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Callaghan MM, Thusoo E, Sharma BD, Getahun F, Stevenson DM, Maranas C, Olson DG, Lynd LR, Amador-Noguez D. Deuterated water as a substrate-agnostic isotope tracer for investigating reversibility and thermodynamics of reactions in central carbon metabolism. Metab Eng 2023; 80:254-266. [PMID: 37923005 DOI: 10.1016/j.ymben.2023.10.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Revised: 10/16/2023] [Accepted: 10/22/2023] [Indexed: 11/07/2023]
Abstract
Stable isotope tracers are a powerful tool for the quantitative analysis of microbial metabolism, enabling pathway elucidation, metabolic flux quantification, and assessment of reaction and pathway thermodynamics. 13C and 2H metabolic flux analysis commonly relies on isotopically labeled carbon substrates, such as glucose. However, the use of 2H-labeled nutrient substrates faces limitations due to their high cost and limited availability in comparison to 13C-tracers. Furthermore, isotope tracer studies in industrially relevant bacteria that metabolize complex substrates such as cellulose, hemicellulose, or lignocellulosic biomass, are challenging given the difficulty in obtaining these as isotopically labeled substrates. In this study, we examine the potential of deuterated water (2H2O) as an affordable, substrate-neutral isotope tracer for studying central carbon metabolism. We apply 2H2O labeling to investigate the reversibility of glycolytic reactions across three industrially relevant bacterial species -C. thermocellum, Z. mobilis, and E. coli-harboring distinct glycolytic pathways with unique thermodynamics. We demonstrate that 2H2O labeling recapitulates previous reversibility and thermodynamic findings obtained with established 13C and 2H labeled nutrient substrates. Furthermore, we exemplify the utility of this 2H2O labeling approach by applying it to high-substrate C. thermocellum fermentations -a setting in which the use of conventional tracers is impractical-thereby identifying the glycolytic enzyme phosphofructokinase as a major bottleneck during high-substrate fermentations and unveiling critical insights that will steer future engineering efforts to enhance ethanol production in this cellulolytic organism. This study demonstrates the utility of deuterated water as a substrate-agnostic isotope tracer for examining flux and reversibility of central carbon metabolic reactions, which yields biological insights comparable to those obtained using costly 2H-labeled nutrient substrates.
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Affiliation(s)
- Melanie M Callaghan
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, USA; Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA
| | - Eashant Thusoo
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, USA; Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA; Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, USA
| | - Bishal D Sharma
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, USA; Thayer School of Engineering, Dartmouth College, Hanover, NH, USA
| | - Fitsum Getahun
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA; Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, USA
| | - David M Stevenson
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, USA; Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA; Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, USA
| | - Costas Maranas
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, USA; Department of Chemical Engineering, The Pennsylvania State University, University Park, PA, USA
| | - Daniel G Olson
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, USA; Thayer School of Engineering, Dartmouth College, Hanover, NH, USA
| | - Lee R Lynd
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, USA; Thayer School of Engineering, Dartmouth College, Hanover, NH, USA
| | - Daniel Amador-Noguez
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, USA; Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA; Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, USA.
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Daley SR, Gallanosa PM, Sparling R. Kinetic characterization of annotated glycolytic enzymes present in cellulose-fermenting Clostridium thermocellum suggests different metabolic roles. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2023; 16:112. [PMID: 37438781 DOI: 10.1186/s13068-023-02362-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Accepted: 06/27/2023] [Indexed: 07/14/2023]
Abstract
BACKGROUND The efficient production of sustainable biofuels is important for the reduction of greenhouse gas emissions. Clostridium thermocellum ATCC 27405 is a candidate for ethanol production from lignocellulosic biomass using consolidated bioprocessing. Fermentation of cellulosic biomass goes through an atypical glycolytic pathway in this thermophilic bacterium, with various glycolytic enzymes capable of utilizing different phosphate donors, including GTP and inorganic pyrophosphate (PPi), in addition to or in place of the usual ATP. C. thermocellum contains three annotated phosphofructokinases (PFK) genes, the expression of which have all been detected through proteomics and transcriptomics. Pfp (Cthe_0347) was previously characterized as pyrophosphate dependent with fructose-6-phosphate (F6P) as its substrate. RESULTS We now demonstrate that this enzyme can also phosphorylate sedoheptulose-7-phosphate (an intermediate in the pentose phosphate pathway), with the Vmax and Km of F6P being approximately 15 folds higher and 43 folds lower, respectively, in comparison to sedoheptulose-7-phosphate. Purified PfkA shows preference for GTP as the phosphate donor as opposed to ATP with a 12.5-fold difference in Km values while phosphorylating F6P. Allosteric regulation is a factor at play in PfkA activity, with F6P exhibiting positive cooperativity, and an apparent requirement for ammonium ions to attain maximal activity. Phosphoenolpyruvate and PPi were the only inhibitors for PfkA determined from the study, which corroborates what is known about enzymes from this subfamily. The activation or inhibition by these ligands lends support to the argument that glycolysis is regulated by metabolites such as PPi and NH4+ in the organism. PfkB, showed no activity with F6P, but had significant activity with fructose, while utilizing either ATP or GTP, making it a fructokinase. Rounding out the upper glycolysis pathway, the identity of the fructose-1,6-bisphosphate aldolase in the genome was verified and reported to have substantial activity with fructose-1,6-bisphosphate, in the presence of the divalent ion, Zn2+. CONCLUSION These findings along with previous proteomic data suggest that Pfp, plays a role in both glycolysis and the pentose phosphate pathway, while PfkA and PfkB may phosphorylate sugars in glycolysis but is responsible for sugar metabolism elsewhere under conditions outside of growth on sufficient cellobiose.
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Affiliation(s)
- Steve R Daley
- Department of Microbiology, University of Manitoba, 213 Buller Building, Winnipeg, MB, R3T 2N2, Canada
| | - Patricia Mae Gallanosa
- 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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Kuil T, Nurminen CMK, van Maris AJA. Pyrophosphate as allosteric regulator of ATP-phosphofructokinase in Clostridium thermocellum and other bacteria with ATP- and PP i-phosphofructokinases. Arch Biochem Biophys 2023; 743:109676. [PMID: 37380119 DOI: 10.1016/j.abb.2023.109676] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Revised: 06/13/2023] [Accepted: 06/17/2023] [Indexed: 06/30/2023]
Abstract
The phosphofructokinase (Pfk) reaction represents one of the key regulatory points in glycolysis. While most organisms encode for Pfks that use ATP as phosphoryl donor, some organisms also encode for PPi-dependent Pfks. Despite this central role, the biochemical characteristics as well as the physiological role of both Pfks is often not known. Clostridium thermocellum is an example of a microorganism that encodes for both Pfks, however, only PPi-Pfk activity has been detected in cell-free extracts and little is known about the regulation and function of both enzymes. In this study, the ATP- and PPi-Pfk of C. thermocellum were purified and biochemically characterized. No allosteric regulators were found for PPi-Pfk amongst common effectors. With fructose-6-P, PPi, fructose-1,6-bisP, and Pi PPi-Pfk showed high specificity (KM < 0.62 mM) and maximum activity (Vmax > 156 U mg-1). In contrast, ATP-Pfk showed much lower affinity (K0.5 of 9.26 mM) and maximum activity (14.5 U mg-1) with fructose-6-P. In addition to ATP, also GTP, UTP and ITP could be used as phosphoryl donors. The catalytic efficiency with GTP was 7-fold higher than with ATP, suggesting that GTP is the preferred substrate. The enzyme was activated by NH4+, and pronounced inhibition was observed with GDP, FBP, PEP, and especially with PPi (Ki of 0.007 mM). Characterization of purified ATP-Pfks originating from eleven different bacteria, encoding for only ATP-Pfk or for both ATP- and PPi-Pfk, identified that PPi inhibition of ATP-Pfks could be a common phenomenon for organisms with a PPi-dependent glycolysis.
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Affiliation(s)
- Teun Kuil
- Department of Industrial Biotechnology, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Carolus M K Nurminen
- Department of Industrial Biotechnology, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Antonius J A van Maris
- Department of Industrial Biotechnology, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Stockholm, Sweden.
