1
|
Ponsetto P, Sasal EM, Mazzoli R, Valetti F, Gilardi G. The potential of native and engineered Clostridia for biomass biorefining. Front Bioeng Biotechnol 2024; 12:1423935. [PMID: 39219620 PMCID: PMC11365079 DOI: 10.3389/fbioe.2024.1423935] [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: 04/26/2024] [Accepted: 08/06/2024] [Indexed: 09/04/2024] Open
Abstract
Since their first industrial application in the acetone-butanol-ethanol (ABE) fermentation in the early 1900s, Clostridia have found large application in biomass biorefining. Overall, their fermentation products include organic acids (e.g., acetate, butyrate, lactate), short chain alcohols (e.g., ethanol, n-butanol, isobutanol), diols (e.g., 1,2-propanediol, 1,3-propanediol) and H2 which have several applications such as fuels, building block chemicals, solvents, food and cosmetic additives. Advantageously, several clostridial strains are able to use cheap feedstocks such as lignocellulosic biomass, food waste, glycerol or C1-gases (CO2, CO) which confer them additional potential as key players for the development of processes less dependent from fossil fuels and with reduced greenhouse gas emissions. The present review aims to provide a survey of research progress aimed at developing Clostridium-mediated biomass fermentation processes, especially as regards strain improvement by metabolic engineering.
Collapse
Affiliation(s)
| | | | - Roberto Mazzoli
- Structural and Functional Biochemistry, Laboratory of Proteomics and Metabolic Engineering of Prokaryotes, Department of Life Sciences and Systems Biology, University of Torino, Torino, Italy
| | | | | |
Collapse
|
2
|
Mazzoli R, Pescarolo S, Gilli G, Gilardi G, Valetti F. Hydrogen production pathways in Clostridia and their improvement by metabolic engineering. Biotechnol Adv 2024; 73:108379. [PMID: 38754796 DOI: 10.1016/j.biotechadv.2024.108379] [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: 12/04/2023] [Revised: 05/13/2024] [Accepted: 05/13/2024] [Indexed: 05/18/2024]
Abstract
Biological production of hydrogen has a tremendous potential as an environmentally sustainable technology to generate a clean fuel. Among the different available methods to produce biohydrogen, dark fermentation features the highest productivity and can be used as a means to dispose of organic waste biomass. Within this approach, Clostridia have the highest theoretical H2 production yield. Nonetheless, most strains show actual yields far lower than the theoretical maximum: improving their efficiency becomes necessary for achieving cost-effective fermentation processes. This review aims at providing a survey of the metabolic network involved in H2 generation in Clostridia and strategies used to improve it through metabolic engineering. Together with current achievements, a number of future perspectives to implement these results will be illustrated.
Collapse
Affiliation(s)
- Roberto Mazzoli
- Structural and Functional Biochemistry, Laboratory of Proteomics and Metabolic Engineering of Prokaryotes, Department of Life Sciences and Systems Biology, University of Torino, Via Accademia Albertina 13, 10123 Torino, Italy.
| | - Simone Pescarolo
- Biology applied to the environment, Laboratories of microbiology and ecotoxicology, Ecobioqual, Environment Park. Via Livorno 60, 10144 Torino, Italy
| | - Giorgio Gilli
- Department of Sciences of Public Health and Pediatrics, School of Medicine, University of Torino, Via Santena 5 bis, 10126 Torino, Italy
| | - Gianfranco Gilardi
- Structural and Functional Biochemistry, Laboratory of Proteomics and Metabolic Engineering of Prokaryotes, Department of Life Sciences and Systems Biology, University of Torino, Via Accademia Albertina 13, 10123 Torino, Italy
| | - Francesca Valetti
- Structural and Functional Biochemistry, Laboratory of Proteomics and Metabolic Engineering of Prokaryotes, Department of Life Sciences and Systems Biology, University of Torino, Via Accademia Albertina 13, 10123 Torino, Italy.
| |
Collapse
|
3
|
Ehsaan M, Yoo M, Kuit W, Foulquier C, Soucaille P, Minton NP. Chromosomal integration of the pSOL1 megaplasmid of Clostridium acetobutylicum for continuous and stable advanced biofuels production. Nat Microbiol 2024; 9:1655-1660. [PMID: 38877224 PMCID: PMC11222136 DOI: 10.1038/s41564-024-01714-w] [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: 05/30/2023] [Accepted: 04/24/2024] [Indexed: 06/16/2024]
Abstract
Biofuel production by Clostridium acetobutylicum is compromised by strain degeneration due to loss of its pSOL1 megaplasmid. Here we used engineering biology to stably integrate pSOL1 into the chromosome together with a synthetic isopropanol pathway. In a membrane bioreactor continuously fed with glucose mineral medium, the final strain produced advanced biofuels, n-butanol and isopropanol, at high yield (0.31 g g-1), titre (15.4 g l-1) and productivity (15.5 g l-1 h-1) without degeneration.
Collapse
Affiliation(s)
- Muhammad Ehsaan
- BBSRC/EPSRC Synthetic Biology Research Centre, School of Life Sciences, Biodiscovery Institute, University of Nottingham, Nottingham, UK
| | - Minyeong Yoo
- BBSRC/EPSRC Synthetic Biology Research Centre, School of Life Sciences, Biodiscovery Institute, University of Nottingham, Nottingham, UK
| | - Wouter Kuit
- BBSRC/EPSRC Synthetic Biology Research Centre, School of Life Sciences, Biodiscovery Institute, University of Nottingham, Nottingham, UK
| | - Céline Foulquier
- TBI, Université de Toulouse, CNRS, INRAE, INSA, Toulouse, France
| | - Philippe Soucaille
- BBSRC/EPSRC Synthetic Biology Research Centre, School of Life Sciences, Biodiscovery Institute, University of Nottingham, Nottingham, UK.
- TBI, Université de Toulouse, CNRS, INRAE, INSA, Toulouse, France.
| | - Nigel P Minton
- BBSRC/EPSRC Synthetic Biology Research Centre, School of Life Sciences, Biodiscovery Institute, University of Nottingham, Nottingham, UK
| |
Collapse
|
4
|
Wang Y, Qian J, Shi T, Wang Y, Ding Q, Ye C. Application of extremophile cell factories in industrial biotechnology. Enzyme Microb Technol 2024; 175:110407. [PMID: 38341913 DOI: 10.1016/j.enzmictec.2024.110407] [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: 12/15/2023] [Revised: 01/24/2024] [Accepted: 01/26/2024] [Indexed: 02/13/2024]
Abstract
Due to the extreme living conditions, extremophiles have unique characteristics in morphology, structure, physiology, biochemistry, molecular evolution mechanism and so on. Extremophiles have superior growth and synthesis capabilities under harsh conditions compared to conventional microorganisms, allowing for unsterilized fermentation processes and thus better performance in low-cost production. In recent years, due to the development and optimization of molecular biology, synthetic biology and fermentation technology, the identification and screening technology of extremophiles has been greatly improved. In this review, we summarize techniques for the identification and screening of extremophiles and review their applications in industrial biotechnology in recent years. In addition, the facts and perspectives gathered in this review suggest that next-generation industrial biotechnology (NGIBs) based on engineered extremophiles holds the promise of simplifying biofuturing processes, establishing open, non-sterilized continuous fermentation production systems, and utilizing low-cost substrates to make NGIBs attractive and cost-effective bioprocessing technologies for sustainable manufacturing.
