached were 5.1 and 29.9 g/L, respectively. CONCLUSIONS Modifications in the organic acid fermentative pathways in Clostridium thermocellum caused an increase in extracellular pyruvate and free amino acids. Adaptive laboratory evolution led to improved growth, and an increase in ethanol yield and production due a mutation in adhE or a disruption in hfsB. Strains with deletions in ldh and pta pathways and subjected to ALE demonstrated undiminished cellulolytic capabilities when cultured on high cellulose loadings.
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Affiliation(s)
- Evert K. Holwerda
- Thayer School of Engineering, Dartmouth College, Hanover, NH 03755 USA
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
| | - Daniel G. Olson
- Thayer School of Engineering, Dartmouth College, Hanover, NH 03755 USA
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
| | | | - David M. Stevenson
- Department of Bacteriology, University of Wisconsin, Madison, WI 53706 USA
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
| | - Sean J. L. Murphy
- Thayer School of Engineering, Dartmouth College, Hanover, NH 03755 USA
| | - Marybeth I. Maloney
- Thayer School of Engineering, Dartmouth College, Hanover, NH 03755 USA
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
| | - Anthony A. Lanahan
- Thayer School of Engineering, Dartmouth College, Hanover, NH 03755 USA
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
| | - Daniel Amador-Noguez
- Department of Bacteriology, University of Wisconsin, Madison, WI 53706 USA
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
| | - Lee R. Lynd
- Thayer School of Engineering, Dartmouth College, Hanover, NH 03755 USA
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
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15
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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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Engineering Clostridium for improved solvent production: recent progress and perspective. Appl Microbiol Biotechnol 2019; 103:5549-5566. [DOI: 10.1007/s00253-019-09916-7] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Revised: 05/15/2019] [Accepted: 05/15/2019] [Indexed: 01/07/2023]
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17
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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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Xin F, Dong W, Zhang W, Ma J, Jiang M. Biobutanol Production from Crystalline Cellulose through Consolidated Bioprocessing. Trends Biotechnol 2019; 37:167-180. [DOI: 10.1016/j.tibtech.2018.08.007] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Revised: 08/22/2018] [Accepted: 08/24/2018] [Indexed: 01/08/2023]
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19
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Papanek B, O’Dell KB, Manga P, Giannone RJ, Klingeman DM, Hettich RL, Brown SD, Guss AM. Transcriptomic and proteomic changes from medium supplementation and strain evolution in high-yielding Clostridium thermocellum strains. ACTA ACUST UNITED AC 2018; 45:1007-1015. [DOI: 10.1007/s10295-018-2073-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2018] [Accepted: 08/18/2018] [Indexed: 01/05/2023]
Abstract
Abstract
Clostridium thermocellum is a potentially useful organism for the production of lignocellulosic biofuels because of its ability to directly deconstruct cellulose and convert it into ethanol. Previously engineered C. thermocellum strains have achieved higher yields and titers of ethanol. These strains often initially grow more poorly than the wild type. Adaptive laboratory evolution and medium supplementation have been used to improve growth, but the mechanism(s) by which growth improves remain(s) unclear. Here, we studied (1) wild-type C. thermocellum, (2) the slow-growing and high-ethanol-yielding mutant AG553, and (3) the faster-growing evolved mutant AG601, each grown with and without added formate. We used a combination of transcriptomics and proteomics to understand the physiological impact of the metabolic engineering, evolution, and medium supplementation. Medium supplementation with formate improved growth in both AG553 and AG601. Expression of C1 metabolism genes varied with formate addition, supporting the hypothesis that the primary benefit of added formate is the supply of C1 units for biosynthesis. Expression of stress response genes such as those involved in the sporulation cascade was dramatically over-represented in AG553, even after the addition of formate, suggesting that the source of the stress may be other issues such as redox imbalances. The sporulation response is absent in evolved strain AG601, suggesting that sporulation limits the growth of engineered strain AG553. A better understanding of the stress response and mechanisms of improved growth hold promise for informing rational improvement of C. thermocellum for lignocellulosic biofuel production.
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Affiliation(s)
- Beth Papanek
- 0000 0004 0446 2659 grid.135519.a Biosciences Division Oak Ridge National Laboratory Oak Ridge TN USA
- 0000 0001 2315 1184 grid.411461.7 Bredesen Center for Interdisciplinary Research and Graduate Education University of Tennessee-Knoxville Knoxville TN USA
- 0000 0004 1936 9991 grid.35403.31 Integrated Bioprocessing Research Laboratory University of Illinois-Urbana-Champaign Urbana IL USA
| | - Kaela B O’Dell
- 0000 0004 0446 2659 grid.135519.a Biosciences Division Oak Ridge National Laboratory Oak Ridge TN USA
| | - Punita Manga
- 0000 0004 0446 2659 grid.135519.a Biosciences Division Oak Ridge National Laboratory Oak Ridge TN USA
- 0000 0001 2315 1184 grid.411461.7 The Graduate School of Genome Science and Technology University of Tennessee-Knoxville Knoxville TN USA
| | - Richard J Giannone
- 0000 0004 0446 2659 grid.135519.a Biosciences Division Oak Ridge National Laboratory Oak Ridge TN USA
| | - Dawn M Klingeman
- 0000 0004 0446 2659 grid.135519.a Biosciences Division Oak Ridge National Laboratory Oak Ridge TN USA
| | - Robert L Hettich
- 0000 0004 0446 2659 grid.135519.a Biosciences Division Oak Ridge National Laboratory Oak Ridge TN USA
| | - Steven D Brown
- 0000 0004 0446 2659 grid.135519.a Biosciences Division Oak Ridge National Laboratory Oak Ridge TN USA
- 0000 0001 2315 1184 grid.411461.7 The Graduate School of Genome Science and Technology University of Tennessee-Knoxville Knoxville TN USA
- LanzaTech Inc 8045 Lamon Ave, Suite 400 60077 Skokie IL USA
| | - Adam M Guss
- 0000 0004 0446 2659 grid.135519.a Biosciences Division Oak Ridge National Laboratory Oak Ridge TN USA
- 0000 0001 2315 1184 grid.411461.7 Bredesen Center for Interdisciplinary Research and Graduate Education University of Tennessee-Knoxville Knoxville TN 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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Williams-Rhaesa AM, Rubinstein GM, Scott IM, Lipscomb GL, Poole Ii FL, Kelly RM, Adams MWW. Engineering redox-balanced ethanol production in the cellulolytic and extremely thermophilic bacterium, Caldicellulosiruptor bescii. Metab Eng Commun 2018; 7:e00073. [PMID: 30009131 PMCID: PMC6041484 DOI: 10.1016/j.mec.2018.e00073] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Revised: 05/16/2018] [Accepted: 05/27/2018] [Indexed: 11/06/2022] Open
