201
|
Transcriptomic profiles of Clostridium ljungdahlii during lithotrophic growth with syngas or H 2 and CO 2 compared to organotrophic growth with fructose. Sci Rep 2017; 7:13135. [PMID: 29030620 PMCID: PMC5640608 DOI: 10.1038/s41598-017-12712-w] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Accepted: 09/14/2017] [Indexed: 01/13/2023] Open
Abstract
Clostridium ljungdahlii derives energy by lithotrophic and organotrophic acetogenesis. C. ljungdahlii was grown organotrophically with fructose and also lithotrophically, either with syngas - a gas mixture containing hydrogen (H2), carbon dioxide (CO2), and carbon monoxide (CO), or with H2 and CO2. Gene expression was compared quantitatively by microarrays using RNA extracted from all three conditions. Gene expression with fructose and with H2/CO2 was compared by RNA-Seq. Upregulated genes with both syngas and H2/CO2 (compared to fructose) point to the urea cycle, uptake and degradation of peptides and amino acids, response to sulfur starvation, potentially NADPH-producing pathways involving (S)-malate and ornithine, quorum sensing, sporulation, and cell wall remodeling, suggesting a global and multicellular response to lithotrophic conditions. With syngas, the upregulated (R)-lactate dehydrogenase gene represents a route of electron transfer from ferredoxin to NAD. With H2/CO2, flavodoxin and histidine biosynthesis genes were upregulated. Downregulated genes corresponded to an intracytoplasmic microcompartment for disposal of methylglyoxal, a toxic byproduct of glycolysis, as 1-propanol. Several cytoplasmic and membrane-associated redox-active protein genes were differentially regulated. The transcriptomic profiles of C. ljungdahlii in lithotrophic and organotrophic growth modes indicate large-scale physiological and metabolic differences, observations that may guide biofuel and commodity chemical production with this species.
Collapse
|
202
|
Evidence of mixotrophic carbon-capture by n-butanol-producer Clostridium beijerinckii. Sci Rep 2017; 7:12759. [PMID: 28986542 PMCID: PMC5630571 DOI: 10.1038/s41598-017-12962-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2016] [Accepted: 09/13/2017] [Indexed: 12/17/2022] Open
Abstract
Recent efforts to combat increasing greenhouse gas emissions include their capture into advanced biofuels, such as butanol. Traditionally, biobutanol research has been centered solely on its generation from sugars. Our results show partial re-assimilation of CO2 and H2 by n-butanol-producer C. beijerinckii. This was detected as synchronous CO2/H2 oscillations by direct (real-time) monitoring of their fermentation gasses. Additional functional analysis demonstrated increased total carbon recovery above heterotrophic values associated to mixotrophic assimilation of synthesis gas (H2, CO2 and CO). This was further confirmed using 13C-Tracer experiments feeding 13CO2 and measuring the resulting labeled products. Genome- and transcriptome-wide analysis revealed transcription of key C-1 capture and additional energy conservation genes, including partial Wood-Ljungdahl and complete reversed pyruvate ferredoxin oxidoreductase / pyruvate-formate-lyase-dependent (rPFOR/Pfl) pathways. Therefore, this report provides direct genetic and physiological evidences of mixotrophic inorganic carbon-capture by C. beijerinckii.
Collapse
|
203
|
Momper L, Kiel Reese B, Zinke L, Wanger G, Osburn MR, Moser D, Amend JP. Major phylum-level differences between porefluid and host rock bacterial communities in the terrestrial deep subsurface. ENVIRONMENTAL MICROBIOLOGY REPORTS 2017; 9:501-511. [PMID: 28677247 DOI: 10.1111/1758-2229.12563] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2016] [Revised: 01/06/2017] [Accepted: 06/19/2017] [Indexed: 06/07/2023]
Abstract
Earth's deep subsurface biosphere (DSB) is home to a vast number and wide variety of microorganisms. Although difficult to access and sample, deep subsurface environments have been probed through drilling programs, exploration of mines and sampling of deeply sourced vents and springs. In an effort to understand the ecology of deep terrestrial habitats, we examined bacterial diversity in the Sanford Underground Research Facility (SURF), the former Homestake gold mine, in South Dakota, USA. Whole genomic DNA was extracted from deeply circulating groundwater and corresponding host rock (at a depth of 1.45 km below ground surface). Pyrotag DNA sequencing of the 16S rRNA gene revealed diverse communities of putative chemolithoautotrophs, aerobic and anaerobic heterotrophs, numerous candidate phyla and unique rock-associated microbial assemblage. There was a clear and near-total separation of communities between SURF deeply circulating fracture fluids and SURF host-rocks. Sequencing data from SURF compared against five similarly sequenced terrestrial subsurface sites in Europe and North America revealed classes Clostridia and Betaproteobacteria were dominant in terrestrial fluids. This study presents a unique analysis showing differences in terrestrial subsurface microbial communities between fracture fluids and host rock through which those fluids permeate.
Collapse
Affiliation(s)
- Lily Momper
- Department of Biological Sciences, Marine Environmental Biology Section, University of Southern California, Los Angeles, CA, USA
| | - Brandi Kiel Reese
- Department of Life Sciences, Texas A&M University, Corpus Christi, TX, USA
| | - Laura Zinke
- Department of Biological Sciences, Marine Environmental Biology Section, University of Southern California, Los Angeles, CA, USA
| | - Greg Wanger
- Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA, USA
- Department of Earth Sciences, University of Southern California, Los Angeles, CA, USA
| | - Magdalena R Osburn
- Department of Earth and Planetary Sciences, Northwestern University, Evanston, IL, USA
| | - Duane Moser
- Division of Earth and Ecosystem Sciences, Desert Research Institute, Las Vegas, NV, USA
| | - Jan P Amend
- Department of Biological Sciences, Marine Environmental Biology Section, University of Southern California, Los Angeles, CA, USA
- Department of Earth Sciences, University of Southern California, Los Angeles, CA, USA
| |
Collapse
|
204
|
Yang G, Jia D, Jin L, Jiang Y, Wang Y, Jiang W, Gu Y. Rapid Generation of Universal Synthetic Promoters for Controlled Gene Expression in Both Gas-Fermenting and Saccharolytic Clostridium Species. ACS Synth Biol 2017; 6:1672-1678. [PMID: 28602076 DOI: 10.1021/acssynbio.7b00155] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Engineering solventogenic clostridia, a group of important industrial microorganisms, to realize their full potential in biorefinery application is still hindered by the absence of plentiful biological parts. Here, we developed an effective approach for rapid generation of a synthetic promoter library in solventogenic clostridia based on a dual-reporter system (catP-lacZ) and a widely used strong thl promoter. The yielded artificial promoters, spanning 2 orders of magnitude, comprised two modular components (the core promoter region and the spacer between RBS and the translation-initiating code), and the strongest promoter had an over 10-fold-higher activity than the original expression part Pthl. The test of these synthetic promoters in controlled expression of sadh and danK in saccharolytic C. acetobutylicum and gas-fermenting C. ljungdahlii, respectively, gave the expected phenotypes, and moreover, showed good correlation between promoter activities and phenotypic changes. The presented wide-strength-range promoters here will be useful for synthetic biology application in solventogenic clostridia.
Collapse
Affiliation(s)
- Gaohua Yang
- Key
Laboratory of Synthetic Biology, Institute of Plant Physiology and
Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Dechen Jia
- Key
Laboratory of Synthetic Biology, Institute of Plant Physiology and
Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Lin Jin
- Key
Laboratory of Synthetic Biology, Institute of Plant Physiology and
Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Yuqian Jiang
- Department
of Biochemistry and Molecular Medicine, University of California at Davis, Sacramento, California 95817, United States
| | - Yong Wang
- Key
Laboratory of Synthetic Biology, Institute of Plant Physiology and
Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Weihong Jiang
- Key
Laboratory of Synthetic Biology, Institute of Plant Physiology and
Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China
- Jiangsu
National Synergetic Innovation Center for Advanced Materials, SICAM, 200 North Zhongshan Road, Nanjing 210009, China
| | - Yang Gu
- Key
Laboratory of Synthetic Biology, Institute of Plant Physiology and
Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China
- Shanghai Collaborative Innovation Center for Biomanufacturing Technology, 130 Meilong Road, Shanghai 200237, China
| |
Collapse
|
205
|
Shen S, Gu Y, Chai C, Jiang W, Zhuang Y, Wang Y. Enhanced alcohol titre and ratio in carbon monoxide-rich off-gas fermentation of Clostridium carboxidivorans through combination of trace metals optimization with variable-temperature cultivation. BIORESOURCE TECHNOLOGY 2017; 239:236-243. [PMID: 28521234 DOI: 10.1016/j.biortech.2017.04.099] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2017] [Revised: 04/23/2017] [Accepted: 04/24/2017] [Indexed: 06/07/2023]
Abstract
Bioconversion of C1 gases to produce chemicals has good application prospects. Here, the combination of trace metals optimization using a statistical method with variable-temperature cultivation was used to enhance alcohol synthesis during CO-rich off-gas fermentation by Clostridium carboxidivorans P7. Based on ATCC medium 1754, the optimum concentration of the trace metals was found to be 5-fold Ni2+, Co2+, SeO42+, and WO42+; 3.48-fold Cu2+; 0.55-fold MoO42+; 0.5-fold Zn2+ and (NH4)2SO4·FeSO4·6H2O; and additional 44.32μM FeCl3·6H2O. The production of alcohol and organic acid changed to 4.40g/L and 0.50g/L from 2.16g/L and 2.37g/L, respectively, yielding an increase of alcohol-to-product ratio from 47.7% to 89.8%. By fermenting with the optimized medium and timed control of the incubation temperature (37°C [0-24h]-25°C [24-144h]), the alcohol titre further increased to 6.97g/L with 1.67g/L butanol and 1.33g/L hexanol, exceeding those previously reported for strain P7.
Collapse
Affiliation(s)
- Shaohuang Shen
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Yang Gu
- Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Changsheng Chai
- Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Weihong Jiang
- Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Yingping Zhuang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Yonghong Wang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China.
| |
Collapse
|
206
|
Igarashi K, Kato S. Extracellular electron transfer in acetogenic bacteria and its application for conversion of carbon dioxide into organic compounds. Appl Microbiol Biotechnol 2017; 101:6301-6307. [PMID: 28748358 DOI: 10.1007/s00253-017-8421-3] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2017] [Revised: 07/04/2017] [Accepted: 07/04/2017] [Indexed: 11/26/2022]
Abstract
Acetogenic bacteria (i.e., acetogens) produce acetate from CO2 during anaerobic chemoautotrophic growth. Because acetogens fix CO2 with high energy efficiency, they have been investigated as biocatalysts of CO2 conversion into valuable chemicals. Recent studies revealed that some acetogens are capable of extracellular electron transfer (EET), which enables electron exchange between microbial cells and extracellular solid materials. Thus, acetogens are promising candidates as biocatalysts in recently developed bioelectrochemical technologies, including microbial electrosynthesis (MES), in which useful chemicals are biologically produced from CO2 using electricity as the energy source. In microbial photoelectrosynthesis, a variant of MES technology, the conversion of CO2 into organic compounds is achieved using light as the sole energy source without an external power supply. In this mini-review, we introduce the general features of bioproduction and EET of acetogens and describe recent progress and future prospects of MES technologies based on the EET capability of acetogens.