Collapse
Affiliation(s)
- Yuzhou Wang
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing 210023, PR China
| | - Jinyi Qian
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing 210023, PR China
| | - Tianqiong Shi
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing 210023, PR China
| | - Yuetong Wang
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing 210023, PR China
| | - Qiang Ding
- School of Life Sciences, Anhui University, Hefei 230601, PR China.
| | - Chao Ye
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing 210023, PR China; Ministry of Education Key Laboratory of NSLSCS.
| |
Collapse
|
5
|
Olavarria K, Becker MV, Sousa DZ, van Loosdrecht MC, Wahl SA. Design and thermodynamic analysis of a pathway enabling anaerobic production of poly-3-hydroxybutyrate in Escherichia coli. Synth Syst Biotechnol 2023; 8:629-639. [PMID: 37823039 PMCID: PMC10562921 DOI: 10.1016/j.synbio.2023.09.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2023] [Revised: 09/14/2023] [Accepted: 09/19/2023] [Indexed: 10/13/2023] Open
Abstract
Utilizing anaerobic metabolisms for the production of biotechnologically relevant products presents potential advantages, such as increased yields and reduced energy dissipation. However, lower energy dissipation may indicate that certain reactions are operating closer to their thermodynamic equilibrium. While stoichiometric analyses and genetic modifications are frequently employed in metabolic engineering, the use of thermodynamic tools to evaluate the feasibility of planned interventions is less documented. In this study, we propose a novel metabolic engineering strategy to achieve an efficient anaerobic production of poly-(R)-3-hydroxybutyrate (PHB) in the model organism Escherichia coli. Our approach involves re-routing of two-thirds of the glycolytic flux through non-oxidative glycolysis and coupling PHB synthesis with NADH re-oxidation. We complemented our stoichiometric analysis with various thermodynamic approaches to assess the feasibility and the bottlenecks in the proposed engineered pathway. According to our calculations, the main thermodynamic bottleneck are the reactions catalyzed by the acetoacetyl-CoA β-ketothiolase (EC 2.3.1.9) and the acetoacetyl-CoA reductase (EC 1.1.1.36). Furthermore, we calculated thermodynamically consistent sets of kinetic parameters to determine the enzyme amounts required for sustaining the conversion fluxes. In the case of the engineered conversion route, the protein pool necessary to sustain the desired fluxes could account for 20% of the whole cell dry weight.
Collapse
Affiliation(s)
- Karel Olavarria
- Laboratory of Microbiology, Wageningen University and Research, Stippenenweg 4, 6708 WE, Wageningen, The Netherlands
- Centre for Living Technologies, Eindhoven-Wageningen-Utrecht Alliance, Princetonlaan 6, 3584 CB, Utrecht, The Netherlands
| | - Marco V. Becker
- Department of Biotechnology, Applied Sciences Faculty, Delft University of Technology, van der Maasweg 9, 2629 HZ, Delft, The Netherlands
| | - Diana Z. Sousa
- Laboratory of Microbiology, Wageningen University and Research, Stippenenweg 4, 6708 WE, Wageningen, The Netherlands
- Centre for Living Technologies, Eindhoven-Wageningen-Utrecht Alliance, Princetonlaan 6, 3584 CB, Utrecht, The Netherlands
| | - Mark C.M. van Loosdrecht
- Department of Biotechnology, Applied Sciences Faculty, Delft University of Technology, van der Maasweg 9, 2629 HZ, Delft, The Netherlands
| | - S. Aljoscha Wahl
- Lehrstuhl für Bioverfahrenstechnik, Friedrich-Alexander-Universität, Paul-Gordan-Strasse 3, 91052, Erlangen, Germany
| |
Collapse
|
6
|
Boudignon E, Foulquier C, Soucaille P. Improvement of the Genome Editing Tools Based on 5FC/5FU Counter Selection in Clostridium acetobutylicum. Microorganisms 2023; 11:2696. [PMID: 38004708 PMCID: PMC10672894 DOI: 10.3390/microorganisms11112696] [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: 10/04/2023] [Revised: 10/27/2023] [Accepted: 11/02/2023] [Indexed: 11/26/2023] Open
Abstract
Several genetic tools have been developed for genome engineering in Clostridium acetobutylicum utilizing 5-fluorouracil (5FU) or 5-fluorocytosine (5FC) resistance as a selection method. In our group, a method based on the integration, by single crossing over, of a suicide plasmid (pCat-upp) followed by selection for the second crossing over using a counter-selectable marker (the upp gene and 5FU resistance) was recently developed for genome editing in C. acetobutylicum. This method allows genome modification without leaving any marker or scar in a strain of C. acetobutylicum that is ∆upp. Unfortunately, 5FU has strong mutagenic properties, inducing mutations in the strain's genome. After numerous applications of the pCat-upp/5FU system for genome modification in C. acetobutylicum, the CAB1060 mutant strain became entirely resistant to 5FU in the presence of the upp gene, resulting in failure when selecting on 5FU for the second crossing over. It was found that the potential repressor of the pyrimidine operon, PyrR, was mutated at position A115, leading to the 5FU resistance of the strain. To fix this problem, we created a corrective replicative plasmid expressing the pyrR gene, which was shown to restore the 5FU sensitivity of the strain. Furthermore, in order to avoid the occurrence of the problem observed with the CAB1060 strain, a preventive suicide plasmid, pCat-upp-pyrR*, was also developed, featuring the introduction of a synthetic codon-optimized pyrR gene, which was referred to as pyrR* with low nucleotide sequence homology to pyrR. Finally, to minimize the mutagenic effect of 5FU, we also improved the pCat-upp/5FU system by reducing the concentration of 5FU from 1 mM to 5 µM using a defined synthetic medium. The optimized system/conditions were used to successfully replace the ldh gene by the sadh-hydG operon to convert acetone into isopropanol.
Collapse
Affiliation(s)
- Eglantine Boudignon
- Toulouse Biotechnology Institute (TBI), National Institute of Applied Sciences (INSA), Université de Toulouse, 135 Avenue de Rangueil, 31077 Toulouse cedex 4, France; (E.B.); (C.F.)
- Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAe), UMR 792, 24 chemin de Borde Rouge-Auzeville, 31326 Castanet-Tolosan, France
- Centre National de la Recherche Scientifique (CNRS), UMR 5504, 16 Avenue Edouard Belin, 31055 Toulouse cedex 4, France
| | - Céline Foulquier
- Toulouse Biotechnology Institute (TBI), National Institute of Applied Sciences (INSA), Université de Toulouse, 135 Avenue de Rangueil, 31077 Toulouse cedex 4, France; (E.B.); (C.F.)
- Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAe), UMR 792, 24 chemin de Borde Rouge-Auzeville, 31326 Castanet-Tolosan, France
- Centre National de la Recherche Scientifique (CNRS), UMR 5504, 16 Avenue Edouard Belin, 31055 Toulouse cedex 4, France
| | - Philippe Soucaille
- Toulouse Biotechnology Institute (TBI), National Institute of Applied Sciences (INSA), Université de Toulouse, 135 Avenue de Rangueil, 31077 Toulouse cedex 4, France; (E.B.); (C.F.)
- Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAe), UMR 792, 24 chemin de Borde Rouge-Auzeville, 31326 Castanet-Tolosan, France
- Centre National de la Recherche Scientifique (CNRS), UMR 5504, 16 Avenue Edouard Belin, 31055 Toulouse cedex 4, France
- (BBSRC)/EPSRC Synthetic Biology Research Centre (SBRC), School of Life Sciences, The University of Nottingham, University Park, Nottingham NG7 2RD, UK
| |
Collapse
|
7
|
Dai K, Qu C, Feng J, Lan Y, Fu H, Wang J. Metabolic engineering of Thermoanaerobacterium aotearoense strain SCUT27 for biofuels production from sucrose and molasses. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2023; 16:155. [PMID: 37865803 PMCID: PMC10589968 DOI: 10.1186/s13068-023-02402-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2023] [Accepted: 09/21/2023] [Indexed: 10/23/2023]
Abstract
BACKGROUND Sucrose-rich sugarcane trash surpasses 28 million tons globally per year. Effective biorefinery systems could convert these biomasses to bioproducts, such as bioethanol from sugarcane sucrose in Brazil. Thermophilic microbes for biofuels have attracted great attention due to their higher fermentation temperature and wide substrate spectrum. However, few thermophiles using sucrose or molasses for biofuels production was reported. Thermoanaerobacterium aotearoense SCUT27 has been considered as an efficient ethanol producer, but it cannot directly utilize sucrose. In this study, various sucrose metabolic pathways were introduced and analyzed in Thermoanaerobaterium. RESULTS The sucrose-6-phosphate hydrolase (scrB), which was from a screened strain Thermoanaerobacterium thermosaccharolyticum G3-1 was overexpressed in T. aotearoense SCUT27 and endowed this strain with the ability to utilize sucrose. In addition, overexpression of the sucrose-specific PTS system (scrA) from Clostridium acetobutylicum accelerated the sucrose transport. To strengthen the alcohols production and substrates metabolism, the redox-sensing transcriptional repressor (rex) in T. aotearoense was further knocked out. Moreover, with the gene arginine repressor (argR) deleted, the ethanologenic mutant P8S10 showed great inhibitors-tolerance and finally accumulated ~ 34 g/L ethanol (a yield of 0.39 g/g sugars) from pretreated cane molasses in 5 L tank by fed-batch fermentation. When introducing butanol synthetic pathway, 3.22 g/L butanol was produced by P8SB4 with a yield of 0.44 g alcohols/g sugars at 50℃. This study demonstrated the potential application of T. aotearoense SCUT27 for ethanol and butanol production from low cost cane molasses. CONCLUSIONS Our work provided strategies for sucrose utilization in thermophiles and improved biofuels production as well as stress tolerances of T. aotearoense SCUT27, demonstrating the potential application of the strain for cost-effective biofuels production from sucrose-based feedstocks.
Collapse
Affiliation(s)
- Kaiqun Dai
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006, China
| | - Chunyun Qu
- College of Light Industry and Food Science, Guangdong Provincial Key Laboratory of Science and Technology of Lingnan Special Food Science and Technology, Zhongkai University of Agriculture and Engineering, Guangzhou, 510225, China
| | - Jun Feng
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006, China
| | - Yang Lan
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006, China
| | - Hongxin Fu
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006, China.
- Guangdong Provincial Key Laboratory of Fermentation and Enzyme Engineering, South China University of Technology, Guangzhou, 510006, China.
| | - Jufang Wang
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006, China.
- Guangdong Provincial Key Laboratory of Fermentation and Enzyme Engineering, South China University of Technology, Guangzhou, 510006, China.
| |
Collapse
|
8
|
Ma Y, Guo N, Li X, Jiang Z, Zhang D, Guo L, Wang Y. Development of an Efficient Recombinant Protein Expression System in Clostridium saccharoperbutylacetonicum Based on the Bacteriophage T7 System. ACS Synth Biol 2023; 12:3092-3105. [PMID: 37712503 DOI: 10.1021/acssynbio.3c00439] [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] [Indexed: 09/16/2023]
Abstract
Recombinant proteins have broad applications. However, there is a lack of a recombinant protein expression system specifically for large-scale production in anaerobic hosts. Here, we developed a powerful and stringently inducible protein expression system based on the bacteriophage T7 system in the strictly anaerobic solvent-producing Clostridium saccharoperbutylacetonicum. With the integration of a codon optimized T7 RNA polymerase into the chromosome, a single plasmid carrying a T7 promoter could efficiently drive high-level expression of the target gene in an orthogonal manner, which was tightly regulated by a lactose-inducible system. Furthermore, by deleting beta-galactosidase genes involved in lactose metabolism, the transcriptional strength was further improved. In the ultimately optimized strain TM-07, the transcriptional strength of the T7 promoter showed 9.5-fold increase compared to the endogenous strong promoter Pthl. The heterologous NADP+-dependent 3-hydroxybutyryl-CoA dehydrogenase (Hbd1) from C. kluyveri was expressed in TM-07, and the yield of the recombinant protein reached 30.4-42.4% of the total cellular protein, surpassing the strong protein expression systems in other Gram-positive bacteria. The relative activity of Hbd1 in the crude enzyme was 198.0 U/mg, which was 8.3-fold higher than the natural activity in C. kluyveri. The relative activity of the purified enzyme reached 467.4 U/mg. To the best of our knowledge, this study represents the first application of the T7 expression system in Clostridium species, and this optimized expression system holds great potential for large-scale endotoxin-free recombinant protein production under strictly anaerobic conditions. This development paves the way for significant advancements in biotechnology and opens up new avenues for industrial applications.
Collapse
Affiliation(s)
- Yuechao Ma
- Department of Biosystems Engineering, Auburn University, Auburn, Alabama 36849, United States
- Center for Bioenergy and Bioproducts, Auburn University, Auburn, Alabama 36849, United States
| | - Na Guo
- Department of Biosystems Engineering, Auburn University, Auburn, Alabama 36849, United States
- Center for Bioenergy and Bioproducts, Auburn University, Auburn, Alabama 36849, United States
| | - Xiao Li
- Department of Crop, Soil and Environmental Sciences, Auburn University, Auburn, Alabama 36849, United States
| | - Zhihua Jiang
- Department of Chemical Engineering, Auburn University, Auburn, Alabama 36849, United States
| | - Dunhua Zhang
- Aquatic Animal Health Research Unit, Agricultural Research Service, USDA, Auburn, Alabama 36832, United States
| | - Liang Guo
- College of Environmental Science and Engineering, Ocean University of China, Qingdao 266100, China
| | - Yi Wang
- Department of Biosystems Engineering, Auburn University, Auburn, Alabama 36849, United States
- Center for Bioenergy and Bioproducts, Auburn University, Auburn, Alabama 36849, United States
| |
Collapse
|
9
|
Boecker S, Schulze P, Klamt S. Growth-coupled anaerobic production of isobutanol from glucose in minimal medium with Escherichia coli. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2023; 16:148. [PMID: 37789464 PMCID: PMC10548627 DOI: 10.1186/s13068-023-02395-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Accepted: 09/18/2023] [Indexed: 10/05/2023]
Abstract
BACKGROUND The microbial production of isobutanol holds promise to become a sustainable alternative to fossil-based synthesis routes for this important chemical. Escherichia coli has been considered as one production host, however, due to redox imbalance, growth-coupled anaerobic production of isobutanol from glucose in E. coli is only possible if complex media additives or small amounts of oxygen are provided. These strategies have a negative impact on product yield, productivity, reproducibility, and production costs. RESULTS In this study, we propose a strategy based on acetate as co-substrate for resolving the redox imbalance. We constructed the E. coli background strain SB001 (ΔldhA ΔfrdA ΔpflB) with blocked pathways from glucose to alternative fermentation products but with an enabled pathway for acetate uptake and subsequent conversion to ethanol via acetyl-CoA. This strain, if equipped with the isobutanol production plasmid pIBA4, showed robust exponential growth (µ = 0.05 h-1) under anaerobic conditions in minimal glucose medium supplemented with small amounts of acetate. In small-scale batch cultivations, the strain reached a glucose uptake rate of 4.8 mmol gDW-1 h-1, a titer of 74 mM and 89% of the theoretical maximal isobutanol/glucose yield, while secreting only small amounts of ethanol synthesized from acetate. Furthermore, we show that the strain keeps a high metabolic activity also in a pulsed fed-batch bioreactor cultivation, even if cell growth is impaired by the accumulation of isobutanol in the medium. CONCLUSIONS This study showcases the beneficial utilization of acetate as a co-substrate and redox sink to facilitate growth-coupled production of isobutanol under anaerobic conditions. This approach holds potential for other applications with different production hosts and/or substrate-product combinations.