Abstract
Caldicellulosiruptor bescii is an extremely thermophilic cellulolytic bacterium with great potential for consolidated bioprocessing of renewable plant biomass. Since it does not natively produce ethanol, metabolic engineering is required to create strains with this capability. Previous efforts involved the heterologous expression of the gene encoding a bifunctional alcohol dehydrogenase, AdhE, which uses NADH as the electron donor to reduce acetyl-CoA to ethanol. Acetyl-CoA produced from sugar oxidation also generates reduced ferredoxin but there is no known pathway for the transfer of electrons from reduced ferredoxin to NAD in C. bescii. Herein, we engineered a strain of C. bescii using a more stable genetic background than previously reported and heterologously-expressed adhE from Clostridium thermocellum (which grows optimally (Topt) at 60 °C) with and without co-expression of the membrane-bound Rnf complex from Thermoanaerobacter sp. X514 (Topt 60 °C). Rnf is an energy-conserving, reduced ferredoxin NAD oxidoreductase encoded by six genes (rnfCDGEAB). It was produced in a catalytically active form in C. bescii that utilized the largest DNA construct to be expressed in this organism. The new genetic lineage containing AdhE resulted in increased ethanol production compared to previous reports. Ethanol production was further enhanced by the presence of Rnf, which also resulted in decreased production of pyruvate, acetoin and an uncharacterized compound as unwanted side-products. Using crystalline cellulose as the growth substrate for the Rnf-containing strain, 75 mM (3.5 g/L) ethanol was produced at 60 °C, which is 5-fold higher than that reported previously. This underlines the importance of redox balancing and paves the way for achieving even higher ethanol titers in C. bescii. New stable genetic background results in higher ethanol production. Ethanol production is enhanced further by reduced ferredoxin NAD oxidoreductase (Rnf). Rnf decreases pyruvate, acetoin and an unknown compound as unwanted side products. Maximum ethanol production is five-times higher than that achieved previously.
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Affiliation(s)
| | - Gabriel M Rubinstein
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA
| | - Israel M Scott
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA
| | - Gina L Lipscomb
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA
| | - Farris L Poole Ii
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA
| | - Robert M Kelly
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC, USA
| | - Michael W W Adams
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA
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Liu H, Sun J, Chang JS, Shukla P. Engineering microbes for direct fermentation of cellulose to bioethanol. Crit Rev Biotechnol 2018; 38:1089-1105. [DOI: 10.1080/07388551.2018.1452891] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Affiliation(s)
- Hao Liu
- State Key Laboratory of Pulp and Paper Engineering, South China University of Technology, Guangzhou, China
| | - Jianliang Sun
- State Key Laboratory of Pulp and Paper Engineering, South China University of Technology, Guangzhou, China
| | - Jo-Shu Chang
- Department of Chemical Engineering, National Cheng Kung University, Tainan, Taiwan, China
| | - Pratyoosh Shukla
- Enzyme Technology and Protein Bioinformatics Laboratory, Department of Microbiology, Maharshi Dayanand University, Rohtak, India
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23
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The features that distinguish lichenases from other polysaccharide-hydrolyzing enzymes and the relevance of lichenases for biotechnological applications. Appl Microbiol Biotechnol 2018; 102:3951-3965. [DOI: 10.1007/s00253-018-8904-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Revised: 02/23/2018] [Accepted: 02/26/2018] [Indexed: 01/16/2023]
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24
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Henske JK, Wilken SE, Solomon KV, Smallwood CR, Shutthanandan V, Evans JE, Theodorou MK, O'Malley MA. Metabolic characterization of anaerobic fungi provides a path forward for bioprocessing of crude lignocellulose. Biotechnol Bioeng 2018; 115:874-884. [DOI: 10.1002/bit.26515] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2017] [Revised: 11/15/2017] [Accepted: 12/08/2017] [Indexed: 12/14/2022]
Affiliation(s)
- John K. Henske
- Department of Chemical EngineeringUniversity of CaliforniaSanta BarbaraCalifornia
| | - St. Elmo Wilken
- Department of Chemical EngineeringUniversity of CaliforniaSanta BarbaraCalifornia
| | - Kevin V. Solomon
- Department of Chemical EngineeringUniversity of CaliforniaSanta BarbaraCalifornia
- Agriculture and Biological EngineeringPurdue UniversityW. LafayetteIndiana
| | - Chuck R. Smallwood
- Environmental Molecular Sciences LaboratoryPacific Northwest National LaboratoryRichlandWashington
| | | | - James E. Evans
- Environmental Molecular Sciences LaboratoryPacific Northwest National LaboratoryRichlandWashington
| | - Michael K. Theodorou
- Animal ProductionWelfare and Veterinary SciencesHarper Adams UniversityNewportShropshireUK
| | - Michelle A. O'Malley
- Department of Chemical EngineeringUniversity of CaliforniaSanta BarbaraCalifornia
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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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Jiang Y, Xin F, Lu J, Dong W, Zhang W, Zhang M, Wu H, Ma J, Jiang M. State of the art review of biofuels production from lignocellulose by thermophilic bacteria. BIORESOURCE TECHNOLOGY 2017. [PMID: 28634129 DOI: 10.1016/j.biortech.2017.05.142] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Biofuels, including ethanol and butanol, are mainly produced by mesophilic solventogenic yeasts and Clostridium species. However, these microorganisms cannot directly utilize lignocellulosic materials, which are abundant, renewable and non-compete with human demand. More recently, thermophilic bacteria show great potential for biofuels production, which could efficiently degrade lignocellulose through the cost effective consolidated bioprocessing. Especially, it could avoid contamination in the whole process owing to its relatively high fermentation temperature. However, wild types thermophiles generally produce low levels of biofuels, hindering their large scale production. This review comprehensively summarizes the state of the art development of biofuels production by reported thermophilic microorganisms, and also concludes strategies to improve biofuels production including the metabolic pathways construction, co-culturing systems and biofuels tolerance. In addition, strategies to further improve butanol production are proposed.
