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Klask CM, Jäger B, Casini I, Angenent LT, Molitor B. Genetic Evidence Reveals the Indispensable Role of the rseC Gene for Autotrophy and the Importance of a Functional Electron Balance for Nitrate Reduction in Clostridium ljungdahlii. Front Microbiol 2022; 13:887578. [PMID: 35615511 PMCID: PMC9124969 DOI: 10.3389/fmicb.2022.887578] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Accepted: 03/31/2022] [Indexed: 11/20/2022] Open
Abstract
For Clostridium ljungdahlii, the RNF complex plays a key role for energy conversion from gaseous substrates such as hydrogen and carbon dioxide. In a previous study, a disruption of RNF-complex genes led to the loss of autotrophy, while heterotrophy was still possible via glycolysis. Furthermore, it was shown that the energy limitation during autotrophy could be lifted by nitrate supplementation, which resulted in an elevated cellular growth and ATP yield. Here, we used CRISPR-Cas12a to delete: (1) the RNF complex-encoding gene cluster rnfCDGEAB; (2) the putative RNF regulator gene rseC; and (3) a gene cluster that encodes for a putative nitrate reductase. The deletion of either rnfCDGEAB or rseC resulted in a complete loss of autotrophy, which could be restored by plasmid-based complementation of the deleted genes. We observed a transcriptional repression of the RNF-gene cluster in the rseC-deletion strain during autotrophy and investigated the distribution of the rseC gene among acetogenic bacteria. To examine nitrate reduction and its connection to the RNF complex, we compared autotrophic and heterotrophic growth of our three deletion strains with either ammonium or nitrate. The rnfCDGEAB- and rseC-deletion strains failed to reduce nitrate as a metabolic activity in non-growing cultures during autotrophy but not during heterotrophy. In contrast, the nitrate reductase deletion strain was able to grow in all tested conditions but lost the ability to reduce nitrate. Our findings highlight the important role of the rseC gene for autotrophy, and in addition, contribute to understand the connection of nitrate reduction to energy metabolism.
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Affiliation(s)
- Christian-Marco Klask
- Environmental Biotechnology Group, Geo- and Environmental Science Center, University of Tübingen, Tübingen, Germany
| | - Benedikt Jäger
- Environmental Biotechnology Group, Geo- and Environmental Science Center, University of Tübingen, Tübingen, Germany
| | - Isabella Casini
- Environmental Biotechnology Group, Geo- and Environmental Science Center, University of Tübingen, Tübingen, Germany
| | - Largus T. Angenent
- Environmental Biotechnology Group, Geo- and Environmental Science Center, University of Tübingen, Tübingen, Germany
- Cluster of Excellence – Controlling Microbes to Fight Infections, University of Tübingen, Tübingen, Germany
- Max Planck Institute for Biology Tübingen, Tübingen, Germany
| | - Bastian Molitor
- Environmental Biotechnology Group, Geo- and Environmental Science Center, University of Tübingen, Tübingen, Germany
- Cluster of Excellence – Controlling Microbes to Fight Infections, University of Tübingen, Tübingen, Germany
- *Correspondence: Bastian Molitor,
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de Lima LA, Ingelman H, Brahmbhatt K, Reinmets K, Barry C, Harris A, Marcellin E, Köpke M, Valgepea K. Faster Growth Enhances Low Carbon Fuel and Chemical Production Through Gas Fermentation. Front Bioeng Biotechnol 2022; 10:879578. [PMID: 35497340 PMCID: PMC9039284 DOI: 10.3389/fbioe.2022.879578] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2022] [Accepted: 03/14/2022] [Indexed: 12/13/2022] Open
Abstract
