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Stefanini R, Karekar S, Ale Enriquez F, Ahring B. Examining homoacetogens in feces from adult and juvenile kangaroos with the aim of finding competitive strains to hydrogenotrophic methanogens. Microbiol Spectr 2024:e0318323. [PMID: 38904373 DOI: 10.1128/spectrum.03183-23] [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: 10/26/2023] [Accepted: 04/13/2024] [Indexed: 06/22/2024] Open
Abstract
We examined the microbial populations present in fecal samples of macropods capable of utilizing a mixture of hydrogen and carbon dioxide (70:30) percent. The feces samples were cultured under anaerobic conditions, and production of methane or acetic acids characteristic for methanogenesis and homoacetogenesis was measured. While the feces of adult macropods mainly produced methane from the substrate, the sample from a 2-month-old juvenile kangaroo only produced acetic acid and no methane. The stable highly enriched culture of the joey kangaroo was sequenced to examine the V3 and V4 regions of the 16S rRNA gene. The results showed that over 70% of gene copies belonged to the Clostridia class, with Paraclostridium and Blautia as the most predominant genera. The culture further showed the presence of Actinomyces spp., a genus which has only been identified in the GI tract of macropods in a few studies, and where none, to our knowledge, have been classified as homoacetogenic. The joey kangaroo mixed culture showed a doubling time of 3.54 h and a specific growth rate of 0.199/h, faster than what has been observed for homoacetogenic bacteria in general. IMPORTANCE Enteric methane emissions from cattle are a significant contributor to greenhouse gas emissions worldwide. Methane emissions not only contribute to climate change but also represent a loss of energy from the animal's diet. However, methanogens play an important role as hydrogen sink to rumen systems; without it, the performance of hydrolytic organisms diminishes. Therefore, effective strategies of methanogen inhibition would be enhanced in conjunction with the addition of alternative hydrogen sinks to the rumen. The significance of our research is to identify homoacetogens present in the GI tract of kangaroos and to present their performance in vitro, demonstrating their capability to serve as alternatives to rumen methanogens.
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Affiliation(s)
- Renan Stefanini
- Bioproducts, Sciences and Engineering Laboratory, Washington State University, Richland, Washington, USA
- Department of Biological Systems Engineering, Washington State University, Pullman, Washington, USA
| | - Supriya Karekar
- Bioproducts, Sciences and Engineering Laboratory, Washington State University, Richland, Washington, USA
- Department of Biological Systems Engineering, Washington State University, Pullman, Washington, USA
| | - Fuad Ale Enriquez
- Bioproducts, Sciences and Engineering Laboratory, Washington State University, Richland, Washington, USA
- The Gene and Linda Voiland School of Chemical Engineering and Bioengineering, Washington State University, Pullman, Washington, USA
| | - Birgitte Ahring
- Bioproducts, Sciences and Engineering Laboratory, Washington State University, Richland, Washington, USA
- Department of Biological Systems Engineering, Washington State University, Pullman, Washington, USA
- The Gene and Linda Voiland School of Chemical Engineering and Bioengineering, Washington State University, Pullman, Washington, USA
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Zhang J, Li F, Liu D, Liu Q, Song H. Engineering extracellular electron transfer pathways of electroactive microorganisms by synthetic biology for energy and chemicals production. Chem Soc Rev 2024; 53:1375-1446. [PMID: 38117181 DOI: 10.1039/d3cs00537b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2023]
Abstract
The excessive consumption of fossil fuels causes massive emission of CO2, leading to climate deterioration and environmental pollution. The development of substitutes and sustainable energy sources to replace fossil fuels has become a worldwide priority. Bio-electrochemical systems (BESs), employing redox reactions of electroactive microorganisms (EAMs) on electrodes to achieve a meritorious combination of biocatalysis and electrocatalysis, provide a green and sustainable alternative approach for bioremediation, CO2 fixation, and energy and chemicals production. EAMs, including exoelectrogens and electrotrophs, perform extracellular electron transfer (EET) (i.e., outward and inward EET), respectively, to exchange energy with the environment, whose rate determines the efficiency and performance of BESs. Therefore, we review the synthetic biology strategies developed in the last decade for engineering EAMs to enhance the EET rate in cell-electrode interfaces for facilitating the production of electricity energy and value-added chemicals, which include (1) progress in genetic manipulation and editing tools to achieve the efficient regulation of gene expression, knockout, and knockdown of EAMs; (2) synthetic biological engineering strategies to enhance the outward EET of exoelectrogens to anodes for electricity power production and anodic electro-fermentation (AEF) for chemicals production, including (i) broadening and strengthening substrate utilization, (ii) increasing the intracellular releasable reducing equivalents, (iii) optimizing c-type cytochrome (c-Cyts) expression and maturation, (iv) enhancing conductive nanowire biosynthesis and modification, (v) promoting electron shuttle biosynthesis, secretion, and immobilization, (vi) engineering global regulators to promote EET rate, (vii) facilitating biofilm formation, and (viii) constructing cell-material hybrids; (3) the mechanisms of inward EET, CO2 fixation pathway, and engineering strategies for improving the inward EET of electrotrophic cells for CO2 reduction and chemical production, including (i) programming metabolic pathways of electrotrophs, (ii) rewiring bioelectrical circuits for enhancing inward EET, and (iii) constructing microbial (photo)electrosynthesis by cell-material hybridization; (4) perspectives on future challenges and opportunities for engineering EET to develop highly efficient BESs for sustainable energy and chemical production. We expect that this review will provide a theoretical basis for the future development of BESs in energy harvesting, CO2 fixation, and chemical synthesis.
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Affiliation(s)
- Junqi Zhang
- Frontier Science Center for Synthetic Biology (Ministry of Education), Key Laboratory of Systems Bioengineering, and School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China.
| | - Feng Li
- Frontier Science Center for Synthetic Biology (Ministry of Education), Key Laboratory of Systems Bioengineering, and School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China.
| | - Dingyuan Liu
- Frontier Science Center for Synthetic Biology (Ministry of Education), Key Laboratory of Systems Bioengineering, and School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China.
| | - Qijing Liu
- Frontier Science Center for Synthetic Biology (Ministry of Education), Key Laboratory of Systems Bioengineering, and School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China.
| | - Hao Song
- Frontier Science Center for Synthetic Biology (Ministry of Education), Key Laboratory of Systems Bioengineering, and School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China.
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Tremblay PL, Zhang T. Genetic tools for the electrotroph Sporomusa ovata and autotrophic biosynthesis. Appl Environ Microbiol 2024; 90:e0175723. [PMID: 38117058 PMCID: PMC10807461 DOI: 10.1128/aem.01757-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Accepted: 11/13/2023] [Indexed: 12/21/2023] Open
Abstract
Sporomusa ovata is a Gram-negative acetogen of the Sporomusaceae family with a unique physiology. This anerobic bacterium is a core microbial catalyst for advanced CO2-based biotechnologies including gas fermentation, microbial electrosynthesis, and hybrid photosystem. Until now, no genetic tools exist for S. ovata, which is a critical obstacle to its optimization as an autotrophic chassis and the acquisition of knowledge about its metabolic capacities. Here, we developed an electroporation protocol for S. ovata. With this procedure, it became possible to introduce replicative plasmids such as pJIR751 and its derivatives into the acetogen. This system was then employed to demonstrate the feasibility of heterologous expression by introducing a functional β-glucuronidase enzyme under the promoters of different strengths in S. ovata. Next, a recombinant S. ovata strain producing the non-native product acetone both from an organic carbon substrate and from CO2 was constructed. Finally, a replicative plasmid capable of integrating itself on the chromosome of the acetogen was developed as a tool for genome editing, and gene deletion was demonstrated. These results indicate that S. ovata can be engineered and provides a first-generation genetic toolbox for the optimization of this biotechnological workhorse.IMPORTANCES. ovata harbors unique features that make it outperform most microbes for autotrophic biotechnologies such as a capacity to acquire electrons from different solid donors, a low H2 threshold, and efficient energy conservation mechanisms. The development of the first-generation genetic instruments described in this study is a key step toward understanding the molecular mechanisms involved in these outstanding metabolic and physiological characteristics. In addition, these tools enable the construction of recombinant S. ovata strains that can synthesize a wider range of products in an efficient manner.
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Affiliation(s)
- Pier-Luc Tremblay
- School of Chemistry, Chemical Engineering, and Life Science, Wuhan University of Technology, Wuhan, China
- Institut WUT-AMU, Wuhan University of Technology, Wuhan, China
- Shaoxing Institute for Advanced Research, Wuhan University of Technology, Shaoxing, China
- Sanya Science and Education Innovation Park, Wuhan University of Technology, Sanya, China
| | - Tian Zhang
- School of Chemistry, Chemical Engineering, and Life Science, Wuhan University of Technology, Wuhan, China
- Institut WUT-AMU, Wuhan University of Technology, Wuhan, China
- Shaoxing Institute for Advanced Research, Wuhan University of Technology, Shaoxing, China
- Sanya Science and Education Innovation Park, Wuhan University of Technology, Sanya, China
- Advanced Engineering Technology Research Institute of Zhongshan City, Wuhan University of Technology, Zhongshan, China
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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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Höfele F, Schoch T, Oberlies C, Dürre P. Heterologous Production of Isopropanol Using Metabolically Engineered Acetobacterium woodii Strains. Bioengineering (Basel) 2023; 10:1381. [PMID: 38135972 PMCID: PMC10741115 DOI: 10.3390/bioengineering10121381] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 11/23/2023] [Accepted: 11/27/2023] [Indexed: 12/24/2023] Open
Abstract
The depletion of fossil fuel resources and the CO2 emissions coupled with petroleum-based industrial processes present a relevant issue for the whole of society. An alternative to the fossil-based production of chemicals is microbial fermentation using acetogens. Acetogenic bacteria are able to metabolize CO or CO2 (+H2) via the Wood-Ljungdahl pathway. As isopropanol is widely used in a variety of industrial branches, it is advantageous to find a fossil-independent production process. In this study, Acetobacterium woodii was employed to produce isopropanol via plasmid-based expression of the enzymes thiolase A, CoA-transferase, acetoacetate decarboxylase and secondary alcohol dehydrogenase. An examination of the enzymes originating from different organisms led to a maximum isopropanol production of 5.64 ± 1.08 mM using CO2 + H2 as the carbon and energy source. To this end, the genes thlA (encoding thiolase A) and ctfA/ctfB (encoding CoA-transferase) of Clostridium scatologenes, adc (encoding acetoacetate decarboxylase) originating from C. acetobutylicum and sadH (encoding secondary alcohol dehydrogenase) of C. beijerinckii DSM 6423 were employed. Since bottlenecks in the isopropanol production pathway are known, optimization of the strain was investigated, resulting in a 2.5-fold increase in isopropanol concentration.