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Affiliation(s)
- Yujia Jiang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211800, PR China
| | - Fengxue Xin
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211800, PR China
| | - Jiasheng Lu
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211800, PR China
| | - Weiliang Dong
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211800, PR China
| | - Wenming Zhang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211800, PR China; Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing Tech University, Nanjing 211800, PR China
| | - Min Zhang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211800, PR China
| | - Hao Wu
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211800, PR China; Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing Tech University, Nanjing 211800, PR China
| | - Jiangfeng Ma
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211800, PR China
| | - Min Jiang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211800, PR China; Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing Tech University, Nanjing 211800, PR China.
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Verbeke TJ, Garcia GM, Elkins JG. The effect of switchgrass loadings on feedstock solubilization and biofuel production by Clostridium thermocellum. BIOTECHNOLOGY FOR BIOFUELS 2017; 10:233. [PMID: 29213307 PMCID: PMC5708108 DOI: 10.1186/s13068-017-0917-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Accepted: 08/08/2017] [Indexed: 05/25/2023]
Abstract
BACKGROUND Efficient deconstruction and bioconversion of solids at high mass loadings is necessary to produce industrially relevant titers of biofuels from lignocellulosic biomass. To date, only a few studies have investigated the effect of solids loadings on microorganisms of interest for consolidated bioprocessing. Here, the effects that various switchgrass loadings have on Clostridium thermocellum solubilization and bioconversion are investigated. RESULTS Clostridium thermocellum was grown for 10 days on 10, 25, or 50 g/L switchgrass or Avicel at equivalent glucan loadings. Avicel was completely consumed at all loadings, but total cellulose solubilization decreased from 63 to 37% as switchgrass loadings increased from 10 to 50 g/L. Washed, spent switchgrass could be additionally hydrolyzed and fermented in second-round fermentations suggesting that access to fermentable substrates was not the limiting factor at higher feedstock loadings. Results from fermentations on Avicel or cellobiose using culture medium supplemented with 50% spent fermentation broth demonstrated that compounds present in the supernatants from the 25 or 50 g/L switchgrass loadings were the most inhibitory to continued fermentation. CONCLUSIONS Recalcitrance alone cannot fully account for differences in solubilization and end-product formation between switchgrass and Avicel at increased substrate loadings. Experiments aimed at separating metabolic inhibition from inhibition of hydrolysis suggest that C. thermocellum's hydrolytic machinery is more vulnerable to inhibition from switchgrass-derived compounds than its fermentative metabolism.
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Affiliation(s)
- Tobin J. Verbeke
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37831-6038 USA
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831-6038 USA
- Present Address: Department of Biological Sciences, University of Calgary, Calgary, AB T2N 1N4 Canada
| | - Gabriela M. Garcia
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37831-6038 USA
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831-6038 USA
| | - James G. Elkins
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37831-6038 USA
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831-6038 USA
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28
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Tian L, Perot SJ, Stevenson D, Jacobson T, Lanahan AA, Amador-Noguez D, Olson DG, Lynd LR. Metabolome analysis reveals a role for glyceraldehyde 3-phosphate dehydrogenase in the inhibition of C. thermocellum by ethanol. BIOTECHNOLOGY FOR BIOFUELS 2017; 10:276. [PMID: 29213320 PMCID: PMC5708176 DOI: 10.1186/s13068-017-0961-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Accepted: 11/06/2017] [Indexed: 06/07/2023]
Abstract
BACKGROUND Clostridium thermocellum is a promising microorganism for conversion of cellulosic biomass to biofuel, without added enzymes; however, the low ethanol titer produced by strains developed thus far is an obstacle to industrial application. RESULTS Here, we analyzed changes in the relative concentration of intracellular metabolites in response to gradual addition of ethanol to growing cultures. For C. thermocellum, we observed that ethanol tolerance, in experiments with gradual ethanol addition, was twofold higher than previously observed in response to a stepwise increase in the ethanol concentration, and appears to be due to a mechanism other than mutation. As ethanol concentrations increased, we found accumulation of metabolites upstream of the glyceraldehyde 3-phosphate dehydrogenase (GAPDH) reaction and depletion of metabolites downstream of that reaction. This pattern was not observed in the more ethanol-tolerant organism Thermoanaerobacterium saccharolyticum. We hypothesize that the Gapdh enzyme may have different properties in the two organisms. Our hypothesis is supported by enzyme assays showing greater sensitivity of the C. thermocellum enzyme to high levels of NADH, and by the increase in ethanol tolerance and production when the T. saccharolyticum gapdh was expressed in C. thermocellum. CONCLUSIONS We have demonstrated that a metabolic bottleneck occurs at the GAPDH reaction when the growth of C. thermocellum is inhibited by high levels of ethanol. We then showed that this bottleneck could be relieved by expression of the gapdh gene from T. saccharolyticum. This enzyme is a promising target for future metabolic engineering work.
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Affiliation(s)
- Liang Tian
- Thayer School of Engineering, Dartmouth College, 14 Engineering Drive, Hanover, NH 03755 USA
- Bioenergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
| | - Skyler J. Perot
- Dartmouth College, Hanover, NH 03755 USA
- Bioenergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
| | - David Stevenson
- Bioenergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
- University of Wisconsin-Madison, Madison, WI 53706 USA
| | - Tyler Jacobson
- Bioenergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
- University of Wisconsin-Madison, Madison, WI 53706 USA
| | - Anthony A. Lanahan
- Thayer School of Engineering, Dartmouth College, 14 Engineering Drive, Hanover, NH 03755 USA
- Bioenergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
| | - Daniel Amador-Noguez
- Bioenergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
- University of Wisconsin-Madison, Madison, WI 53706 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 37831 USA
| | - 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 37831 USA
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Zheng T, Cui J, Bae HR, Lynd LR, Olson DG. Expression of adhA from different organisms in Clostridium thermocellum. BIOTECHNOLOGY FOR BIOFUELS 2017; 10:251. [PMID: 29213311 PMCID: PMC5707802 DOI: 10.1186/s13068-017-0940-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/07/2017] [Accepted: 10/19/2017] [Indexed: 06/07/2023]
Abstract
BACKGROUND Clostridium thermocellum is a cellulolytic anaerobic thermophile that is a promising candidate for consolidated bioprocessing of lignocellulosic biomass into biofuels such as ethanol. It was previously shown that expressing Thermoanaerobacterium saccharolyticum adhA in C. thermocellum increases ethanol yield.In this study, we investigated expression of adhA genes from different organisms in Clostridium thermocellum. METHODS Based on sequence identity to T. saccharolyticum adhA, we chose adhA genes from 10 other organisms: Clostridium botulinum, Methanocaldococcus bathoardescens, Thermoanaerobacterium ethanolicus, Thermoanaerobacter mathranii, Thermococcus strain AN1, Thermoanaerobacterium thermosaccharolyticum, Caldicellulosiruptor saccharolyticus, Fervidobacterium nodosum, Marinitoga piezophila, and Thermotoga petrophila. All 11 adhA genes (including T. saccharolyticum adhA) were expressed in C. thermocellum and fermentation end products were analyzed. RESULTS All 11 adhA genes increased C. thermocellum ethanol yield compared to the empty-vector control. C. botulinum and T. ethanolicus adhA genes generated significantly higher ethanol yield than T. saccharolyticum adhA. CONCLUSION Our results indicated that expressing adhA is an effective method of increasing ethanol yield in wild-type C. thermocellum, and that this appears to be a general property of adhA genes.