Collapse
Affiliation(s)
- Kensuke Igarashi
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 2-17-2-1 Tsukisamu-Higashi, Toyohira-ku, Sapporo, Hokkaido, 062-8517, Japan
| | - Souichiro Kato
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 2-17-2-1 Tsukisamu-Higashi, Toyohira-ku, Sapporo, Hokkaido, 062-8517, Japan.
- Division of Applied Bioscience, Graduate School of Agriculture, Hokkaido University, Kita-9 Nishi-9, Kita-ku, Sapporo, Hokkaido, 060-8589, Japan.
| |
Collapse
|
207
|
De Tissera S, Köpke M, Simpson SD, Humphreys C, Minton NP, Dürre P. Syngas Biorefinery and Syngas Utilization. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2017. [DOI: 10.1007/10_2017_5] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
|
208
|
Continuous Ethanol Production from Synthesis Gas by Clostridium ragsdalei in a Trickle-Bed Reactor. FERMENTATION-BASEL 2017. [DOI: 10.3390/fermentation3020023] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
|
209
|
|
210
|
Maintenance of ATP Homeostasis Triggers Metabolic Shifts in Gas-Fermenting Acetogens. Cell Syst 2017; 4:505-515.e5. [PMID: 28527885 DOI: 10.1016/j.cels.2017.04.008] [Citation(s) in RCA: 90] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Revised: 02/12/2017] [Accepted: 04/18/2017] [Indexed: 12/31/2022]
Abstract
Acetogens are promising cell factories for producing fuels and chemicals from waste feedstocks via gas fermentation, but quantitative characterization of carbon, energy, and redox metabolism is required to guide their rational metabolic engineering. Here, we explore acetogen gas fermentation using physiological, metabolomics, and transcriptomics data for Clostridium autoethanogenum steady-state chemostat cultures grown on syngas at various gas-liquid mass transfer rates. We observe that C. autoethanogenum shifts from acetate to ethanol production to maintain ATP homeostasis at higher biomass concentrations but reaches a limit at a molar acetate/ethanol ratio of ∼1. This regulatory mechanism eventually leads to depletion of the intracellular acetyl-CoA pool and collapse of metabolism. We accurately predict growth phenotypes using a genome-scale metabolic model. Modeling revealed that the methylene-THF reductase reaction was ferredoxin reducing. This work provides a reference dataset to advance the understanding and engineering of arguably the first carbon fixation pathway on Earth.
Collapse
|
211
|
Islam MA, Hadadi N, Ataman M, Hatzimanikatis V, Stephanopoulos G. Exploring biochemical pathways for mono-ethylene glycol (MEG) synthesis from synthesis gas. Metab Eng 2017; 41:173-181. [PMID: 28433737 DOI: 10.1016/j.ymben.2017.04.005] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2016] [Revised: 12/28/2016] [Accepted: 04/16/2017] [Indexed: 10/19/2022]
Abstract
Mono-ethylene glycol (MEG) is an important petrochemical with widespread use in numerous consumer products. The current industrial MEG-production process relies on non-renewable fossil fuel-based feedstocks, such as petroleum, natural gas, and naphtha; hence, it is useful to explore alternative routes of MEG-synthesis from gases as they might provide a greener and more sustainable alternative to the current production methods. Technologies of synthetic biology and metabolic engineering of microorganisms can be deployed for the expression of new biochemical pathways for MEG-synthesis from gases, provided that such promising alternative routes are first identified. We used the BNICE.ch algorithm to develop novel and previously unknown biological pathways to MEG from synthesis gas by leveraging the Wood-Ljungdahl pathway of carbon fixation of acetogenic bacteria. We developed a set of useful pathway pruning and analysis criteria to systematically assess thousands of pathways generated by BNICE.ch. Published genome-scale models of Moorella thermoacetica and Clostridium ljungdahlii were used to perform the pathway yield calculations and in-depth analyses of seven (7) newly developed biological MEG-producing pathways from gases, including CO2, CO, and H2. These analyses helped identify not only better candidate pathways, but also superior chassis organisms that can be used for metabolic engineering of the candidate pathways. The pathway generation, pruning, and detailed analysis procedures described in this study can also be used to develop biochemical pathways for other commodity chemicals from gaseous substrates.
Collapse
Affiliation(s)
- M Ahsanul Islam
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, United States
| | - Noushin Hadadi
- Institute of Chemical Sciences and Engineering, Ecole Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | - Meric Ataman
- Institute of Chemical Sciences and Engineering, Ecole Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | - Vassily Hatzimanikatis
- Institute of Chemical Sciences and Engineering, Ecole Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland.
| | - Gregory Stephanopoulos
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, United States.
| |
Collapse
|
212
|
Heijstra BD, Leang C, Juminaga A. Gas fermentation: cellular engineering possibilities and scale up. Microb Cell Fact 2017; 16:60. [PMID: 28403896 PMCID: PMC5389167 DOI: 10.1186/s12934-017-0676-y] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2016] [Accepted: 04/04/2017] [Indexed: 12/11/2022] Open
Abstract
Low carbon fuels and chemicals can be sourced from renewable materials such as biomass or from industrial and municipal waste streams. Gasification of these materials allows all of the carbon to become available for product generation, a clear advantage over partial biomass conversion into fermentable sugars. Gasification results into a synthesis stream (syngas) containing carbon monoxide (CO), carbon dioxide (CO2), hydrogen (H2) and nitrogen (N2). Autotrophy-the ability to fix carbon such as CO2 is present in all domains of life but photosynthesis alone is not keeping up with anthropogenic CO2 output. One strategy is to curtail the gaseous atmospheric release by developing waste and syngas conversion technologies. Historically microorganisms have contributed to major, albeit slow, atmospheric composition changes. The current status and future potential of anaerobic gas-fermenting bacteria with special focus on acetogens are the focus of this review.
Collapse
Affiliation(s)
| | - Ching Leang
- LanzaTech, Inc., 8045 Lamon Ave, Suite 400, Skokie, IL USA
| | - Alex Juminaga
- LanzaTech, Inc., 8045 Lamon Ave, Suite 400, Skokie, IL USA
| |
Collapse
|
213
|
Metals and minerals as a biotechnology feedstock: engineering biomining microbiology for bioenergy applications. Curr Opin Biotechnol 2017; 45:144-155. [PMID: 28371651 DOI: 10.1016/j.copbio.2017.03.009] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2016] [Revised: 03/04/2017] [Accepted: 03/10/2017] [Indexed: 01/06/2023]
Abstract
Developing new feedstocks for the efficient production of biochemicals and biofuels will be a critical challenge as we diversify away from petrochemicals. One possible opportunity is the utilization of sulfide-based minerals in the Earth's crust. Non-photosynthetic chemolithoautotrophic bacteria are starting to be developed to produce biochemicals from CO2 using energy obtained from the oxidation of inorganic feedstocks. Biomining of metals like gold and copper already exploit the native metabolism of these bacteria and these represent perhaps the largest-scale bioprocesses ever developed. The metabolic engineering of these bacteria could be a desirable alternative to classical heterotrophic bioproduction. In this review, we discuss biomining operations and the challenges and advances in the engineering of associated chemolithoautotrophic bacteria for biofuel production. The co-generation of biofuels integrated with mining operations is a largely unexplored opportunity that will require advances in fundamental microbiology and the development of new genetic tools and techniques for these organisms. Although this approach is presently in its infancy, the production of biochemicals using energy from non-petroleum mineral resources is an exciting new biotechnology opportunity.
Collapse
|
214
|
Homolactic Acid Fermentation by the Genetically Engineered Thermophilic Homoacetogen Moorella thermoacetica ATCC 39073. Appl Environ Microbiol 2017; 83:AEM.00247-17. [PMID: 28159797 DOI: 10.1128/aem.00247-17] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2017] [Accepted: 01/31/2017] [Indexed: 11/20/2022] Open
Abstract
For the efficient production of target metabolites from carbohydrates, syngas, or H2-CO2 by genetically engineered Moorella thermoacetica, the control of acetate production (a main metabolite of M. thermoacetica) is desired. Although propanediol utilization protein (PduL) was predicted to be a phosphotransacetylase (PTA) involved in acetate production in M. thermoacetica, this has not been confirmed. Our findings described herein directly demonstrate that two putative PduL proteins, encoded by Moth_0864 (pduL1) and Moth_1181 (pduL2), are involved in acetate formation as PTAs. To disrupt these genes, we replaced each gene with a lactate dehydrogenase gene from Thermoanaerobacter pseudethanolicus ATCC 33223 (T-ldh). The acetate production from fructose as the sole carbon source by the pduL1 deletion mutant was not deficient, whereas the disruption of pduL2 significantly decreased the acetate yield to approximately one-third that of the wild-type strain. The double-deletion (both pduL genes) mutant did not produce acetate but produced only lactate as the end product from fructose. These results suggest that both pduL genes are associated with acetate formation via acetyl-coenzyme A (acetyl-CoA) and that their disruption enables a shift in the homoacetic pathway to the genetically synthesized homolactic pathway via pyruvate.IMPORTANCE This is the first report, to our knowledge, on the experimental identification of PTA genes in M. thermoacetica and the shift of the native homoacetic pathway to the genetically synthesized homolactic pathway by their disruption on a sugar platform.
Collapse
|
215
|
Xu H, Liang C, Yuan Z, Xu J, Hua Q, Guo Y. A study of CO/syngas bioconversion by Clostridium autoethanogenum with a flexible gas-cultivation system. Enzyme Microb Technol 2017; 101:24-29. [PMID: 28433187 DOI: 10.1016/j.enzmictec.2017.03.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2016] [Revised: 02/23/2017] [Accepted: 03/09/2017] [Indexed: 10/20/2022]
Abstract
Bioconversion of CO/syngas to produce ethanol is a novel route in bioethanol production, which can be accomplished by some acetogens. Specific culture vessels and techniques are needed to cultivate these microorganisms since they are anaerobic and substrates are gaseous. In this work, gas-sampling bag was applied as a gas-cultivation system to study CO/syngas bioconversion by Clostridium autoethanogenum and was demonstrated to be efficient because of its flexibility and excellent ability to maintain the headspace atmosphere. C. autoethanogenum can use CO as the sole carbon and energy source to produce ethanol, acetate as well as CO2. In the experimental range, higher ethanol production was favored by higher yeast extract concentrations, and the maximum ethanol concentration of 3.45g/L was obtained at 1.0g/L of yeast extract. Study with various bottled gases showed that C. autoethanogenum preferred to use CO other than CO2 and produced the highest level of ethanol with 100% CO as the substrate. C. autoethanogenum can also utilize biomass-generated syngas (36.2% CO, 23.0% H2, 15.4% CO2, 11.3% N2), but the process proceeded slowly and insufficiently due to the presence of O2 and C2H2. In our study, C. autoethanogenum showed a better performance in the bioconversion of CO to ethanol than Clostridium ljungdahlii, a strain which has been most studied, and for both strains, ethanol production was promoted by supplementing 0.5g/L of acetate.