Gas fermentation offers both fossil carbon-free sustainable production of fuels and chemicals and recycling of gaseous and solid waste using gas-fermenting microbes. Bioprocess development, systems-level analysis of biocatalyst metabolism, and engineering of cell factories are advancing the widespread deployment of the commercialised technology. Acetogens are particularly attractive biocatalysts but effects of the key physiological parameter–specific growth rate (μ)—on acetogen metabolism and the gas fermentation bioprocess have not been established yet. Here, we investigate the μ-dependent bioprocess performance of the model-acetogen Clostridium autoethanogenum in CO and syngas (CO + CO2+H2) grown chemostat cultures and assess systems-level metabolic responses using gas analysis, metabolomics, transcriptomics, and metabolic modelling. We were able to obtain steady-states up to μ ∼2.8 day−1 (∼0.12 h−1) and show that faster growth supports both higher yields and productivities for reduced by-products ethanol and 2,3-butanediol. Transcriptomics data revealed differential expression of 1,337 genes with increasing μ and suggest that C. autoethanogenum uses transcriptional regulation to a large extent for facilitating faster growth. Metabolic modelling showed significantly increased fluxes for faster growing cells that were, however, not accompanied by gene expression changes in key catabolic pathways for CO and H2 metabolism. Cells thus seem to maintain sufficient “baseline” gene expression to rapidly respond to CO and H2 availability without delays to kick-start metabolism. Our work advances understanding of transcriptional regulation in acetogens and shows that faster growth of the biocatalyst improves the gas fermentation bioprocess.
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Affiliation(s)
- Lorena Azevedo de Lima
- ERA Chair in Gas Fermentation Technologies, Institute of Technology, University of Tartu, Tartu, Estonia
| | - Henri Ingelman
- ERA Chair in Gas Fermentation Technologies, Institute of Technology, University of Tartu, Tartu, Estonia
| | - Kush Brahmbhatt
- ERA Chair in Gas Fermentation Technologies, Institute of Technology, University of Tartu, Tartu, Estonia
| | - Kristina Reinmets
- ERA Chair in Gas Fermentation Technologies, Institute of Technology, University of Tartu, Tartu, Estonia
| | - Craig Barry
- Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, St. Lucia, QLD, Australia
| | | | - Esteban Marcellin
- Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, St. Lucia, QLD, Australia
| | | | - Kaspar Valgepea
- ERA Chair in Gas Fermentation Technologies, Institute of Technology, University of Tartu, Tartu, Estonia
- *Correspondence: Kaspar Valgepea,
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Abstract
Microbes that can recycle one-carbon (C1) greenhouse gases into fuels and chemicals are vital for the biosustainability of future industries. Acetogens are the most efficient known microbes for fixing carbon oxides CO2 and CO. Understanding proteome allocation is important for metabolic engineering as it dictates metabolic fitness. Here, we use absolute proteomics to quantify intracellular concentrations for >1,000 proteins in the model acetogen Clostridium autoethanogenum grown autotrophically on three gas mixtures (CO, CO+H2, or CO+CO2+H2). We detect the prioritization of proteome allocation for C1 fixation and the significant expression of proteins involved in the production of acetate and ethanol as well as proteins with unclear functions. The data also revealed which isoenzymes are likely relevant in vivo for CO oxidation, H2 metabolism, and ethanol production. The integration of proteomic and metabolic flux data demonstrated that enzymes catalyze high fluxes with high concentrations and high in vivo catalytic rates. We show that flux adjustments were dominantly accompanied by changing enzyme catalytic rates rather than concentrations. IMPORTANCE Acetogen bacteria are important for maintaining biosustainability as they can recycle gaseous C1 waste feedstocks (e.g., industrial waste gases and syngas from gasified biomass or municipal solid waste) into fuels and chemicals. Notably, the acetogen Clostridium autoethanogenum is being used as a cell factory in industrial-scale gas fermentation. Here, we perform reliable absolute proteome quantification for the first time in an acetogen. This is important as our work advances both rational metabolic engineering of acetogen cell factories and accurate in silico reconstruction of their phenotypes. Furthermore, this absolute proteomics data set serves as a reference toward a better systems-level understanding of the ancient metabolism of acetogens.