Collapse
Affiliation(s)
- Simon Boecker
- Analysis and Redesign of Biological Networks, Max Planck Institute for Dynamics of Complex Technical Systems, Sandtorstr. 1, 39106, Magdeburg, Germany
- University of Applied Sciences Berlin, Seestr. 64, 13347, Berlin, Germany
| | - Peter Schulze
- Physical and Chemical Foundations of Process Engineering, Max Planck Institute for Dynamics of Complex Technical Systems, Sandtorstr. 1, 39106, Magdeburg, Germany
| | - Steffen Klamt
- Analysis and Redesign of Biological Networks, Max Planck Institute for Dynamics of Complex Technical Systems, Sandtorstr. 1, 39106, Magdeburg, Germany.
| |
Collapse
|
10
|
Omorotionmwan BB, Wang H, Baker JP, Gizynski K, Yoo M, Akaluka C, Zhang Y, Minton NP. Chromosomal engineering of inducible isopropanol- butanol-ethanol production in Clostridium acetobutylicum. Front Bioeng Biotechnol 2023; 11:1218099. [PMID: 37397966 PMCID: PMC10312008 DOI: 10.3389/fbioe.2023.1218099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2023] [Accepted: 06/05/2023] [Indexed: 07/04/2023] Open
Abstract
The use of environmentally damaging petrochemical feedstocks can be displaced by fermentation processes based on engineered microbial chassis that recycle biomass-derived carbon into chemicals and fuels. The stable retention of introduced genes, designed to extend product range and/or increase productivity, is essential. Accordingly, we have created multiply marked auxotrophic strains of Clostridium acetobutylicum that provide distinct loci (pyrE, argH, purD, pheA) at which heterologous genes can be rapidly integrated using allele-coupled exchange (ACE). For each locus, ACE-mediated insertion is conveniently selected on the basis of the restoration of prototrophy on minimal media. The Clostridioides difficile gene (tcdR) encoding an orthogonal sigma factor (TcdR) was integrated at the pyrE locus under the control of the lactose-inducible, bgaR::PbgaL promoter to allow the simultaneous control of genes/operons inserted at other disparate loci (purD and pheA) that had been placed under the control of the PtcdB promoter. In control experiments, dose-dependent expression of a catP reporter gene was observed with increasing lactose concentration. At the highest doses tested (10 mM) the level of expression was over 10-fold higher than if catP was placed directly under the control of bgaR::PbgaL and over 2-fold greater than achieved using the strong Pfdx promoter of the Clostridium sporogenes ferredoxin gene. The utility of the system was demonstrated in the production of isopropanol by the C. acetobutylicum strain carrying an integrated copy of tcdR following the insertion of a synthetic acetone operon (ctfA/B, adc) at the purD locus and a gene (sadh) encoding a secondary dehydrogenase at pheA. Lactose induction (10 mM) resulted in the production of 4.4 g/L isopropanol and 19.8 g/L Isopropanol-Butanol-Ethanol mixture.
Collapse
Affiliation(s)
- Bunmi B. Omorotionmwan
- Clostridia Research Group, BBSRC/EPSRC Synthetic Biology Research Centre (SBRC), Biodiscovery Institute, School of Life Sciences, The University of Nottingham, Nottingham, United Kingdom
| | - Hengzheng Wang
- Clostridia Research Group, BBSRC/EPSRC Synthetic Biology Research Centre (SBRC), Biodiscovery Institute, School of Life Sciences, The University of Nottingham, Nottingham, United Kingdom
| | - Jonathan P. Baker
- Clostridia Research Group, BBSRC/EPSRC Synthetic Biology Research Centre (SBRC), Biodiscovery Institute, School of Life Sciences, The University of Nottingham, Nottingham, United Kingdom
| | - Krzysztof Gizynski
- Clostridia Research Group, BBSRC/EPSRC Synthetic Biology Research Centre (SBRC), Biodiscovery Institute, School of Life Sciences, The University of Nottingham, Nottingham, United Kingdom
| | - Minyeong Yoo
- Clostridia Research Group, BBSRC/EPSRC Synthetic Biology Research Centre (SBRC), Biodiscovery Institute, School of Life Sciences, The University of Nottingham, Nottingham, United Kingdom
| | - Cynthia Akaluka
- Clostridia Research Group, BBSRC/EPSRC Synthetic Biology Research Centre (SBRC), Biodiscovery Institute, School of Life Sciences, The University of Nottingham, Nottingham, United Kingdom
| | - Ying Zhang
- Clostridia Research Group, BBSRC/EPSRC Synthetic Biology Research Centre (SBRC), Biodiscovery Institute, School of Life Sciences, The University of Nottingham, Nottingham, United Kingdom
| | - Nigel P. Minton
- Clostridia Research Group, BBSRC/EPSRC Synthetic Biology Research Centre (SBRC), Biodiscovery Institute, School of Life Sciences, The University of Nottingham, Nottingham, United Kingdom
- NIHR Nottingham Biomedical Research Centre, Nottingham University Hospitals NHS Trust and the University of Nottingham, Nottingham, United Kingdom
| |
Collapse
|
11
|
Jang YS, Kim WJ, Im JA, Palaniswamy S, Yao Z, Lee HL, Yoon YR, Seong HJ, Papoutsakis ET, Lee SY. Efforts to install a heterologous Wood-Ljungdahl pathway in Clostridium acetobutylicum enable the identification of the native tetrahydrofolate (THF) cycle and result in early induction of solvents. Metab Eng 2023; 77:188-198. [PMID: 37054966 DOI: 10.1016/j.ymben.2023.04.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2022] [Revised: 03/05/2023] [Accepted: 04/10/2023] [Indexed: 04/15/2023]
Abstract
Here, we report the construction of a Clostridium acetobutylicum strain ATCC 824 (pCD07239) by heterologous expression of carbonyl branch genes (CD630_0723∼CD630_0729) from Clostridium difficile, aimed at installing a heterologous Wood-Ljungdahl pathway (WLP). As part of this effort, in order to validate the methyl branch of the WLP in the C. acetobutylicum, we performed 13C-tracing analysis on knockdown mutants of four genes responsible for the formation of 5-methyl-tetrahydrofolate (5-methyl-THF) from formate: CA_C3201, CA_C2310, CA_C2083, and CA_C0291. While C. acetobutylicum 824 (pCD07239) could not grow autotrophically, in heterotrophic fermentation, it began producing butanol at the early growth phase (OD600 of 0.80; 0.162 g/L butanol). In contrast, solvent production in the parent strain did not begin until the early stationary phase (OD600 of 7.40). This study offers valuable insights for future research on biobutanol production during the early growth phase.