Collapse
Affiliation(s)
- Huijuan Xu
- CAS Key Laboratory of Renewable Energy, Guangzhou Institute of Energy Conversion, Chinese Academy of Sciences, Guangzhou, China
| | - Cuiyi Liang
- CAS Key Laboratory of Renewable Energy, Guangzhou Institute of Energy Conversion, Chinese Academy of Sciences, Guangzhou, China
| | - Zhenhong Yuan
- CAS Key Laboratory of Renewable Energy, Guangzhou Institute of Energy Conversion, Chinese Academy of Sciences, Guangzhou, China.
| | - Jingliang Xu
- CAS Key Laboratory of Renewable Energy, Guangzhou Institute of Energy Conversion, Chinese Academy of Sciences, Guangzhou, China.
| | - Qiang Hua
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| | - Ying Guo
- CAS Key Laboratory of Renewable Energy, Guangzhou Institute of Energy Conversion, Chinese Academy of Sciences, Guangzhou, China
| |
Collapse
|
216
|
Puig S, Ganigué R, Batlle-Vilanova P, Balaguer MD, Bañeras L, Colprim J. Tracking bio-hydrogen-mediated production of commodity chemicals from carbon dioxide and renewable electricity. BIORESOURCE TECHNOLOGY 2017; 228:201-209. [PMID: 28063363 DOI: 10.1016/j.biortech.2016.12.035] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2016] [Revised: 12/08/2016] [Accepted: 12/09/2016] [Indexed: 05/28/2023]
Abstract
This study reveals that reduction of carbon dioxide (CO2) to commodity chemicals can be functionally compartmentalized in bioelectrochemical systems. In the present example, a syntrophic consortium composed by H2-producers (Rhodobacter sp.) in the biofilm is combined with carboxidotrophic Clostridium species, mainly found in the bulk liquid. The performance of these H2-mediated electricity-driven systems could be tracked by the activity of a biological H2 sensory protein identified at cathode potentials between -0.2V and -0.3V vs SHE. This seems to point out that such signal is not strain specific, but could be detected in any organism containing hydrogenases. Thus, the findings of this work open the door to the development of a biosensor application or soft sensors for monitoring such systems.
Collapse
Affiliation(s)
- Sebastià Puig
- LEQUIA, Institute of the Environment, University of Girona, Campus de Montilivi, Carrer Maria Aurèlia Capmany, 69, E-17003 Girona, Catalonia, Spain.
| | - Ramon Ganigué
- LEQUIA, Institute of the Environment, University of Girona, Campus de Montilivi, Carrer Maria Aurèlia Capmany, 69, E-17003 Girona, Catalonia, Spain; Centre of Microbial Ecology and Technology, Ghent University, Coupure Links 653, B-9000 Ghent, Belgium
| | - Pau Batlle-Vilanova
- LEQUIA, Institute of the Environment, University of Girona, Campus de Montilivi, Carrer Maria Aurèlia Capmany, 69, E-17003 Girona, Catalonia, Spain; Department of Innovation and Technology, FCC Aqualia, Balmes Street, 36, 6th Floor, 08007 Barcelona, Spain
| | - M Dolors Balaguer
- LEQUIA, Institute of the Environment, University of Girona, Campus de Montilivi, Carrer Maria Aurèlia Capmany, 69, E-17003 Girona, Catalonia, Spain
| | - Lluís Bañeras
- Molecular Microbial Ecology Group, Institute of Aquatic Ecology, University of Girona, E-17071 Girona, Spain
| | - Jesús Colprim
- LEQUIA, Institute of the Environment, University of Girona, Campus de Montilivi, Carrer Maria Aurèlia Capmany, 69, E-17003 Girona, Catalonia, Spain
| |
Collapse
|
217
|
Biofilm Formation by Clostridium ljungdahlii Is Induced by Sodium Chloride Stress: Experimental Evaluation and Transcriptome Analysis. PLoS One 2017; 12:e0170406. [PMID: 28118386 PMCID: PMC5261816 DOI: 10.1371/journal.pone.0170406] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2016] [Accepted: 01/04/2017] [Indexed: 01/08/2023] Open
Abstract
The acetogen Clostridium ljungdahlii is capable of syngas fermentation and microbial electrosynthesis. Biofilm formation could benefit both these applications, but was not yet reported for C. ljungdahlii. Biofilm formation does not occur under standard growth conditions, but attachment or aggregation could be induced by different stresses. The strongest biofilm formation was observed with the addition of sodium chloride. After 3 days of incubation, the biomass volume attached to a plastic surface was 20 times higher with than without the addition of 200 mM NaCl to the medium. The addition of NaCl also resulted in biofilm formation on glass, graphite and glassy carbon, the latter two being often used electrode materials for microbial electrosynthesis. Biofilms were composed of extracellular proteins, polysaccharides, as well as DNA, while pilus-like appendages were observed with, but not without, the addition of NaCl. A transcriptome analysis comparing planktonic (no NaCl) and biofilm (NaCl addition) cells showed that C. ljungdahlii coped with the salt stress by the upregulation of the general stress response, Na+ export and osmoprotectant accumulation. A potential role for poly-N-acetylglucosamines and D-alanine in biofilm formation was found. Flagellar motility was downregulated, while putative type IV pili biosynthesis genes were not expressed. Moreover, the gene expression analysis suggested the involvement of the transcriptional regulators LexA, Spo0A and CcpA in stress response and biofilm formation. This study showed that NaCl addition might be a valuable strategy to induce biofilm formation by C. ljungdahlii, which can improve the efficacy of syngas fermentation and microbial electrosynthesis applications.
Collapse
|
218
|
Liew F, Henstra AM, Kӧpke M, Winzer K, Simpson SD, Minton NP. Metabolic engineering of Clostridium autoethanogenum for selective alcohol production. Metab Eng 2017; 40:104-114. [PMID: 28111249 PMCID: PMC5367853 DOI: 10.1016/j.ymben.2017.01.007] [Citation(s) in RCA: 130] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2016] [Revised: 11/01/2016] [Accepted: 01/19/2017] [Indexed: 01/27/2023]
Abstract
Gas fermentation using acetogenic bacteria such as Clostridium autoethanogenum offers an attractive route for production of fuel ethanol from industrial waste gases. Acetate reduction to acetaldehyde and further to ethanol via an aldehyde: ferredoxin oxidoreductase (AOR) and alcohol dehydrogenase has been postulated alongside the classic pathway of ethanol formation via a bi-functional aldehyde/alcohol dehydrogenase (AdhE). Here we demonstrate that AOR is critical to ethanol formation in acetogens and inactivation of AdhE led to consistently enhanced autotrophic ethanol production (up to 180%). Using ClosTron and allelic exchange mutagenesis, which was demonstrated for the first time in an acetogen, we generated single mutants as well as double mutants for both aor and adhE isoforms to confirm the role of each gene. The aor1+2 double knockout strain lost the ability to convert exogenous acetate, propionate and butyrate into the corresponding alcohols, further highlighting the role of these enzymes in catalyzing the thermodynamically unfavourable reduction of carboxylic acids into alcohols. 180% improvement in C. autoethanogenum ethanol production via metabolic engineering. Confirmed role of AOR in autotrophic ethanol production of acetogens. Generated both aor and adhE mutants of C. autoethanogenum.. Demonstrated allelic exchange mutagenesis for stable deletions in acetogens. Inactivation of adhE and aor2, but not aor1, improves autotrophic ethanol production.
Collapse
Affiliation(s)
- Fungmin Liew
- BBSRC/EPSRC Synthetic Biology Research Centre (SBRC), School of Life Sciences, University Park, The University of Nottingham, Nottingham NG7 2RD, UK; LanzaTech Inc., 8045 Lamon Avenue, Suite 400, Skokie, IL, USA
| | - Anne M Henstra
- BBSRC/EPSRC Synthetic Biology Research Centre (SBRC), School of Life Sciences, University Park, The University of Nottingham, Nottingham NG7 2RD, UK
| | - Michael Kӧpke
- LanzaTech Inc., 8045 Lamon Avenue, Suite 400, Skokie, IL, USA
| | - Klaus Winzer
- BBSRC/EPSRC Synthetic Biology Research Centre (SBRC), School of Life Sciences, University Park, The University of Nottingham, Nottingham NG7 2RD, UK
| | - Sean D Simpson
- LanzaTech Inc., 8045 Lamon Avenue, Suite 400, Skokie, IL, USA
| | - Nigel P Minton
- BBSRC/EPSRC Synthetic Biology Research Centre (SBRC), School of Life Sciences, University Park, The University of Nottingham, Nottingham NG7 2RD, UK.
| |
Collapse
|
219
|
Genomic reconstruction of multiple lineages of uncultured benthic archaea suggests distinct biogeochemical roles and ecological niches. ISME JOURNAL 2017; 11:1118-1129. [PMID: 28085154 DOI: 10.1038/ismej.2016.189] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Revised: 11/10/2016] [Accepted: 11/19/2016] [Indexed: 01/14/2023]
Abstract
Genomic bins belonging to multiple archaeal lineages were recovered from distinct redox regimes in sediments of the White Oak River estuary. The reconstructed archaeal genomes were identified as belonging to the rice cluster subgroups III and V (RC-III, RC-V), the Marine Benthic Group D (MBG-D), and a newly described archaeal class, the Theionarchaea. The metabolic capabilities of these uncultured archaea were inferred and indicated a common capability for extracellular protein degradation, supplemented by other pathways. The multiple genomic bins within the MBG-D archaea shared a nearly complete reductive acetyl-CoA pathway suggesting acetogenic capabilities. In contrast, the RC-III metabolism appeared centered on the degradation of detrital proteins and production of H2, whereas the RC-V archaea lacked capabilities for protein degradation and uptake, and appeared to be specialized on carbohydrate fermentation. The Theionarchaea appeared as complex metabolic hybrids; encoding a complete tricarboxylic acid cycle permitting carbon (acetyl-CoA) oxidation, together with a complete reductive acetyl-CoA pathway and sulfur reduction by a sulfhydrogenase. The differentiated inferred capabilities of these uncultured archaeal lineages indicated lineage-specific linkages with the nitrogen, carbon and sulfur cycles. The predicted metabolisms of these archaea suggest preferences for distinct geochemical niches within the estuarine sedimentary environment.