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Affiliation(s)
- Franziska Höfele
- Institute of Molecular Biology and Biotechnology of Prokaryotes, Ulm University, 89081 Ulm, Germany
| | - Teresa Schoch
- Institute of Microbiology and Biotechnology, Ulm University, 89081 Ulm, Germany (C.O.); (P.D.)
| | - Catarina Oberlies
- Institute of Microbiology and Biotechnology, Ulm University, 89081 Ulm, Germany (C.O.); (P.D.)
| | - Peter Dürre
- Institute of Microbiology and Biotechnology, Ulm University, 89081 Ulm, Germany (C.O.); (P.D.)
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Kurt E, Qin J, Williams A, Zhao Y, Xie D. Perspectives for Using CO 2 as a Feedstock for Biomanufacturing of Fuels and Chemicals. Bioengineering (Basel) 2023; 10:1357. [PMID: 38135948 PMCID: PMC10740661 DOI: 10.3390/bioengineering10121357] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Revised: 11/20/2023] [Accepted: 11/24/2023] [Indexed: 12/24/2023] Open
Abstract
Microbial cell factories offer an eco-friendly alternative for transforming raw materials into commercially valuable products because of their reduced carbon impact compared to conventional industrial procedures. These systems often depend on lignocellulosic feedstocks, mainly pentose and hexose sugars. One major hurdle when utilizing these sugars, especially glucose, is balancing carbon allocation to satisfy energy, cofactor, and other essential component needs for cellular proliferation while maintaining a robust yield. Nearly half or more of this carbon is inevitably lost as CO2 during the biosynthesis of regular metabolic necessities. This loss lowers the production yield and compromises the benefit of reducing greenhouse gas emissions-a fundamental advantage of biomanufacturing. This review paper posits the perspectives of using CO2 from the atmosphere, industrial wastes, or the exhausted gases generated in microbial fermentation as a feedstock for biomanufacturing. Achieving the carbon-neutral or -negative goals is addressed under two main strategies. The one-step strategy uses novel metabolic pathway design and engineering approaches to directly fix the CO2 toward the synthesis of the desired products. Due to the limitation of the yield and efficiency in one-step fixation, the two-step strategy aims to integrate firstly the electrochemical conversion of the exhausted CO2 into C1/C2 products such as formate, methanol, acetate, and ethanol, and a second fermentation process to utilize the CO2-derived C1/C2 chemicals or co-utilize C5/C6 sugars and C1/C2 chemicals for product formation. The potential and challenges of using CO2 as a feedstock for future biomanufacturing of fuels and chemicals are also discussed.
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Affiliation(s)
- Elif Kurt
- Department of Chemical Engineering, University of Massachusetts, Lowell, MA 01854, USA; (E.K.); (J.Q.); (A.W.)
| | - Jiansong Qin
- Department of Chemical Engineering, University of Massachusetts, Lowell, MA 01854, USA; (E.K.); (J.Q.); (A.W.)
| | - Alexandria Williams
- Department of Chemical Engineering, University of Massachusetts, Lowell, MA 01854, USA; (E.K.); (J.Q.); (A.W.)
| | - Youbo Zhao
- Physical Sciences Inc., 20 New England Business Ctr., Andover, MA 01810, USA;
| | - Dongming Xie
- Department of Chemical Engineering, University of Massachusetts, Lowell, MA 01854, USA; (E.K.); (J.Q.); (A.W.)
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Nwaokorie UJ, Reinmets K, de Lima LA, Pawar PR, Shaikh KM, Harris A, Köpke M, Valgepea K. Deletion of genes linked to the C 1-fixing gene cluster affects growth, by-products, and proteome of Clostridium autoethanogenum. Front Bioeng Biotechnol 2023; 11:1167892. [PMID: 37265994 PMCID: PMC10230548 DOI: 10.3389/fbioe.2023.1167892] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Accepted: 05/03/2023] [Indexed: 06/03/2023] Open
Abstract
Gas fermentation has emerged as a sustainable route to produce fuels and chemicals by recycling inexpensive one-carbon (C1) feedstocks from gaseous and solid waste using gas-fermenting microbes. Currently, acetogens that utilise the Wood-Ljungdahl pathway to convert carbon oxides (CO and CO2) into valuable products are the most advanced biocatalysts for gas fermentation. However, our understanding of the functionalities of the genes involved in the C1-fixing gene cluster and its closely-linked genes is incomplete. Here, we investigate the role of two genes with unclear functions-hypothetical protein (hp; LABRINI_07945) and CooT nickel binding protein (nbp; LABRINI_07950)-directly adjacent and expressed at similar levels to the C1-fixing gene cluster in the gas-fermenting model-acetogen Clostridium autoethanogenum. Targeted deletion of either the hp or nbp gene using CRISPR/nCas9, and phenotypic characterisation in heterotrophic and autotrophic batch and autotrophic bioreactor continuous cultures revealed significant growth defects and altered by-product profiles for both ∆hp and ∆nbp strains. Variable effects of gene deletion on autotrophic batch growth on rich or minimal media suggest that both genes affect the utilisation of complex nutrients. Autotrophic chemostat cultures showed lower acetate and ethanol production rates and higher carbon flux to CO2 and biomass for both deletion strains. Additionally, proteome analysis revealed that disruption of either gene affects the expression of proteins of the C1-fixing gene cluster and ethanol synthesis pathways. Our work contributes to a better understanding of genotype-phenotype relationships in acetogens and offers engineering targets to improve carbon fixation efficiency in gas fermentation.
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Affiliation(s)
- Ugochi Jennifer Nwaokorie
- 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
| | - Lorena Azevedo de Lima
- ERA Chair in Gas Fermentation Technologies, Institute of Technology, University of Tartu, Tartu, Estonia
| | - Pratik Rajendra Pawar
- ERA Chair in Gas Fermentation Technologies, Institute of Technology, University of Tartu, Tartu, Estonia
| | | | | | | | - Kaspar Valgepea
- ERA Chair in Gas Fermentation Technologies, Institute of Technology, University of Tartu, Tartu, Estonia
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Lo J, Wu C, Humphreys JR, Yang B, Jiang Z, Wang X, Maness P, Tsesmetzis N, Xiong W. Thermodynamic and Kinetic Modeling Directs Pathway Optimization for Isopropanol Production in a Gas-Fermenting Bacterium. mSystems 2023; 8:e0127422. [PMID: 36971551 PMCID: PMC10134883 DOI: 10.1128/msystems.01274-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/29/2023] Open
Abstract
Highly efficient bioproduction from gaseous substrates (e.g., hydrogen and carbon oxides) will require systematic optimization of the host microbes. To date, the rational redesign of gas-fermenting bacteria is still in its infancy, due in part to the lack of quantitative and precise metabolic knowledge that can direct strain engineering.
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Moreira JPC, Heap JT, Alves JI, Domingues L. Developing a genetic engineering method for Acetobacterium wieringae to expand one-carbon valorization pathways. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2023; 16:24. [PMID: 36788587 PMCID: PMC9930230 DOI: 10.1186/s13068-023-02259-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Accepted: 01/05/2023] [Indexed: 02/16/2023]
Abstract
BACKGROUND Developing new bioprocesses to produce chemicals and fuels with reduced production costs will greatly facilitate the replacement of fossil-based raw materials. In most fermentation bioprocesses, the feedstock usually represents the highest cost, which becomes the target for cost reduction. Additionally, the biorefinery concept advocates revenue growth from the production of several compounds using the same feedstock. Taken together, the production of bio commodities from low-cost gas streams containing CO, CO2, and H2, obtained from the gasification of any carbon-containing waste streams or off-gases from heavy industry (steel mills, processing plants, or refineries), embodies an opportunity for affordable and renewable chemical production. To achieve this, by studying non-model autotrophic acetogens, current limitations concerning low growth rates, toxicity by gas streams, and low productivity may be overcome. The Acetobacterium wieringae strain JM is a novel autotrophic acetogen that is capable of producing acetate and ethanol. It exhibits faster growth rates on various gaseous compounds, including carbon monoxide, compared to other Acetobacterium species, making it potentially useful for industrial applications. The species A. wieringae has not been genetically modified, therefore developing a genetic engineering method is important for expanding its product portfolio from gas fermentation and overall improving the characteristics of this acetogen for industrial demands. RESULTS This work reports the development and optimization of an electrotransformation protocol for A. wieringae strain JM, which can also be used in A. wieringae DSM 1911, and A. woodii DSM 1030. We also show the functionality of the thiamphenicol resistance marker, catP, and the functionality of the origins of replication pBP1, pCB102, pCD6, and pIM13 in all tested Acetobacterium strains, with transformation efficiencies of up to 2.0 × 103 CFU/μgDNA. Key factors affecting electrotransformation efficiency include OD600 of cell harvesting, pH of resuspension buffer, the field strength of the electric pulse, and plasmid amount. Using this method, the acetone production operon from Clostridium acetobutylicum was efficiently introduced in all tested Acetobacterium spp., leading to non-native biochemical acetone production via plasmid-based expression. CONCLUSIONS A. wieringae can be electrotransformed at high efficiency using different plasmids with different replication origins. The electrotransformation procedure and tools reported here unlock the genetic and metabolic manipulation of the biotechnologically relevant A. wieringae strains. For the first time, non-native acetone production is shown in A. wieringae.