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Affiliation(s)
- Tianyong Zheng
- Department of Biological Sciences, Dartmouth College, Hanover, NH 03755 USA
- Bioenergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37830 USA
| | - Jingxuan Cui
- Department of Biological Sciences, Dartmouth College, Hanover, NH 03755 USA
- Bioenergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37830 USA
| | - Hye Ri Bae
- Bioenergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37830 USA
- Thayer School of Engineering, Dartmouth College, 14 Engineering Drive, Hanover, NH 03755 USA
| | - Lee R. Lynd
- Department of Biological Sciences, Dartmouth College, Hanover, NH 03755 USA
- Bioenergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37830 USA
- Thayer School of Engineering, Dartmouth College, 14 Engineering Drive, Hanover, NH 03755 USA
| | - Daniel G. Olson
- Bioenergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37830 USA
- Thayer School of Engineering, Dartmouth College, 14 Engineering Drive, Hanover, NH 03755 USA
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30
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Sander K, Asano KG, Bhandari D, Van Berkel GJ, Brown SD, Davison B, Tschaplinski TJ. Targeted redox and energy cofactor metabolomics in Clostridium thermocellum and Thermoanaerobacterium saccharolyticum. BIOTECHNOLOGY FOR BIOFUELS 2017; 10:270. [PMID: 29213318 PMCID: PMC5707896 DOI: 10.1186/s13068-017-0960-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/16/2017] [Accepted: 11/06/2017] [Indexed: 06/07/2023]
Abstract
BACKGROUND Clostridium thermocellum and Thermoanaerobacterium saccharolyticum are prominent candidate biocatalysts that, together, can enable the direct biotic conversion of lignocellulosic biomass to ethanol. The imbalance and suboptimal turnover rates of redox cofactors are currently hindering engineering efforts to achieve higher bioproductivity in both organisms. Measuring relevant intracellular cofactor concentrations will help understand redox state of these cofactors and help identify a strategy to overcome these limitations; however, metabolomic determinations of these labile metabolites have historically proved challenging. RESULTS Through our validations, we verified the handling and storage stability of these metabolites, and verified extraction matrices and extraction solvent were not suppressing mass spectrometry signals. We recovered adenylate energy charge ratios (a main quality indicator) above 0.82 for all extractions. NADH/NAD+ values of 0.26 and 0.04 for an adhE-deficient strain of C. thermocellum and its parent, respectively, reflect the expected shift to a more reduced redox potential when a species lacks the ability to re-oxidize NADH by synthesizing ethanol. This method failed to yield reliable results with C. bescii and poor-growing strains of T. saccharolyticum. CONCLUSIONS Our validated protocols demonstrate and validate the extraction and analysis of selected redox and energy-related metabolites from two candidate consolidated bioprocessing biocatalysts, C. thermocellum and T. saccharolyticum. This development and validation highlights the important, but often neglected, need to optimize and validate metabolomic protocols when adapting them to new cell or tissue types.
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Affiliation(s)
- Kyle Sander
- Department of Chemical and Biomolecular Engineering, University of Tennessee, Knoxville, TN USA
- Bredesen Center for Interdisciplinary Graduate Research and Education, University of Tennessee, Knoxville, TN USA
- BioEnergy Sciences Center, Oak Ridge National Laboratory, Oak Ridge, TN USA
| | - Keiji G. Asano
- Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN USA
- BioEnergy Sciences Center, Oak Ridge National Laboratory, Oak Ridge, TN USA
| | - Deepak Bhandari
- Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN USA
- BioEnergy Sciences Center, Oak Ridge National Laboratory, Oak Ridge, TN USA
- Present Address: Centers for Disease Control and Prevention, Atlanta, GA USA
| | - Gary J. Van Berkel
- Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN USA
- BioEnergy Sciences Center, Oak Ridge National Laboratory, Oak Ridge, TN USA
| | - Steven D. Brown
- Bredesen Center for Interdisciplinary Graduate Research and Education, University of Tennessee, Knoxville, TN USA
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN USA
- Present Address: LanzaTech, Skokie, IL USA
| | - Brian Davison
- Department of Chemical and Biomolecular Engineering, University of Tennessee, Knoxville, TN USA
- Bredesen Center for Interdisciplinary Graduate Research and Education, University of Tennessee, Knoxville, TN USA
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN USA
- BioEnergy Sciences Center, Oak Ridge National Laboratory, Oak Ridge, TN USA
| | - Timothy J. Tschaplinski
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN USA
- BioEnergy Sciences Center, Oak Ridge National Laboratory, Oak Ridge, TN USA
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31
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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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Akinosho H, Yee K, Rodriguez M, Muchero W, Yoo CG, Li M, Thompson O, Pu Y, Brown S, Mielenz J, Ragauskas AJ. Lignin Exhibits Recalcitrance‐Associated Features Following the Consolidated Bioprocessing of
Populus trichocarpa
Natural Variants. ChemistrySelect 2017. [DOI: 10.1002/slct.201701572] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Hannah Akinosho
- BioEnergy Science Center Oak Ridge National Laboratory Oak Ridge TN 37831
- Biosciences Division Oak Ridge National Laboratory Oak Ridge TN 37831
- Department of Chemistry and Biochemistry, G eorgia Institute of Technology Atlanta GA 30332
| | - Kelsey Yee
- BioEnergy Science Center Oak Ridge National Laboratory Oak Ridge TN 37831
- Biosciences Division Oak Ridge National Laboratory Oak Ridge TN 37831
| | - Miguel Rodriguez
- BioEnergy Science Center Oak Ridge National Laboratory Oak Ridge TN 37831
- Biosciences Division Oak Ridge National Laboratory Oak Ridge TN 37831