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Schroeder WL, Kuil T, van Maris AJA, Olson DG, Lynd LR, Maranas CD. A detailed genome-scale metabolic model of Clostridium thermocellum investigates sources of pyrophosphate for driving glycolysis. Metab Eng 2023; 77:306-322. [PMID: 37085141 DOI: 10.1016/j.ymben.2023.04.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Revised: 03/24/2023] [Accepted: 04/08/2023] [Indexed: 04/23/2023]
Abstract
Lignocellulosic biomass is an abundant and renewable source of carbon for chemical manufacturing, yet it is cumbersome in conventional processes. A promising, and increasingly studied, candidate for lignocellulose bioprocessing is the thermophilic anaerobe Clostridium thermocellum given its potential to produce ethanol, organic acids, and hydrogen gas from lignocellulosic biomass under high substrate loading. Possessing an atypical glycolytic pathway which substitutes GTP or pyrophosphate (PPi) for ATP in some steps, including in the energy-investment phase, identification, and manipulation of PPi sources are key to engineering its metabolism. Previous efforts to identify the primary pyrophosphate have been unsuccessful. Here, we explore pyrophosphate metabolism through reconstructing, updating, and analyzing a new genome-scale stoichiometric model for C. thermocellum, iCTH669. Hundreds of changes to the former GEM, iCBI655, including correcting cofactor usages, addressing charge and elemental balance, standardizing biomass composition, and incorporating the latest experimental evidence led to a MEMOTE score improvement to 94%. We found agreement of iCTH669 model predictions across all available fermentation and biomass yield datasets. The feasibility of hundreds of PPi synthesis routes, newly identified and previously proposed, were assessed through the lens of the iCTH669 model including biomass synthesis, tRNA synthesis, newly identified sources, and previously proposed PPi-generating cycles. In all cases, the metabolic cost of PPi synthesis is at best equivalent to investment of one ATP suggesting no direct energetic advantage for the cofactor substitution in C. thermocellum. Even though no unique source of PPi could be gleaned by the model, by combining with gene expression data two most likely scenarios emerge. First, previously investigated PPi sources likely account for most PPi production in wild-type strains. Second, alternate metabolic routes as encoded by iCTH669 can collectively maintain PPi levels even when previously investigated synthesis cycles are disrupted. Model iCTH669 is available at github.com/maranasgroup/iCTH669.
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Affiliation(s)
- Wheaton L Schroeder
- Department of Chemical Engineering, The Pennsylvania State University, University Park, PA, USA; Center for Bioenergy Innovation, Oak Ridge, TN, USA
| | - Teun Kuil
- Department of Industrial Biotechnology, School of Engineering Sciences in Chemistry Biotechnology and Health, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Antonius J A van Maris
- Department of Industrial Biotechnology, School of Engineering Sciences in Chemistry Biotechnology and Health, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Daniel G Olson
- Center for Bioenergy Innovation, Oak Ridge, TN, USA; Thayer School of Engineering, Dartmouth College, Hanover, NH, USA
| | - Lee R Lynd
- Center for Bioenergy Innovation, Oak Ridge, TN, USA; Thayer School of Engineering, Dartmouth College, Hanover, NH, USA
| | - Costas D Maranas
- Department of Chemical Engineering, The Pennsylvania State University, University Park, PA, USA; Center for Bioenergy Innovation, Oak Ridge, TN, USA.
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5
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Liu Q, Sun S, Chen S, Su Y, Wang Y, Tang F, Zhao C, Li L. A novel dehydrocoenzyme activator combined with a composite microbial agent TY for enhanced bioremediation of crude oil-contaminated soil. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2023; 331:117246. [PMID: 36642048 DOI: 10.1016/j.jenvman.2023.117246] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 12/30/2022] [Accepted: 01/04/2023] [Indexed: 06/17/2023]
Abstract
Bioaugmentation (BA) and biostimulation (BS) synergistic remediation is an effective remediation strategy for oil-contaminated soil. In this study, the optimal combination system of composite microbial agent TY (Achromobacter: Pseudomona = 2:1) and dehydrocoenzyme activator (NaNO3 (7.0 g/L), (NH4)2HPO4 (1.0 g/L), riboflavin (6.0 mg/L)) was screened. Under the best combination system, the degradation rate of crude oil in oil-contaminated soil reached 79.44% after 60 d, which was 1.74 times and 1.23 times higher than that of compound microbial agent TY treatment and dehydrogenase activator treatment, respectively. In addition, a highly efficient combination system was found to target the degradation of oil C10-C28 fractions by gas chromatography (GC). The increased abundance of dehydrogenase coenzymes such as flavin nucleotides (FAD and FMN), coenzyme I (NAD+, Co I) and coenzyme II (NADP+, Co II) as well as dioxygenases and monooxygenases promote the degradation of crude oil. Furthermore, the dominant genera at the genus level in soil were analyzed by high-throughput sequencing, which were Nocardioides (46.48%-56.07%), Gordonia (11.40%-14.61%), Intrasporangiaceae (5.05%-10.58%), Pseudomonas (1.39%-1.92%) and Dietzia (0.64%-2.77%). Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) analysis showed that the abundance of genes associated with crude oil degradation such as ABC transporters (2.89%), fatty acid (1.04%), carbon metabolism (4.5%) and aromatic compound (0.92%) was assigned enhanced after 60 d of remediation. These results indicated that the combination system of the compound bacterium TY and the dehydrocoenzyme activator is a propective option for the bioremediation of oil-contaminated soil.
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Affiliation(s)
- Qiyou Liu
- College of Chemistry and Chemical Engineering, China University of Petroleum (East China), Qingdao, 266580, PR China; State Key Laboratory of Petroleum Pollution Control, Qingdao, 266580, PR China.
| | - Shuo Sun
- College of Chemistry and Chemical Engineering, China University of Petroleum (East China), Qingdao, 266580, PR China; State Key Laboratory of Petroleum Pollution Control, Qingdao, 266580, PR China
| | - Shuiquan Chen
- College of Energy and Mining Engineering, Shandong University of Science and Technology, Qingdao, 266590, PR China
| | - Yuhua Su
- College of Chemistry and Chemical Engineering, China University of Petroleum (East China), Qingdao, 266580, PR China; State Key Laboratory of Petroleum Pollution Control, Qingdao, 266580, PR China
| | - Yaru Wang
- College of Chemistry and Chemical Engineering, China University of Petroleum (East China), Qingdao, 266580, PR China; State Key Laboratory of Petroleum Pollution Control, Qingdao, 266580, PR China
| | - Fang Tang
- College of Chemistry and Chemical Engineering, China University of Petroleum (East China), Qingdao, 266580, PR China; State Key Laboratory of Petroleum Pollution Control, Qingdao, 266580, PR China
| | - Chaocheng Zhao
- College of Chemistry and Chemical Engineering, China University of Petroleum (East China), Qingdao, 266580, PR China; State Key Laboratory of Petroleum Pollution Control, Qingdao, 266580, PR China
| | - Lin Li
- College of Safety and Environmental Engineering, Shandong University of Science and Technology, Qingdao, 266590, PR China
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The Roles of Nicotinamide Adenine Dinucleotide Phosphate Reoxidation and Ammonium Assimilation in the Secretion of Amino Acids as Byproducts of Clostridium thermocellum. Appl Environ Microbiol 2023; 89:e0175322. [PMID: 36625594 PMCID: PMC9888227 DOI: 10.1128/aem.01753-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Clostridium thermocellum is a cellulolytic thermophile that is considered for the consolidated bioprocessing of lignocellulose to ethanol. Improvements in ethanol yield are required for industrial implementation, but the incompletely understood causes of amino acid secretion impede progress. In this study, amino acid secretion was investigated via gene deletions in ammonium-regulated, nicotinamide adenine dinucleotide phosphate (NADPH)-supplying and NADPH-consuming pathways as well as via physiological characterization in cellobiose-limited or ammonium-limited chemostats. First, the contribution of the NADPH-supplying malate shunt was studied with strains using either the NADPH-yielding malate shunt (Δppdk) or a redox-independent conversion of PEP to pyruvate (Δppdk ΔmalE::Peno-pyk). In the latter, branched-chain amino acids, especially valine, were significantly reduced, whereas the ethanol yield increased from 46 to 60%, suggesting that the secretion of these amino acids balances the NADPH surplus from the malate shunt. The unchanged amino acid secretion in Δppdk falsified a previous hypothesis on an ammonium-regulated PEP-to-pyruvate flux redistribution. The possible involvement of another NADPH-supplier, namely, NADH-dependent reduced ferredoxin:NADP+ oxidoreductase (nfnAB), was also excluded. Finally, the deletion of glutamate synthase (gogat) in ammonium assimilation resulted in the upregulation of NADPH-linked glutamate dehydrogenase activity and decreased amino acid yields. Since gogat in C. thermocellum is putatively annotated as ferredoxin-linked, a claim which is supported by the product redistribution observed in this study, this deletion likely replaced ferredoxin with NADPH in ammonium assimilation. Overall, these findings indicate that a need to reoxidize NADPH is driving the observed amino acid secretion, likely at the expense of the NADH needed for ethanol formation. This suggests that metabolic engineering strategies that simplify the redox metabolism and ammonium assimilation can contribute to increased ethanol yields. IMPORTANCE Improving the ethanol yield of C. thermocellum is important for the industrial implementation of this microorganism in consolidated bioprocessing. A central role of NADPH in driving amino acid byproduct formation was demonstrated by eliminating the NADPH-supplying malate shunt and separately by changing the cofactor specificity in ammonium assimilation. With amino acid secretion diverting carbon and electrons away from ethanol, these insights are important for further metabolic engineering to reach industrial requirements on ethanol yield. This study also provides chemostat data that are relevant for training genome-scale metabolic models and for improving the validity of their predictions, especially considering the reduced degree-of-freedom in the redox metabolism of the strains generated here. In addition, this study advances the fundamental understanding on the mechanisms underlying amino acid secretion in cellulolytic Clostridia as well as on the regulation and cofactor specificity in ammonium assimilation. Together, these efforts aid in the development of C. thermocellum for the sustainable consolidated bioprocessing of lignocellulose to ethanol with minimal pretreatment.