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Affiliation(s)
- João P. C. Moreira
- grid.10328.380000 0001 2159 175XCEB - Centre of Biological Engineering, University of Minho, 4710-057 Braga, Portugal ,LABBELS - Associate Laboratory, Braga/Guimarães, Portugal
| | - John T. Heap
- grid.4563.40000 0004 1936 8868School of Life Sciences, University of Nottingham, Biodiscovery Institute, University Park, Nottingham, NG7 2RD UK
| | - Joana I. Alves
- grid.10328.380000 0001 2159 175XCEB - Centre of Biological Engineering, University of Minho, 4710-057 Braga, Portugal ,LABBELS - Associate Laboratory, Braga/Guimarães, Portugal
| | - Lucília Domingues
- CEB - Centre of Biological Engineering, University of Minho, 4710-057, Braga, Portugal. .,LABBELS - Associate Laboratory, Braga/Guimarães, Portugal.
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Liu Z, Xue X, Cai W, Cui K, Patil SA, Guo K. Recent progress on microbial electrosynthesis reactors and strategies to enhance the reactor performance. Biochem Eng J 2022. [DOI: 10.1016/j.bej.2022.108745] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
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11
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Lo J, Humphreys JR, Magnusson L, Wachter B, Urban C, Hebdon SD, Xiong W, Chou KJ, Ching Maness P. Acetogenic production of 3-Hydroxybutyrate using a native 3-Hydroxybutyryl-CoA Dehydrogenase. Front Microbiol 2022; 13:948369. [PMID: 36003933 PMCID: PMC9393629 DOI: 10.3389/fmicb.2022.948369] [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: 05/19/2022] [Accepted: 07/11/2022] [Indexed: 11/16/2022] Open
Abstract
3-Hydroxybutyrate (3HB) is a product of interest as it is a precursor to the commercially produced bioplastic polyhydroxybutyrate. It can also serve as a platform for fine chemicals, medicines, and biofuels, making it a value-added product and feedstock. Acetogens non-photosynthetically fix CO2 into acetyl-CoA and have been previously engineered to convert acetyl-CoA into 3HB. However, as acetogen metabolism is poorly understood, those engineering efforts have had varying levels of success. 3HB, using acetyl-CoA as a precursor, can be synthesized by a variety of different pathways. Here we systematically compare various pathways to produce 3HB in acetogens and discover a native (S)-3-hydroxybutyryl-CoA dehydrogenase, hbd2, responsible for endogenous 3HB production. In conjunction with the heterologous thiolase atoB and CoA transferase ctfAB, hbd2 overexpression improves yields of 3HB on both sugar and syngas (CO/H2/CO2), outperforming the other tested pathways. These results uncovered a previously unknown 3HB production pathway, inform data from prior metabolic engineering efforts, and have implications for future physiological and biotechnological anaerobic research.
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Sanford PA, Woolston BM. Expanding the genetic engineering toolbox for the metabolically flexible acetogen Eubacterium limosum. J Ind Microbiol Biotechnol 2022; 49:6650221. [PMID: 35881468 PMCID: PMC9559302 DOI: 10.1093/jimb/kuac019] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Accepted: 06/30/2022] [Indexed: 11/14/2022]
Abstract
Acetogenic bacteria are an increasingly popular choice for producing fuels and chemicals from single carbon (C1) substrates. Eubacterium limosum is a promising acetogen with several native advantages, including the ability to catabolize a wide repertoire of C1 feedstocks and the ability to grow well on agar plates. However, despite its promise as a strain for synthetic biology and metabolic engineering, there are insufficient engineering tools and molecular biology knowledge to leverage its native strengths for these applications. To capitalize on the natural advantages of this organism, here we extended its limited engineering toolbox. We evaluated the copy number of three common plasmid origins of replication and devised a method of controlling copy number and heterologous gene expression level by modulating antibiotic concentration. We further quantitatively assessed the strength and regulatory tightness of a panel of promoters, developing a series of well-characterized vectors for gene expression at varying levels. In addition, we developed a black/white colorimetric genetic reporter assay and leveraged the high oxygen tolerance of E. limosum to develop a simple and rapid transformation protocol that enables benchtop transformation. Finally, we developed two new antibiotic selection markers—doubling the number available for this organism. These developments will enable enhanced metabolic engineering and synthetic biology work with E. limosum.
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Affiliation(s)
- Patrick A Sanford
- Department of Chemical Engineering, Northeastern University, 360 Huntington Avenue, 223 Cullinane, Boston, MA 02115, USA
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13
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A clean in-frame knockout system for gene deletion in Acetobacterium woodii. J Biotechnol 2022; 353:9-18. [PMID: 35659892 DOI: 10.1016/j.jbiotec.2022.05.013] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 05/27/2022] [Accepted: 05/28/2022] [Indexed: 11/24/2022]
Abstract
Acetogenic bacteria produce acetate following the fixation of CO2 via the Wood-Ljungdahl pathway. As such, they represent excellent process organisms for the production of novel chemicals and fuels from this waste greenhouse gas. Acetobacterium woodii is the model acetogen and numerous studies have been conducted investigating its biochemistry, gas consumption and use as a production chassis. However, there are a dearth of available tools for A. woodii gene modification which limits the research options available for genetic studies. Here, the previously proposed Clostridia Roadmap is implemented in A. woodii leading to the derivation of a knockout system for the generation of clean, in-frame deletions. The replicon of the Gram-positive plasmid pCD6 that originated in Clostridioides difficile was identified as being replication-defective in A. woodii, a property that was exploited to construct a pseudo-suicide knockout plasmid which was used to generate an auxotrophic, pyrE mutant. This allowed the subsequent use of a heterologous pyrE gene (from Clostridium acetobutylicum) as a counter selection marker and the deletion of a number of genes by allelic exchange. Specific mutants generated were affected in growth on glucose, fructose and ethanol as a consequence of deletion of fruA, pstG and adhE, respectively.
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Lauer I, Philipps G, Jennewein S. Metabolic engineering of Clostridium ljungdahlii for the production of hexanol and butanol from CO 2 and H 2. Microb Cell Fact 2022; 21:85. [PMID: 35568911 PMCID: PMC9107641 DOI: 10.1186/s12934-022-01802-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Accepted: 04/11/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The replacement of fossil fuels and petrochemicals with sustainable alternatives is necessary to mitigate the effects of climate change and also to counteract diminishing fossil resources. Acetogenic microorganisms such as Clostridium spp. are promising sources of fuels and basic chemical precursors because they efficiently utilize CO and CO2 as carbon source. However the conversion into high titers of butanol and hexanol is challenging. RESULTS Using a metabolic engineering approach we transferred a 17.9-kb gene cluster via conjugation, containing 13 genes from C. kluyveri and C. acetobutylicum for butanol and hexanol biosynthesis, into C. ljungdahlii. Plasmid-based expression resulted in 1075 mg L-1 butanol and 133 mg L-1 hexanol from fructose in complex medium, and 174 mg L-1 butanol and 15 mg L-1 hexanol from gaseous substrate (20% CO2 and 80% H2) in minimal medium. Product formation was increased by the genomic integration of the heterologous gene cluster. We confirmed the expression of all 13 enzymes by targeted proteomics and identified potential rate-limiting steps. Then, we removed the first-round selection marker using CRISPR/Cas9 and integrated an additional 7.8 kb gene cluster comprising 6 genes from C. carboxidivorans. This led to a significant increase in the hexanol titer (251 mg L-1) at the expense of butanol (158 mg L-1), when grown on CO2 and H2 in serum bottles. Fermentation of this strain at 2-L scale produced 109 mg L-1 butanol and 393 mg L-1 hexanol. CONCLUSIONS We thus confirmed the function of the butanol/hexanol biosynthesis genes and achieved hexanol biosynthesis in the syngas-fermenting species C. ljungdahlii for the first time, reaching the levels produced naturally by C. carboxidivorans. The genomic integration strain produced hexanol without selection and is therefore suitable for continuous fermentation processes.
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Affiliation(s)
- Ira Lauer
- Department for Industrial Biotechnology, Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Forckenbeckstr. 6, 52074, Aachen, Germany
| | - Gabriele Philipps
- Department for Industrial Biotechnology, Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Forckenbeckstr. 6, 52074, Aachen, Germany
| | - Stefan Jennewein
- Department for Industrial Biotechnology, Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Forckenbeckstr. 6, 52074, Aachen, Germany.
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15
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Rybnicky GA, Fackler NA, Karim AS, Köpke M, Jewett MC. Spacer2PAM: A computational framework to guide experimental determination of functional CRISPR-Cas system PAM sequences. Nucleic Acids Res 2022; 50:3523-3534. [PMID: 35258601 PMCID: PMC8990532 DOI: 10.1093/nar/gkac142] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Revised: 02/12/2022] [Accepted: 02/15/2022] [Indexed: 11/17/2022] Open
Abstract
RNA-guided nucleases from CRISPR-Cas systems expand opportunities for precise, targeted genome modification. Endogenous CRISPR-Cas systems in many prokaryotes are attractive to circumvent expression, functionality, and unintended activity hurdles posed by heterologous CRISPR-Cas effectors. However, each CRISPR-Cas system recognizes a unique set of protospacer adjacent motifs (PAMs), which requires identification by extensive screening of randomized DNA libraries. This challenge hinders development of endogenous CRISPR-Cas systems, especially those based on multi-protein effectors and in organisms that are slow-growing or have transformation idiosyncrasies. To address this challenge, we present Spacer2PAM, an easy-to-use, easy-to-interpret R package built to predict and guide experimental determination of functional PAM sequences for any CRISPR-Cas system given its corresponding CRISPR array as input. Spacer2PAM can be used in a 'Quick' method to generate a single PAM prediction or in a 'Comprehensive' method to inform targeted PAM libraries small enough to screen in difficult to transform organisms. We demonstrate Spacer2PAM by predicting PAM sequences for industrially relevant organisms and experimentally identifying seven PAM sequences that mediate interference from the Spacer2PAM-informed PAM library for the type I-B CRISPR-Cas system from Clostridium autoethanogenum. We anticipate that Spacer2PAM will facilitate the use of endogenous CRISPR-Cas systems for industrial biotechnology and synthetic biology.