Collapse
|
220
|
Clomburg JM, Crumbley AM, Gonzalez R. Industrial biomanufacturing: The future of chemical production. Science 2017; 355:355/6320/aag0804. [DOI: 10.1126/science.aag0804] [Citation(s) in RCA: 271] [Impact Index Per Article: 38.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2016] [Accepted: 10/21/2016] [Indexed: 12/18/2022]
Abstract
The current model for industrial chemical manufacturing employs large-scale megafacilities that benefit from economies of unit scale. However, this strategy faces environmental, geographical, political, and economic challenges associated with energy and manufacturing demands. We review how exploiting biological processes for manufacturing (i.e., industrial biomanufacturing) addresses these concerns while also supporting and benefiting from economies of unit number. Key to this approach is the inherent small scale and capital efficiency of bioprocesses and the ability of engineered biocatalysts to produce designer products at high carbon and energy efficiency with adjustable output, at high selectivity, and under mild process conditions. The biological conversion of single-carbon compounds represents a test bed to establish this paradigm, enabling rapid, mobile, and widespread deployment, access to remote and distributed resources, and adaptation to new and changing markets.
Collapse
|
221
|
Abstract
Alcohols (CnHn+2OH) are classified into primary, secondary, and tertiary alcohols, which can be branched or unbranched. They can also feature more than one OH-group (two OH-groups = diol; three OH-groups = triol). Presently, except for ethanol and sugar alcohols, they are mainly produced from fossil-based resources, such as petroleum, gas, and coal. Methanol and ethanol have the highest annual production volume accounting for 53 and 91 million tons/year, respectively. Most alcohols are used as fuels (e.g., ethanol), solvents (e.g., butanol), and chemical intermediates.This chapter gives an overview of recent research on the production of short-chain unbranched alcohols (C1-C5), focusing in particular on propanediols (1,2- and 1,3-propanediol), butanols, and butanediols (1,4- and 2,3-butanediol). It also provides a short summary on biobased higher alcohols (>C5) including branched alcohols.
Collapse
|
222
|
Dürre P. Gas fermentation - a biotechnological solution for today's challenges. Microb Biotechnol 2017; 10:14-16. [PMID: 27790842 PMCID: PMC5270713 DOI: 10.1111/1751-7915.12431] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2016] [Accepted: 09/24/2016] [Indexed: 12/01/2022] Open
Affiliation(s)
- Peter Dürre
- Institut für Mikrobiologie und BiotechnologieUniversität UlmUlmGermany
| |
Collapse
|
223
|
Huang H, Chai C, Li N, Rowe P, Minton NP, Yang S, Jiang W, Gu Y. CRISPR/Cas9-Based Efficient Genome Editing in Clostridium ljungdahlii, an Autotrophic Gas-Fermenting Bacterium. ACS Synth Biol 2016; 5:1355-1361. [PMID: 27276212 DOI: 10.1021/acssynbio.6b00044] [Citation(s) in RCA: 126] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Acetogenic bacteria have the potential to convert single carbon gases (CO and CO2) into a range of bulk chemicals and fuels. Realization of their full potential is being impeded by the absence of effective genetic tools for high throughput genome modification. Here we report the development of a highly efficient CRISPR/Cas9 system for rapid genome editing of Clostridium ljungdahlii, a paradigm for the commercial production of ethanol from synthesis gas. Following the experimental selection of two promoters (Pthl and ParaE) for expression of cas9 and the requisite single guide RNA (sgRNA), the efficiency of system was tested by making precise deletions of four genes, pta, adhE1, ctf and pyrE. Deletion efficiencies were 100%, >75%, 100% and >50%, respectively. The system overcomes the deficiencies of currently available tools (more rapid, no added antibiotic resistance gene, scarless and minimal polar effects) and will find utility in other acetogens, including the pathogen Clostridium difficile.
Collapse
Affiliation(s)
- He Huang
- Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences , Shanghai 200032, China
| | - Changsheng Chai
- Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences , Shanghai 200032, China
| | - Ning Li
- Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences , Shanghai 200032, China
| | - Pete Rowe
- Clostridia Research Group, BBSRC/EPSRC Synthetic Biology Research Centre (SBRC), School of Life Sciences, University of Nottingham , Nottingham, NG7 2RD, U.K
| | - Nigel P Minton
- Clostridia Research Group, BBSRC/EPSRC Synthetic Biology Research Centre (SBRC), School of Life Sciences, University of Nottingham , Nottingham, NG7 2RD, U.K
| | - Sheng Yang
- Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences , Shanghai 200032, China
- Jiangsu National Synergetic Innovation Center for Advanced Materials, SICAM , 200 North Zhongshan Road, Nanjing 210009, China
| | - Weihong Jiang
- Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences , Shanghai 200032, China
- Jiangsu National Synergetic Innovation Center for Advanced Materials, SICAM , 200 North Zhongshan Road, Nanjing 210009, China
| | - Yang Gu
- Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences , Shanghai 200032, China
- Shanghai Collaborative Innovation Center for Biomanufacturing Technology , 130 Meilong Road, Shanghai 200237, China
| |
Collapse
|
224
|
Whitham JM, Schulte MJ, Bobay BG, Bruno-Barcena JM, Chinn MS, Flickinger MC, Pawlak JJ, Grunden AM. Characterization of Clostridium ljungdahlii OTA1: a non-autotrophic hyper ethanol-producing strain. Appl Microbiol Biotechnol 2016; 101:1615-1630. [PMID: 27866253 DOI: 10.1007/s00253-016-7978-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Revised: 10/27/2016] [Accepted: 10/31/2016] [Indexed: 02/07/2023]
Abstract
A Clostridium ljungdahlii lab-isolated spontaneous-mutant strain, OTA1, has been shown to produce twice as much ethanol as the C. ljungdahlii ATCC 55383 strain when cultured in a mixotrophic medium containing fructose and syngas. Whole-genome sequencing identified four unique single nucleotide polymorphisms (SNPs) in the C. ljungdahlii OTA1 genome. Among these, two SNPs were found in the gene coding for AcsA and HemL, enzymes involved in acetyl-CoA formation from CO/CO2. Homology models of the respective mutated enzymes revealed alterations in the size and hydrogen bonding of the amino acids in their active sites. Failed attempts to grow OTA1 autotrophically suggested that one or both of these mutated genes prevented acetyl-CoA synthesis from CO/CO2, demonstrating that its activity was required for autotrophic growth by C. ljungdahlii. An inoperable Wood-Ljungdahl pathway resulted in higher CO2 and ethanol yields and lower biomass and acetate yields compared to WT for multiple growth conditions including heterotrophic and mixotrophic conditions. The two other SNPs identified in the C. ljungdahlii OTA1 genome were in genes coding for transcriptional regulators (CLJU_c09320 and CLJU_c18110) and were found to be responsible for deregulated expression of co-localized arginine catabolism and 2-deoxy-D-ribose catabolism genes. Growth medium supplementation experiments suggested that increased arginine metabolism and 2-deoxy-D-ribose were likely to have minor effects on biomass and fermentation product yields. In addition, in silico flux balance analysis simulating mixotrophic and heterotrophic conditions showed no change in flux to ethanol when flux through HemL was changed whereas limited flux through AcsA increased the ethanol flux for both simulations. In characterizing the effects of the SNPs identified in the C. ljungdahlii OTA1 genome, a non-autotrophic hyper ethanol-producing strain of C. ljungdahlii was identified that has utility for further physiology and strain performance studies and as a biocatalyst for industrial applications.
Collapse
Affiliation(s)
- Jason M Whitham
- Department of Plant and Microbial Biology, North Carolina State University, 4548 Thomas Hall, Campus Box 7615, Raleigh, NC, 27695-7615, USA
| | - Mark J Schulte
- Department of Chemical and Biomolecular Engineering, 196 Golden LEAF Biomanufacturing Training and Education Center, North Carolina State University, Raleigh, NC, 27695, USA
| | - Benjamin G Bobay
- Duke University NMR Center, Duke University Medical Center, Duke University, Durham, NC, 27710, USA
| | - Jose M Bruno-Barcena
- Department of Plant and Microbial Biology, North Carolina State University, 4548 Thomas Hall, Campus Box 7615, Raleigh, NC, 27695-7615, USA
| | - Mari S Chinn
- Department of Biological and Agricultural Engineering, North Carolina State University, 277 Weaver Labs, Campus Box 7625, Raleigh, NC, 27695-7625, USA
| | - Michael C Flickinger
- Department of Chemical and Biomolecular Engineering, 196 Golden LEAF Biomanufacturing Training and Education Center, North Carolina State University, Raleigh, NC, 27695, USA
| | - Joel J Pawlak
- Department of Forest Biomaterials, North Carolina State University, 2028C Biltmore Hall, Campus Box 8001, Raleigh, NC, 27695-8001, USA
| | - Amy M Grunden
- Department of Plant and Microbial Biology, North Carolina State University, 4548 Thomas Hall, Campus Box 7615, Raleigh, NC, 27695-7615, USA.
| |
Collapse
|
225
|
Richter H, Molitor B, Diender M, Sousa DZ, Angenent LT. A Narrow pH Range Supports Butanol, Hexanol, and Octanol Production from Syngas in a Continuous Co-culture of Clostridium ljungdahlii and Clostridium kluyveri with In-Line Product Extraction. Front Microbiol 2016; 7:1773. [PMID: 27877166 PMCID: PMC5099930 DOI: 10.3389/fmicb.2016.01773] [Citation(s) in RCA: 93] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2016] [Accepted: 10/21/2016] [Indexed: 12/19/2022] Open
Abstract
Carboxydotrophic bacteria (CTB) have received attention due to their ability to synthesize commodity chemicals from producer gas and synthesis gas (syngas). CTB have an important advantage of a high product selectivity compared to chemical catalysts. However, the product spectrum of wild-type CTB is narrow. Our objective was to investigate whether a strategy of combining two wild-type bacterial strains into a single, continuously fed bioprocessing step would be promising to broaden the product spectrum. Here, we have operated a syngas-fermentation process with Clostridium ljungdahlii and Clostridium kluyveri with in-line product extraction through gas stripping and product condensing within the syngas recirculation line. The main products from C. ljungdahlii fermentation at a pH of 6.0 were ethanol and acetate at net volumetric production rates of 65.5 and 431 mmol C·L−1·d−1, respectively. An estimated 2/3 of total ethanol produced was utilized by C. kluyveri to chain elongate with the reverse β-oxidation pathway, resulting in n-butyrate and n-caproate at net rates of 129 and 70 mmol C·L−1·d−1, respectively. C. ljungdahlii likely reduced the produced carboxylates to their corresponding alcohols with the reductive power from syngas. This resulted in the longer-chain alcohols n-butanol, n-hexanol, and n-octanol at net volumetric production rates of 39.2, 31.7, and 0.045 mmol C·L−1·d−1, respectively. The continuous production of the longer-chain alcohols occurred only within a narrow pH spectrum of 5.7–6.4 due to the pH discrepancy between the two strains. Regardless whether other wild-type strains could overcome this pH discrepancy, the specificity (mol carbon in product per mol carbon in all other liquid products) for each longer-chain alcohol may never be high in a single bioprocessing step. This, because two bioprocesses compete for intermediates (i.e., carboxylates): (1) chain elongation; and (2) biological reduction. This innate competition resulted in a mixture of n-butanol and n-hexanol with traces of n-octanol.