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Increasing the Thermodynamic Driving Force of the Phosphofructokinase Reaction in
Clostridium thermocellum. Appl Environ Microbiol 2022; 88:e0125822. [PMID: 36286488 PMCID: PMC9680637 DOI: 10.1128/aem.01258-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The ability to control the distribution of thermodynamic driving force throughout a metabolic pathway is likely to be an important tool for metabolic engineering. The phosphofructokinase reaction is a key enzyme in Embden-Mayerhof-Parnas glycolysis and therefore improving the thermodynamic driving force of this reaction in
C. thermocellum
is believed to enable higher product titers.
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8
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Functional analysis of H +-pumping membrane-bound pyrophosphatase, ADP-glucose synthase, and pyruvate phosphate dikinase as pyrophosphate sources in Clostridium thermocellum. Appl Environ Microbiol 2021; 88:e0185721. [PMID: 34936842 PMCID: PMC8863071 DOI: 10.1128/aem.01857-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The atypical glycolysis of Clostridium thermocellum is characterized by the use of pyrophosphate (PPi) as phosphoryl donor for phosphofructokinase (Pfk) and pyruvate phosphate dikinase (Ppdk) reactions. Previously, biosynthetic PPi was calculated to be stoichiometrically insufficient to drive glycolysis. This study investigates the role of a H+-pumping membrane-bound pyrophosphatase, glycogen cycling, a predicted Ppdk-malate shunt cycle and acetate cycling in generating PPi. Knockout studies and enzyme assays confirmed that clo1313_0823 encodes a membrane-bound pyrophosphatase. Additionally, clo1313_0717-0718 was confirmed to encode ADP-glucose synthase by knockouts, glycogen measurements in C. thermocellum and heterologous expression in E. coli. Unexpectedly, individually-targeted gene deletions of the four putative PPi sources did not have a significant phenotypic effect. Although combinatorial deletion of all four putative PPi sources reduced the growth rate by 22% (0.30±0.01 h-1) and the biomass yield by 38% (0.18±0.00 gbiomass gsubstrate-1), this change was much smaller than what would be expected for stoichiometrically essential PPi-supplying mechanisms. Growth-arrested cells of the quadruple knockout readily fermented cellobiose indicating that the unknown PPi-supplying mechanisms are independent of biosynthesis. An alternative hypothesis that ATP-dependent Pfk activity circumvents a need for PPi altogether, was falsified by enzyme assays, heterologous expression of candidate genes and whole-genome sequencing. As a secondary outcome, enzymatic assays confirmed functional annotation of clo1313_1832 as ATP- and GTP-dependent fructokinase. These results indicate that the four investigated PPi sources individually and combined play no significant PPi-supplying role and the true source(s) of PPi, or alternative phosphorylating mechanisms, that drive glycolysis in C. thermocellum remain(s) elusive. IMPORTANCE Increased understanding of the central metabolism of C. thermocellum is important from a fundamental as well as from a sustainability and industrial perspective. In addition to showing that H+-pumping membrane-bound PPase, glycogen cycling, a Ppdk-malate shunt cycle, and acetate cycling are not significant sources of PPi supply, this study adds functional annotation of four genes and availability of an updated PPi stoichiometry from biosynthesis to the scientific domain. Together, this aids future metabolic engineering attempts aimed to improve C. thermocellum as a cell factory for sustainable and efficient production of ethanol from lignocellulosic material through consolidated bioprocessing with minimal pretreatment. Getting closer to elucidating the elusive source of PPi, or alternative phosphorylating mechanisms, for the atypical glycolysis is itself of fundamental importance. Additionally, the findings of this study directly contribute to investigations into trade-offs between thermodynamic driving force versus energy yield of PPi- and ATP-dependent glycolysis.
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Hofmann J, Bitew MA, Kuba M, De Souza DP, Newton HJ, Sansom FM. Characterisation of putative lactate synthetic pathways of Coxiella burnetii. PLoS One 2021; 16:e0255925. [PMID: 34388185 PMCID: PMC8362950 DOI: 10.1371/journal.pone.0255925] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2021] [Accepted: 07/26/2021] [Indexed: 11/19/2022] Open
Abstract
The zoonotic pathogen Coxiella burnetii, the causative agent of the human disease Q fever, is an ever-present danger to global public health. Investigating novel metabolic pathways necessary for C. burnetii to replicate within its unusual intracellular niche may identify new therapeutic targets. Recent studies employing stable isotope labelling established the ability of C. burnetii to synthesize lactate, despite the absence of an annotated synthetic pathway on its genome. A noncanonical lactate synthesis pathway could provide a novel anti-Coxiella target if it is essential for C. burnetii pathogenesis. In this study, two C. burnetii proteins, CBU1241 and CBU0823, were chosen for analysis based on their similarities to known lactate synthesizing enzymes. Recombinant GST-CBU1241, a putative malate dehydrogenase (MDH), did not produce measurable lactate in in vitro lactate dehydrogenase (LDH) activity assays and was confirmed to function as an MDH. Recombinant 6xHis-CBU0823, a putative NAD+-dependent malic enzyme, was shown to have both malic enzyme activity and MDH activity, however, did not produce measurable lactate in either LDH or malolactic enzyme activity assays in vitro. To examine potential lactate production by CBU0823 more directly, [13C]glucose labelling experiments compared label enrichment within metabolic pathways of a cbu0823 transposon mutant and the parent strain. No difference in lactate production was observed, but the loss of CBU0823 significantly reduced 13C-incorporation into glycolytic and TCA cycle intermediates. This disruption to central carbon metabolism did not have any apparent impact on intracellular replication within THP-1 cells. This research provides new information about the mechanism of lactate biosynthesis within C. burnetii, demonstrating that CBU1241 is not multifunctional, at least in vitro, and that CBU0823 also does not synthesize lactate. Although critical for normal central carbon metabolism of C. burnetii, loss of CBU0823 did not significantly impair replication of the bacterium inside cells.