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Affiliation(s)
- Grant A Rybnicky
- Chemistry of Life Processes Institute, Northwestern University, Evanston, IL, 60208, USA,Center for Synthetic Biology, Northwestern University, Evanston, IL, 60208, USA,Interdisciplinary Biological Sciences Graduate Program, Northwestern University, Evanston, IL, 60208, USA
| | | | - Ashty S Karim
- Chemistry of Life Processes Institute, Northwestern University, Evanston, IL, 60208, USA,Center for Synthetic Biology, Northwestern University, Evanston, IL, 60208, USA,Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL 60208, USA
| | | | - Michael C Jewett
- To whom correspondence should be addressed. Tel: +1 847 467 5007; Fax: +1 847 467 5007;
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16
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Development of highly characterized genetic bioparts for efficient gene expression in CO2-fixing Eubacterium limosum. Metab Eng 2022; 72:215-226. [DOI: 10.1016/j.ymben.2022.03.016] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Revised: 03/20/2022] [Accepted: 03/26/2022] [Indexed: 12/22/2022]
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17
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Flaiz M, Baur T, Gaibler J, Kröly C, Dürre P. Establishment of Green- and Red-Fluorescent Reporter Proteins Based on the Fluorescence-Activating and Absorption-Shifting Tag for Use in Acetogenic and Solventogenic Anaerobes. ACS Synth Biol 2022; 11:953-967. [PMID: 35081709 DOI: 10.1021/acssynbio.1c00554] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Anaerobic bacteria are promising biocatalysts to produce industrially relevant products from nonfood feedstocks. Several anaerobes are genetically accessible, and various molecular tools for metabolic engineering are available. Still, the use of bright fluorescent reporters, which are commonly used in molecular biological approaches is limited under anaerobic conditions. Therefore, the establishment of different anaerobic fluorescent reporter proteins is of great interest. Here, we present the establishment of the green- and red-fluorescent reporter proteins greenFAST and redFAST for use in different solventogenic and acetogenic bacteria. Green fluorescence of greenFAST was bright in Clostridium saccharoperbutylacetonicum, Clostridium acetobutylicum, Acetobacterium woodii, and Eubacterium limosum, while only C. saccharoperbutylacetonicum showed bright red fluorescence when producing redFAST. We used both reporter proteins in C. saccharoperbutylacetonicum for multicolor approaches. These include the investigation of the co-culture dynamics of metabolically engineered strains. Moreover, we established a tightly regulated inducible two-plasmid system and used greenFAST and redFAST to track the coexistence and interaction of both plasmids under anaerobic conditions in C. saccharoperbutylacetonicum. The establishment of greenFAST and redFAST as fluorescent reporters opens the door for further multicolor approaches to investigate cell dynamics, gene expression, or protein localization under anaerobic conditions.
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Affiliation(s)
- Maximilian Flaiz
- Institute of Microbiology and Biotechnology, University of Ulm, Albert-Einstein-Allee 11, 89081 Ulm, Germany
| | - Tina Baur
- Institute of Microbiology and Biotechnology, University of Ulm, Albert-Einstein-Allee 11, 89081 Ulm, Germany
| | - Jana Gaibler
- Institute of Microbiology and Biotechnology, University of Ulm, Albert-Einstein-Allee 11, 89081 Ulm, Germany
| | - Christian Kröly
- Institute of Microbiology and Biotechnology, University of Ulm, Albert-Einstein-Allee 11, 89081 Ulm, Germany
| | - Peter Dürre
- Institute of Microbiology and Biotechnology, University of Ulm, Albert-Einstein-Allee 11, 89081 Ulm, Germany
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18
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Hoyt KO, Woolston BM. Adapting isotopic tracer and metabolic flux analysis approaches to study C1 metabolism. Curr Opin Biotechnol 2022; 75:102695. [PMID: 35182834 DOI: 10.1016/j.copbio.2022.102695] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 01/20/2022] [Accepted: 01/27/2022] [Indexed: 12/20/2022]
Abstract
Single-carbon (C1, or one-carbon) substrates are promising feedstocks for sustainable biofuel and biochemical production. Crucial to the goal of engineering C1-utilizing strains for improved production is a quantitative understanding of the organization, regulation and rates of the reactions that underpin C1 metabolism. 13C Metabolic flux analysis (MFA) is a well-established platform for interrogating these questions with multi-carbon substrates, and uses the differential labeling of metabolites that results from feeding a substrate with position-specific incorporation of 13C in order to infer quantitative fluxes and pathway topology. Adapting isotopic tracer approaches to C1 metabolism, where position-specific substrate labeling is impossible, requires additional experimental considerations. Here we review recent studies that have developed isotopic tracer approaches to overcome the challenge of uniform metabolite labeling and provide quantitative insight into C1 metabolism.
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Affiliation(s)
- Kathryn O Hoyt
- Department of Chemical Engineering, 201 Cullinane, Northeastern University, 360 Huntington Avenue, Boston, MA 02115-5000, USA
| | - Benjamin M Woolston
- Department of Chemical Engineering, 201 Cullinane, Northeastern University, 360 Huntington Avenue, Boston, MA 02115-5000, USA.
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19
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Establishing Butyribacterium methylotrophicum as a platform organism for the production of biocommodities from liquid C1 metabolites. Appl Environ Microbiol 2022; 88:e0239321. [PMID: 35138930 DOI: 10.1128/aem.02393-21] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Using the Wood-Ljungdahl pathway, acetogens can non-photosynthetically fix gaseous C1 molecules preventing them from entering the atmosphere. Many acetogens can also grow on liquid C1 compounds such as formate and methanol which avoid the storage and mass transfer issues associated with gaseous C1 compounds. Substrate redox state also plays an important role in acetogen metabolism and can modulate products formed by these organisms. Butyribacterium methylotrophicum is an acetogen known for its ability to synthesize longer-chained molecules such as butyrate and butanol, which have significantly higher value than acetate or ethanol, from one-carbon (C1) compounds. We explored B. methylotrophicum's C1 metabolism by varying substrates, substrate concentrations and substrate feeding strategies to improve four-carbon product titers. Our results showed that formate utilization by B. methylotrophicum favored acetate production and methanol utilization favored butyrate production. Co-feeding of both substrates produced a high butyrate titer of 4 g/L when methanol was supplied in excess to formate. Testing of formate feeding strategies, in the presence of methanol, led to further increases in the butyrate to acetate ratio. Mixotrophic growth of liquid and gaseous C1 substrates expanded the B. methylotrophicum product profile as ethanol, butanol and lactate were produced in these conditions. We also showed that B. methylotrophicum is capable of producing caproate, a six-carbon product, presumably through chain elongation cycles of the reverse β-oxidation pathway. Furthermore, we demonstrated butanol production via heterologous gene expression. Our results indicate that both selection of appropriate substrates and genetic engineering play important roles in determining titers of desired products. Importance. Acetogenic bacteria can fix single-carbon (C1) molecules. However, improvements are needed to overcome poor product titers. Butyribacterium methylotrophicum can naturally ferment C1 compounds into longer-chained molecules such as butyrate alongside traditional acetate. Here we show that B. methylotrophicum can effectively grow on formate and methanol to produce high titers of butyrate. We improved ratios of butyrate to acetate through adjusted formate feeding strategies and produced higher value six-carbon molecules. We also expanded the B. methylotrophicum product profile with the addition of C1 gases as the organism produced ethanol, butanol and lactate. Furthermore, we developed a transformation protocol for B. methylotrophicum to facilitate genetic engineering of this organism for the circular bioeconomy.
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Arslan K, Schoch T, Höfele F, Herrschaft S, Oberlies C, Bengelsdorf F, Veiga MC, Dürre P, Kennes C. Engineering
Acetobacterium woodii
for the production of isopropanol and acetone from carbon dioxide and hydrogen. Biotechnol J 2022; 17:e2100515. [DOI: 10.1002/biot.202100515] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Revised: 01/10/2022] [Accepted: 01/11/2022] [Indexed: 11/12/2022]
Affiliation(s)
- Kübra Arslan
- Chemical Enginering Laboratory, Faculty of Sciences and Centre for Advanced Scientific Research (CICA), BIOENGIN group University of La Coruña Rúa da Fraga 10 La Coruña 15008 Spain
| | - Teresa Schoch
- Institute of Microbiology and Biotechnology University of Ulm Albert‐Einstein‐Allee 11 Ulm 89081 Germany
| | - Franziska Höfele
- Institute of Microbiology and Biotechnology University of Ulm Albert‐Einstein‐Allee 11 Ulm 89081 Germany
| | - Sabrina Herrschaft
- Institute of Microbiology and Biotechnology University of Ulm Albert‐Einstein‐Allee 11 Ulm 89081 Germany
| | - Catarina Oberlies
- Institute of Microbiology and Biotechnology University of Ulm Albert‐Einstein‐Allee 11 Ulm 89081 Germany
| | - Frank Bengelsdorf
- Institute of Microbiology and Biotechnology University of Ulm Albert‐Einstein‐Allee 11 Ulm 89081 Germany
| | - María C. Veiga
- Chemical Enginering Laboratory, Faculty of Sciences and Centre for Advanced Scientific Research (CICA), BIOENGIN group University of La Coruña Rúa da Fraga 10 La Coruña 15008 Spain
| | - Peter Dürre
- Institute of Microbiology and Biotechnology University of Ulm Albert‐Einstein‐Allee 11 Ulm 89081 Germany
| | - Christian Kennes
- Chemical Enginering Laboratory, Faculty of Sciences and Centre for Advanced Scientific Research (CICA), BIOENGIN group University of La Coruña Rúa da Fraga 10 La Coruña 15008 Spain
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21
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Kajla S, Kumari R, Nagi GK. Microbial CO2 fixation and biotechnology in reducing industrial CO2 emissions. Arch Microbiol 2022; 204:149. [DOI: 10.1007/s00203-021-02677-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Revised: 10/20/2021] [Accepted: 10/21/2021] [Indexed: 11/30/2022]
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22
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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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23
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Hong Y, Zeng AP. Biosynthesis Based on One-Carbon Mixotrophy. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2022; 180:351-371. [DOI: 10.1007/10_2021_198] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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24
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Abel AJ, Hilzinger JM, Arkin AP, Clark DS. Systems-informed genome mining for electroautotrophic microbial production. Bioelectrochemistry 2022; 145:108054. [DOI: 10.1016/j.bioelechem.2022.108054] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Revised: 12/15/2021] [Accepted: 01/06/2022] [Indexed: 01/09/2023]
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25
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Benalcázar EA, Noorman H, Filho RM, Posada JA. Decarbonizing ethanol production via gas fermentation: impact of the CO/H2/CO2 mix source on greenhouse gas emissions and production costs. Comput Chem Eng 2022. [DOI: 10.1016/j.compchemeng.2022.107670] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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26
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Lee J. Lessons from Clostridial Genetics: Toward Engineering Acetogenic Bacteria. BIOTECHNOL BIOPROC E 2021. [DOI: 10.1007/s12257-021-0062-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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27
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Valorisation of CO2 into Value-Added Products via Microbial Electrosynthesis (MES) and Electro-Fermentation Technology. FERMENTATION-BASEL 2021. [DOI: 10.3390/fermentation7040291] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Microbial electrocatalysis reckons on microbes as catalysts for reactions occurring at electrodes. Microbial fuel cells and microbial electrolysis cells are well-known in this context; both prefer the oxidation of organic and inorganic matter for producing electricity. Notably, the synthesis of high energy-density chemicals (fuels) or their precursors by microorganisms using bio-cathode to yield electrical energy is called Microbial Electrosynthesis (MES), giving an exceptionally appealing novel way for producing beneficial products from electricity and wastewater. This review accentuates the concept, importance and opportunities of MES, as an emerging discipline at the nexus of microbiology and electrochemistry. Production of organic compounds from MES is considered as an effective technique for the generation of various beneficial reduced end-products (like acetate and butyrate) as well as in reducing the load of CO2 from the atmosphere to mitigate the harmful effect of greenhouse gases in global warming. Although MES is still an emerging technology, this method is not thoroughly known. The authors have focused on MES, as it is the next transformative, viable alternative technology to decrease the repercussions of surplus carbon dioxide in the environment along with conserving energy.