Collapse
Affiliation(s)
- Yu-Sin Jang
- Division of Applied Life Science (BK21 Four), Department of Applied Life Chemistry, Institute of Agriculture & Life Science (IALS), Gyeongsang National University (GNU), Jinju, 52828, Republic of Korea.
| | - Won Jun Kim
- Metabolic and Biomolecular Engineering National Research Laboratory, Department of Chemical and Biomolecular Engineering (BK21 Four Program), Institute for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea
| | - Jung Ae Im
- Metabolic and Biomolecular Engineering National Research Laboratory, Department of Chemical and Biomolecular Engineering (BK21 Four Program), Institute for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea
| | - Sampathkumar Palaniswamy
- Division of Applied Life Science (BK21 Four), Department of Applied Life Chemistry, Institute of Agriculture & Life Science (IALS), Gyeongsang National University (GNU), Jinju, 52828, Republic of Korea
| | - Zhuang Yao
- Division of Applied Life Science (BK21 Four), Department of Applied Life Chemistry, Institute of Agriculture & Life Science (IALS), Gyeongsang National University (GNU), Jinju, 52828, Republic of Korea
| | - Haeng Lim Lee
- Division of Applied Life Science (BK21 Four), Department of Applied Life Chemistry, Institute of Agriculture & Life Science (IALS), Gyeongsang National University (GNU), Jinju, 52828, Republic of Korea
| | - Ye Rin Yoon
- Division of Applied Life Science (BK21 Four), Department of Applied Life Chemistry, Institute of Agriculture & Life Science (IALS), Gyeongsang National University (GNU), Jinju, 52828, Republic of Korea
| | - Hyeon Jeong Seong
- Division of Applied Life Science (BK21 Four), Department of Applied Life Chemistry, Institute of Agriculture & Life Science (IALS), Gyeongsang National University (GNU), Jinju, 52828, Republic of Korea
| | - Eleftherios T Papoutsakis
- Delaware Biotechnology Institute, University of Delaware, 590 Avenue 1743, Newark, DE, 19713, USA; Department of Biological Sciences, University of Delaware, 118 Wolf Hall, Newark, DE, 19716, USA
| | - Sang Yup Lee
- Metabolic and Biomolecular Engineering National Research Laboratory, Department of Chemical and Biomolecular Engineering (BK21 Four Program), Institute for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea.
| |
Collapse
|
12
|
Guo X, Zhang H, Feng J, Yang L, Luo K, Fu H, Wang J. De novo biosynthesis of butyl butyrate in engineered Clostridium tyrobutyricum. Metab Eng 2023; 77:64-75. [PMID: 36948242 DOI: 10.1016/j.ymben.2023.03.009] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Revised: 03/07/2023] [Accepted: 03/20/2023] [Indexed: 03/24/2023]
Abstract
Butyl butyrate has broad applications in foods, cosmetics, solvents, and biofuels. Microbial synthesis of bio-based butyl butyrate has been regarded as a promising approach recently. Herein, we engineered Clostridium tyrobutyricum ATCC 25755 to achieve de novo biosynthesis of butyl butyrate from fermentable sugars. Through introducing the butanol synthetic pathway (enzyme AdhE2), screening alcohol acyltransferases (AATs), adjusting transcription of VAAT and adhE2 (i.e., optimizing promoter), and efficient supplying butyryl-CoA, an excellent engineered strain, named MUV3, was obtained with ability to produce 4.58 g/L butyl butyrate at 25 °C with glucose in serum bottles. More NADH is needed for butyl butyrate synthesis, thus mannitol (the more reduced substrate) was employed to produce butyl butyrate. Ultimately, 62.59 g/L butyl butyrate with a selectivity of 95.97%, and a yield of 0.21 mol/mol was obtained under mannitol with fed-batch fermentation in a 5 L bioreactor, which is the highest butyl butyrate titer reported so far. Altogether, this study presents an anaerobic fermentative platform for de novo biosynthesis of butyl butyrate in one step, which lays the foundation for butyl butyrate biosynthesis from renewable biomass feedstocks.
Collapse
Affiliation(s)
- Xiaolong Guo
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006, China
| | - Huihui Zhang
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006, China
| | - Jun Feng
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006, China
| | - Lu Yang
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006, China
| | - Kui Luo
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006, China
| | - Hongxin Fu
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006, China; Guangdong Provincial Key Laboratory of Fermentation and Enzyme Engineering, South China University of Technology, Guangzhou, 510006, China.
| | - Jufang Wang
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006, China; Guangdong Provincial Key Laboratory of Fermentation and Enzyme Engineering, South China University of Technology, Guangzhou, 510006, China.
| |
Collapse
|
13
|
Philp J. Bioeconomy and net-zero carbon: lessons from Trends in Biotechnology, volume 1, issue 1. Trends Biotechnol 2023; 41:307-322. [PMID: 36272819 DOI: 10.1016/j.tibtech.2022.09.016] [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: 07/04/2022] [Revised: 09/15/2022] [Accepted: 09/23/2022] [Indexed: 11/06/2022]
Abstract
Many biotechnology applications tend to be for low production volumes and relatively high-value products such as insulin and vaccines. More difficult to perfect at scale are bioprocesses for high-volume products with lower value, especially if the target product is a reduced chemical such as a solvent or a plastic. Historically, industrial microbiology succeeded under special circumstances when fossil feedstocks were either unavailable or expensive. Inevitably, as these circumstances relaxed, bioprocesses struggled to compete with petrochemistry. Why try to compete? Fossil resources will be phased out in the coming decades in the struggle with climate change. To reach net-zero carbon by 2050 will require all sectors to transition, not only energy and transportation. This may herald a new opportunity for industrial bioprocesses with much better tools.
Collapse
Affiliation(s)
- Jim Philp
- Organization for Economic Cooperation and Development (OECD), Paris, France.
| |
Collapse
|
14
|
Madhavan A, Arun KB, Sindhu R, Nair BG, Pandey A, Awasthi MK, Szakacs G, Binod P. Design and genome engineering of microbial cell factories for efficient conversion of lignocellulose to fuel. BIORESOURCE TECHNOLOGY 2023; 370:128555. [PMID: 36586428 DOI: 10.1016/j.biortech.2022.128555] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Revised: 12/26/2022] [Accepted: 12/27/2022] [Indexed: 06/17/2023]
Abstract
The gradually increasing need for fossil fuels demands renewable biofuel substitutes. This has fascinated an increasing investigation to design innovative energy fuels that have comparable Physico-chemical and combustion characteristics with fossil-derived fuels. The efficient microbes for bioenergy synthesis desire the proficiency to consume a large quantity of carbon substrate, transfer various carbohydrates through efficient metabolic pathways, capability to withstand inhibitory components and other degradation compounds, and improve metabolic fluxes to synthesize target compounds. Metabolically engineered microbes could be an efficient methodology for synthesizing biofuel from cellulosic biomass by cautiously manipulating enzymes and metabolic pathways. This review offers a comprehensive perspective on the trends and advances in metabolic and genetic engineering technologies for advanced biofuel synthesis by applying various heterologous hosts. Probable technologies include enzyme engineering, heterologous expression of multiple genes, CRISPR-Cas technologies for genome editing, and cell surface display.