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Affiliation(s)
- Janine Hofmann
- Faculty of Veterinary and Agricultural Sciences, Asia-Pacific Centre for Animal Health, Melbourne Veterinary School, University of Melbourne, Parkville, Victoria, Australia
| | - Mebratu A. Bitew
- Department of Pathology, Microbiology and Immunology, University of California, Davis, California, United States of America
| | - Miku Kuba
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - David P. De Souza
- Metabolomics Australia, The Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria, Australia
| | - Hayley J. Newton
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Fiona M. Sansom
- Faculty of Veterinary and Agricultural Sciences, Asia-Pacific Centre for Animal Health, Melbourne Veterinary School, University of Melbourne, Parkville, Victoria, Australia
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10
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Koendjbiharie JG, van Kranenburg R, Kengen SWM. The PEP-pyruvate-oxaloacetate node: variation at the heart of metabolism. FEMS Microbiol Rev 2021; 45:fuaa061. [PMID: 33289792 PMCID: PMC8100219 DOI: 10.1093/femsre/fuaa061] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Accepted: 11/18/2020] [Indexed: 12/15/2022] Open
Abstract
At the junction between the glycolysis and the tricarboxylic acid cycle-as well as various other metabolic pathways-lies the phosphoenolpyruvate (PEP)-pyruvate-oxaloacetate node (PPO-node). These three metabolites form the core of a network involving at least eleven different types of enzymes, each with numerous subtypes. Obviously, no single organism maintains each of these eleven enzymes; instead, different organisms possess different subsets in their PPO-node, which results in a remarkable degree of variation, despite connecting such deeply conserved metabolic pathways as the glycolysis and the tricarboxylic acid cycle. The PPO-node enzymes play a crucial role in cellular energetics, with most of them involved in (de)phosphorylation of nucleotide phosphates, while those responsible for malate conversion are important redox enzymes. Variations in PPO-node therefore reflect the different energetic niches that organisms can occupy. In this review, we give an overview of the biochemistry of these eleven PPO-node enzymes. We attempt to highlight the variation that exists, both in PPO-node compositions, as well as in the roles that the enzymes can have within those different settings, through various recent discoveries in both bacteria and archaea that reveal deviations from canonical functions.
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Affiliation(s)
- Jeroen G Koendjbiharie
- Laboratory of Microbiology, Wageningen University, Stippeneng4, 6708 WE Wageningen, The Netherlands
| | - Richard van Kranenburg
- Laboratory of Microbiology, Wageningen University, Stippeneng4, 6708 WE Wageningen, The Netherlands
- Corbion, Arkelsedijk 46, 4206 AC Gorinchem, The Netherlands
| | - Servé W M Kengen
- Laboratory of Microbiology, Wageningen University, Stippeneng4, 6708 WE Wageningen, The Netherlands
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Metabolic Fluxes of Nitrogen and Pyrophosphate in Chemostat Cultures of Clostridium thermocellum and Thermoanaerobacterium saccharolyticum. Appl Environ Microbiol 2020; 86:AEM.01795-20. [PMID: 32978139 PMCID: PMC7657619 DOI: 10.1128/aem.01795-20] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Accepted: 09/17/2020] [Indexed: 01/29/2023] Open
Abstract
Clostridium thermocellum and Thermoanaerobacterium saccharolyticum were grown in cellobiose-limited chemostat cultures at a fixed dilution rate. C. thermocellum produced acetate, ethanol, formate, and lactate. Surprisingly, and in contrast to batch cultures, in cellobiose-limited chemostat cultures of T. saccharolyticum, ethanol was the main fermentation product. Enzyme assays confirmed that in C. thermocellum, glycolysis proceeds via pyrophosphate (PPi)-dependent phosphofructokinase (PFK), pyruvate-phosphate dikinase (PPDK), as well as a malate shunt for the conversion of phosphoenolpyruvate (PEP) to pyruvate. Pyruvate kinase activity was not detectable. In T. saccharolyticum, ATP but not PPi served as cofactor for the PFK reaction. High activities of both pyruvate kinase and PPDK were present, whereas the activities of a malate shunt enzymes were low in T. saccharolyticum In C. thermocellum, glycolysis via PPi-PFK and PPDK obeys the equation glucose + 5 NDP + 3 PPi → 2 pyruvate + 5 NTP + Pi (where NDP is nucleoside diphosphate and NTP is nucleoside triphosphate). Metabolic flux analysis of chemostat data with the wild type and a deletion mutant of the proton-pumping pyrophosphatase showed that a PPi-generating mechanism must be present that operates according to ATP + Pi → ADP + PPi Both organisms also produced significant amounts of amino acids in cellobiose-limited cultures. It was anticipated that this phenomenon would be suppressed by growth under nitrogen limitation. Surprisingly, nitrogen-limited chemostat cultivation of wild-type C. thermocellum revealed a bottleneck in pyruvate oxidation, as large amounts of pyruvate and amino acids, mainly valine, were excreted; up to 50% of the nitrogen consumed was excreted again as amino acids.IMPORTANCE This study discusses the fate of pyrophosphate in the metabolism of two thermophilic anaerobes that lack a soluble irreversible pyrophosphatase as present in Escherichia coli but instead use a reversible membrane-bound proton-pumping enzyme. In such organisms, the charging of tRNA with amino acids may become more reversible. This may contribute to the observed excretion of amino acids during sugar fermentation by Clostridium thermocellum and Thermoanaerobacterium saccharolyticum Calculation of the energetic advantage of reversible pyrophosphate-dependent glycolysis, as occurs in Clostridium thermocellum, could not be properly evaluated, as currently available genome-scale models neglect the anabolic generation of pyrophosphate in, for example, polymerization of amino acids to protein. This anabolic pyrophosphate replaces ATP and thus saves energy. Its amount is, however, too small to cover the pyrophosphate requirement of sugar catabolism in glycolysis. Consequently, pyrophosphate for catabolism is generated according to ATP + Pi → ADP + PPi.
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Wu C, Cano M, Gao X, Lo J, Maness P, Xiong W. A quantitative lens on anaerobic life: leveraging the state-of-the-art fluxomics approach to explore clostridial metabolism. Curr Opin Biotechnol 2020; 64:47-54. [DOI: 10.1016/j.copbio.2019.09.012] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Revised: 09/02/2019] [Accepted: 09/12/2019] [Indexed: 10/25/2022]
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Koendjbiharie JG, Post WB, Palmer MM, van Kranenburg R. Effects of CO 2 limitation on the metabolism of Pseudoclostridium thermosuccinogenes. BMC Microbiol 2020; 20:149. [PMID: 32513108 PMCID: PMC7282089 DOI: 10.1186/s12866-020-01835-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Accepted: 05/28/2020] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND Bio-based succinic acid holds promise as a sustainable platform chemical. Its production through microbial fermentation concurs with the fixation of CO2, through the carboxylation of phosphoenolpyruvate. Here, we studied the effect of the available CO2 on the metabolism of Pseudoclostridium thermosuccinogenes, the only known succinate producing thermophile. Batch cultivations in bioreactors sparged with 1 and 20% CO2 were conducted that allowed us to carefully study the effect of CO2 limitation. RESULTS Formate yield was greatly reduced at low CO2 concentrations, signifying a switch from pyruvate formate lyase (PFL) to pyruvate:ferredoxin oxidoreductase (PFOR) for acetyl-CoA formation. The corresponding increase in endogenous CO2 production (by PFOR) enabled succinic acid production to be largely maintained as its yield was reduced by only 26%, thus also maintaining the concomitant NADH re-oxidation, essential for regenerating NAD+ for glycolysis. Acetate yield was slightly reduced as well, while that of lactate was slightly increased. CO2 limitation also prompted the formation of significant amounts of ethanol, which is only marginally produced during CO2 excess. Altogether, the changes in fermentation product yields result in increased ferredoxin and NAD+ reduction, and increased NADPH oxidation during CO2 limitation, which must be linked to reshuffled (trans) hydrogenation mechanisms of those cofactors, in order to keep them balanced. RNA sequencing, to investigate transcriptional effects of CO2 limitation, yielded only ambiguous results regarding the known (trans) hydrogenation mechanisms. CONCLUSIONS The results hinted at a decreased NAD+/NADH ratio, which could ultimately be responsible for the stress observed during CO2 limitation. Clear overexpression of an alcohol dehydrogenase (adhE) was observed, which may explain the increased ethanol production, while no changes were seen for PFL and PFOR expression that could explain the anticipated switch based on the fermentation results.
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Affiliation(s)
| | | | - Martí Munar Palmer
- Laboratory of Microbiology, Wageningen University, Wageningen, Netherlands
| | - Richard van Kranenburg
- Corbion, Gorinchem, Netherlands. .,Laboratory of Microbiology, Wageningen University, Wageningen, Netherlands.