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Jia D, He M, Tian Y, Shen S, Zhu X, Wang Y, Zhuang Y, Jiang W, Gu Y. Metabolic Engineering of Gas-Fermenting Clostridium ljungdahlii for Efficient Co-production of Isopropanol, 3-Hydroxybutyrate, and Ethanol. ACS Synth Biol 2021; 10:2628-2638. [PMID: 34549587 DOI: 10.1021/acssynbio.1c00235] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Rational design and modification of autotrophic bacteria to efficiently produce high-value chemicals and biofuels are crucial for establishing a sustainable and economically viable process for one-carbon (C1) source utilization, which, however, remains a challenge in metabolic engineering. In this study, autotrophic Clostridium ljungdahlii was metabolically engineered to efficiently co-produce three important bulk chemicals, isopropanol, 3-hydroxybutyrate (3-HB), and ethanol (together, IHE), using syngas (CO2/CO). An artificial isopropanol-producing pathway was first constructed and optimized in C. ljungdahlii to achieve an efficient production of isopropanol and an unexpected product, 3-HB. Based on this finding, an endogenous active dehydrogenase capable of converting acetoacetate to 3-HB was identified in C. ljungdahlii, thereby revealing an efficient 3-HB-producing pathway. The engineered strain was further optimized to reassimilate acetic acid and synthesize 3-HB by introducing heterologous functional genes. Finally, the best-performing strain was able to produce 13.4, 3.0, and 28.4 g/L of isopropanol, 3-HB, and ethanol, respectively, in continuous gas fermentation. Therefore, this work represents remarkable progress in microbial production of bulk chemicals using C1 gases.
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Affiliation(s)
- Dechen Jia
- Key Laboratory of Synthetic Biology, The State Key Laboratory of Plant Carbon-Nitrogen Assimilation, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Meiyu He
- Key Laboratory of Synthetic Biology, The State Key Laboratory of Plant Carbon-Nitrogen Assimilation, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
- Key Laboratory of Plant Stress Biology, State Key Laboratory of Cotton Biology, School of Life Sciences, Henan University, Kaifeng 475004, China
| | - Yi Tian
- Key Laboratory of Synthetic Biology, The State Key Laboratory of Plant Carbon-Nitrogen Assimilation, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
- Key Laboratory of Plant Stress Biology, State Key Laboratory of Cotton Biology, School of Life Sciences, Henan University, Kaifeng 475004, China
| | - Shaohuang Shen
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Xianfeng Zhu
- Key Laboratory of Plant Stress Biology, State Key Laboratory of Cotton Biology, School of Life Sciences, Henan University, Kaifeng 475004, China
| | - Yonghong Wang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Yingping Zhuang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Weihong Jiang
- Key Laboratory of Synthetic Biology, The State Key Laboratory of Plant Carbon-Nitrogen Assimilation, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Yang Gu
- Key Laboratory of Synthetic Biology, The State Key Laboratory of Plant Carbon-Nitrogen Assimilation, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
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Hexanol biosynthesis from syngas by Clostridium carboxidivorans P7 - product toxicity, temperature dependence and in situ extraction. Heliyon 2021; 7:e07732. [PMID: 34409191 PMCID: PMC8361263 DOI: 10.1016/j.heliyon.2021.e07732] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Revised: 05/17/2021] [Accepted: 08/03/2021] [Indexed: 11/08/2022] Open
Abstract
Clostridium carboxidivorans converts syngas into industrial alcohols like hexanol, but titers may be limited by product toxicity. Investigation of IC50 at 30 °C (17.5 mM) and 37 °C (11.8 mM) revealed increased hexanol tolerance at lower temperatures. To avoid product toxicity, oleyl alcohol was added as an extraction solvent, increasing hexanol production nearly 2.5-fold to 23.9 mM (2.4 g/L) at 30 °C. This titer exceeds the concentration that is acutely toxic in the absence of a solvent, confirming the hypothesis that current hexanol production is limited by product toxicity. The solvent however had no positive effect at 37 °C. Furthermore, C. carboxidivorans cell membranes adapted to the higher temperature by incorporating more saturated fatty acids, but surprisingly not to hexanol. Corn oil and sunflower seed oil were tested as alternative, inexpensive extraction solvents. Hexanol titers were similar with all solvents, but oleyl alcohol achieved the highest extraction efficiency.
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30
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Debabov VG. Acetogens: Biochemistry, Bioenergetics, Genetics, and Biotechnological Potential. Microbiology (Reading) 2021. [DOI: 10.1134/s0026261721030024] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
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Flaiz M, Ludwig G, Bengelsdorf FR, Dürre P. Production of the biocommodities butanol and acetone from methanol with fluorescent FAST-tagged proteins using metabolically engineered strains of Eubacterium limosum. BIOTECHNOLOGY FOR BIOFUELS 2021; 14:117. [PMID: 33971948 PMCID: PMC8111989 DOI: 10.1186/s13068-021-01966-2] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Accepted: 04/29/2021] [Indexed: 05/12/2023]
Abstract
BACKGROUND The interest in using methanol as a substrate to cultivate acetogens increased in recent years since it can be sustainably produced from syngas and has the additional benefit of reducing greenhouse gas emissions. Eubacterium limosum is one of the few acetogens that can utilize methanol, is genetically accessible and, therefore, a promising candidate for the recombinant production of biocommodities from this C1 carbon source. Although several genetic tools are already available for certain acetogens including E. limosum, the use of brightly fluorescent reporter proteins is still limited. RESULTS In this study, we expanded the genetic toolbox of E. limosum by implementing the fluorescence-activating and absorption shifting tag (FAST) as a fluorescent reporter protein. Recombinant E. limosum strains that expressed the gene encoding FAST in an inducible and constitutive manner were constructed. Cultivation of these recombinant strains resulted in brightly fluorescent cells even under anaerobic conditions. Moreover, we produced the biocommodities butanol and acetone from methanol with recombinant E. limosum strains. Therefore, we used E. limosum cultures that produced FAST-tagged fusion proteins of the bifunctional acetaldehyde/alcohol dehydrogenase or the acetoacetate decarboxylase, respectively, and determined the fluorescence intensity and product concentrations during growth. CONCLUSIONS The addition of FAST as an oxygen-independent fluorescent reporter protein expands the genetic toolbox of E. limosum. Moreover, our results show that FAST-tagged fusion proteins can be constructed without negatively impacting the stability, functionality, and productivity of the resulting enzyme. Finally, butanol and acetone can be produced from methanol using recombinant E. limosum strains expressing genes encoding fluorescent FAST-tagged fusion proteins.
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Affiliation(s)
- Maximilian Flaiz
- Institute of Microbiology and Biotechnology, Ulm University, Albert-Einstein-Allee 11, 89081, Ulm, Germany.
| | - Gideon Ludwig
- Institute of Microbiology and Biotechnology, Ulm University, Albert-Einstein-Allee 11, 89081, Ulm, Germany
| | - Frank R Bengelsdorf
- Institute of Microbiology and Biotechnology, Ulm University, Albert-Einstein-Allee 11, 89081, Ulm, Germany
| | - Peter Dürre
- Institute of Microbiology and Biotechnology, Ulm University, Albert-Einstein-Allee 11, 89081, Ulm, Germany
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Weitz S, Hermann M, Linder S, Bengelsdorf FR, Takors R, Dürre P. Isobutanol Production by Autotrophic Acetogenic Bacteria. Front Bioeng Biotechnol 2021; 9:657253. [PMID: 33912549 PMCID: PMC8072342 DOI: 10.3389/fbioe.2021.657253] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Accepted: 03/22/2021] [Indexed: 02/04/2023] Open
Abstract
Two different isobutanol synthesis pathways were cloned into and expressed in the two model acetogenic bacteria Acetobacterium woodii and Clostridium ljungdahlii. A. woodii is specialized on using CO2 + H2 gas mixtures for growth and depends on sodium ions for ATP generation by a respective ATPase and Rnf system. On the other hand, C. ljungdahlii grows well on syngas (CO + H2 + CO2 mixture) and depends on protons for energy conservation. The first pathway consisted of ketoisovalerate ferredoxin oxidoreductase (Kor) from Clostridium thermocellum and bifunctional aldehyde/alcohol dehydrogenase (AdhE2) from C. acetobutylicum. Three different kor gene clusters are annotated in C. thermocellum and were all tested. Only in recombinant A. woodii strains, traces of isobutanol could be detected. Additional feeding of ketoisovalerate increased isobutanol production to 2.9 mM under heterotrophic conditions using kor3 and to 1.8 mM under autotrophic conditions using kor2. In C. ljungdahlii, isobutanol could only be detected upon additional ketoisovalerate feeding under autotrophic conditions. kor3 proved to be the best suited gene cluster. The second pathway consisted of ketoisovalerate decarboxylase from Lactococcus lactis and alcohol dehydrogenase from Corynebacterium glutamicum. For increasing the carbon flux to ketoisovalerate, genes encoding ketol-acid reductoisomerase, dihydroxy-acid dehydratase, and acetolactate synthase from C. ljungdahlii were subcloned downstream of adhA. Under heterotrophic conditions, A. woodii produced 0.2 mM isobutanol and 0.4 mM upon additional ketoisovalerate feeding. Under autotrophic conditions, no isobutanol formation could be detected. Only upon additional ketoisovalerate feeding, recombinant A. woodii produced 1.5 mM isobutanol. With C. ljungdahlii, no isobutanol was formed under heterotrophic conditions and only 0.1 mM under autotrophic conditions. Additional feeding of ketoisovalerate increased these values to 1.5 mM and 0.6 mM, respectively. A further increase to 2.4 mM and 1 mM, respectively, could be achieved upon inactivation of the ilvE gene in the recombinant C. ljungdahlii strain. Engineering the coenzyme specificity of IlvC of C. ljungdahlii from NADPH to NADH did not result in improved isobutanol production.
