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Ingelman H, Heffernan JK, Harris A, Brown SD, Shaikh KM, Saqib AY, Pinheiro MJ, de Lima LA, Martinez KR, Gonzalez-Garcia RA, Hawkins G, Daleiden J, Tran L, Zeleznik H, Jensen RO, Reynoso V, Schindel H, Jänes J, Simpson SD, Köpke M, Marcellin E, Valgepea K. Autotrophic adaptive laboratory evolution of the acetogen Clostridium autoethanogenum delivers the gas-fermenting strain LAbrini with superior growth, products, and robustness. N Biotechnol 2024; 83:S1871-6784(24)00023-2. [PMID: 38871051 DOI: 10.1016/j.nbt.2024.06.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2024] [Revised: 06/05/2024] [Accepted: 06/10/2024] [Indexed: 06/15/2024]
Abstract
Microbes able to convert gaseous one-carbon (C1) waste feedstocks are increasingly important to transition to the sustainable production of renewable chemicals and fuels. Acetogens are interesting biocatalysts since gas fermentation using Clostridium autoethanogenum has been commercialised. However, most acetogen strains need complex nutrients, display slow growth, and are not robust for bioreactor fermentations. In this work, we used three different and independent adaptive laboratory evolution (ALE) strategies to evolve the wild-type C. autoethanogenum to grow faster, without yeast extract and to be robust in operating continuous bioreactor cultures. Multiple evolved strains with improved phenotypes were isolated on minimal media with one strain, named "LAbrini", exhibiting superior performance regarding the maximum specific growth rate, product profile, and robustness in continuous cultures. Whole-genome sequencing of the evolved strains identified 25 mutations. Of particular interest are two genes that acquired seven different mutations across the three ALE strategies, potentially as a result of convergent evolution. Reverse genetic engineering of mutations in potentially sporulation-related genes CLAU_3129 (spo0A) and CLAU_1957 recovered all three superior features of our ALE strains through triggering significant proteomic rearrangements. This work provides a robust C. autoethanogenum strain "LAbrini" to accelerate phenotyping and genetic engineering and to better understand acetogen metabolism.
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Affiliation(s)
- Henri Ingelman
- ERA Chair in Gas Fermentation Technologies, Institute of Bioengineering, University of Tartu, 50411 Tartu, Estonia
| | - James K Heffernan
- Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, 4072 St. Lucia, Australia
| | | | | | | | - Asfand Yar Saqib
- ERA Chair in Gas Fermentation Technologies, Institute of Bioengineering, University of Tartu, 50411 Tartu, Estonia
| | - Marina J Pinheiro
- ERA Chair in Gas Fermentation Technologies, Institute of Bioengineering, University of Tartu, 50411 Tartu, Estonia
| | - Lorena Azevedo de Lima
- ERA Chair in Gas Fermentation Technologies, Institute of Bioengineering, University of Tartu, 50411 Tartu, Estonia
| | - Karen Rodriguez Martinez
- Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, 4072 St. Lucia, Australia
| | - Ricardo A Gonzalez-Garcia
- Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, 4072 St. Lucia, Australia
| | | | | | | | | | | | | | | | - Jürgen Jänes
- Institute of Molecular Systems Biology, ETH Zürich, 8049 Zürich, Switzerland
| | | | | | - Esteban Marcellin
- Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, 4072 St. Lucia, Australia.
| | - Kaspar Valgepea
- ERA Chair in Gas Fermentation Technologies, Institute of Bioengineering, University of Tartu, 50411 Tartu, Estonia.