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In Vivo Thermodynamic Analysis of Glycolysis in Clostridium thermocellum and Thermoanaerobacterium saccharolyticum Using 13C and 2H Tracers. mSystems 2020; 5:5/2/e00736-19. [PMID: 32184362 PMCID: PMC7380578 DOI: 10.1128/msystems.00736-19] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
Thermodynamics constitutes a key determinant of flux and enzyme efficiency in metabolic networks. Here, we provide new insights into the divergent thermodynamics of the glycolytic pathways of C. thermocellum and T. saccharolyticum, two industrially relevant thermophilic bacteria whose metabolism still is not well understood. We report that while the glycolytic pathway in T. saccharolyticum is as thermodynamically favorable as that found in model organisms, such as E. coli or Saccharomyces cerevisiae, the glycolytic pathway of C. thermocellum operates near equilibrium. The use of a near-equilibrium glycolytic pathway, with potentially increased ATP yield, by this cellulolytic microbe may represent an evolutionary adaptation to growth on cellulose, but it has the drawback of being highly susceptible to product feedback inhibition. The results of this study will facilitate future engineering of high-performance strains capable of transforming cellulosic biomass to biofuels at high yields and titers. Clostridium thermocellum and Thermoanaerobacterium saccharolyticum are thermophilic anaerobic bacteria with complementary metabolic capabilities that utilize distinct glycolytic pathways for the conversion of cellulosic sugars to biofuels. We integrated quantitative metabolomics with 2H and 13C metabolic flux analysis to investigate the in vivo reversibility and thermodynamics of the central metabolic networks of these two microbes. We found that the glycolytic pathway in C. thermocellum operates remarkably close to thermodynamic equilibrium, with an overall drop in Gibbs free energy 5-fold lower than that of T. saccharolyticum or anaerobically grown Escherichia coli. The limited thermodynamic driving force of glycolysis in C. thermocellum could be attributed in large part to the small free energy of the phosphofructokinase reaction producing fructose bisphosphate. The ethanol fermentation pathway was also substantially more reversible in C. thermocellum than in T. saccharolyticum. These observations help explain the comparatively low ethanol titers of C. thermocellum and suggest engineering interventions that can be used to increase its ethanol productivity and glycolytic rate. In addition to thermodynamic analysis, we used our isotope tracer data to reconstruct the T. saccharolyticum central metabolic network, revealing exclusive use of the Embden-Meyerhof-Parnas (EMP) pathway for glycolysis, a bifurcated tricarboxylic acid (TCA) cycle, and a sedoheptulose bisphosphate bypass active within the pentose phosphate pathway. IMPORTANCE Thermodynamics constitutes a key determinant of flux and enzyme efficiency in metabolic networks. Here, we provide new insights into the divergent thermodynamics of the glycolytic pathways of C. thermocellum and T. saccharolyticum, two industrially relevant thermophilic bacteria whose metabolism still is not well understood. We report that while the glycolytic pathway in T. saccharolyticum is as thermodynamically favorable as that found in model organisms, such as E. coli or Saccharomyces cerevisiae, the glycolytic pathway of C. thermocellum operates near equilibrium. The use of a near-equilibrium glycolytic pathway, with potentially increased ATP yield, by this cellulolytic microbe may represent an evolutionary adaptation to growth on cellulose, but it has the drawback of being highly susceptible to product feedback inhibition. The results of this study will facilitate future engineering of high-performance strains capable of transforming cellulosic biomass to biofuels at high yields and titers.
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Usai G, Cirrincione S, Re A, Manfredi M, Pagnani A, Pessione E, Mazzoli R. Clostridium cellulovorans metabolism of cellulose as studied by comparative proteomic approach. J Proteomics 2020; 216:103667. [DOI: 10.1016/j.jprot.2020.103667] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Revised: 12/31/2019] [Accepted: 01/22/2020] [Indexed: 12/15/2022]
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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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Rozova ON, Mustakhimov II, But SY, Reshetnikov AS, Khmelenina VN. Role of the malic enzyme in metabolism of the halotolerant methanotroph Methylotuvimicrobium alcaliphilum 20Z. PLoS One 2019; 14:e0225054. [PMID: 31738793 PMCID: PMC6860931 DOI: 10.1371/journal.pone.0225054] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Accepted: 10/28/2019] [Indexed: 01/10/2023] Open
Abstract
The bacteria utilizing methane as a growth substrate (methanotrophs) are important constituents of the biosphere. Methanotrophs mitigate the emission of anthropogenic and natural greenhouse gas methane to the environment and are the promising agents for future biotechnologies. Many aspects of CH4 bioconversion by methanotrophs require further clarification. This study was aimed at characterizing the biochemical properties of the malic enzyme (Mae) from the halotolerant obligate methanotroph Methylotuvimicrobium alcaliphilum 20Z. The His6-tagged Mae was obtained by heterologous expression in Escherichia coli BL21 (DE3) and purified by affinity metal chelating chromatography. As determined by gel filtration and non-denaturating gradient gel electrophoresis, the molecular mass of the native enzyme is 260 kDa. The homotetrameric Mae (65x4 kDa) catalyzed an irreversible NAD+-dependent reaction of L-malate decarboxylation into pyruvate with a specific activity of 32 ± 2 units mg-1 and Km value of 5.5 ± 0.8 mM for malate and 57 ± 5 μM for NAD+. The disruption of the mae gene by insertion mutagenesis resulted in a 20-fold increase in intracellular malate level in the mutant compared to the wild type strain. Based on both enzyme and mutant properties, we conclude that the malic enzyme is involved in the control of intracellular L-malate level in Mtm. alcaliphilum 20Z. Genomic analysis has revealed that Maes present in methanotrophs fall into two different clades in the amino acid-based phylogenetic tree, but no correlation of the division with taxonomic affiliations of the host bacteria was observed.
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Affiliation(s)
- Olga N. Rozova
- Federal Research Center “Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences”, G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Pushchino, Moscow Region, Russia
| | - Ildar I. Mustakhimov
- Federal Research Center “Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences”, G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Pushchino, Moscow Region, Russia
| | - Sergei Y. But
- Federal Research Center “Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences”, G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Pushchino, Moscow Region, Russia
| | - Aleksandr S. Reshetnikov
- Federal Research Center “Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences”, G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Pushchino, Moscow Region, Russia
| | - Valentina N. Khmelenina
- Federal Research Center “Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences”, G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Pushchino, Moscow Region, Russia
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Rozova ON, Khmelenina VN, Mustakhimov II, But SY, Trotsenko YA. Properties of Malic Enzyme from the Aerobic Methanotroph Methylosinus trichosporium. BIOCHEMISTRY (MOSCOW) 2019; 84:390-397. [PMID: 31228930 DOI: 10.1134/s0006297919040060] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Recombinant malic enzyme from the aerobic methanotroph Methylosinus trichosporium was obtained by heterologous expression in Escherichia coli and purified by affinity metal-chelating chromatography. The homohexameric enzyme of 6×80 kDa catalyzed the reversible reaction of oxidative decarboxylation of malate to pyruvate in the presence of mono- and divalent cations and NADP+ as a cofactor. The kcat/Km ratio indicated much higher catalytic efficiency of the malate decarboxylation reaction as compared with the pyruvate carboxylation reaction. Analysis of the protein sequence revealed that the C-region of the enzyme contains a large domain homologous to phosphoacetyltransferase, but no phosphoacetyltransferase activity was detected either for a full chimeric malic enzyme or for the C-end fragment obtained as a separate protein. This C-end domain promoted activity of the malic enzyme.