Collapse
Affiliation(s)
- Aravind Madhavan
- School of Biotechnology, Amrita Vishwa Vidyapeetham, Amritapuri, Kollam 690525 Kerala, India.
| | - K B Arun
- Department of Life Sciences, CHRIST (Deemed to be University), Bengaluru 560029, Karnataka, India
| | - Raveendran Sindhu
- Department of Food Technology, TKM Institute of Technology, Kollam 689 122, India
| | - Bipin G Nair
- School of Biotechnology, Amrita Vishwa Vidyapeetham, Amritapuri, Kollam 690525 Kerala, India
| | - Ashok Pandey
- Center for Innovation and Translational Research, CSIR-Indian Institute of Toxicology Research, Lucknow 226 001, India; Sustainability Cluster, School of Engineering, University of Petroleum and Energy Studies, Dehradun 248007, Uttarkhand, India; Centre for Energy and Environmental Sustainability, Lucknow 226 029, Uttar Pradesh, India
| | - Mukesh Kumar Awasthi
- College of Natural Resources and Environment, Northwest A & F University, Yangling, Shaanxi 712 100, China
| | - George Szakacs
- Budapest University of Technology and Economics, Department of Applied Biotechnology and Food Science, 1111 Budapest, Szent Gellert ter 4, Hungary
| | - Parameswaran Binod
- Microbial Processes and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology, Trivandrum 695 019, India
| |
Collapse
|
15
|
Rajpurohit H, Eiteman MA. Nutrient-Limited Operational Strategies for the Microbial Production of Biochemicals. Microorganisms 2022; 10:2226. [PMID: 36363817 PMCID: PMC9695796 DOI: 10.3390/microorganisms10112226] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 10/31/2022] [Accepted: 11/07/2022] [Indexed: 08/24/2023] Open
Abstract
Limiting an essential nutrient has a profound impact on microbial growth. The notion of growth under limited conditions was first described using simple Monod kinetics proposed in the 1940s. Different operational modes (chemostat, fed-batch processes) were soon developed to address questions related to microbial physiology and cell maintenance and to enhance product formation. With more recent developments of metabolic engineering and systems biology, as well as high-throughput approaches, the focus of current engineers and applied microbiologists has shifted from these fundamental biochemical processes. This review draws attention again to nutrient-limited processes. Indeed, the sophisticated gene editing tools not available to pioneers offer the prospect of metabolic engineering strategies which leverage nutrient limited processes. Thus, nutrient- limited processes continue to be very relevant to generate microbially derived biochemicals.
Collapse
Affiliation(s)
| | - Mark A. Eiteman
- School of Chemical, Materials and Biomedical Engineering, University of Georgia, Athens, GA 30602, USA
| |
Collapse
|
16
|
Fernandes APM, Ferreira AM, Sebastião M, Santos R, Neves CMSS, Coutinho JAP. First Stage of the Development of an Eco-Friendly Detergent Formulation for Efficient Removal of Carbonized Soil. Molecules 2022; 27:molecules27217460. [PMID: 36364294 PMCID: PMC9656870 DOI: 10.3390/molecules27217460] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Revised: 10/19/2022] [Accepted: 10/28/2022] [Indexed: 11/06/2022] Open
Abstract
Detergent formulations for cleaning a carbonized soil—degreasers—typically comprise surfactants, organic solvents, phosphate-based cleaning agents, and alkaline agents, which results in high pH values (>11) that raise human and environmental risks. It is important to develop eco-friendly and safer degreasers, while maintaining their cleaning efficiency. In this work, simple degreaser formulations, with a pH below 11 and without phosphates, were developed by using a mixture of solvent, surfactant, and water to remove carbonized soil. The efficiency of the new degreaser formulations (with 5 wt% solvent, 5 wt% nonionic or ionic surfactant, and 90 wt% water) was evaluated by an abrasion test in the removal of carbonized soil from ceramic and stainless steel surfaces and compared with a commercial product. The results obtained show that the formulations comprising isopropylene glycol (IPG) with C11−C13 9EOs and diethylene glycol butyl ether (BDG) with octyltrimethylammonium octanoate ([N1118][C8O2]) present the best cleaning efficiency for both surfaces. The composition of these formulations was optimized for each surface using a mixture design. The resulting formulations, despite having a simpler composition, a pH lower than 11, and being phosphate-free, presented a cleaning efficiency equal or slightly higher than the commercial control. These results show that it is possible to design degreasers that are much less aggressive to the environment and user, while simultaneously fulfilling the market requirements.
Collapse
Affiliation(s)
| | - Ana M. Ferreira
- CICECO—Aveiro Institute of Materials, Chemistry Department, University of Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal
| | - Marco Sebastião
- Mistolin S.A., Zona Industrial de Vagos Lt 58, 3840-385 Vagos, Portugal
| | - Ricardo Santos
- Mistolin S.A., Zona Industrial de Vagos Lt 58, 3840-385 Vagos, Portugal
| | - Catarina M. S. S. Neves
- CICECO—Aveiro Institute of Materials, Chemistry Department, University of Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal
- Correspondence:
| | - João A. P. Coutinho
- CICECO—Aveiro Institute of Materials, Chemistry Department, University of Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal
| |
Collapse
|
17
|
Identification of serine/threonine kinases that regulate metabolism and sporulation in Clostridium beijerinckii. Appl Microbiol Biotechnol 2022; 106:7563-7575. [DOI: 10.1007/s00253-022-12234-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2022] [Revised: 09/17/2022] [Accepted: 10/07/2022] [Indexed: 11/02/2022]
|
18
|
Re A, Mazzoli R. Current progress on engineering microbial strains and consortia for production of cellulosic butanol through consolidated bioprocessing. Microb Biotechnol 2022; 16:238-261. [PMID: 36168663 PMCID: PMC9871528 DOI: 10.1111/1751-7915.14148] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Revised: 08/01/2022] [Accepted: 09/07/2022] [Indexed: 01/27/2023] Open
Abstract
In the last decades, fermentative production of n-butanol has regained substantial interest mainly owing to its use as drop-in-fuel. The use of lignocellulose as an alternative to traditional acetone-butanol-ethanol fermentation feedstocks (starchy biomass and molasses) can significantly increase the economic competitiveness of biobutanol over production from non-renewable sources (petroleum). However, the low cost of lignocellulose is offset by its high recalcitrance to biodegradation which generally requires chemical-physical pre-treatment and multiple bioreactor-based processes. The development of consolidated processing (i.e., single-pot fermentation) can dramatically reduce lignocellulose fermentation costs and promote its industrial application. Here, strategies for developing microbial strains and consortia that feature both efficient (hemi)cellulose depolymerization and butanol production will be depicted, that is, rational metabolic engineering of native (hemi)cellulolytic or native butanol-producing or other suitable microorganisms; protoplast fusion of (hemi)cellulolytic and butanol-producing strains; and co-culture of (hemi)cellulolytic and butanol-producing microbes. Irrespective of the fermentation feedstock, biobutanol production is inherently limited by the severe toxicity of this solvent that challenges process economic viability. Hence, an overview of strategies for developing butanol hypertolerant strains will be provided.