Collapse
Affiliation(s)
- Hanno Richter
- Department for Biological and Environmental Engineering, Cornell University Ithaca, NY, USA
| | - Bastian Molitor
- Department for Biological and Environmental Engineering, Cornell University Ithaca, NY, USA
| | - Martijn Diender
- Laboratory of Microbiology, Wageningen University Wageningen, Netherlands
| | - Diana Z Sousa
- Laboratory of Microbiology, Wageningen University Wageningen, Netherlands
| | - Largus T Angenent
- Department for Biological and Environmental Engineering, Cornell UniversityIthaca, NY, USA; Atkinson Center for a Sustainable Future, Cornell UniversityIthaca, NY, USA
| |
Collapse
|
226
|
Deutzmann JS, Spormann AM. Enhanced microbial electrosynthesis by using defined co-cultures. ISME JOURNAL 2016; 11:704-714. [PMID: 27801903 DOI: 10.1038/ismej.2016.149] [Citation(s) in RCA: 65] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2016] [Revised: 09/02/2016] [Accepted: 09/18/2016] [Indexed: 01/23/2023]
Abstract
Microbial uptake of free cathodic electrons presents a poorly understood aspect of microbial physiology. Uptake of cathodic electrons is particularly important in microbial electrosynthesis of sustainable fuel and chemical precursors using only CO2 and electricity as carbon, electron and energy source. Typically, large overpotentials (200 to 400 mV) were reported to be required for cathodic electron uptake during electrosynthesis of, for example, methane and acetate, or low electrosynthesis rates were observed. To address these limitations and to explore conceptual alternatives, we studied defined co-cultures metabolizing cathodic electrons. The Fe(0)-corroding strain IS4 was used to catalyze the electron uptake reaction from the cathode forming molecular hydrogen as intermediate, and Methanococcus maripaludis and Acetobacterium woodii were used as model microorganisms for hydrogenotrophic synthesis of methane and acetate, respectively. The IS4-M. maripaludis co-cultures achieved electromethanogenesis rates of 0.1-0.14 μmol cm-2 h-1 at -400 mV vs standard hydrogen electrode and 0.6-0.9 μmol cm-2 h-1 at -500 mV. Co-cultures of strain IS4 and A. woodii formed acetate at rates of 0.21-0.23 μmol cm-2 h-1 at -400 mV and 0.57-0.74 μmol cm-2 h-1 at -500 mV. These data show that defined co-cultures coupling cathodic electron uptake with synthesis reactions via interspecies hydrogen transfer may lay the foundation for an engineering strategy for microbial electrosynthesis.
Collapse
Affiliation(s)
- Jörg S Deutzmann
- Department of Civil and Environmental Engineering, Stanford University, Stanford, CA, USA
| | - Alfred M Spormann
- Department of Civil and Environmental Engineering, Stanford University, Stanford, CA, USA.,Department of Chemical Engineering, Stanford University, Stanford, CA, USA
| |
Collapse
|
227
|
Gonzalez JE, Antoniewicz MR. Tracing metabolism from lignocellulosic biomass and gaseous substrates to products with stable-isotopes. Curr Opin Biotechnol 2016; 43:86-95. [PMID: 27780112 DOI: 10.1016/j.copbio.2016.10.002] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2016] [Revised: 10/03/2016] [Accepted: 10/05/2016] [Indexed: 12/12/2022]
Abstract
Engineered microbes offer a practical and sustainable alternative to traditional industrial approaches. To increase the economic feasibility of biological processes, microbial isolates are engineered to take up inexpensive feedstocks (including lignocellulosic biomass, syngas, methane, and carbon dioxide), and convert them into substrates of central metabolism and further into value-added products. To trace the metabolism of these feedstocks into products, isotopic tracers are applied together with isotopomer analysis techniques such as 13C-metabolic flux analysis to provide a detailed picture of pathway utilization. Flux data is then integrated with kinetic models and constraint-based approaches to identify metabolic bottlenecks, propose novel metabolic engineering strategies, and improve process performance.
Collapse
Affiliation(s)
- Jacqueline E Gonzalez
- Department of Chemical and Biomolecular Engineering, Metabolic Engineering and Systems Biology Laboratory, University of Delaware, Newark, DE 19716, USA
| | - Maciek R Antoniewicz
- Department of Chemical and Biomolecular Engineering, Metabolic Engineering and Systems Biology Laboratory, University of Delaware, Newark, DE 19716, USA.
| |
Collapse
|
228
|
May HD, Evans PJ, LaBelle EV. The bioelectrosynthesis of acetate. Curr Opin Biotechnol 2016; 42:225-233. [PMID: 27743996 DOI: 10.1016/j.copbio.2016.09.004] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2016] [Revised: 08/16/2016] [Accepted: 09/12/2016] [Indexed: 12/22/2022]
Abstract
Risks associated with climate change are driving the search for new technologies to produce fuels and chemicals. The microbial electrosynthesis of chemical compounds, using electricity and CO2 as feedstock and microbes to deliver the catalysts, has the potential to be one of those technologies. Central to the production of multicarbon compounds by this process is the bioelectrosynthesis of acetate (electroacetogenesis), and significant improvements in productivity and insightful discoveries concerning the extracellular transfer of electrons to the acetogenic microorganisms have been made recently. This review examines these advances and how they are influencing the development of microbial electrosynthesis into a new biotechnology for the sustainable production of fuels and chemicals.
Collapse
Affiliation(s)
- Harold D May
- Department of Microbiology & Immunology, Marine Biomedicine & Environmental Science Center, Medical University of South Carolina, Hollings Marine Laboratory, 331 Fort Johnson Road, Charleston, SC 29412-9112, USA.
| | - Patrick J Evans
- CDM Smith, 14432 S.E. Eastgate Way, Suite 100, Bellevue, WA 98007, USA
| | - Edward V LaBelle
- Department of Microbiology & Immunology, Marine Biomedicine & Environmental Science Center, Medical University of South Carolina, Hollings Marine Laboratory, 331 Fort Johnson Road, Charleston, SC 29412-9112, USA
| |
Collapse
|
229
|
In silico metabolic engineering of Clostridium ljungdahlii for synthesis gas fermentation. Metab Eng 2016; 38:389-400. [PMID: 27720802 DOI: 10.1016/j.ymben.2016.10.002] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2016] [Revised: 08/19/2016] [Accepted: 10/05/2016] [Indexed: 02/01/2023]
Abstract
Synthesis gas fermentation is one of the most promising routes to convert synthesis gas (syngas; mainly comprised of H2 and CO) to renewable liquid fuels and chemicals by specialized bacteria. The most commonly studied syngas fermenting bacterium is Clostridium ljungdahlii, which produces acetate and ethanol as its primary metabolic byproducts. Engineering of C. ljungdahlii metabolism to overproduce ethanol, enhance the synthesize of the native byproducts lactate and 2,3-butanediol, and introduce the synthesis of non-native products such as butanol and butyrate has substantial commercial value. We performed in silico metabolic engineering studies using a genome-scale reconstruction of C. ljungdahlii metabolism and the OptKnock computational framework to identify gene knockouts that were predicted to enhance the synthesis of these native products and non-native products, introduced through insertion of the necessary heterologous pathways. The OptKnock derived strategies were often difficult to assess because increase product synthesis was invariably accompanied by decreased growth. Therefore, the OptKnock strategies were further evaluated using a spatiotemporal metabolic model of a syngas bubble column reactor, a popular technology for large-scale gas fermentation. Unlike flux balance analysis, the bubble column model accounted for the complex tradeoffs between increased product synthesis and reduced growth rates of engineered mutants within the spatially varying column environment. The two-stage methodology for deriving and evaluating metabolic engineering strategies was shown to yield new C. ljungdahlii gene targets that offer the potential for increased product synthesis under realistic syngas fermentation conditions.
Collapse
|
230
|
CO 2 fixation by anaerobic non-photosynthetic mixotrophy for improved carbon conversion. Nat Commun 2016; 7:12800. [PMID: 27687501 PMCID: PMC5056431 DOI: 10.1038/ncomms12800] [Citation(s) in RCA: 91] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2016] [Accepted: 08/01/2016] [Indexed: 01/09/2023] Open
Abstract
Maximizing the conversion of biogenic carbon feedstocks into chemicals and fuels is essential for fermentation processes as feedstock costs and processing is commonly the greatest operating expense. Unfortunately, for most fermentations, over one-third of sugar carbon is lost to CO2 due to the decarboxylation of pyruvate to acetyl-CoA and limitations in the reducing power of the bio-feedstock. Here we show that anaerobic, non-photosynthetic mixotrophy, defined as the concurrent utilization of organic (for example, sugars) and inorganic (for example, CO2) substrates in a single organism, can overcome these constraints to increase product yields and reduce overall CO2 emissions. As a proof-of-concept, Clostridium ljungdahlii was engineered to produce acetone and achieved a mass yield 138% of the previous theoretical maximum using a high cell density continuous fermentation process. In addition, when enough reductant (that is, H2) is provided, the fermentation emits no CO2. Finally, we show that mixotrophy is a general trait among acetogens.
Collapse
|
231
|
Shin J, Song Y, Jeong Y, Cho BK. Analysis of the Core Genome and Pan-Genome of Autotrophic Acetogenic Bacteria. Front Microbiol 2016; 7:1531. [PMID: 27733845 PMCID: PMC5039349 DOI: 10.3389/fmicb.2016.01531] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Accepted: 09/12/2016] [Indexed: 01/07/2023] Open
Abstract
Acetogens are obligate anaerobic bacteria capable of reducing carbon dioxide (CO2) to multicarbon compounds coupled to the oxidation of inorganic substrates, such as hydrogen (H2) or carbon monoxide (CO), via the Wood-Ljungdahl pathway. Owing to the metabolic capability of CO2 fixation, much attention has been focused on understanding the unique pathways associated with acetogens, particularly their metabolic coupling of CO2 fixation to energy conservation. Most known acetogens are phylogenetically and metabolically diverse bacteria present in 23 different bacterial genera. With the increased volume of available genome information, acetogenic bacterial genomes can be analyzed by comparative genome analysis. Even with the genetic diversity that exists among acetogens, the Wood-Ljungdahl pathway, a central metabolic pathway, and cofactor biosynthetic pathways are highly conserved for autotrophic growth. Additionally, comparative genome analysis revealed that most genes in the acetogen-specific core genome were associated with the Wood-Ljungdahl pathway. The conserved enzymes and those predicted as missing can provide insight into biological differences between acetogens and allow for the discovery of promising candidates for industrial applications.