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Pavan M, Reinmets K, Garg S, Mueller AP, Marcellin E, Köpke M, Valgepea K. Advances in systems metabolic engineering of autotrophic carbon oxide-fixing biocatalysts towards a circular economy. Metab Eng 2022; 71:117-141. [DOI: 10.1016/j.ymben.2022.01.015] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 01/24/2022] [Accepted: 01/25/2022] [Indexed: 12/16/2022]
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Zhang C, Nie X, Zhang H, Wu Y, He H, Yang C, Jiang W, Gu Y. Functional dissection and modulation of the BirA protein for improved autotrophic growth of gas-fermenting Clostridium ljungdahlii. Microb Biotechnol 2021; 14:2072-2089. [PMID: 34291572 PMCID: PMC8449670 DOI: 10.1111/1751-7915.13884] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Accepted: 06/22/2021] [Indexed: 11/28/2022] Open
Abstract
Gas-fermenting Clostridium species can convert one-carbon gases (CO2 /CO) into a variety of chemicals and fuels, showing excellent application prospects in green biological manufacturing. The discovery of crucial genes and proteins with novel functions is important for understanding and further optimization of these autotrophic bacteria. Here, we report that the Clostridium ljungdahlii BirA protein (ClBirA) plays a pleiotropic regulator role, which, together with its biotin protein ligase (BPL) activity, enables an effective control of autotrophic growth of C. ljungdahlii. The structural modulation of ClBirA, combined with the in vivo and in vitro analyses, further reveals the action mechanism of ClBirA's dual roles as well as their interaction in C. ljungdahlii. Importantly, an atypical, flexible architecture of the binding site was found to be employed by ClBirA in the regulation of a lot of essential pathway genes, thereby expanding BirA's target genes to a broader range in clostridia. Based on these findings, molecular modification of ClBirA was performed, and an improved cellular performance of C. ljungdahlii was achieved in gas fermentation. This work reveals a previously unknown potent role of BirA in gas-fermenting clostridia, providing new perspective for understanding and engineering these autotrophic bacteria.
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Affiliation(s)
- Can Zhang
- Key Laboratory of Synthetic BiologyThe State Key Laboratory of Plant Carbon‐Nitrogen AssimilationCAS Center for Excellence in Molecular Plant SciencesShanghai Institute of Plant Physiology and EcologyChinese Academy of SciencesShanghai200032China
- University of Chinese Academy of SciencesBeijingChina
| | - Xiaoqun Nie
- Key Laboratory of Synthetic BiologyThe State Key Laboratory of Plant Carbon‐Nitrogen AssimilationCAS Center for Excellence in Molecular Plant SciencesShanghai Institute of Plant Physiology and EcologyChinese Academy of SciencesShanghai200032China
| | - Huan Zhang
- Key Laboratory of Synthetic BiologyThe State Key Laboratory of Plant Carbon‐Nitrogen AssimilationCAS Center for Excellence in Molecular Plant SciencesShanghai Institute of Plant Physiology and EcologyChinese Academy of SciencesShanghai200032China
- University of Chinese Academy of SciencesBeijingChina
| | - Yuwei Wu
- Key Laboratory of Synthetic BiologyThe State Key Laboratory of Plant Carbon‐Nitrogen AssimilationCAS Center for Excellence in Molecular Plant SciencesShanghai Institute of Plant Physiology and EcologyChinese Academy of SciencesShanghai200032China
- University of Chinese Academy of SciencesBeijingChina
| | - Huiqi He
- Key Laboratory of Synthetic BiologyThe State Key Laboratory of Plant Carbon‐Nitrogen AssimilationCAS Center for Excellence in Molecular Plant SciencesShanghai Institute of Plant Physiology and EcologyChinese Academy of SciencesShanghai200032China
| | - Chen Yang
- Key Laboratory of Synthetic BiologyThe State Key Laboratory of Plant Carbon‐Nitrogen AssimilationCAS Center for Excellence in Molecular Plant SciencesShanghai Institute of Plant Physiology and EcologyChinese Academy of SciencesShanghai200032China
| | - Weihong Jiang
- Key Laboratory of Synthetic BiologyThe State Key Laboratory of Plant Carbon‐Nitrogen AssimilationCAS Center for Excellence in Molecular Plant SciencesShanghai Institute of Plant Physiology and EcologyChinese Academy of SciencesShanghai200032China