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Affiliation(s)
- Sandra Weitz
- Institut für Mikrobiologie und Biotechnologie, Universität Ulm, Ulm, Germany
| | - Maria Hermann
- Institut für Bioverfahrenstechnik, Universität Stuttgart, Stuttgart, Germany
| | - Sonja Linder
- Institut für Mikrobiologie und Biotechnologie, Universität Ulm, Ulm, Germany
| | - Frank R Bengelsdorf
- Institut für Mikrobiologie und Biotechnologie, Universität Ulm, Ulm, Germany
| | - Ralf Takors
- Institut für Bioverfahrenstechnik, Universität Stuttgart, Stuttgart, Germany
| | - Peter Dürre
- Institut für Mikrobiologie und Biotechnologie, Universität Ulm, Ulm, Germany
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Fackler N, Heijstra BD, Rasor BJ, Brown H, Martin J, Ni Z, Shebek KM, Rosin RR, Simpson SD, Tyo KE, Giannone RJ, Hettich RL, Tschaplinski TJ, Leang C, Brown SD, Jewett MC, Köpke M. Stepping on the Gas to a Circular Economy: Accelerating Development of Carbon-Negative Chemical Production from Gas Fermentation. Annu Rev Chem Biomol Eng 2021; 12:439-470. [PMID: 33872517 DOI: 10.1146/annurev-chembioeng-120120-021122] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Owing to rising levels of greenhouse gases in our atmosphere and oceans, climate change poses significant environmental, economic, and social challenges globally. Technologies that enable carbon capture and conversion of greenhouse gases into useful products will help mitigate climate change by enabling a new circular carbon economy. Gas fermentation usingcarbon-fixing microorganisms offers an economically viable and scalable solution with unique feedstock and product flexibility that has been commercialized recently. We review the state of the art of gas fermentation and discuss opportunities to accelerate future development and rollout. We discuss the current commercial process for conversion of waste gases to ethanol, including the underlying biology, challenges in process scale-up, and progress on genetic tool development and metabolic engineering to expand the product spectrum. We emphasize key enabling technologies to accelerate strain development for acetogens and other nonmodel organisms.
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Affiliation(s)
- Nick Fackler
- LanzaTech Inc., Skokie, Illinois 60077, USA; , , , , , ,
| | | | - Blake J Rasor
- Department of Chemical and Biological Engineering, Chemistry of Life Processes Institute, and Center for Synthetic Biology, Northwestern University, Evanston, Illinois 60208, USA; , , , , , ,
| | - Hunter Brown
- Department of Chemical and Biological Engineering, Chemistry of Life Processes Institute, and Center for Synthetic Biology, Northwestern University, Evanston, Illinois 60208, USA; , , , , , ,
| | - Jacob Martin
- Department of Chemical and Biological Engineering, Chemistry of Life Processes Institute, and Center for Synthetic Biology, Northwestern University, Evanston, Illinois 60208, USA; , , , , , ,
| | - Zhuofu Ni
- Department of Chemical and Biological Engineering, Chemistry of Life Processes Institute, and Center for Synthetic Biology, Northwestern University, Evanston, Illinois 60208, USA; , , , , , ,
| | - Kevin M Shebek
- Department of Chemical and Biological Engineering, Chemistry of Life Processes Institute, and Center for Synthetic Biology, Northwestern University, Evanston, Illinois 60208, USA; , , , , , ,
| | - Rick R Rosin
- LanzaTech Inc., Skokie, Illinois 60077, USA; , , , , , ,
| | - Séan D Simpson
- LanzaTech Inc., Skokie, Illinois 60077, USA; , , , , , ,
| | - Keith E Tyo
- Department of Chemical and Biological Engineering, Chemistry of Life Processes Institute, and Center for Synthetic Biology, Northwestern University, Evanston, Illinois 60208, USA; , , , , , ,
| | - Richard J Giannone
- Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA; ,
| | - Robert L Hettich
- Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA; ,
| | | | - Ching Leang
- LanzaTech Inc., Skokie, Illinois 60077, USA; , , , , , ,
| | - Steven D Brown
- LanzaTech Inc., Skokie, Illinois 60077, USA; , , , , , ,
| | - Michael C Jewett
- Department of Chemical and Biological Engineering, Chemistry of Life Processes Institute, and Center for Synthetic Biology, Northwestern University, Evanston, Illinois 60208, USA; , , , , , , .,Robert H. Lurie Comprehensive Cancer Center and Simpson Querrey Institute, Northwestern University, Chicago, Illinois 60611, USA
| | - Michael Köpke
- LanzaTech Inc., Skokie, Illinois 60077, USA; , , , , , ,
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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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Abstract
Goal of sustainable carbon neutral economy can be achieved by designing an efficient CO2 reduction system to generate biofuels, in particular, by mimicking the mechanism of natural photosynthesis using semiconducting nanomaterials interfaced with electroactive bacteria (EAB) in a photosynthetic microbial electrosynthesis (PMES) system. This review paper presents an overview of the recent advancements in the biohybrid photoanode and photocathode materials. We discuss the reaction mechanism observed at photoanode and photocathode to enhance our understanding on the solar driven MES. We extend the discussion by showcasing the potential activity of EABs toward high selectivity and production rates for desirable products by manipulating their genomic sequence. Additionally, the critical challenges associated in scaling up the PMES system including the strategies for diminution of reactive oxygen species, low solubility of CO2 in the typical electrolytes, low selectivity of product species are presented along with the suggestions of alternative strategies to achieve economically viable generation of (bio)commodities.
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Mann M, Wittke D, Büchs J. Online monitoring applying the anaerobic respiratory monitoring system reveals iron(II) limitation in YTF medium for Clostridium ljungdahlii. Eng Life Sci 2021; 21:19-28. [PMID: 33531887 PMCID: PMC7837299 DOI: 10.1002/elsc.202000054] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Revised: 10/19/2020] [Accepted: 10/19/2020] [Indexed: 12/13/2022] Open
Abstract
Online monitoring of microbial cultures is an effective approach for studying both aerobic and anaerobic microorganisms. Especially in small-scale cultivations, several parallel online monitored experiments can generate a detailed understanding of the cultivation, compared to a situation where a few data points are generated from time course sampling and offline analysis. However, the availability of small-scale online monitoring devices for acetogenic organisms is limited. In this study, the previously reported anaerobic Respiration Activity MOnitoring System (anaRAMOS) device was adapted for online monitoring of Clostridium ljungdahlii (C. ljungdahlii) cultures with fructose as the carbon source. The anaRAMOS was applied to identify conversion of different carbon sources present in commonly used YTF medium. An iron(II) deficiency was discovered in this medium for C. ljungdahlii. Addition of iron(II) to the YTF medium reduced the cultivation time and increased biomass yield of C. ljungdahlii cultures by 50% and 40%, respectively. The measurement of the carbon dioxide transfer rate was used to calculated the iron(II) contained in complex components. By demonstrating the application of the anaRAMOS device for medium optimization, it is proven that the described online monitoring device has potential for use in process development.
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Affiliation(s)
- Marcel Mann
- AVT – Biochemical EngineeringRWTH Aachen UniversityAachenGermany
| | - Darina Wittke
- AVT – Biochemical EngineeringRWTH Aachen UniversityAachenGermany
| | - Jochen Büchs
- AVT – Biochemical EngineeringRWTH Aachen UniversityAachenGermany
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Wiechmann A, Trifunović D, Klein S, Müller V. Homologous production, one-step purification, and proof of Na + transport by the Rnf complex from Acetobacterium woodii, a model for acetogenic conversion of C1 substrates to biofuels. BIOTECHNOLOGY FOR BIOFUELS 2020; 13:208. [PMID: 33342435 PMCID: PMC7751120 DOI: 10.1186/s13068-020-01851-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Accepted: 12/04/2020] [Indexed: 05/25/2023]
Abstract
BACKGROUND Capture and storage of the energy carrier hydrogen as well as of the greenhouse gas carbon dioxide are two major problems that mankind faces currently. Chemical catalysts have been developed, but only recently a group of anaerobic bacteria that convert hydrogen and carbon dioxide to acetate, formate, or biofuels such as ethanol has come into focus, the acetogenic bacteria. These biocatalysts produce the liquid organic hydrogen carrier formic acid from H2 + CO2 or even carbon monoxide with highest rates ever reported. The autotrophic, hydrogen-oxidizing, and CO2-reducing acetogens have in common a specialized metabolism to catalyze CO2 reduction, the Wood-Ljungdahl pathway (WLP). The WLP does not yield net ATP, but is hooked up to a membrane-bound respiratory chain that enables ATP synthesis coupled to CO2 fixation. The nature of the respiratory enzyme has been an enigma since the discovery of these bacteria and has been unraveled in this study. RESULTS We have produced a His-tagged variant of the ferredoxin:NAD oxidoreductase (Rnf complex) from the model acetogen Acetobacterium woodii, solubilized the enzyme from the cytoplasmic membrane, and purified it by Ni2+-NTA affinity chromatography. The enzyme was incorporated into artificial liposomes and catalyzed Na+ transport coupled to ferredoxin-dependent NAD reduction. Our results using the purified enzyme do not only verify that the Rnf complex from A. woodii is Na+-dependent, they also demonstrate for the first time that this membrane-embedded molecular engine creates a Na+ gradient across the membrane of A. woodii which can be used for ATP synthesis. DISCUSSION We present a protocol for homologous production and purification for an Rnf complex. The enzyme catalyzed electron-transfer driven Na+ export and, thus, our studies provided the long-awaited biochemical proof that the Rnf complex is a respiratory enzyme.