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Affiliation(s)
- O N Rozova
- G. K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Federal Research Center "Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences", Pushchino, Moscow Region, 142290, Russia
| | - V N Khmelenina
- G. K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Federal Research Center "Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences", Pushchino, Moscow Region, 142290, Russia.
| | - I I Mustakhimov
- G. K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Federal Research Center "Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences", Pushchino, Moscow Region, 142290, Russia
| | - S Y But
- G. K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Federal Research Center "Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences", Pushchino, Moscow Region, 142290, Russia
| | - Yu A Trotsenko
- G. K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Federal Research Center "Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences", Pushchino, Moscow Region, 142290, Russia
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Masukagami Y, Tivendale KA, Browning GF, Sansom FM. Analysis of the Mycoplasma bovis lactate dehydrogenase reveals typical enzymatic activity despite the presence of an atypical catalytic site motif. MICROBIOLOGY-SGM 2019; 164:186-193. [PMID: 29393016 DOI: 10.1099/mic.0.000600] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
The lactate dehydrogenase (LDH) of Mycoplasma genitalium has been predicted to also act as a malate dehydrogenase (MDH), but there has been no experimental validation of this hypothesized dual function for any mollicute. Our analysis of the metabolite profile of Mycoplasma bovis using gas chromatography/mass spectrometry (GC/MS) and liquid chromatography/mass spectrometry (LC/MS) detected malate, suggesting that there may be MDH activity in M. bovis. To investigate whether the putative l-LDH enzyme of M. bovis has a dual function (MDH and LDH), we performed bioinformatic and functional biochemical analyses. Although the amino acid sequence and predicted structural analysis of M. bovisl-LDH revealed unusual residues within the catalytic site, suggesting that it may have the flexibility to possess a dual function, our biochemical studies using recombinant M. bovis -LDH did not detect any MDH activity. However, we did show that the enzyme has typical LDH activity that could be inhibited by both MDH substrates oxaloacetate (OAA) and malate, suggesting that these substrates may be able to bind to M. bovis LDH. Inhibition of the conversion of pyruvate to lactate by OAA may be one method the mycoplasma cell uses to reduce the potential for accumulation of intracellular lactate.
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Affiliation(s)
- Yumiko Masukagami
- Asia-Pacific Centre for Animal Health, Melbourne Veterinary School, Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Parkville, VIC, Australia
| | - Kelly Anne Tivendale
- Asia-Pacific Centre for Animal Health, Melbourne Veterinary School, Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Parkville, VIC, Australia
| | - Glenn Francis Browning
- Asia-Pacific Centre for Animal Health, Melbourne Veterinary School, Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Parkville, VIC, Australia
| | - Fiona Margaret Sansom
- Asia-Pacific Centre for Animal Health, Melbourne Veterinary School, Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Parkville, VIC, Australia
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Koendjbiharie JG, Wevers K, van Kranenburg R. Assessing Cofactor Usage in Pseudoclostridium thermosuccinogenes via Heterologous Expression of Central Metabolic Enzymes. Front Microbiol 2019; 10:1162. [PMID: 31178853 PMCID: PMC6543838 DOI: 10.3389/fmicb.2019.01162] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Accepted: 05/07/2019] [Indexed: 11/13/2022] Open
Abstract
Pseudoclostridium thermosuccinogenes and Hungateiclostridium thermocellum are being studied for their potential to contribute to a more sustainable bio-based economy. Both species were shown previously to rely on GTP or pyrophosphate instead of ATP as cofactors in specific reactions of central energy metabolism for reasons that are not well understood yet. Since it is often impossible to predict cofactor specificity from the primary protein structure, thirteen enzymes from P. thermosuccinogenes were cloned and heterologous expressed in Escherichia coli to assess the cofactor usage in vitro and paint a more complete picture of the cofactor usage in the central metabolism of P. thermosuccinogenes. The assays were conducted with heat-treated E. coli cell-free extract devoid of background activity to allow the quick assessment of a relatively large number of (thermophilic) enzymes. Selected enzymes were also purified to allow the determination of the enzyme kinetics for competing cofactors. Following the results of the glucokinase (GK), galactokinase, xylulokinase (XK), and ribokinase assays, it seems that phosphorylation of monosaccharides by and large is mainly GTP-dependent. Some possible implications of this relating to the adenylate/guanylate energy charge are discussed here. Besides the highly expressed pyrophosphate-dependent 6-phosphofructokinase, another 6-phosphofructokinase was found to be equally dependent on ATP and GTP, while no 6-phosphofructokinase activity could be demonstrated for a third. Both type I glyceraldehyde 3-phosphate dehydrogenases were found to be NAD+-dependent, and further, acetate kinase, isocitrate dehydrogenase, and three enzymes predicted to be responsible for the interconversion of phosphoenolpyruvate and pyruvate (i.e., pyruvate kinase; pyruvate, phosphate dikinase; phosphoenolpyruvate synthase), were also assessed.
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Affiliation(s)
| | - Kimberly Wevers
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, Netherlands
| | - Richard van Kranenburg
- Corbion, Gorinchem, Netherlands
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, Netherlands
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Xiong W, Lo J, Chou KJ, Wu C, Magnusson L, Dong T, Maness P. Isotope-Assisted Metabolite Analysis Sheds Light on Central Carbon Metabolism of a Model Cellulolytic Bacterium Clostridium thermocellum. Front Microbiol 2018; 9:1947. [PMID: 30190711 PMCID: PMC6115520 DOI: 10.3389/fmicb.2018.01947] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Accepted: 07/31/2018] [Indexed: 01/01/2023] Open
Abstract
Cellulolytic bacteria have the potential to perform lignocellulose hydrolysis and fermentation simultaneously. The metabolic pathways of these bacteria, therefore, require more comprehensive and quantitative understanding. Using isotope tracer, gas chromatography-mass spectrometry, and metabolic flux modeling, we decipher the metabolic network of Clostridium thermocellum, a model cellulolytic bacterium which represents as an attractive platform for conversion of lignocellulose to dedicated products. We uncover that the Embden-Meyerhof-Parnas (EMP) pathway is the predominant glycolytic route whereas the Entner-Doudoroff (ED) pathway and oxidative pentose phosphate pathway are inactive. We also observe that C. thermocellum's TCA cycle is initiated by both Si- and Re-citrate synthase, and it is disconnected between 2-oxoglutarate and oxaloacetate in the oxidative direction; C. thermocellum uses a citramalate shunt to synthesize isoleucine; and both the one-carbon pathway and the malate shunt are highly active in this bacterium. To gain a quantitative understanding, we further formulate a fluxome map to quantify the metabolic fluxes through central metabolic pathways. This work represents the first global in vivo investigation of the principal carbon metabolism of C. thermocellum. Our results elucidate the unique structure of metabolic network in this cellulolytic bacterium and demonstrate the capability of isotope-assisted metabolite studies in understanding microbial metabolism of industrial interests.
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Affiliation(s)
- Wei Xiong
- National Renewable Energy Laboratory, Golden, CO, United States
| | - Jonathan Lo
- National Renewable Energy Laboratory, Golden, CO, United States
| | | | - Chao Wu
- National Renewable Energy Laboratory, Golden, CO, United States
| | | | - Tao Dong
- National Renewable Energy Laboratory, Golden, CO, United States
| | - PinChing Maness
- National Renewable Energy Laboratory, Golden, CO, United States
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Investigating the Central Metabolism of Clostridium thermosuccinogenes. Appl Environ Microbiol 2018; 84:AEM.00363-18. [PMID: 29678919 DOI: 10.1128/aem.00363-18] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2018] [Accepted: 04/15/2018] [Indexed: 01/28/2023] Open
Abstract
Clostridium thermosuccinogenes is a thermophilic anaerobic bacterium able to convert various carbohydrates to succinate and acetate as main fermentation products. Genomes of the four publicly available strains have been sequenced, and the genome of the type strain has been closed. The annotated genomes were used to reconstruct the central metabolism, and enzyme assays were used to validate annotations and to determine cofactor specificity. The genes were identified for the pathways to all fermentation products, as well as for the Embden-Meyerhof-Parnas pathway and the pentose phosphate pathway. Notably, a candidate transaldolase was lacking, and transcriptomics during growth on glucose versus that on xylose did not provide any leads to potential transaldolase genes or alternative pathways connecting the C5 with the C3/C6 metabolism. Enzyme assays showed xylulokinase to prefer GTP over ATP, which could be of importance for engineering xylose utilization in related thermophilic species of industrial relevance. Furthermore, the gene responsible for malate dehydrogenase was identified via heterologous expression in Escherichia coli and subsequent assays with the cell extract, which has proven to be a simple and powerful method for the basal characterization of thermophilic enzymes.IMPORTANCE Running industrial fermentation processes at elevated temperatures has several advantages, including reduced cooling requirements, increased reaction rates and solubilities, and a possibility to perform simultaneous saccharification and fermentation of a pretreated biomass. Most studies with thermophiles so far have focused on bioethanol production. Clostridium thermosuccinogenes seems an attractive production organism for organic acids, succinic acid in particular, from lignocellulosic biomass-derived sugars. This study provides valuable insights into its central metabolism and GTP and PPi cofactor utilization.