| | - Wellington Muchero
- BioEnergy Science Center Oak Ridge National Laboratory Oak Ridge TN 37831
- Biosciences Division Oak Ridge National Laboratory Oak Ridge TN 37831
| | - Chang Geun Yoo
- Department of Chemical and Biomolecular Engineering & Department of Forestry Center for Renewable Carbon at Wildlife, and Fisheries University of Tennessee Knoxville TN 37996
- BioEnergy Science Center Oak Ridge National Laboratory Oak Ridge TN 37831
- Biosciences Division Oak Ridge National Laboratory Oak Ridge TN 37831
| | - Mi Li
- Department of Chemical and Biomolecular Engineering & Department of Forestry Center for Renewable Carbon at Wildlife, and Fisheries University of Tennessee Knoxville TN 37996
- BioEnergy Science Center Oak Ridge National Laboratory Oak Ridge TN 37831
- Biosciences Division Oak Ridge National Laboratory Oak Ridge TN 37831
| | - Olivia Thompson
- BioEnergy Science Center Oak Ridge National Laboratory Oak Ridge TN 37831
- Biosciences Division Oak Ridge National Laboratory Oak Ridge TN 37831
| | - Yunqiao Pu
- BioEnergy Science Center Oak Ridge National Laboratory Oak Ridge TN 37831
- Biosciences Division Oak Ridge National Laboratory Oak Ridge TN 37831
| | - Steven Brown
- BioEnergy Science Center Oak Ridge National Laboratory Oak Ridge TN 37831
- Biosciences Division Oak Ridge National Laboratory Oak Ridge TN 37831
| | - Johnathan Mielenz
- BioEnergy Science Center Oak Ridge National Laboratory Oak Ridge TN 37831
- Biosciences Division Oak Ridge National Laboratory Oak Ridge TN 37831
| | - Arthur J. Ragauskas
- Department of Chemical and Biomolecular Engineering & Department of Forestry Center for Renewable Carbon at Wildlife, and Fisheries University of Tennessee Knoxville TN 37996
- BioEnergy Science Center Oak Ridge National Laboratory Oak Ridge TN 37831
- Biosciences Division Oak Ridge National Laboratory Oak Ridge TN 37831
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Holistic bioengineering: rewiring central metabolism for enhanced bioproduction. Biochem J 2017; 474:3935-3950. [PMID: 29146872 PMCID: PMC5688466 DOI: 10.1042/bcj20170377] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Revised: 10/17/2017] [Accepted: 10/20/2017] [Indexed: 12/29/2022]
Abstract
What does it take to convert a living organism into a truly productive biofactory? Apart from optimizing biosynthesis pathways as standalone units, a successful bioengineering approach must bend the endogenous metabolic network of the host, and especially its central metabolism, to support the bioproduction process. In practice, this usually involves three complementary strategies which include tuning-down or abolishing competing metabolic pathways, increasing the availability of precursors of the desired biosynthesis pathway, and ensuring high availability of energetic resources such as ATP and NADPH. In this review, we explore these strategies, focusing on key metabolic pathways and processes, such as glycolysis, anaplerosis, the TCA (tricarboxylic acid) cycle, and NADPH production. We show that only a holistic approach for bioengineering — considering the metabolic network of the host organism as a whole, rather than focusing on the production pathway alone — can truly mold microorganisms into efficient biofactories.
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34
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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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35
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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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36
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Xu T, Li Y, He Z, Van Nostrand JD, Zhou J. Cas9 Nickase-Assisted RNA Repression Enables Stable and Efficient Manipulation of Essential Metabolic Genes in Clostridium cellulolyticum. Front Microbiol 2017; 8:1744. [PMID: 28936208 PMCID: PMC5594222 DOI: 10.3389/fmicb.2017.01744] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Accepted: 08/28/2017] [Indexed: 11/16/2022] Open
Abstract
Essential gene functions remain largely underexplored in bacteria. Clostridium cellulolyticum is a promising candidate for consolidated bioprocessing; however, its genetic manipulation to reduce the formation of less-valuable acetate is technically challenging due to the essentiality of acetate-producing genes. Here we developed a Cas9 nickase-assisted chromosome-based RNA repression to stably manipulate essential genes in C. cellulolyticum. Our plasmid-based expression of antisense RNA (asRNA) molecules targeting the phosphotransacetylase (pta) gene successfully reduced the enzymatic activity by 35% in cellobiose-grown cells, metabolically decreased the acetate titer by 15 and 52% in wildtype transformants on cellulose and xylan, respectively. To control both acetate and lactate simultaneously, we transformed the repression plasmid into lactate production-deficient mutant and found the plasmid delivery reduced acetate titer by more than 33%, concomitant with negligible lactate formation. The strains with pta gene repression generally diverted more carbon into ethanol. However, further testing on chromosomal integrants that were created by double-crossover recombination exhibited only very weak repression because DNA integration dramatically lessened gene dosage. With the design of a tandem repetitive promoter-driven asRNA module and the use of a new Cas9 nickase genome editing tool, a chromosomal integrant (LM3P) was generated in a single step and successfully enhanced RNA repression, with a 27% decrease in acetate titer on cellulose in antibiotic-free medium. These results indicate the effectiveness of tandem promoter-driven RNA repression modules in promoting gene repression in chromosomal integrants. Our combinatorial method using a Cas9 nickase genome editing tool to integrate the gene repression module demonstrates easy-to-use and high-efficiency advantages, paving the way for stably manipulating genes, even essential ones, for functional characterization and microbial engineering.