Collapse
Affiliation(s)
- Jongoh Shin
- Systems and Synthetic Biology Laboratory, Department of Biological Sciences and KI for the BioCentury, Korea Advanced Institute of Science and Technology Daejeon, South Korea
| | - Yoseb Song
- Systems and Synthetic Biology Laboratory, Department of Biological Sciences and KI for the BioCentury, Korea Advanced Institute of Science and Technology Daejeon, South Korea
| | - Yujin Jeong
- Systems and Synthetic Biology Laboratory, Department of Biological Sciences and KI for the BioCentury, Korea Advanced Institute of Science and Technology Daejeon, South Korea
| | - Byung-Kwan Cho
- Systems and Synthetic Biology Laboratory, Department of Biological Sciences and KI for the BioCentury, Korea Advanced Institute of Science and TechnologyDaejeon, South Korea; Intelligent Synthetic Biology CenterDaejeon, South Korea
| |
Collapse
|
232
|
Claassens NJ, Sousa DZ, dos Santos VAPM, de Vos WM, van der Oost J. Harnessing the power of microbial autotrophy. Nat Rev Microbiol 2016; 14:692-706. [DOI: 10.1038/nrmicro.2016.130] [Citation(s) in RCA: 150] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
|
233
|
Pyne ME, Liu X, Moo-Young M, Chung DA, Chou CP. Genome-directed analysis of prophage excision, host defence systems, and central fermentative metabolism in Clostridium pasteurianum. Sci Rep 2016; 6:26228. [PMID: 27641836 PMCID: PMC5027557 DOI: 10.1038/srep26228] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2015] [Accepted: 04/29/2016] [Indexed: 11/09/2022] Open
Abstract
Clostridium pasteurianum is emerging as a prospective host for the production of biofuels and chemicals, and has recently been shown to directly consume electric current. Despite this growing biotechnological appeal, the organism’s genetics and central metabolism remain poorly understood. Here we present a concurrent genome sequence for the C. pasteurianum type strain and provide extensive genomic analysis of the organism’s defence mechanisms and central fermentative metabolism. Next generation genome sequencing produced reads corresponding to spontaneous excision of a novel phage, designated φ6013, which could be induced using mitomycin C and detected using PCR and transmission electron microscopy. Methylome analysis of sequencing reads provided a near-complete glimpse into the organism’s restriction-modification systems. We also unveiled the chief C. pasteurianum Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) locus, which was found to exemplify a Type I-B system. Finally, we show that C. pasteurianum possesses a highly complex fermentative metabolism whereby the metabolic pathways enlisted by the cell is governed by the degree of reductance of the substrate. Four distinct fermentation profiles, ranging from exclusively acidogenic to predominantly alcohologenic, were observed through redox consideration of the substrate. A detailed discussion of the organism’s central metabolism within the context of metabolic engineering is provided.
Collapse
Affiliation(s)
- Michael E Pyne
- Department of Chemical Engineering, University of Waterloo, Waterloo, Ontario, Canada
| | - Xuejia Liu
- Department of Chemical Engineering, University of Waterloo, Waterloo, Ontario, Canada
| | - Murray Moo-Young
- Department of Chemical Engineering, University of Waterloo, Waterloo, Ontario, Canada
| | - Duane A Chung
- Department of Chemical Engineering, University of Waterloo, Waterloo, Ontario, Canada.,Department of Pathology and Molecular Medicine, McMaster University, Ontario, Canada.,Algaeneers Inc. and Neemo Inc., Hamilton, Ontario, Canada
| | - C Perry Chou
- Department of Chemical Engineering, University of Waterloo, Waterloo, Ontario, Canada
| |
Collapse
|
234
|
Abstract
Thermophilic microorganisms as well as acetogenic bacteria are both considered ancient. Interestingly, only a few species of bacteria, all belonging to the family Thermoanaerobacteraceae, are described to conserve energy from acetate formation with hydrogen as electron donor and carbon dioxide as electron acceptor. This review reflects the metabolic differences between Moorella spp., Thermoanaerobacter kivui and Thermacetogenium phaeum, with focus on the biochemistry of autotrophic growth and energy conservation. The potential of these thermophilic acetogens for biotechnological applications is discussed briefly.
Collapse
Affiliation(s)
- Mirko Basen
- Department of Molecular Microbiology and Bioenergetics, Institute of Molecular Biosciences, Johann Wolfgang Goethe University, Frankfurt Am Main, Germany
| | - Volker Müller
- Department of Molecular Microbiology and Bioenergetics, Institute of Molecular Biosciences, Johann Wolfgang Goethe University, Frankfurt Am Main, Germany.
| |
Collapse
|
235
|
Clostridia: a flexible microbial platform for the production of alcohols. Curr Opin Chem Biol 2016; 35:65-72. [PMID: 27619003 DOI: 10.1016/j.cbpa.2016.08.024] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2016] [Revised: 08/22/2016] [Accepted: 08/24/2016] [Indexed: 11/22/2022]
Abstract
Solventogenic clostridia are native producers of ethanol and many higher alcohols employing a broad range of cheap renewable substrates, such as lignocellulosic materials and C1 gases (CO and CO2). These characteristics enable solventogenic clostridia to act as flexible microbial platforms for the production of liquid biofuels. With the rapid development of genetic tools in recent years, the intrinsic intractability of clostridia has been largely overcome, thus, engineering clostridia for production of chemicals and fuels has attracted increasing interests. Here, we provide an overview of recent progress in the production of alcohols based on solventogenic clostridia. Saccharolytic, cellulolytic and gas-fermenting clostridia are discussed, with a special focus on strategies for metabolic engineering to enable and to improve clostridia for the production of higher alcohols.
Collapse
|
236
|
Molitor B, Richter H, Martin ME, Jensen RO, Juminaga A, Mihalcea C, Angenent LT. Carbon recovery by fermentation of CO-rich off gases - Turning steel mills into biorefineries. BIORESOURCE TECHNOLOGY 2016; 215:386-396. [PMID: 27095410 DOI: 10.1016/j.biortech.2016.03.094] [Citation(s) in RCA: 87] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Revised: 03/16/2016] [Accepted: 03/17/2016] [Indexed: 05/08/2023]
Abstract
Technological solutions to reduce greenhouse gas (GHG) emissions from anthropogenic sources are required. Heavy industrial processes, such as steel making, contribute considerably to GHG emissions. Fermentation of carbon monoxide (CO)-rich off gases with wild-type acetogenic bacteria can be used to produce ethanol, acetate, and 2,3-butanediol, thereby, reducing the carbon footprint of heavy industries. Here, the processes for the production of ethanol from CO-rich off gases are discussed and a perspective on further routes towards an integrated biorefinery at a steel mill is given. Recent achievements in genetic engineering as well as integration of other biotechnology platforms to increase the product portfolio are summarized. Already, yields have been increased and the portfolio of products broadened. To develop a commercially viable process, however, the extraction from dilute product streams is a critical step and alternatives to distillation are discussed. Finally, another critical step is waste(water) treatment with the possibility to recover resources.
Collapse
Affiliation(s)
- Bastian Molitor
- Department of Biological and Environmental Engineering, Cornell University, Riley-Robb Hall, Ithaca, NY 14853, United States
| | - Hanno Richter
- Department of Biological and Environmental Engineering, Cornell University, Riley-Robb Hall, Ithaca, NY 14853, United States
| | - Michael E Martin
- LanzaTech, 8045 Lamon Avenue, Suite 400, Skokie, IL 60077, United States
| | - Rasmus O Jensen
- LanzaTech, 8045 Lamon Avenue, Suite 400, Skokie, IL 60077, United States
| | - Alex Juminaga
- LanzaTech, 8045 Lamon Avenue, Suite 400, Skokie, IL 60077, United States
| | | | - Largus T Angenent
- Department of Biological and Environmental Engineering, Cornell University, Riley-Robb Hall, Ithaca, NY 14853, United States.
| |
Collapse
|
237
|
Tortajada M. New waves underneath the purple strain. Microb Biotechnol 2016; 10:1297-1299. [PMID: 27573515 PMCID: PMC5658615 DOI: 10.1111/1751-7915.12409] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2016] [Accepted: 08/05/2016] [Indexed: 11/30/2022] Open
Abstract
Successful merging of chemical and biotechnological operations is essential to achieve cost‐efficient industrialization of bio‐based processes. The demonstration of the use of syngas, derived from microwave assisted pyrolysis of municipal solid waste, for the improved growth and poly‐3‐hydroxybutyrate production in Rhodospirillium rubrum, stands out as an example of the synergistic contribution of chemical engineering and applied microbiology to sustainable biomaterial manufacturing, paving the way to similar applications for other syngas derived bioproducts.
Collapse
Affiliation(s)
- Marta Tortajada
- BIOPOLIS S.L., Parc Científic Universitat de València. C/Catedrático Agustín Escardino, 9, Paterna, Valencia, 46980, Spain
| |
Collapse
|
238
|
Lee SH, Yun EJ, Kim J, Lee SJ, Um Y, Kim KH. Biomass, strain engineering, and fermentation processes for butanol production by solventogenic clostridia. Appl Microbiol Biotechnol 2016; 100:8255-71. [PMID: 27531513 DOI: 10.1007/s00253-016-7760-9] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2016] [Revised: 07/26/2016] [Accepted: 07/28/2016] [Indexed: 12/14/2022]
Abstract
Butanol is considered an attractive biofuel and a commercially important bulk chemical. However, economical production of butanol by solventogenic clostridia, e.g., via fermentative production of acetone-butanol-ethanol (ABE), is hampered by low fermentation performance, mainly as a result of toxicity of butanol to microorganisms and high substrate costs. Recently, sugars from marine macroalgae and syngas were recognized as potent carbon sources in biomass feedstocks that are abundant and do not compete for arable land with edible crops. With the aid of systems metabolic engineering, many researchers have developed clostridial strains with improved performance on fermentation of these substrates. Alternatively, fermentation strategies integrated with butanol recovery processes such as adsorption, gas stripping, liquid-liquid extraction, and pervaporation have been designed to increase the overall titer of butanol and volumetric productivity. Nevertheless, for economically feasible production of butanol, innovative strategies based on recent research should be implemented. This review describes and discusses recent advances in the development of biomass feedstocks, microbial strains, and fermentation processes for butanol production.
Collapse
Affiliation(s)
- Sang-Hyun Lee
- Department of Biotechnology, Graduate School, Korea University, Seoul, 02841, South Korea
| | - Eun Ju Yun
- Department of Biotechnology, Graduate School, Korea University, Seoul, 02841, South Korea
| | - Jungyeon Kim
- Department of Biotechnology, Graduate School, Korea University, Seoul, 02841, South Korea
| | - Sang Jun Lee
- Biosystems and Bioengineering Program, University of Science and Technology and Microbiomics and Immunity Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 34141, South Korea
| | - Youngsoon Um
- Clean Energy Research Center, Korea Institute of Science and Technology, Seoul, 02792, South Korea
| | - Kyoung Heon Kim
- Department of Biotechnology, Graduate School, Korea University, Seoul, 02841, South Korea.
| |
Collapse
|
239
|
Expanding the molecular toolkit for the homoacetogen Clostridium ljungdahlii. Sci Rep 2016; 6:31518. [PMID: 27527841 PMCID: PMC4985741 DOI: 10.1038/srep31518] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2016] [Accepted: 07/20/2016] [Indexed: 01/10/2023] Open
Abstract
Increasing interest in homoacetogenic bacteria for the production of biochemicals and biofuels requisites the development of new genetic tools for these atypical production organisms. An attractive host for the conversion of synthesis gas or electricity into multi-carbon compounds is Clostridium ljungdahlii. So far only limited achievements in modifying this organism towards the production of industrially relevant compounds have been made. Therefore, there is still a strong need for developing new and optimizing existing genetic tools to efficiently access its metabolism. Here, we report on the development of a stable and reproducible transformation protocol that is applicable to C. ljungdahlii and several other clostridial species. Further, we demonstrate the functionality of a temperature-sensitive origin of replication in combination with a fluorescence marker system as important tools for future genetic engineering of this host for microbial bioproduction.