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Dash S, Khodayari A, Zhou J, Holwerda EK, Olson DG, Lynd LR, Maranas CD. Development of a core Clostridium thermocellum kinetic metabolic model consistent with multiple genetic perturbations. BIOTECHNOLOGY FOR BIOFUELS 2017; 10:108. [PMID: 28469704 PMCID: PMC5414155 DOI: 10.1186/s13068-017-0792-2] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/29/2016] [Accepted: 04/18/2017] [Indexed: 06/07/2023]
Abstract
BACKGROUND Clostridium thermocellum is a Gram-positive anaerobe with the ability to hydrolyze and metabolize cellulose into biofuels such as ethanol, making it an attractive candidate for consolidated bioprocessing (CBP). At present, metabolic engineering in C. thermocellum is hindered due to the incomplete description of its metabolic repertoire and regulation within a predictive metabolic model. Genome-scale metabolic (GSM) models augmented with kinetic models of metabolism have been shown to be effective at recapitulating perturbed metabolic phenotypes. RESULTS In this effort, we first update a second-generation genome-scale metabolic model (iCth446) for C. thermocellum by correcting cofactor dependencies, restoring elemental and charge balances, and updating GAM and NGAM values to improve phenotype predictions. The iCth446 model is next used as a scaffold to develop a core kinetic model (k-ctherm118) of the C. thermocellum central metabolism using the Ensemble Modeling (EM) paradigm. Model parameterization is carried out by simultaneously imposing fermentation yield data in lactate, malate, acetate, and hydrogen production pathways for 19 measured metabolites spanning a library of 19 distinct single and multiple gene knockout mutants along with 18 intracellular metabolite concentration data for a Δgldh mutant and ten experimentally measured Michaelis-Menten kinetic parameters. CONCLUSIONS The k-ctherm118 model captures significant metabolic changes caused by (1) nitrogen limitation leading to increased yields for lactate, pyruvate, and amino acids, and (2) ethanol stress causing an increase in intracellular sugar phosphate concentrations (~1.5-fold) due to upregulation of cofactor pools. Robustness analysis of k-ctherm118 alludes to the presence of a secondary activity of ketol-acid reductoisomerase and possible regulation by valine and/or leucine pool levels. In addition, cross-validation and robustness analysis allude to missing elements in k-ctherm118 and suggest additional experiments to improve kinetic model prediction fidelity. Overall, the study quantitatively assesses the advantages of EM-based kinetic modeling towards improved prediction of C. thermocellum metabolism and develops a predictive kinetic model which can be used to design biofuel-overproducing strains.
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Affiliation(s)
- Satyakam Dash
- Department of Chemical Engineering, The Pennsylvania State University, 126 Land and Water Research Building, University Park, PA 16802 USA
| | - Ali Khodayari
- Department of Chemical Engineering, The Pennsylvania State University, 126 Land and Water Research Building, University Park, PA 16802 USA
| | - Jilai Zhou
- Thayer School of Engineering at Dartmouth College, Hanover, NH USA
| | | | - Daniel G. Olson
- Thayer School of Engineering at Dartmouth College, Hanover, NH USA
| | - Lee R. Lynd
- Thayer School of Engineering at Dartmouth College, Hanover, NH USA
| | - Costas D. Maranas
- Department of Chemical Engineering, The Pennsylvania State University, 126 Land and Water Research Building, University Park, PA 16802 USA
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Rydzak T, Garcia D, Stevenson DM, Sladek M, Klingeman DM, Holwerda EK, Amador-Noguez D, Brown SD, Guss AM. Deletion of Type I glutamine synthetase deregulates nitrogen metabolism and increases ethanol production in Clostridium thermocellum. Metab Eng 2017; 41:182-191. [PMID: 28400329 DOI: 10.1016/j.ymben.2017.04.002] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2016] [Revised: 03/27/2017] [Accepted: 04/07/2017] [Indexed: 12/25/2022]
Abstract
Clostridium thermocellum rapidly deconstructs cellulose and ferments resulting hydrolysis products into ethanol and other products, and is thus a promising platform organism for the development of cellulosic biofuel production via consolidated bioprocessing. While recent metabolic engineering strategies have targeted eliminating canonical fermentation products (acetate, lactate, formate, and H2), C. thermocellum also secretes amino acids, which has limited ethanol yields in engineered strains to approximately 70% of the theoretical maximum. To investigate approaches to decrease amino acid secretion, we attempted to reduce ammonium assimilation by deleting the Type I glutamine synthetase (glnA) in an essentially wild type strain of C. thermocellum. Deletion of glnA reduced levels of secreted valine and total amino acids by 53% and 44% respectively, and increased ethanol yields by 53%. RNA-seq analysis revealed that genes encoding the RNF-complex were more highly expressed in ΔglnA and may have a role in improving NADH-availability for ethanol production. While a significant up-regulation of genes involved in nitrogen assimilation and urea uptake suggested that deletion of glnA induces a nitrogen starvation response, metabolomic analysis showed an increase in intracellular glutamine levels indicative of nitrogen-rich conditions. We propose that deletion of glnA causes deregulation of nitrogen metabolism, leading to overexpression of nitrogen metabolism genes and, in turn, elevated glutamine levels. Here we demonstrate that perturbation of nitrogen assimilation is a promising strategy to redirect flux from the production of nitrogenous compounds toward biofuels in C. thermocellum.
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Affiliation(s)
- Thomas Rydzak
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States; BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - David Garcia
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States; BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - David M Stevenson
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, United States
| | - Margaret Sladek
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States; BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Dawn M Klingeman
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States; BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Evert K Holwerda
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States; Thayer School of Engineering at Dartmouth College, Hanover, NH, United States
| | - Daniel Amador-Noguez
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, United States
| | - Steven D Brown
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States; BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Adam M Guss
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States; BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN, United States.
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Taillefer M, Sparling R. Glycolysis as the Central Core of Fermentation. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2017; 156:55-77. [PMID: 26907549 DOI: 10.1007/10_2015_5003] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The increasing concerns of greenhouse gas emissions have increased the interest in dark fermentation as a means of productions for industrial chemicals, especially from renewable cellulosic biomass. However, the metabolism, including glycolysis, of many candidate organisms for cellulosic biomass conversion through consolidated bioprocessing is still poorly understood and the genomes have only recently been sequenced. Because a variety of industrial chemicals are produced directly from sugar metabolism, the careful understanding of glycolysis from a genomic and biochemical point of view is essential in the development of strategies for increasing product yields and therefore increasing industrial potential. The current review discusses the different pathways available for glycolysis along with unexpected variations from traditional models, especially in the utilization of alternate energy intermediates (GTP, pyrophosphate). This reinforces the need for a careful description of interactions between energy metabolites and glycolysis enzymes for understanding carbon and electron flux regulation.
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Affiliation(s)
- M Taillefer
- Department of Microbiology, University of Manitoba, Winnipeg, MB, Canada, R3T 2N2
| | - R Sparling
- Department of Microbiology, University of Manitoba, Winnipeg, MB, Canada, R3T 2N2.
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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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CO2-fixing one-carbon metabolism in a cellulose-degrading bacterium Clostridium thermocellum. Proc Natl Acad Sci U S A 2016; 113:13180-13185. [PMID: 27794122 DOI: 10.1073/pnas.1605482113] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Clostridium thermocellum can ferment cellulosic biomass to formate and other end products, including CO2 This organism lacks formate dehydrogenase (Fdh), which catalyzes the reduction of CO2 to formate. However, feeding the bacterium 13C-bicarbonate and cellobiose followed by NMR analysis showed the production of 13C-formate in C. thermocellum culture, indicating the presence of an uncharacterized pathway capable of converting CO2 to formate. Combining genomic and experimental data, we demonstrated that the conversion of CO2 to formate serves as a CO2 entry point into the reductive one-carbon (C1) metabolism, and internalizes CO2 via two biochemical reactions: the reversed pyruvate:ferredoxin oxidoreductase (rPFOR), which incorporates CO2 using acetyl-CoA as a substrate and generates pyruvate, and pyruvate-formate lyase (PFL) converting pyruvate to formate and acetyl-CoA. We analyzed the labeling patterns of proteinogenic amino acids in individual deletions of all five putative PFOR mutants and in a PFL deletion mutant. We identified two enzymes acting as rPFOR, confirmed the dual activities of rPFOR and PFL crucial for CO2 uptake, and provided physical evidence of a distinct in vivo "rPFOR-PFL shunt" to reduce CO2 to formate while circumventing the lack of Fdh. Such a pathway precedes CO2 fixation via the reductive C1 metabolic pathway in C. thermocellum These findings demonstrated the metabolic versatility of C. thermocellum, which is thought of as primarily a cellulosic heterotroph but is shown here to be endowed with the ability to fix CO2 as well.