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Affiliation(s)
- Anja Wiechmann
- Molecular Microbiology and Bioenergetics, Institute of Molecular Biosciences, Goethe University Frankfurt, Max-von-Laue Str. 9, 60438, Frankfurt am Main, Germany
| | - Dragan Trifunović
- Molecular Microbiology and Bioenergetics, Institute of Molecular Biosciences, Goethe University Frankfurt, Max-von-Laue Str. 9, 60438, Frankfurt am Main, Germany
| | - Sophie Klein
- Molecular Microbiology and Bioenergetics, Institute of Molecular Biosciences, Goethe University Frankfurt, Max-von-Laue Str. 9, 60438, Frankfurt am Main, Germany
| | - Volker Müller
- Molecular Microbiology and Bioenergetics, Institute of Molecular Biosciences, Goethe University Frankfurt, Max-von-Laue Str. 9, 60438, Frankfurt am Main, Germany.
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38
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Lo J, Humphreys JR, Jack J, Urban C, Magnusson L, Xiong W, Gu Y, Ren ZJ, Maness PC. The Metabolism of Clostridium ljungdahlii in Phosphotransacetylase Negative Strains and Development of an Ethanologenic Strain. Front Bioeng Biotechnol 2020; 8:560726. [PMID: 33195125 PMCID: PMC7653027 DOI: 10.3389/fbioe.2020.560726] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2020] [Accepted: 10/05/2020] [Indexed: 11/13/2022] Open
Abstract
The sustainable production of chemicals from non-petrochemical sources is one of the greatest challenges of our time. CO2 release from industrial activity is not environmentally friendly yet provides an inexpensive feedstock for chemical production. One means of addressing this problem is using acetogenic bacteria to produce chemicals from CO2, waste streams, or renewable resources. Acetogens are attractive hosts for chemical production for many reasons: they can utilize a variety of feedstocks that are renewable or currently waste streams, can capture waste carbon sources and covert them to products, and can produce a variety of chemicals with greater carbon efficiency over traditional fermentation technologies. Here we investigated the metabolism of Clostridium ljungdahlii, a model acetogen, to probe carbon and electron partitioning and understand what mechanisms drive product formation in this organism. We utilized CRISPR/Cas9 and an inducible riboswitch to target enzymes involved in fermentation product formation. We focused on the genes encoding phosphotransacetylase (pta), aldehyde ferredoxin oxidoreductases (aor1 and aor2), and bifunctional alcohol/aldehyde dehydrogenases (adhE1 and adhE2) and performed growth studies under a variety of conditions to probe the role of those enzymes in the metabolism. Finally, we demonstrated a switch from acetogenic to ethanologenic metabolism by these manipulations, providing an engineered bacterium with greater application potential in biorefinery industry.
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Affiliation(s)
- Jonathan Lo
- National Renewable Energy Laboratory, Golden, CO, United States
| | | | - Joshua Jack
- Andlinger Center for Energy and Environment, Princeton University, Princeton, NJ, United States
| | - Chris Urban
- National Renewable Energy Laboratory, Golden, CO, United States
| | | | - Wei Xiong
- National Renewable Energy Laboratory, Golden, CO, United States
| | - Yang Gu
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Zhiyong Jason Ren
- Andlinger Center for Energy and Environment, Princeton University, Princeton, NJ, United States
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Synthetic Biology on Acetogenic Bacteria for Highly Efficient Conversion of C1 Gases to Biochemicals. Int J Mol Sci 2020; 21:ijms21207639. [PMID: 33076477 PMCID: PMC7589590 DOI: 10.3390/ijms21207639] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 10/13/2020] [Accepted: 10/13/2020] [Indexed: 12/13/2022] Open
Abstract
Synthesis gas, which is mainly produced from fossil fuels or biomass gasification, consists of C1 gases such as carbon monoxide, carbon dioxide, and methane as well as hydrogen. Acetogenic bacteria (acetogens) have emerged as an alternative solution to recycle C1 gases by converting them into value-added biochemicals using the Wood-Ljungdahl pathway. Despite the advantage of utilizing acetogens as biocatalysts, it is difficult to develop industrial-scale bioprocesses because of their slow growth rates and low productivities. To solve these problems, conventional approaches to metabolic engineering have been applied; however, there are several limitations owing to the lack of required genetic bioparts for regulating their metabolic pathways. Recently, synthetic biology based on genetic parts, modules, and circuit design has been actively exploited to overcome the limitations in acetogen engineering. This review covers synthetic biology applications to design and build industrial platform acetogens.
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40
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Charubin K, Streett H, Papoutsakis ET. Development of Strong Anaerobic Fluorescent Reporters for Clostridium acetobutylicum and Clostridium ljungdahlii Using HaloTag and SNAP-tag Proteins. Appl Environ Microbiol 2020; 86:e01271-20. [PMID: 32769192 PMCID: PMC7531948 DOI: 10.1128/aem.01271-20] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Accepted: 08/04/2020] [Indexed: 12/12/2022] Open
Abstract
One of the biggest limitations in the study and engineering of anaerobic Clostridium organisms is the lack of strong fluorescent reporters capable of strong and real-time fluorescence. Recently, we developed a strong fluorescent reporter system for Clostridium organisms based on the FAST protein. Here, we report the development of two new strong fluorescent reporter systems for Clostridium organisms based on the HaloTag and SNAP-tag proteins, which produce strong fluorescent signals when covalently bound to fluorogenic ligands. These new fluorescent reporters are orthogonal to the FAST ligands and to each other, allowing for simultaneous labeling and visualization. We used HaloTag and SNAP-tag to label the strictly anaerobic organisms Clostridium acetobutylicum and Clostridium ljungdahlii We have also identified a new strong promoter for protein expression in C. acetobutylicum, based on the phosphotransacetylase gene (pta) from C. ljungdahlii Furthermore, the HaloTag and the SNAP-tag, in combination with the previously described FAST system, were successfully used to measure cell populations in bacterial mixed cultures and showed the simultaneous orthogonal labeling of HaloTag and SNAP-tag together with the FAST protein reporter. Finally, we show the expression of recombinant fusion protein of FAST and the ZapA division protein (from C. acetobutylicum) in C. ljungdahlii. The availability of multiple strong fluorescent reporters is a major addition to the genetic toolkit of Clostridium and other anaerobes that will lead to better understanding of these unique organisms.IMPORTANCE Up to this point, assays and methods involving fluorescent reporter proteins were unavailable or limited in Clostridium organisms and other strict anaerobes. Green fluorescent protein (GFP), mCherry, and flavin-binding proteins (and their derivatives) have been used only in a few clostridia with limited success and yielded low fluorescence compared to aerobic microbial systems. Recently, we reported a new strong fluorescent reporter system based on the FAST protein as a first step in expanding the fluorescence-based reporters for Clostridium and other anaerobic microbial platforms. Additional strong orthogonal fluorescent proteins, with distinct emission spectra are needed to allow for (i) multispecies tracking within the growing field of microbial cocultures and microbiomes, (ii) protein localization and tracking in anaerobes, and (iii) identification and development of natural and synthetic promoters, ribosome-binding sites (RBS), and terminators for optimal protein expression in anaerobes. Here, we present two new strong fluorescent reporter systems based on the HaloTag and SNAP-tag proteins.
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Affiliation(s)
- Kamil Charubin
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, Delaware, USA
- Delaware Biotechnology Institute, University of Delaware, Newark, Delaware, USA
| | - Hannah Streett
- Delaware Biotechnology Institute, University of Delaware, Newark, Delaware, USA
- Department of Biological Sciences, University of Delaware, Newark, Delaware, USA
| | - Eleftherios Terry Papoutsakis
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, Delaware, USA
- Delaware Biotechnology Institute, University of Delaware, Newark, Delaware, USA
- Department of Biological Sciences, University of Delaware, Newark, Delaware, USA
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Review—Microbial Electrosynthesis: A Way Towards The Production of Electro-Commodities Through Carbon Sequestration with Microbes as Biocatalysts. JOURNAL OF THE ELECTROCHEMICAL SOCIETY 2020. [DOI: 10.1149/1945-7111/abb836] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
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Affiliation(s)
- Cláudio J. R. Frazão
- TU Dresden Institute of Natural Materials Technology Bergstraße 120 01062 Dresden Germany
| | - Thomas Walther
- TU Dresden Institute of Natural Materials Technology Bergstraße 120 01062 Dresden Germany
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Jeong J, Kim JY, Park B, Choi IG, Chang IS. Genetic engineering system for syngas-utilizing acetogen, Eubacterium limosum KIST612. ACTA ACUST UNITED AC 2020. [DOI: 10.1016/j.biteb.2020.100452] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
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Xia PF, Casini I, Schulz S, Klask CM, Angenent LT, Molitor B. Reprogramming Acetogenic Bacteria with CRISPR-Targeted Base Editing via Deamination. ACS Synth Biol 2020; 9:2162-2171. [PMID: 32610012 DOI: 10.1021/acssynbio.0c00226] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Acetogenic bacteria are rising in popularity as chassis microbes for biotechnology due to their capability of converting inorganic one-carbon (C1) gases to organic chemicals. To fully uncover the potential of acetogenic bacteria, synthetic biology tools are imperative to either engineer designed functions or to interrogate the physiology. Here, we report a genome-editing tool at a one-nucleotide resolution, namely base editing, for acetogenic bacteria based on CRISPR-targeted deamination. This tool combines nuclease deactivated Cas9 with activation-induced cytidine deaminase to enable cytosine-to-thymine substitution without DNA cleavage, homology-directed repair, and donor DNA, which are generally the bottlenecks for applying conventional CRISPR-Cas systems in bacteria. We designed and validated a modularized base-editing tool in the model acetogenic bacterium Clostridium ljungdahlii. The editing principles were investigated, and an in-silico analysis revealed the capability of base editing across the genome and the potential for off-target events. Moreover, genes related to acetate and ethanol production were disrupted individually by installing premature STOP codons to reprogram carbon flux toward improved acetate production. This resulted in engineered C. ljungdahlii strains with the desired phenotypes and stable genotypes. Our base-editing tool promotes the application and research in acetogenic bacteria and provides a blueprint to upgrade CRISPR-Cas-based genome editing in bacteria in general.