| | - Yang Gu
- Key Laboratory of Synthetic BiologyThe State Key Laboratory of Plant Carbon‐Nitrogen AssimilationCAS Center for Excellence in Molecular Plant SciencesShanghai Institute of Plant Physiology and EcologyChinese Academy of SciencesShanghai200032China
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Fackler N, Heffernan J, Juminaga A, Doser D, Nagaraju S, Gonzalez-Garcia RA, Simpson SD, Marcellin E, Köpke M. Transcriptional control of Clostridium autoethanogenum using CRISPRi. Synth Biol (Oxf) 2021; 6:ysab008. [PMID: 33928195 PMCID: PMC8062849 DOI: 10.1093/synbio/ysab008] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Revised: 01/15/2021] [Accepted: 02/01/2021] [Indexed: 02/06/2023] Open
Abstract
Gas fermentation by Clostridium autoethanogenum is a commercial process for the sustainable biomanufacturing of fuels and valuable chemicals using abundant, low-cost C1 feedstocks (CO and CO2) from sources such as inedible biomass, unsorted and nonrecyclable municipal solid waste, and industrial emissions. Efforts toward pathway engineering and elucidation of gene function in this microbe have been limited by a lack of genetic tools to control gene expression and arduous genome engineering methods. To increase the pace of progress, here we developed an inducible CRISPR interference (CRISPRi) system for C. autoethanogenum and applied that system toward transcriptional repression of genes with ostensibly crucial functions in metabolism.
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Affiliation(s)
| | - James Heffernan
- Australian Institute for Bioengineering and Nanotechnology, ARC Centre of Excellence in Synthetic Biology & Metabolomics Australia, The University of Queensland, Brisbane, Queensland, 4072 Australia
| | | | | | | | - R Axayacatl Gonzalez-Garcia
- Australian Institute for Bioengineering and Nanotechnology, ARC Centre of Excellence in Synthetic Biology & Metabolomics Australia, The University of Queensland, Brisbane, Queensland, 4072 Australia
| | | | - Esteban Marcellin
- Australian Institute for Bioengineering and Nanotechnology, ARC Centre of Excellence in Synthetic Biology & Metabolomics Australia, The University of Queensland, Brisbane, Queensland, 4072 Australia
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Bourgade B, Minton NP, Islam MA. Genetic and metabolic engineering challenges of C1-gas fermenting acetogenic chassis organisms. FEMS Microbiol Rev 2021; 45:fuab008. [PMID: 33595667 PMCID: PMC8351756 DOI: 10.1093/femsre/fuab008] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Accepted: 01/15/2021] [Indexed: 12/11/2022] Open
Abstract
Unabated mining and utilisation of petroleum and petroleum resources and their conversion to essential fuels and chemicals have drastic environmental consequences, contributing to global warming and climate change. In addition, fossil fuels are finite resources, with a fast-approaching shortage. Accordingly, research efforts are increasingly focusing on developing sustainable alternatives for chemicals and fuels production. In this context, bioprocesses, relying on microorganisms, have gained particular interest. For example, acetogens use the Wood-Ljungdahl pathway to grow on single carbon C1-gases (CO2 and CO) as their sole carbon source and produce valuable products such as acetate or ethanol. These autotrophs can, therefore, be exploited for large-scale fermentation processes to produce industrially relevant chemicals from abundant greenhouse gases. In addition, genetic tools have recently been developed to improve these chassis organisms through synthetic biology approaches. This review will focus on the challenges of genetically and metabolically modifying acetogens. It will first discuss the physical and biochemical obstacles complicating successful DNA transfer in these organisms. Current genetic tools developed for several acetogens, crucial for strain engineering to consolidate and expand their catalogue of products, will then be described. Recent tool applications for metabolic engineering purposes to allow redirection of metabolic fluxes or production of non-native compounds will lastly be covered.