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Kwon HJ, Lee J, Kwon SJ, Lee HS. Development of a genetic engineering toolbox for syngas-utilizing acetogen Clostridium sp. AWRP. Microb Cell Fact 2024; 23:6. [PMID: 38172811 PMCID: PMC10763472 DOI: 10.1186/s12934-023-02272-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Accepted: 12/12/2023] [Indexed: 01/05/2024] Open
Abstract
BACKGROUND Clostridium sp. AWRP (AWRP) is a novel acetogenic bacterium isolated under high partial pressure of carbon monoxide (CO) and can be one of promising candidates for alcohol production from carbon oxides. Compared to model strains such as C. ljungdahlii and C. autoethanogenum, however, genetic manipulation of AWRP has not been established, preventing studies on its physiological characteristics and metabolic engineering. RESULTS We were able to demonstrate the genetic domestication of AWRP, including transformation of shuttle plasmids, promoter characterization, and genome editing. From the conjugation experiment with E. coli S17-1, among the four replicons tested (pCB102, pAMβ1, pIP404, and pIM13), three replicated in AWRP but pCB102 was the only one that could be transferred by electroporation. DNA methylation in E. coli significantly influenced transformation efficiencies in AWRP: the highest transformation efficiencies (102-103 CFU/µg) were achieved with unmethylated plasmid DNA. Determination of strengths of several clostridial promoters enabled the establishment of a CRISPR/Cas12a genome editing system based on Acidaminococcus sp. BV3L6 cas12a gene; interestingly, the commonly used CRISPR/Cas9 system did not work in AWRP, although it expressed the weakest promoter (C. acetobutylicum Pptb) tested. This system was successfully employed for the single gene deletion (xylB and pyrE) and double deletion of two prophage gene clusters. CONCLUSIONS The presented genome editing system allowed us to achieve several genome manipulations, including double deletion of two large prophage groups. The genetic toolbox developed in this study will offer a chance for deeper studies on Clostridium sp. AWRP for syngas fermentation and carbon dioxide (CO2) sequestration.
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Affiliation(s)
- Hae Jun Kwon
- Marine Biotechnology Research Center, Korea Institute of Ocean Science and Technology, Busan, Republic of Korea
| | - Joungmin Lee
- Marine Biotechnology Research Center, Korea Institute of Ocean Science and Technology, Busan, Republic of Korea.
| | - Soo Jae Kwon
- Marine Biotechnology Research Center, Korea Institute of Ocean Science and Technology, Busan, Republic of Korea
- KIOST School, University of Science and Technology, Busan, Republic of Korea
| | - Hyun Sook Lee
- Marine Biotechnology Research Center, Korea Institute of Ocean Science and Technology, Busan, Republic of Korea.
- KIOST School, University of Science and Technology, Busan, Republic of Korea.
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Perret L, Boukis N, Sauer J. Synthesis gas fermentation at high cell density: How pH and hydrogen partial pressure affect productivity and product ratio in continuous fermentation. BIORESOURCE TECHNOLOGY 2024; 391:129894. [PMID: 37866768 DOI: 10.1016/j.biortech.2023.129894] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 10/17/2023] [Accepted: 10/17/2023] [Indexed: 10/24/2023]
Abstract
For the first time, syngas fermentation was operated continuously with total cell retention and process pressures up to 4barg in long-term runs of up to 3000 hours. Throughout this time, the process was stable. The measured data have shown that hydrogen uptake and ethanol space-time yield are highest at a slightly reduced pH of 5.7 compared to pH5.9. Even lower pH values lead to higher acetic acid to ethanol product ratios, while C2space-time yields remain constant. Increasing the hydrogen partial pressure to 1.52bar resulted in a significant increase in hydrogen uptake rate and ethanol formation. An ethanol space-time yield of 10mmolL-1h-1 was short-term achieved, being the highest space-time yield measured to date for the wild type of C. ljungdahlii. Hydrogen uptake above a theoretical equilibrium concentration of [Formula: see text] is significantly reduced, indicating an inhibition of an enzymatic reaction.
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Affiliation(s)
- Lukas Perret
- Institute of Catalysis Research and Technology, Karlsruhe Institute of Technology, Hermann-von-Helmholtz-Platz 1, Eggenstein-Leopoldshafen 76344, Baden-Wurttemberg, Germany.
| | - Nikolaos Boukis
- Institute of Catalysis Research and Technology, Karlsruhe Institute of Technology, Hermann-von-Helmholtz-Platz 1, Eggenstein-Leopoldshafen 76344, Baden-Wurttemberg, Germany
| | - Jörg Sauer
- Institute of Catalysis Research and Technology, Karlsruhe Institute of Technology, Hermann-von-Helmholtz-Platz 1, Eggenstein-Leopoldshafen 76344, Baden-Wurttemberg, Germany
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