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Thompson RA, Dahal S, Garcia S, Nookaew I, Trinh CT. Exploring complex cellular phenotypes and model-guided strain design with a novel genome-scale metabolic model of Clostridium thermocellum DSM 1313 implementing an adjustable cellulosome. BIOTECHNOLOGY FOR BIOFUELS 2016; 9:194. [PMID: 27602057 PMCID: PMC5012057 DOI: 10.1186/s13068-016-0607-x] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2016] [Accepted: 08/26/2016] [Indexed: 05/06/2023]
Abstract
BACKGROUND Clostridium thermocellum is a gram-positive thermophile that can directly convert lignocellulosic material into biofuels. The metabolism of C. thermocellum contains many branches and redundancies which limit biofuel production, and typical genetic techniques are time-consuming. Further, the genome sequence of a genetically tractable strain C. thermocellum DSM 1313 has been recently sequenced and annotated. Therefore, developing a comprehensive, predictive, genome-scale metabolic model of DSM 1313 is desired for elucidating its complex phenotypes and facilitating model-guided metabolic engineering. RESULTS We constructed a genome-scale metabolic model iAT601 for DSM 1313 using the KEGG database as a scaffold and an extensive literature review and bioinformatic analysis for model refinement. Next, we used several sets of experimental data to train the model, e.g., estimation of the ATP requirement for growth-associated maintenance (13.5 mmol ATP/g DCW/h) and cellulosome synthesis (57 mmol ATP/g cellulosome/h). Using our tuned model, we investigated the effect of cellodextrin lengths on cell yields, and could predict in silico experimentally observed differences in cell yield based on which cellodextrin species is assimilated. We further employed our tuned model to analyze the experimentally observed differences in fermentation profiles (i.e., the ethanol to acetate ratio) between cellobiose- and cellulose-grown cultures and infer regulatory mechanisms to explain the phenotypic differences. Finally, we used the model to design over 250 genetic modification strategies with the potential to optimize ethanol production, 6155 for hydrogen production, and 28 for isobutanol production. CONCLUSIONS Our developed genome-scale model iAT601 is capable of accurately predicting complex cellular phenotypes under a variety of conditions and serves as a high-quality platform for model-guided strain design and metabolic engineering to produce industrial biofuels and chemicals of interest.
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Affiliation(s)
- R. Adam Thompson
- Bredesen Center for Interdisciplinary Research and Graduate Education, University of Tennessee, Knoxville, TN 37996 USA
- Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
| | - Sanjeev Dahal
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
- Comparative Genomics Group, Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
| | - Sergio Garcia
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
- Department of Chemical and Biomolecular Engineering, University of Tennessee, 1512 Middle Dr., DO#432, Knoxville, TN 37996 USA
| | - Intawat Nookaew
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
- Comparative Genomics Group, Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
- Department of Biomedical Informatics, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, AR 72205 USA
| | - Cong T. Trinh
- Bredesen Center for Interdisciplinary Research and Graduate Education, University of Tennessee, Knoxville, TN 37996 USA
- Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
- Department of Chemical and Biomolecular Engineering, University of Tennessee, 1512 Middle Dr., DO#432, Knoxville, TN 37996 USA
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Sander K, Wilson CM, Rodriguez M, Klingeman DM, Rydzak T, Davison BH, Brown SD. Clostridium thermocellum DSM 1313 transcriptional responses to redox perturbation. BIOTECHNOLOGY FOR BIOFUELS 2015; 8:211. [PMID: 26692898 PMCID: PMC4676874 DOI: 10.1186/s13068-015-0394-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2015] [Accepted: 11/24/2015] [Indexed: 05/21/2023]
Abstract
BACKGROUND Clostridium thermocellum is a promising consolidated bioprocessing candidate organism capable of directly converting lignocellulosic biomass to ethanol. Current ethanol yields, productivities, and growth inhibitions are industrial deployment impediments for commodity fuel production by this bacterium. Redox imbalance under certain conditions and in engineered strains may contribute to incomplete substrate utilization and may direct fermentation products to undesirable overflow metabolites. Towards a better understanding of redox metabolism in C. thermocellum, we established continuous growth conditions and analyzed global gene expression during addition of two stress chemicals (methyl viologen and hydrogen peroxide) which changed the fermentation redox potential. RESULTS The addition of methyl viologen to C. thermocellum DSM 1313 chemostat cultures caused an increase in ethanol and lactate yields. A lower fermenter redox potential was observed in response to methyl viologen exposure, which correlated with a decrease in cell yield and significant differential expression of 123 genes (log2 > 1.5 or log2 < -1.5, with a 5 % false discovery rate). Expression levels decreased in four main redox-active systems during methyl viologen exposure; the [NiFe] hydrogenase, sulfate transport and metabolism, ammonia assimilation (GS-GOGAT), and porphyrin/siroheme biosynthesis. Genes encoding sulfate transport and reduction and porphyrin/siroheme biosynthesis are co-located immediately downstream of a putative iscR regulatory gene, which may be a cis-regulatory element controlling expression of these genes. Other genes showing differential expression during methyl viologen exposure included transporters and transposases. CONCLUSIONS The differential expression results from this study support a role for C. thermocellum genes for sulfate transport/reduction, glutamate synthase-glutamine synthetase (the GS-GOGAT system), and porphyrin biosynthesis being involved in redox metabolism and homeostasis. This global profiling study provides gene targets for future studies to elucidate the relative contributions of prospective pathways for co-factor pool re-oxidation and C. thermocellum redox homeostasis.
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Affiliation(s)
- Kyle Sander
- />Bredesen Center for Interdisciplinary Research and Graduate Education, University of Tennessee, Knoxville, TN 37996 USA
- />BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
- />Department of Chemical and Biomolecular Engineering, University of Tennessee, Knoxville, TN 37996 USA
| | - Charlotte M. Wilson
- />BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
- />Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
| | - Miguel Rodriguez
- />BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
- />Biosciences 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
| | - 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
| | - Brian H. Davison
- />Bredesen Center for Interdisciplinary Research and Graduate Education, University of Tennessee, Knoxville, TN 37996 USA
- />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
- />Bredesen Center for Interdisciplinary Research and Graduate Education, University of Tennessee, Knoxville, TN 37996 USA
- />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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Elimination of formate production in Clostridium thermocellum. J Ind Microbiol Biotechnol 2015; 42:1263-72. [PMID: 26162629 PMCID: PMC4536278 DOI: 10.1007/s10295-015-1644-3] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2015] [Accepted: 06/15/2015] [Indexed: 02/05/2023]
Abstract
The ability of Clostridium thermocellum to rapidly degrade cellulose and ferment resulting hydrolysis products into ethanol makes it a promising platform organism for cellulosic biofuel production via consolidated bioprocessing. Currently, however, ethanol yield is far below theoretical maximum due to branched product pathways that divert carbon and electrons towards formate, H2, lactate, acetate, and secreted amino acids. To redirect carbon and electron flux away from formate, genes encoding pyruvate:formate lyase (pflB) and PFL-activating enzyme (pflA) were deleted. Formate production in the resulting Δpfl strain was eliminated and acetate production decreased by 50 % on both complex and defined medium. The growth rate of the Δpfl strain decreased by 2.9-fold on defined medium and biphasic growth was observed on complex medium. Supplementation of defined medium with 2 mM formate restored Δpfl growth rate to 80 % of the parent strain. The role of pfl in metabolic engineering strategies and C1 metabolism is discussed.
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