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Affiliation(s)
- Tao Xu
- Institute for Environmental Genomics and Department of Microbiology and Plant Biology, University of Oklahoma, NormanOK, United States
| | - Yongchao Li
- Institute for Environmental Genomics and Department of Microbiology and Plant Biology, University of Oklahoma, NormanOK, United States
| | - Zhili He
- Institute for Environmental Genomics and Department of Microbiology and Plant Biology, University of Oklahoma, NormanOK, United States
| | - Joy D. Van Nostrand
- Institute for Environmental Genomics and Department of Microbiology and Plant Biology, University of Oklahoma, NormanOK, United States
| | - Jizhong Zhou
- Institute for Environmental Genomics and Department of Microbiology and Plant Biology, University of Oklahoma, NormanOK, United States
- Earth Sciences Division, Lawrence Berkeley National Laboratory, BerkeleyCA, United States
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua UniversityBeijing, China
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37
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Thompson RA, Trinh CT. Overflow metabolism and growth cessation in Clostridium thermocellum DSM1313 during high cellulose loading fermentations. Biotechnol Bioeng 2017; 114:2592-2604. [PMID: 28671264 DOI: 10.1002/bit.26374] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2017] [Revised: 06/25/2017] [Accepted: 06/27/2017] [Indexed: 12/31/2022]
Abstract
As a model thermophilic bacterium for the production of second-generation biofuels, the metabolism of Clostridium thermocellum has been widely studied. However, most studies have characterized C. thermocellum metabolism for growth at relatively low substrate concentrations. This outlook is not industrially relevant, however, as commercial viability requires substrate loadings of at least 100 g/L cellulosic materials. Recently, a wild-type C. thermocellum DSM1313 was cultured on high cellulose loading batch fermentations and reported to produce a wide range of fermentative products not seen at lower substrate concentrations, opening the door for a more in-depth analysis of how this organism will behave in industrially relevant conditions. In this work, we elucidated the interconnectedness of overflow metabolism and growth cessation in C. thermocellum during high cellulose loading batch fermentations (100 g/L). Metabolic flux and thermodynamic analyses suggested that hydrogen and formate accumulation perturbed the complex redox metabolism and limited conversion of pyruvate to acetyl-CoA conversion, likely leading to overflow metabolism and growth cessation in C. thermocellum. Pyruvate formate lyase (PFL) acts as an important redox valve and its flux is inhibited by formate accumulation. Finally, we demonstrated that manipulation of fermentation conditions to alleviate hydrogen accumulation could dramatically alter the fate of pyruvate, providing valuable insight into process design for enhanced C. thermocellum production of chemicals and biofuels. Biotechnol. Bioeng. 2017;114: 2592-2604. © 2017 Wiley Periodicals, Inc.
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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, Tennessee.,BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, Tennessee
| | - Cong T Trinh
- Bredesen Center for Interdisciplinary Research and Graduate Education, The University of Tennessee, Knoxville and Oak Ridge National Laboratory, Oak Ridge, Tennessee.,BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, Tennessee.,Department of Chemical and Biomolecular Engineering, The University of Tennessee, Knoxville, Tennessee
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38
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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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39
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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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Kim SK, Groom J, Chung D, Elkins J, Westpheling J. Expression of a heat-stable NADPH-dependent alcohol dehydrogenase from Thermoanaerobacter pseudethanolicus 39E in Clostridium thermocellum 1313 results in increased hydroxymethylfurfural resistance. BIOTECHNOLOGY FOR BIOFUELS 2017; 10:66. [PMID: 28331542 PMCID: PMC5353787 DOI: 10.1186/s13068-017-0750-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2016] [Accepted: 03/09/2017] [Indexed: 05/26/2023]
Abstract
BACKGROUND Resistance to deconstruction is a major limitation to the use of lignocellulosic biomass as a substrate for the production of fuels and chemicals. Consolidated bioprocessing (CBP), the use of microbes for the simultaneous hydrolysis of lignocellulose into soluble sugars and fermentation of the resulting sugars to products of interest, is a potential solution to this obstacle. The pretreatment of plant biomass, however, releases compounds that are inhibitory to the growth of microbes used for CBP. RESULTS Heterologous expression of the Thermoanaerobacter pseudethanolicus 39E bdhA gene, that encodes an alcohol dehydrogenase, in Clostridium thermocellum significantly increased resistance to furan derivatives at concentrations found in acid-pretreated biomass. The mechanism of detoxification of hydroxymethylfurfural was shown to be primarily reduction using NADPH as the cofactor. In addition, we report the construction of new expression vectors for homologous and heterologous expression in C. thermocellum. These vectors use regulatory signals from both C. bescii (the S-layer promoter) and C. thermocellum (the enolase promoter) shown to efficiently drive expression of the BdhA enzyme. CONCLUSIONS Toxic compounds present in lignocellulose hydrolysates that inhibit cell growth and product formation are obstacles to the commercialization of fuels and chemicals from biomass. Expression of genes that reduce the effect of these inhibitors, such as furan derivatives, will serve to enable commercial processes using plant biomass for the production of fuels and chemicals.
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Affiliation(s)
- Sun-Ki Kim
- Department of Genetics, University of Georgia, Athens, GA USA
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN USA
| | - Joseph Groom
- Department of Genetics, University of Georgia, Athens, GA USA
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN USA
| | - Daehwan Chung
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO USA
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN USA
| | - James Elkins
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN USA
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN USA
| | - Janet Westpheling
- Department of Genetics, University of Georgia, Athens, GA USA
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN USA
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Verbeke TJ, Giannone RJ, Klingeman DM, Engle NL, Rydzak T, Guss AM, Tschaplinski TJ, Brown SD, Hettich RL, Elkins JG. Pentose sugars inhibit metabolism and increase expression of an AgrD-type cyclic pentapeptide in Clostridium thermocellum. Sci Rep 2017; 7:43355. [PMID: 28230109 PMCID: PMC5322536 DOI: 10.1038/srep43355] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2016] [Accepted: 01/18/2017] [Indexed: 12/22/2022] Open
Abstract
Clostridium thermocellum could potentially be used as a microbial biocatalyst to produce renewable fuels directly from lignocellulosic biomass due to its ability to rapidly solubilize plant cell walls. While the organism readily ferments sugars derived from cellulose, pentose sugars from xylan are not metabolized. Here, we show that non-fermentable pentoses inhibit growth and end-product formation during fermentation of cellulose-derived sugars. Metabolomic experiments confirmed that xylose is transported intracellularly and reduced to the dead-end metabolite xylitol. Comparative RNA-seq analysis of xylose-inhibited cultures revealed several up-regulated genes potentially involved in pentose transport and metabolism, which were targeted for disruption. Deletion of the ATP-dependent transporter, CbpD partially alleviated xylose inhibition. A putative xylitol dehydrogenase, encoded by Clo1313_0076, was also deleted resulting in decreased total xylitol production and yield by 41% and 46%, respectively. Finally, xylose-induced inhibition corresponds with the up-regulation and biogenesis of a cyclical AgrD-type, pentapeptide. Medium supplementation with the mature cyclical pentapeptide also inhibits bacterial growth. Together, these findings provide new foundational insights needed for engineering improved pentose utilizing strains of C. thermocellum and reveal the first functional Agr-type cyclic peptide to be produced by a thermophilic member of the Firmicutes.