Collapse
|
240
|
Bengelsdorf FR, Poehlein A, Linder S, Erz C, Hummel T, Hoffmeister S, Daniel R, Dürre P. Industrial Acetogenic Biocatalysts: A Comparative Metabolic and Genomic Analysis. Front Microbiol 2016; 7:1036. [PMID: 27458439 PMCID: PMC4935695 DOI: 10.3389/fmicb.2016.01036] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2016] [Accepted: 06/20/2016] [Indexed: 01/28/2023] Open
Abstract
Synthesis gas (syngas) fermentation by anaerobic acetogenic bacteria employing the Wood–Ljungdahl pathway is a bioprocess for production of biofuels and biocommodities. The major fermentation products of the most relevant biocatalytic strains (Clostridium ljungdahlii, C. autoethanogenum, C. ragsdalei, and C. coskatii) are acetic acid and ethanol. A comparative metabolic and genomic analysis using the mentioned biocatalysts might offer targets for metabolic engineering and thus improve the production of compounds apart from ethanol. Autotrophic growth and product formation of the four wild type (WT) strains were compared in uncontrolled batch experiments. The genomes of C. ragsdalei and C. coskatii were sequenced and the genome sequences of all four biocatalytic strains analyzed in comparative manner. Growth and product spectra (acetate, ethanol, 2,3-butanediol) of C. autoethanogenum, C. ljungdahlii, and C. ragsdalei were rather similar. In contrast, C. coskatii produced significantly less ethanol and its genome sequence lacks two genes encoding aldehyde:ferredoxin oxidoreductases (AOR). Comparative genome sequence analysis of the four WT strains revealed high average nucleotide identity (ANI) of C. ljungdahlii and C. autoethanogenum (99.3%) and C. coskatii (98.3%). In contrast, C. ljungdahlii WT and C. ragsdalei WT showed an ANI-based similarity of only 95.8%. Additionally, recombinant C. ljungdahlii strains were constructed that harbor an artificial acetone synthesis operon (ASO) consisting of the following genes: adc, ctfA, ctfB, and thlA (encoding acetoacetate decarboxylase, acetoacetyl-CoA:acetate/butyrate:CoA-transferase subunits A and B, and thiolase) under the control of thlA promoter (PthlA) from C. acetobutylicum or native pta-ack promoter (Ppta-ack) from C. ljungdahlii. Respective recombinant strains produced 2-propanol rather than acetone, due to the presence of a NADPH-dependent primary-secondary alcohol dehydrogenase that converts acetone to 2-propanol. Furthermore, the ClosTronTM system was used to construct an adhE1 integration mutant. These results provide extensive insights into genetic features of industrially relevant bacterial biocatalysts and expand the toolbox for metabolic engineering of acetogenic bacteria able to ferment syngas.
Collapse
Affiliation(s)
| | - Anja Poehlein
- Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Georg-August University Göttingen Göttingen, Germany
| | - Sonja Linder
- Institut für Mikrobiologie und Biotechnologie, Universität Ulm Ulm, Germany
| | - Catarina Erz
- Institut für Mikrobiologie und Biotechnologie, Universität Ulm Ulm, Germany
| | - Tim Hummel
- Institut für Mikrobiologie und Biotechnologie, Universität Ulm Ulm, Germany
| | | | - Rolf Daniel
- Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Georg-August University Göttingen Göttingen, Germany
| | - Peter Dürre
- Institut für Mikrobiologie und Biotechnologie, Universität Ulm Ulm, Germany
| |
Collapse
|
241
|
Yang C, Mi L, Hu X, Liu J, Wang J. Investigation into Host Selection of the Cecal Acetogen Population in Rabbits after Weaning. PLoS One 2016; 11:e0158768. [PMID: 27379387 PMCID: PMC4933399 DOI: 10.1371/journal.pone.0158768] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2016] [Accepted: 06/18/2016] [Indexed: 01/13/2023] Open
Abstract
Homoacetogenic bacteria have received attention as a hydrogenotrophic population that offers a significant energetic advantage to the host animal. Reductive acetogenesis is likely an important hydrogen disposal mechanism in the cecum of rabbits. However, molecular ecology information about cecal acetogen candidates has rarely been reported. To better understand the effect of host selection in the rabbit cecal acetogen community with respect to growth, rabbits at four different age stages (30, 60, 120 and 180 days) with the same diet were studied. Although the abundance of potential acetogens and methanogens was high in the cecum of rabbits undergoing growth, many novel potential acetogen populations were observed in the cecum of rabbits across all age groups. Young and adult rabbits had their own distinct acetogen community although they received the same diet, which suggests that as the rabbit ages, acetogens in the cecum undergo developmental changes because of host selection that are independent of diet, and perhaps the different acetogen communities result in different hydrogenotrophic characteristics. The within-group similarity increased with age, indicating that the acetogen community converges to a more homogeneous and stable arrangement with aging.
Collapse
Affiliation(s)
- Chunlei Yang
- Institute of Dairy Science, MoE Key Laboratory of Molecular Animal Nutrition, College of Animal Sciences, Zhejiang University, Hangzhou 310058, China
| | - Lan Mi
- Institute of Dairy Science, MoE Key Laboratory of Molecular Animal Nutrition, College of Animal Sciences, Zhejiang University, Hangzhou 310058, China
| | - Xialu Hu
- Institute of Dairy Science, MoE Key Laboratory of Molecular Animal Nutrition, College of Animal Sciences, Zhejiang University, Hangzhou 310058, China
| | - Jianxin Liu
- Institute of Dairy Science, MoE Key Laboratory of Molecular Animal Nutrition, College of Animal Sciences, Zhejiang University, Hangzhou 310058, China
| | - Jiakun Wang
- Institute of Dairy Science, MoE Key Laboratory of Molecular Animal Nutrition, College of Animal Sciences, Zhejiang University, Hangzhou 310058, China
- * E-mail:
| |
Collapse
|
242
|
Hoffmeister S, Gerdom M, Bengelsdorf FR, Linder S, Flüchter S, Öztürk H, Blümke W, May A, Fischer RJ, Bahl H, Dürre P. Acetone production with metabolically engineered strains of Acetobacterium woodii. Metab Eng 2016; 36:37-47. [DOI: 10.1016/j.ymben.2016.03.001] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2015] [Revised: 02/15/2016] [Accepted: 03/10/2016] [Indexed: 01/26/2023]
|
243
|
Abstract
Acetogenic bacteria are a diverse group of strictly anaerobic bacteria that utilize the Wood-Ljungdahl pathway for CO2 fixation and energy conservation. These microorganisms play an important part in the global carbon cycle and are a key component of the anaerobic food web. Their most prominent metabolic feature is autotrophic growth with molecular hydrogen and carbon dioxide as the substrates. However, most members also show an outstanding metabolic flexibility for utilizing a vast variety of different substrates. In contrast to autotrophic growth, which is hardly competitive, metabolic flexibility is seen as a key ability of acetogens to compete in ecosystems and might explain the almost-ubiquitous distribution of acetogenic bacteria in anoxic environments. This review covers the latest findings with respect to the heterotrophic metabolism of acetogenic bacteria, including utilization of carbohydrates, lactate, and different alcohols, especially in the model acetogen Acetobacterium woodii Modularity of metabolism, a key concept of pathway design in synthetic biology, together with electron bifurcation, to overcome energetic barriers, appears to be the basis for the amazing substrate spectrum. At the same time, acetogens depend on only a relatively small number of enzymes to expand the substrate spectrum. We will discuss the energetic advantages of coupling CO2 reduction to fermentations that exploit otherwise-inaccessible substrates and the ecological advantages, as well as the biotechnological applications of the heterotrophic metabolism of acetogens.
Collapse
|
244
|
Breitkopf R, Uhlig R, Drenckhan T, Fischer RJ. Two propanediol utilization-like proteins of Moorella thermoacetica with phosphotransacetylase activity. Extremophiles 2016; 20:653-61. [PMID: 27338272 DOI: 10.1007/s00792-016-0854-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2015] [Accepted: 06/14/2016] [Indexed: 12/16/2022]
Abstract
Moorella thermoacetica is one of the model acetogenic bacteria for the resolution of the Wood-Ljungdahl (acetyl-CoA) pathway in which CO2 is autotrophically assimilated yielding acetyl-CoA as central intermediate. Its further conversion into acetate relies on subsequent phosphotransacetylase (PTA) and acetate kinase reactions. However, the genome of M. thermoacetica contains no pta homologous gene. It has been speculated that the moth_0864 and moth_1181 gene products sharing similarities with an evolutionarily distinct phosphotransacylase involved in 1,2-propanediol utilization (PDUL) of Salmonella enterica act as PTAs in M. thermoacetica. Here, we demonstrate specific PTA activities with acetyl-CoA as substrate of 9.05 and 2.03 U/mg for the recombinant enzymes PDUL1 (Moth_1181) and PDUL2 (Moth_0864), respectively. Both showed maximal activity at 65 °C and pH 7.6. Native proteins (90 kDa) are homotetramers composed of four subunits with apparent molecular masses of about 23 kDa. Thus, one or both PDULs of M. thermoacetica might act as PTAs in vivo catalyzing the penultimate step of the Wood-Ljungdahl pathway toward the formation of acetate. In silico analysis underlined that up to now beside of M. thermoacetica, only Sporomusa ovata contains only PDUL like class(III)-PTAs but no other phosphotransacetylases or phosphotransbutyrylases (PTBs).