Collapse
Affiliation(s)
- Angela Re
- Centre for Sustainable Future TechnologiesFondazione Istituto Italiano di TecnologiaTorinoItaly,Department of Applied Science and TechnologyPolitecnico di TorinoTurinItaly
| | - Roberto Mazzoli
- Structural and Functional Biochemistry, Laboratory of Proteomics and Metabolic Engineering of Prokaryotes, Department of Life Sciences and Systems BiologyUniversity of TorinoTorinoItaly
| |
Collapse
|
19
|
Pregnon G, Minton NP, Soucaille P. Genome Sequence of Eubacterium limosum B2 and Evolution for Growth on a Mineral Medium with Methanol and CO2 as Sole Carbon Sources. Microorganisms 2022; 10:microorganisms10091790. [PMID: 36144392 PMCID: PMC9503626 DOI: 10.3390/microorganisms10091790] [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: 07/20/2022] [Revised: 08/23/2022] [Accepted: 09/01/2022] [Indexed: 11/16/2022] Open
Abstract
Eubacterium limosum is an acetogen that can produce butyrate along with acetate as the main fermentation end-product from methanol, a promising C1 feedstock. Although physiological characterization of E. limosum B2 during methylotrophy was previously performed, the strain was cultured in a semi-defined medium, limiting the scope for further metabolic insights. Here, we sequenced the complete genome of the native strain and performed adaptive laboratory evolution to sustain growth on methanol mineral medium. The evolved population significantly improved its maximal growth rate by 3.45-fold. Furthermore, three clones from the evolved population were isolated on methanol mineral medium without cysteine by the addition of sodium thiosulfate. To identify mutations related to growth improvement, the whole genomes of wild-type E. limosum B2, the 10th, 25th, 50th, and 75th generations, and the three clones were sequenced. We explored the total proteomes of the native and the best evolved clone (n°2) and noticed significant differences in proteins involved in gluconeogenesis, anaplerotic reactions, and sulphate metabolism. Furthermore, a homologous recombination was found in subunit S of the type I restriction-modification system between both strains, changing the structure of the subunit, its sequence recognition and the methylome of the evolved clone. Taken together, the genomic, proteomic and methylomic data suggest a possible epigenetic mechanism of metabolic regulation.
Collapse
Affiliation(s)
- Guillaume Pregnon
- INSA, UPS, INP, Toulouse Biotechnology Institute (TBI), Université de Toulouse, 31400 Toulouse, France
| | - Nigel P. Minton
- BBSRC/EPSRC Synthetic Biology Research Centre (SBRC), School of Life Sciences, University Park, The University of Nottingham, Nottingham NG7 2RD, UK
| | - Philippe Soucaille
- INSA, UPS, INP, Toulouse Biotechnology Institute (TBI), Université de Toulouse, 31400 Toulouse, France
- BBSRC/EPSRC Synthetic Biology Research Centre (SBRC), School of Life Sciences, University Park, The University of Nottingham, Nottingham NG7 2RD, UK
- Correspondence: ; Tel.: +33-(0)-561-559-452
| |
Collapse
|
20
|
Chang WL, Hou W, Xu M, Yang ST. High-rate continuous n-butanol production by Clostridium acetobutylicum from glucose and butyric acid in a single-pass fibrous bed bioreactor. Biotechnol Bioeng 2022; 119:3474-3486. [PMID: 36059064 DOI: 10.1002/bit.28223] [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: 07/06/2022] [Revised: 08/15/2022] [Accepted: 09/01/2022] [Indexed: 11/07/2022]
Abstract
Biobutanol produced in acetone-butanol-ethanol (ABE) fermentation at batch mode cannot compete with chemically derived butanol because of the low reactor productivity. Continuous fermentation can dramatically enhance productivity and lower capital and operating costs but are rarely used in industrial fermentation because of increased risks in culture degeneration, cell washout, and contamination. In this study, cells of the asporogenous Clostridium acetobutylicum ATCC55025 were immobilized in a single-pass fibrous-bed bioreactor (FBB) for continuous production of butanol from glucose and butyrate at various dilution rates. Butyric acid in the feed medium helped maintaining cells in the solventogenic phase for stable continuous butanol production. At the dilution rate of 1.88 h-1 , butanol was produced at 9.55 g/L with a yield of 0.24 g/g and productivity of 16.8 g/L/h, which was the highest productivity ever achieved for biobutanol fermentation and an 80-fold improvement over the conventional ABE fermentation. The extremely high productivity was attributed to the high density of viable cells (~100 g/L at >70% viability) immobilized in the fibrous matrix, which also enabled the cells to better tolerate butanol and butyric acid. The FBB was stable for continuous operation for an extended period of over one month. This article is protected by copyright. All rights reserved.
Collapse
Affiliation(s)
- Wei-Lun Chang
- William G. Lowrie Department of Chemical and Biomolecular Engineering, The Ohio State University, 151 West Woodruff Avenue, Columbus, OH, 43210, USA
| | - Wenjie Hou
- William G. Lowrie Department of Chemical and Biomolecular Engineering, The Ohio State University, 151 West Woodruff Avenue, Columbus, OH, 43210, USA.,College of Life Science, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Mengmeng Xu
- William G. Lowrie Department of Chemical and Biomolecular Engineering, The Ohio State University, 151 West Woodruff Avenue, Columbus, OH, 43210, USA
| | - Shang-Tian Yang
- William G. Lowrie Department of Chemical and Biomolecular Engineering, The Ohio State University, 151 West Woodruff Avenue, Columbus, OH, 43210, USA
| |
Collapse
|
21
|
Butanol recovery from synthetic fermentation broth by vacuum distillation in a rotating packed bed. Sep Purif Technol 2022. [DOI: 10.1016/j.seppur.2022.121551] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
22
|
Molecular characterization of the missing electron pathways for butanol synthesis in Clostridium acetobutylicum. Nat Commun 2022; 13:4691. [PMID: 35948538 PMCID: PMC9365771 DOI: 10.1038/s41467-022-32269-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Accepted: 07/22/2022] [Indexed: 12/02/2022] Open
Abstract
Clostridium acetobutylicum is a promising biocatalyst for the renewable production of n-butanol. Several metabolic strategies have already been developed to increase butanol yields, most often based on carbon pathway redirection. However, it has previously demonstrated that the activities of both ferredoxin-NADP+ reductase and ferredoxin-NAD+ reductase, whose encoding genes remain unknown, are necessary to produce the NADPH and the extra NADH needed for butanol synthesis under solventogenic conditions. Here, we purify, identify and partially characterize the proteins responsible for both activities and demonstrate the involvement of the identified enzymes in butanol synthesis through a reverse genetic approach. We further demonstrate the yield of butanol formation is limited by the level of expression of CA_C0764, the ferredoxin-NADP+ reductase encoding gene and the bcd operon, encoding a ferredoxin-NAD+ reductase. The integration of these enzymes into metabolic engineering strategies introduces opportunities for developing a homobutanologenic C. acetobutylicum strain. Ferredoxin-NAD(P) + oxidoreductases are important enzymes for redox balancing in n-butanol production by Clostridium acetobutylicum, but the encoding genes remain unknown. Here, the authors identify the long sought-after genes and increase n-butanol production by optimizing the levels of the two enzymes.
Collapse
|
23
|
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.
Collapse
|
24
|
Sheldon RA, Brady D. Green Chemistry, Biocatalysis, and the Chemical Industry of the Future. CHEMSUSCHEM 2022; 15:e202102628. [PMID: 35026060 DOI: 10.1002/cssc.202102628] [Citation(s) in RCA: 39] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2021] [Revised: 01/11/2022] [Indexed: 06/14/2023]
Abstract
In the movement to decarbonize our economy and move away from fossil fuels we will need to harness the waste products of our activities, such as waste lignocellulose, methane, and carbon dioxide. Our wastes need to be integrated into a circular economy where used products are recycled into a manufacturing carbon cycle. Key to this will be the recycling of plastics at the resin and monomer levels. Biotechnology is well suited to a future chemical industry that must adapt to widely distributed and diverse biological chemical feedstocks. Our increasing mastery of biotechnology is allowing us to develop enzymes and organisms that can synthesize a widening selection of desirable bulk chemicals, including plastics, at commercially viable productivities. Integration of bioreactors with electrochemical systems will permit new production opportunities with enhanced productivities and the advantage of using a low-carbon electricity from renewable and sustainable sources.