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Affiliation(s)
- Tobin J Verbeke
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA.,Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Richard J Giannone
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA.,Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Dawn M Klingeman
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA.,Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Nancy L Engle
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA.,Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Thomas Rydzak
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA.,Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Adam M Guss
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA.,Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Timothy J Tschaplinski
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA.,Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Steven D Brown
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA.,Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Robert L Hettich
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA.,Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - James G Elkins
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA.,Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
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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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Artzi L, Bayer EA, Moraïs S. Cellulosomes: bacterial nanomachines for dismantling plant polysaccharides. Nat Rev Microbiol 2017; 15:83-95. [PMID: 27941816 DOI: 10.1038/nrmicro.2016.164] [Citation(s) in RCA: 223] [Impact Index Per Article: 31.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Cellulosomes are multienzyme complexes that are produced by anaerobic cellulolytic bacteria for the degradation of lignocellulosic biomass. They comprise a complex of scaffoldin, which is the structural subunit, and various enzymatic subunits. The intersubunit interactions in these multienzyme complexes are mediated by cohesin and dockerin modules. Cellulosome-producing bacteria have been isolated from a large variety of environments, which reflects their prevalence and the importance of this microbial enzymatic strategy. In a given species, cellulosomes exhibit intrinsic heterogeneity, and between species there is a broad diversity in the composition and configuration of cellulosomes. With the development of modern technologies, such as genomics and proteomics, the full protein content of cellulosomes and their expression levels can now be assessed and the regulatory mechanisms identified. Owing to their highly efficient organization and hydrolytic activity, cellulosomes hold immense potential for application in the degradation of biomass and are the focus of much effort to engineer an ideal microorganism for the conversion of lignocellulose to valuable products, such as biofuels.
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Affiliation(s)
- Lior Artzi
- Department of Biomolecular Sciences, The Weizmann Institute of Science, 234 Herzl Street, Rehovot 7610001, Israel
| | - Edward A Bayer
- Department of Biomolecular Sciences, The Weizmann Institute of Science, 234 Herzl Street, Rehovot 7610001, Israel
| | - Sarah Moraïs
- Department of Biomolecular Sciences, The Weizmann Institute of Science, 234 Herzl Street, Rehovot 7610001, Israel
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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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45
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Poudel S, Giannone RJ, Rodriguez M, Raman B, Martin MZ, Engle NL, Mielenz JR, Nookaew I, Brown SD, Tschaplinski TJ, Ussery D, Hettich RL. Integrated omics analyses reveal the details of metabolic adaptation of Clostridium thermocellum to lignocellulose-derived growth inhibitors released during the deconstruction of switchgrass. BIOTECHNOLOGY FOR BIOFUELS 2017; 10:14. [PMID: 28077967 PMCID: PMC5223564 DOI: 10.1186/s13068-016-0697-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2016] [Accepted: 12/24/2016] [Indexed: 05/03/2023]
Abstract
BACKGROUND Clostridium thermocellum is capable of solubilizing and converting lignocellulosic biomass into ethanol. Although much of the work-to-date has centered on characterizing this microbe's growth on model cellulosic substrates, such as cellobiose, Avicel, or filter paper, it is vitally important to understand its metabolism on more complex, lignocellulosic substrates to identify relevant industrial bottlenecks that could undermine efficient biofuel production. To this end, we have examined a time course progression of C. thermocellum grown on switchgrass to assess the metabolic and protein changes that occur during the conversion of plant biomass to ethanol. RESULTS The most striking feature of the metabolome was the observed accumulation of long-chain, branched fatty acids over time, implying an adaptive restructuring of C. thermocellum's cellular membrane as the culture progresses. This is undoubtedly a response to the gradual accumulation of lignocellulose-derived inhibitory compounds as the organism deconstructs the switchgrass to access the embedded cellulose. Corroborating the metabolomics data, proteomic analysis revealed a corresponding time-dependent increase in various enzymes, including those involved in the interconversion of branched amino acids valine, leucine, and isoleucine to iso- and anteiso-fatty acid precursors. Additionally, the metabolic accumulation of hemicellulose-derived sugars and sugar alcohols concomitant with increased abundance of enzymes involved in C5 sugar metabolism/pentose phosphate pathway indicates that C. thermocellum shifts glycolytic intermediates to alternate pathways to modulate overall carbon flux in response to C5 sugar metabolites that increase during lignocellulose deconstruction. CONCLUSIONS Integrated omic platforms provided complementary systems biological information that highlight C. thermocellum's specific response to cytotoxic inhibitors released during the deconstruction and utilization of switchgrass. These additional viewpoints allowed us to fully realize the level to which the organism adapts to an increasingly challenging culture environment-information that will prove critical to C. thermocellum's industrial efficacy.