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Affiliation(s)
- Peng-Fei Xia
- Environmental Biotechnology Group, Center for Applied Geosciences, University of Tübingen, 72074 Tübingen, Germany
| | - Isabella Casini
- Environmental Biotechnology Group, Center for Applied Geosciences, University of Tübingen, 72074 Tübingen, Germany
| | - Sarah Schulz
- Environmental Biotechnology Group, Center for Applied Geosciences, University of Tübingen, 72074 Tübingen, Germany
| | - Christian-Marco Klask
- Environmental Biotechnology Group, Center for Applied Geosciences, University of Tübingen, 72074 Tübingen, Germany
| | - Largus T. Angenent
- Environmental Biotechnology Group, Center for Applied Geosciences, University of Tübingen, 72074 Tübingen, Germany
- AG Angenent, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
| | - Bastian Molitor
- Environmental Biotechnology Group, Center for Applied Geosciences, University of Tübingen, 72074 Tübingen, Germany
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Ethanol Metabolism Dynamics in Clostridium ljungdahlii Grown on Carbon Monoxide. Appl Environ Microbiol 2020; 86:AEM.00730-20. [PMID: 32414802 DOI: 10.1128/aem.00730-20] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Accepted: 05/11/2020] [Indexed: 01/10/2023] Open
Abstract
Bioethanol production from syngas using acetogenic bacteria has attracted considerable attention in recent years. However, low ethanol yield is the biggest challenge that prevents the commercialization of syngas fermentation into biofuels using microbial catalysts. The present study demonstrated that ethanol metabolism plays an important role in recycling NADH/NAD+ during autotrophic growth. Deletion of bifunctional aldehyde/alcohol dehydrogenase (adhE) genes leads to significant growth deficiencies in gas fermentation. Using specific fermentation technology in which the gas pressure and pH were constantly controlled at 0.1 MPa and 6.0, respectively, we revealed that ethanol was formed during the exponential phase, closely accompanied by biomass production. Then, ethanol was oxidized to acetate via the aldehyde ferredoxin oxidoreductase pathway in Clostridium ljungdahlii A metabolic experiment using 13C-labeled ethanol and acetate, redox balance analysis, and comparative transcriptomic analysis demonstrated that ethanol production and reuse shared the metabolic pathway but occurred at different growth phases.IMPORTANCE Ethanol production from carbon monoxide (CO) as a carbon and energy source by Clostridium ljungdahlii and "Clostridium autoethanogenum" is currently being commercialized. During gas fermentation, ethanol synthesis is NADH-dependent. However, ethanol oxidation and its regulatory mechanism remain incompletely understood. Energy metabolism analysis demonstrated that reduced ferredoxin is the sole source of NADH formation by the Rnf-ATPase system, which provides ATP for cell growth during CO fermentation. Therefore, ethanol production is tightly linked to biomass production (ATP production). Clarification of the mechanism of ethanol oxidation and biosynthesis can provide an important reference for generating high-ethanol-yield strains of C. ljungdahlii in the future.
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Flaiz M, Baur T, Brahner S, Poehlein A, Daniel R, Bengelsdorf FR. Caproicibacter fermentans gen. nov., sp. nov., a new caproate-producing bacterium and emended description of the genus Caproiciproducens. Int J Syst Evol Microbiol 2020; 70:4269-4279. [DOI: 10.1099/ijsem.0.004283] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A strictly anaerobic bacterial strain designated EA1T was isolated from an enrichment culture inoculated with biogas reactor content. Cells of strain EA1T are spore-forming rods (1–3×0.4–0.8 µm) and stain Gram-negative, albeit they possess a Gram-positive type of cell-wall ultrastructure. Growth of strain EA1T was observed at 30 and 37 °C and within a pH range of pH 5–9. The major components recovered in the fatty acid fraction were C14:0, C16:0, C16:0 DMA (dimethyl acetal) and C16:1
ω7c. Strain EA1T fermented several mono- and disaccharides. Metabolic end products from fructose were acetate, butyrate, caproate and lactate. Furthermore, ethanol, CO2 and H2 were identified as products. The genome consists of a chromosome (3.9 Mbp) with 3797 predicted protein-encoding genes and a G+C content of 51.25 mol%. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain EA1T represents a novel taxon within the family
Oscillospiraceae
. The most closely related type strains of EA1T, based on 16S rRNA gene sequence identity, are
Caproiciproducens galactitolivorans
BS-1T (94.9 %), [
Clostridium
] leptum DSM 753T (93.8 %), [
Clostridium
] sporosphaeroides DSM 1294T (91.7 %) and
Ruminococcus bromii
ATCC 27255T (91.0 %). Further phenotypic characteristics of strain EA1T differentiate it from related, validly described bacterial species. Strain EA1T represents a novel genus and novel species within the family
Oscillospiraceae
. The proposed name is Caproicibacter fermentans gen. nov., sp. nov. The type strain is EA1T (DSM 107079T=JCM 33110T).
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Affiliation(s)
- Maximilian Flaiz
- Institut für Mikrobiologie und Biotechnologie, Universität Ulm, Albert-Einstein-Allee 11, 89081 Ulm, Germany
| | - Tina Baur
- Institut für Mikrobiologie und Biotechnologie, Universität Ulm, Albert-Einstein-Allee 11, 89081 Ulm, Germany
| | - Sven Brahner
- Institut für Mikrobiologie und Biotechnologie, Universität Ulm, Albert-Einstein-Allee 11, 89081 Ulm, Germany
| | - Anja Poehlein
- Genomic and Applied Microbiology & Göttingen Genomics Laboratory, Georg-August University Göttingen, Grisebachstr. 8, D-37077 Göttingen, Germany
| | - Rolf Daniel
- Genomic and Applied Microbiology & Göttingen Genomics Laboratory, Georg-August University Göttingen, Grisebachstr. 8, D-37077 Göttingen, Germany
| | - Frank R. Bengelsdorf
- Institut für Mikrobiologie und Biotechnologie, Universität Ulm, Albert-Einstein-Allee 11, 89081 Ulm, Germany
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Zhang L, Zhao R, Jia D, Jiang W, Gu Y. Engineering Clostridium ljungdahlii as the gas-fermenting cell factory for the production of biofuels and biochemicals. Curr Opin Chem Biol 2020; 59:54-61. [PMID: 32480247 DOI: 10.1016/j.cbpa.2020.04.010] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Revised: 04/08/2020] [Accepted: 04/12/2020] [Indexed: 01/08/2023]
Abstract
Clostridium ljungdahlii is a representative autotrophic gas-fermenting acetogen capable of converting CO2 and CO into biomass and multiple metabolites. The carbon fixation and conversion based on C. ljungdahlii have great potential for the sustainable production of bulk biochemicals and biofuels using industrial syngas and waste gases. With substantial recent advances in genetic manipulation tools, it has become possible to study and improve the metabolic capability of C. ljungdahlii in gas fermentation. The product scope of C. ljungdahlii has been expanded through the introduction of heterologous production pathways followed by the modification of native metabolic networks. In addition, progress has been made in understanding the physiological and metabolic mechanisms of this anaerobe, contributing to strain designs for expected phenotypes. In this review, we highlight the latest research progresses regarding C. ljungdahlii and discuss the next steps to comprehensively understand and engineer this bacterium for an improved bacterial gas bioconversion platform.
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Affiliation(s)
- Lu Zhang
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China; University of Chinese Academy of Sciences, Beijing, China
| | - Ran Zhao
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China; University of Chinese Academy of Sciences, Beijing, China
| | - Dechen Jia
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China; University of Chinese Academy of Sciences, Beijing, China
| | - Weihong Jiang
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China.
| | - Yang Gu
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China.
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Abstract
Clostridia are a group of Gram-positive anaerobic bacteria of medical and industrial importance for which limited genetic methods are available. Here, we demonstrate an approach to make large genomic deletions and insertions in the model Clostridium phytofermentans by combining designed group II introns (targetrons) and Cre recombinase. We apply these methods to delete a 50-gene prophage island by programming targetrons to position markerless lox66 and lox71 sites, which mediate deletion of the intervening 39-kb DNA region using Cre recombinase. Gene expression and growth of the deletion strain showed that the prophage genes contribute to fitness on nonpreferred carbon sources. We also inserted an inducible fluorescent reporter gene into a neutral genomic site by recombination-mediated cassette exchange (RMCE) between genomic and plasmid-based tandem lox sites bearing heterospecific spacers to prevent intracassette recombination. These approaches generally enable facile markerless genome engineering in clostridia to study their genome structure and regulation.IMPORTANCE Clostridia are anaerobic bacteria with important roles in intestinal and soil microbiomes. The inability to experimentally modify the genomes of clostridia has limited their study and application in biotechnology. Here, we developed a targetron-recombinase system to efficiently make large targeted genomic deletions and insertions using the model Clostridium phytofermentans We applied this approach to reveal the importance of a prophage to host fitness and introduce an inducible reporter by recombination-mediated cassette exchange.
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49
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Application of bioelectrochemical systems for carbon dioxide sequestration and concomitant valuable recovery: A review. MATERIALS SCIENCE FOR ENERGY TECHNOLOGIES 2019. [DOI: 10.1016/j.mset.2019.08.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
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50
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Deciphering mixotrophic Clostridium formicoaceticum metabolism and energy conservation: Genomic analysis and experimental studies. Genomics 2019; 111:1687-1694. [DOI: 10.1016/j.ygeno.2018.11.020] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Revised: 11/07/2018] [Accepted: 11/16/2018] [Indexed: 01/01/2023]
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