Collapse
Affiliation(s)
- Ronja Breitkopf
- BBSRC/EPSRC Synthetic Biology Research Centre, School of Life Sciences, University of Nottingham, Nottingham, NG7 2RD, UK
| | - Ronny Uhlig
- Abteilung Mikrobiologie, Institut für Biowissenschaften, Universität Rostock, Albert-Einstein-Str. 3, 18059, Rostock, Germany
| | - Tina Drenckhan
- Abteilung Mikrobiologie, Institut für Biowissenschaften, Universität Rostock, Albert-Einstein-Str. 3, 18059, Rostock, Germany
| | - Ralf-Jörg Fischer
- Abteilung Mikrobiologie, Institut für Biowissenschaften, Universität Rostock, Albert-Einstein-Str. 3, 18059, Rostock, Germany.
| |
Collapse
|
245
|
Volpers M, Claassens NJ, Noor E, van der Oost J, de Vos WM, Kengen SWM, Martins dos Santos VAP. Integrated In Silico Analysis of Pathway Designs for Synthetic Photo-Electro-Autotrophy. PLoS One 2016; 11:e0157851. [PMID: 27336167 PMCID: PMC4919048 DOI: 10.1371/journal.pone.0157851] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2015] [Accepted: 06/06/2016] [Indexed: 11/22/2022] Open
Abstract
The strong advances in synthetic biology enable the engineering of novel functions and complex biological features in unprecedented ways, such as implementing synthetic autotrophic metabolism into heterotrophic hosts. A key challenge for the sustainable production of fuels and chemicals entails the engineering of synthetic autotrophic organisms that can effectively and efficiently fix carbon dioxide by using sustainable energy sources. This challenge involves the integration of carbon fixation and energy uptake systems. A variety of carbon fixation pathways and several types of photosystems and other energy uptake systems can be chosen and, potentially, modularly combined to design synthetic autotrophic metabolism. Prior to implementation, these designs can be evaluated by the combination of several computational pathway analysis techniques. Here we present a systematic, integrated in silico analysis of photo-electro-autotrophic pathway designs, consisting of natural and synthetic carbon fixation pathways, a proton-pumping rhodopsin photosystem for ATP regeneration and an electron uptake pathway. We integrated Flux Balance Analysis of the heterotrophic chassis Escherichia coli with kinetic pathway analysis and thermodynamic pathway analysis (Max-min Driving Force). The photo-electro-autotrophic designs are predicted to have a limited potential for anaerobic, autotrophic growth of E. coli, given the relatively low ATP regenerating capacity of the proton pumping rhodopsin photosystems and the high ATP maintenance of E. coli. If these factors can be tackled, our analysis indicates the highest growth potential for the natural reductive tricarboxylic acid cycle and the synthetic pyruvate synthase–pyruvate carboxylate -glyoxylate bicycle. Both carbon fixation cycles are very ATP efficient, while maintaining fast kinetics, which also results in relatively low estimated protein costs for these pathways. Furthermore, the synthetic bicycles are highly thermodynamic favorable under conditions analysed. However, the most important challenge identified for improving photo-electro-autotrophic growth is increasing the proton-pumping rate of the rhodopsin photosystems, allowing for higher ATP regeneration. Alternatively, other designs of autotrophy may be considered, therefore the herein presented integrated modeling approach allows synthetic biologists to evaluate and compare complex pathway designs before experimental implementation.
Collapse
Affiliation(s)
- Michael Volpers
- Laboratory of Systems and Synthetic Biology, Wageningen University, Dreijenplein 10, 6703 HB, Wageningen, The Netherlands
- LifeGlimmer GmbH, Markelstr. 39a, 12136, Berlin, Germany
| | - Nico J. Claassens
- Laboratory of Microbiology, Wageningen University, Dreijenplein 10, 6703 HB, Wageningen, The Netherlands
| | - Elad Noor
- Institute of Molecular Systems Biology, ETH Zürich, Auguste-Piccard-Hof 1, 8093, Zürich, Switzerland
| | - John van der Oost
- Laboratory of Microbiology, Wageningen University, Dreijenplein 10, 6703 HB, Wageningen, The Netherlands
| | - Willem M. de Vos
- Laboratory of Microbiology, Wageningen University, Dreijenplein 10, 6703 HB, Wageningen, The Netherlands
- Department of Bacteriology and Immunology, Helsinki University, Haartmaninkatu 3, 00014, Helsinki, Finland
| | - Servé W. M. Kengen
- Laboratory of Microbiology, Wageningen University, Dreijenplein 10, 6703 HB, Wageningen, The Netherlands
| | - Vitor A. P. Martins dos Santos
- Laboratory of Systems and Synthetic Biology, Wageningen University, Dreijenplein 10, 6703 HB, Wageningen, The Netherlands
- LifeGlimmer GmbH, Markelstr. 39a, 12136, Berlin, Germany
- * E-mail:
| |
Collapse
|
246
|
Genome Sequence of the Acetogenic Bacterium Moorella mulderi DSM 14980T. GENOME ANNOUNCEMENTS 2016; 4:4/3/e00444-16. [PMID: 27231372 PMCID: PMC4882953 DOI: 10.1128/genomea.00444-16] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Here, we report the draft genome sequence of Moorella mulderi DSM 14980T, a thermophilic acetogenic bacterium, which is able to grow autotrophically on H2 plus CO2 using the Wood-Ljungdahl pathway. The genome consists of a circular chromosome (2.99 Mb).
Collapse
|
247
|
Insights into CO2 Fixation Pathway of Clostridium autoethanogenum by Targeted Mutagenesis. mBio 2016; 7:mBio.00427-16. [PMID: 27222467 PMCID: PMC4895105 DOI: 10.1128/mbio.00427-16] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
The future sustainable production of chemicals and fuels from nonpetrochemical resources and reduction of greenhouse gas emissions are two of the greatest societal challenges. Gas fermentation, which utilizes the ability of acetogenic bacteria such as Clostridium autoethanogenum to grow and convert CO2 and CO into low-carbon fuels and chemicals, could potentially provide solutions to both. Acetogens fix these single-carbon gases via the Wood-Ljungdahl pathway. Two enzyme activities are predicted to be essential to the pathway: carbon monoxide dehydrogenase (CODH), which catalyzes the reversible oxidation of CO to CO2, and acetyl coenzyme A (acetyl-CoA) synthase (ACS), which combines with CODH to form a CODH/ACS complex for acetyl-CoA fixation. Despite their pivotal role in carbon fixation, their functions have not been confirmed in vivo. By genetically manipulating all three CODH isogenes (acsA, cooS1, and cooS2) of C. autoethanogenum, we highlighted the functional redundancies of CODH by demonstrating that cooS1 and cooS2 are dispensable for autotrophy. Unexpectedly, the cooS1 inactivation strain showed a significantly reduced lag phase and a higher growth rate than the wild type on H2 and CO2. During heterotrophic growth on fructose, the acsA inactivation strain exhibited 61% reduced biomass and the abolishment of acetate production (a hallmark of acetogens), in favor of ethanol, lactate, and 2,3-butanediol production. A translational readthrough event was discovered in the uniquely truncated (compared to those of other acetogens) C. autoethanogenum acsA gene. Insights gained from studying the function of CODH enhance the overall understanding of autotrophy and can be used for optimization of biotechnological production of ethanol and other commodities via gas fermentation. Gas fermentation is an emerging technology that converts the greenhouse gases CO2 and CO in industrial waste gases and gasified biomass into fuels and chemical commodities. Acetogenic bacteria such as Clostridium autoethanogenum are central to this bioprocess, but the molecular and genetic characterization of this microorganism is currently lacking. By targeting all three of the isogenes encoding carbon monoxide dehydrogenase (CODH) in C. autoethanogenum, we identified the most important CODH isogene for carbon fixation and demonstrated that genetic inactivation of CODH could improve autotrophic growth. This study shows that disabling of the Wood-Ljungdahl pathway via the inactivation of acsA (encodes CODH) significantly impairs heterotrophic growth and alters the product profile by abolishing acetate production. Moreover, we discovered a previously undescribed mechanism for controlling the production of this enzyme. This study provides valuable insights into the acetogenic pathway and can be used for the development of more efficient and productive strains for gas fermentation.
Collapse
|
248
|
Liew F, Martin ME, Tappel RC, Heijstra BD, Mihalcea C, Köpke M. Gas Fermentation-A Flexible Platform for Commercial Scale Production of Low-Carbon-Fuels and Chemicals from Waste and Renewable Feedstocks. Front Microbiol 2016; 7:694. [PMID: 27242719 PMCID: PMC4862988 DOI: 10.3389/fmicb.2016.00694] [Citation(s) in RCA: 206] [Impact Index Per Article: 25.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2016] [Accepted: 04/26/2016] [Indexed: 12/13/2022] Open
Abstract
There is an immediate need to drastically reduce the emissions associated with global fossil fuel consumption in order to limit climate change. However, carbon-based materials, chemicals, and transportation fuels are predominantly made from fossil sources and currently there is no alternative source available to adequately displace them. Gas-fermenting microorganisms that fix carbon dioxide (CO2) and carbon monoxide (CO) can break this dependence as they are capable of converting gaseous carbon to fuels and chemicals. As such, the technology can utilize a wide range of feedstocks including gasified organic matter of any sort (e.g., municipal solid waste, industrial waste, biomass, and agricultural waste residues) or industrial off-gases (e.g., from steel mills or processing plants). Gas fermentation has matured to the point that large-scale production of ethanol from gas has been demonstrated by two companies. This review gives an overview of the gas fermentation process, focusing specifically on anaerobic acetogens. Applications of synthetic biology and coupling gas fermentation to additional processes are discussed in detail. Both of these strategies, demonstrated at bench-scale, have abundant potential to rapidly expand the commercial product spectrum of gas fermentation and further improve efficiencies and yields.
Collapse
|
249
|
Pal P, Nayak J. Acetic Acid Production and Purification: Critical Review Towards Process Intensification. SEPARATION AND PURIFICATION REVIEWS 2016. [DOI: 10.1080/15422119.2016.1185017] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
|
250
|
Islam MA, Zengler K, Edwards EA, Mahadevan R, Stephanopoulos G. Investigating Moorella thermoacetica metabolism with a genome-scale constraint-based metabolic model. Integr Biol (Camb) 2016; 7:869-82. [PMID: 25994252 DOI: 10.1039/c5ib00095e] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Moorella thermoacetica is a strictly anaerobic, endospore-forming, and metabolically versatile acetogenic bacterium capable of conserving energy by both autotrophic (acetogenesis) and heterotrophic (homoacetogenesis) modes of metabolism. Its metabolic diversity and the ability to efficiently convert a wide range of compounds, including syngas (CO + H2) into acetyl-CoA have made this thermophilic bacterium a promising host for industrial biotechnology applications. However, lack of detailed information on M. thermoacetica's metabolism is a major impediment to its use as a microbial cell factory. In order to overcome this issue, a genome-scale constraint-based metabolic model of Moorella thermoacetica, iAI558, has been developed using its genome sequence and physiological data from published literature. The reconstructed metabolic network of M. thermoacetica comprises 558 metabolic genes, 705 biochemical reactions, and 698 metabolites. Of the total 705 model reactions, 680 are gene-associated while the rest are non-gene associated reactions. The model, in addition to simulating both autotrophic and heterotrophic growth of M. thermoacetica, revealed degeneracy in its TCA-cycle, a common characteristic of anaerobic metabolism. Furthermore, the model helped elucidate the poorly understood energy conservation mechanism of M. thermoacetica during autotrophy. Thus, in addition to generating experimentally testable hypotheses regarding its physiology, such a detailed model will facilitate rapid strain designing and metabolic engineering of M. thermoacetica for industrial applications.
Collapse
Affiliation(s)
- M Ahsanul Islam
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
| | | | | | | | | |
Collapse
|