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Affiliation(s)
- Suresh Poudel
- Biosciences Division, Oak Ridge National Lab, Oak Ridge, TN 37831 USA
- Department of Genome Science and Technology, University of Tennessee, Knoxville, TN 37996 USA
| | | | - Miguel Rodriguez
- Biosciences Division, Oak Ridge National Lab, Oak Ridge, TN 37831 USA
| | - Babu Raman
- Biosciences Division, Oak Ridge National Lab, Oak Ridge, TN 37831 USA
- Dow AgroSciences, 9330 Zionsville Road, Indianapolis, IN 46268 USA
| | - Madhavi Z. Martin
- Biosciences Division, Oak Ridge National Lab, Oak Ridge, TN 37831 USA
| | - Nancy L. Engle
- Biosciences Division, Oak Ridge National Lab, Oak Ridge, TN 37831 USA
| | | | - Intawat Nookaew
- Biosciences Division, Oak Ridge National Lab, Oak Ridge, TN 37831 USA
- Department of Biomedical Informatics, University of Arkansas for Medical Sciences, Little Rock, AR 72205 USA
| | - Steven D. Brown
- Biosciences Division, Oak Ridge National Lab, Oak Ridge, TN 37831 USA
- Department of Genome Science and Technology, University of Tennessee, Knoxville, TN 37996 USA
| | | | - David Ussery
- Biosciences Division, Oak Ridge National Lab, Oak Ridge, TN 37831 USA
- Department of Biomedical Informatics, University of Arkansas for Medical Sciences, Little Rock, AR 72205 USA
| | - Robert L. Hettich
- Chemical Sciences Division, Oak Ridge National Lab, Oak Ridge, TN 37831 USA
- Department of Genome Science and Technology, University of Tennessee, Knoxville, TN 37996 USA
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46
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Macaya-Sanz D, Chen J, Kalluri UC, Muchero W, Tschaplinski TJ, Gunter LE, Simon SJ, Biswal AK, Bryan AC, Payyavula R, Xie M, Yang Y, Zhang J, Mohnen D, Tuskan GA, DiFazio SP. Agronomic performance of Populus deltoides trees engineered for biofuel production. BIOTECHNOLOGY FOR BIOFUELS 2017; 10:253. [PMID: 29213313 PMCID: PMC5707814 DOI: 10.1186/s13068-017-0934-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Accepted: 10/19/2017] [Indexed: 05/02/2023]
Abstract
BACKGROUND One of the major barriers to the development of lignocellulosic feedstocks is the recalcitrance of plant cell walls to deconstruction and saccharification. Recalcitrance can be reduced by targeting genes involved in cell wall biosynthesis, but this can have unintended consequences that compromise the agronomic performance of the trees under field conditions. Here we report the results of a field trial of fourteen distinct transgenic Populus deltoides lines that had previously demonstrated reduced recalcitrance without yield penalties under greenhouse conditions. RESULTS Survival and productivity of the trial were excellent in the first year, and there was little evidence for reduced performance of the transgenic lines with modified target gene expression. Surprisingly, the most striking phenotypic effects in this trial were for two empty-vector control lines that had modified bud set and bud flush. This is most likely due to somaclonal variation or insertional mutagenesis. Traits related to yield, crown architecture, herbivory, pathogen response, and frost damage showed few significant differences between target gene transgenics and empty vector controls. However, there were a few interesting exceptions. Lines overexpressing the DUF231 gene, a putative O-acetyltransferase, showed early bud flush and marginally increased height growth. Lines overexpressing the DUF266 gene, a putative glycosyltransferase, had significantly decreased stem internode length and slightly higher volume index. Finally, lines overexpressing the PFD2 gene, a putative member of the prefoldin complex, had a slightly reduced volume index. CONCLUSIONS This field trial demonstrates that these cell wall modifications, which decreased cell wall recalcitrance under laboratory conditions, did not seriously compromise first-year performance in the field, despite substantial challenges, including an outbreak of a stem boring insect (Gypsonoma haimbachiana), attack by a leaf rust pathogen (Melampsora spp.), and a late frost event. This bodes well for the potential utility of these lines as advanced biofuels feedstocks.
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Affiliation(s)
- David Macaya-Sanz
- Department of Biology, West Virginia University, Morgantown, WV 26506 USA
| | - Jin‐Gui Chen
- BioEnergy Science Center and Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
| | - Udaya C. Kalluri
- BioEnergy Science Center and Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
| | - Wellington Muchero
- BioEnergy Science Center and Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
| | - Timothy J. Tschaplinski
- BioEnergy Science Center and Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
| | - Lee E. Gunter
- BioEnergy Science Center and Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
| | - Sandra J. Simon
- Department of Biology, West Virginia University, Morgantown, WV 26506 USA
| | - Ajaya K. Biswal
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602 USA
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602 USA
| | - Anthony C. Bryan
- BioEnergy Science Center and Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
| | - Raja Payyavula
- BioEnergy Science Center and Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
| | - Meng Xie
- BioEnergy Science Center and Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
| | - Yongil Yang
- BioEnergy Science Center and Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
| | - Jin Zhang
- BioEnergy Science Center and Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
| | - Debra Mohnen
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602 USA
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602 USA
| | - Gerald A. Tuskan
- BioEnergy Science Center and Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
| | - Stephen P. DiFazio
- Department of Biology, West Virginia University, Morgantown, WV 26506 USA
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47
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Ábrego U, Chen Z, Wan C. Consolidated Bioprocessing Systems for Cellulosic Biofuel Production. ADVANCES IN BIOENERGY 2017. [DOI: 10.1016/bs.aibe.2017.01.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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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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Olson DG, Hörl M, Fuhrer T, Cui J, Zhou J, Maloney MI, Amador-Noguez D, Tian L, Sauer U, Lynd LR. Glycolysis without pyruvate kinase in Clostridium thermocellum. Metab Eng 2016; 39:169-180. [PMID: 27914869 DOI: 10.1016/j.ymben.2016.11.011] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2016] [Revised: 10/21/2016] [Accepted: 11/30/2016] [Indexed: 01/05/2023]
Abstract
The metabolism of Clostridium thermocellum is notable in that it assimilates sugar via the EMP pathway but does not possess a pyruvate kinase enzyme. In the wild type organism, there are three proposed pathways for conversion of phosphoenolpyruvate (PEP) to pyruvate, which differ in their cofactor usage. One path uses pyruvate phosphate dikinase (PPDK), another pathway uses the combined activities of PEP carboxykinase (PEPCK) and oxaloacetate decarboxylase (ODC). Yet another pathway, the malate shunt, uses the combined activities of PEPCK, malate dehydrogenase and malic enzyme. First we showed that there is no flux through the ODC pathway by enzyme assay. Flux through the remaining two pathways (PPDK and malate shunt) was determined by dynamic 13C labeling. In the wild-type strain, the malate shunt accounts for about 33±2% of the flux to pyruvate, with the remainder via the PPDK pathway. Deletion of the ppdk gene resulted in a redirection of all pyruvate flux through the malate shunt. This provides the first direct evidence of the in-vivo function of the malate shunt.
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Affiliation(s)
- 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.
| | - Manuel Hörl
- Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Tobias Fuhrer
- Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Jingxuan Cui
- Thayer School of Engineering, Dartmouth College, Hanover, NH 03755, USA; BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37830, USA
| | - Jilai Zhou
- 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
| | - Daniel Amador-Noguez
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706, 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
| | - Uwe Sauer
- Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - 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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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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