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Affiliation(s)
- Barbara Bourgade
- Department of Chemical Engineering, Loughborough University, Loughborough, Leicestershire, LE11 3TU, UK
| | - Nigel P Minton
- BBSRC/EPSRC Synthetic Biology Research Centre (SBRC), School of Life Sciences, University Park, University of Nottingham, Nottingham, Nottinghamshire, NG7 2RD, UK
| | - M Ahsanul Islam
- Department of Chemical Engineering, Loughborough University, Loughborough, Leicestershire, LE11 3TU, UK
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Shi XC, Tremblay PL, Wan L, Zhang T. Improved robustness of microbial electrosynthesis by adaptation of a strict anaerobic microbial catalyst to molecular oxygen. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 754:142440. [PMID: 33254866 DOI: 10.1016/j.scitotenv.2020.142440] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Revised: 08/24/2020] [Accepted: 09/13/2020] [Indexed: 06/12/2023]
Abstract
Microbial electrosynthesis (MES) and other bioprocesses such as syngas fermentation developed for energy storage and the conversion of carbon dioxide into valuable chemicals often employs acetogens as microbial catalysts. Acetogens are sensitive to molecular oxygen, which means that bioproduction reactors must be maintained under strict anaerobic conditions. This requirement increases cost and does not eliminate the possibility of O2 leakage. For MES, the risk is even greater since the system generates O2 when water splitting is the anodic reaction. Here, we show that O2 from the anode of a MES reactor diffuses into the cathode chamber where strict anaerobes reduce CO2. To overcome this drawback, a stepwise adaptive laboratory evolution (ALE) strategy is used to develop the O2 tolerance of the acetogen Sporomusa ovata. Two heavily-mutated S. ovata strains growing well autotrophically in the presence of 0.5 to 5% O2 were obtained. The adapted strains were more performant in the MES system than the wild type converting electrical energy and CO2 into acetate 1.5 fold faster. This study shows that the O2 tolerance of acetogens can be increased, which leads to improvement of the performance and robustness of energy-storage bioprocesses such as MES where O2 is an inhibitor.
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Affiliation(s)
- Xiao-Chen Shi
- State Key Laboratory of Silicate Materials for Architectures, Wuhan University of Technology, Wuhan 430070, PR China; School of Chemistry, Chemical Engineering and Life Science, Wuhan University of Technology, Wuhan 430070, PR China; School of Materials Science and Engineering, Wuhan University of Technology, Wuhan 430070, PR China
| | - Pier-Luc Tremblay
- State Key Laboratory of Silicate Materials for Architectures, Wuhan University of Technology, Wuhan 430070, PR China; School of Chemistry, Chemical Engineering and Life Science, Wuhan University of Technology, Wuhan 430070, PR China
| | - Lulu Wan
- State Key Laboratory of Silicate Materials for Architectures, Wuhan University of Technology, Wuhan 430070, PR China; School of Chemistry, Chemical Engineering and Life Science, Wuhan University of Technology, Wuhan 430070, PR China; School of Materials Science and Engineering, Wuhan University of Technology, Wuhan 430070, PR China
| | - Tian Zhang
- State Key Laboratory of Silicate Materials for Architectures, Wuhan University of Technology, Wuhan 430070, PR China; School of Chemistry, Chemical Engineering and Life Science, Wuhan University of Technology, Wuhan 430070, PR China; School of Materials Science and Engineering, Wuhan University of Technology, Wuhan 430070, PR China.
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Köpke M, Simpson SD. Pollution to products: recycling of ‘above ground’ carbon by gas fermentation. Curr Opin Biotechnol 2020; 65:180-189. [DOI: 10.1016/j.copbio.2020.02.017] [Citation(s) in RCA: 72] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Revised: 02/21/2020] [Accepted: 02/26/2020] [Indexed: 02/01/2023]
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