Collapse
Affiliation(s)
- Roger A Sheldon
- Molecular Sciences Institute, School of Chemistry, University of the Witwatersrand, 1 Jan Smuts Avenue, Braamfontein, Johannesburg, 2000, South Africa
- Department of Biotechnology, Delft University of Technology, Section BOC, van der Maasweg 9, 2629 HZ, Delft, Netherlands
| | - Dean Brady
- Molecular Sciences Institute, School of Chemistry, University of the Witwatersrand, 1 Jan Smuts Avenue, Braamfontein, Johannesburg, 2000, South Africa
| |
Collapse
|
25
|
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.
Collapse
|
26
|
Abstract
Abstract
In the last decade, there was observed a growing demand for both n-butanol as a potential fuel or fuel additive, and propylene as the only raw material for production of alcohol and other more bulky propylene chemical derivatives with faster growing outputs (polymers, propylene oxide, and acrylic acid). The predictable oilfield depletion and the European Green Deal adoption stimulated interest in alternative processes for n-butanol production, especially those involving bio-based materials. Their commercialization will promote additional market penetration of n-butanol for its application as a basic chemical. We analyze briefly the current status of two most advanced bio-based processes, i.e. ethanol–to-n-butanol and acetone–butanol–ethanol (ABE) fermentation. In the second part of the review, studies of n-butanol and ABE conversion to valuable products are considered with an emphasis on the most perspective catalytic systems and variants of the future processes realization.
Collapse
Affiliation(s)
- Larisa Pinaeva
- Department of Technology of Catalytic Processes, Boreskov Institute of Catalysis , Novosibirsk 630090 , Russia
| | - Alexandr Noskov
- Department of Technology of Catalytic Processes, Boreskov Institute of Catalysis , Novosibirsk 630090 , Russia
| |
Collapse
|
27
|
Bahls MO, Platz L, Morgado G, Schmidt GW, Panke S. Directed evolution of biofuel-responsive biosensors for automated optimization of branched-chain alcohol biosynthesis. Metab Eng 2021; 69:98-111. [PMID: 34767976 DOI: 10.1016/j.ymben.2021.10.014] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Revised: 10/21/2021] [Accepted: 10/31/2021] [Indexed: 12/18/2022]
Abstract
The biosynthesis of short-chain alcohols is a carbon-neutral alternative to petroleum-derived production, but strain screening operations are encumbered by laborious analytics. Here, we built, characterized and applied whole cell biosensors by directed evolution of the transcription factor AlkS for screening microbial strain libraries producing industrially relevant alcohols. A selected AlkS variant was applied for in situ product detection in two screening applications concerning key steps in alcohol production. Further, the biosensor strains enabled the implementation of an automated, robotic platform-based workflow with data clustering, which readily allowed the identification of significantly improved strain variants for isopentanol production.
Collapse
Affiliation(s)
- Maximilian O Bahls
- Department of Biosystems Science and Engineering, ETH Zurich, Switzerland
| | - Lukas Platz
- Department of Biosystems Science and Engineering, ETH Zurich, Switzerland
| | - Gaspar Morgado
- Department of Biosystems Science and Engineering, ETH Zurich, Switzerland
| | - Gregor W Schmidt
- Department of Biosystems Science and Engineering, ETH Zurich, Switzerland
| | - Sven Panke
- Department of Biosystems Science and Engineering, ETH Zurich, Switzerland.
| |
Collapse
|
28
|
Zhang J, Shi K, Zhu Y, An Z, Wang W, Ma X, Shu X, Song H, Xiang X, He J. Interfacial Sites in Ag Supported Layered Double Oxide for Dehydrogenation Coupling of Ethanol to n-Butanol. ChemistryOpen 2021; 10:1095-1103. [PMID: 33496388 PMCID: PMC8562315 DOI: 10.1002/open.202000295] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 01/07/2021] [Indexed: 11/12/2022] Open
Abstract
Upgrading of ethanol to n-butanol through dehydrogenation coupling has received increasing attention due to the wide application of n-butanol. But the enhancement of ethanol dehydrogenation and followed coupling to produce high selectivity to n-butanol is still highly desired. Our previous work has reported an acid-base-Ag synergistic catalysis, with Ag particles supported on Mg and Al-containing layered double oxides (Ag/MgAl-LDO). Here, Ag-LDO interfaces have been manipulated for dehydrogenation coupling of ethanol to n-butanol by tailoring the size of Ag particles and the interactions between Ag and LDO. It has been revealed that increasing the population of surface Ag sites at Ag-LDO interfaces promotes not only the dehydrogenation of ethanol to acetaldehyde but also the subsequent aldol condensation of generated acetaldehyde. A selectivity of up to 76 % to n-butanol with an ethanol conversion of 44 % has been achieved on Ag/LDO with abundant interfacial Ag sites, much superior to the state-of-the-art catalysts.
Collapse
Affiliation(s)
- Jian Zhang
- State Key Laboratory of Chemical Resource Engineering & BeijingAdvanced Innovation Center for Soft Matter Science and EngineeringBeijing University of Chemical TechnologyBox 98, 15 Beisanhuan DongluBeijing100029China
| | - Kai Shi
- State Key Laboratory of Chemical Resource Engineering & BeijingAdvanced Innovation Center for Soft Matter Science and EngineeringBeijing University of Chemical TechnologyBox 98, 15 Beisanhuan DongluBeijing100029China
| | - Yanru Zhu
- State Key Laboratory of Chemical Resource Engineering & BeijingAdvanced Innovation Center for Soft Matter Science and EngineeringBeijing University of Chemical TechnologyBox 98, 15 Beisanhuan DongluBeijing100029China
| | - Zhe An
- State Key Laboratory of Chemical Resource Engineering & BeijingAdvanced Innovation Center for Soft Matter Science and EngineeringBeijing University of Chemical TechnologyBox 98, 15 Beisanhuan DongluBeijing100029China
| | - Wanning Wang
- State Key Laboratory of Chemical Resource Engineering & BeijingAdvanced Innovation Center for Soft Matter Science and EngineeringBeijing University of Chemical TechnologyBox 98, 15 Beisanhuan DongluBeijing100029China
| | - Xiaodan Ma
- State Key Laboratory of Chemical Resource Engineering & BeijingAdvanced Innovation Center for Soft Matter Science and EngineeringBeijing University of Chemical TechnologyBox 98, 15 Beisanhuan DongluBeijing100029China
| | - Xin Shu
- State Key Laboratory of Chemical Resource Engineering & BeijingAdvanced Innovation Center for Soft Matter Science and EngineeringBeijing University of Chemical TechnologyBox 98, 15 Beisanhuan DongluBeijing100029China
| | - Hongyan Song
- State Key Laboratory of Chemical Resource Engineering & BeijingAdvanced Innovation Center for Soft Matter Science and EngineeringBeijing University of Chemical TechnologyBox 98, 15 Beisanhuan DongluBeijing100029China
| | - Xu Xiang
- State Key Laboratory of Chemical Resource Engineering & BeijingAdvanced Innovation Center for Soft Matter Science and EngineeringBeijing University of Chemical TechnologyBox 98, 15 Beisanhuan DongluBeijing100029China
| | - Jing He
- State Key Laboratory of Chemical Resource Engineering & BeijingAdvanced Innovation Center for Soft Matter Science and EngineeringBeijing University of Chemical TechnologyBox 98, 15 Beisanhuan DongluBeijing100029China
| |
Collapse
|
29
|
Li Q, Zhang J, Yang J, Jiang Y, Yang S. Recent progress on n-butanol production by lactic acid bacteria. World J Microbiol Biotechnol 2021; 37:205. [PMID: 34698975 DOI: 10.1007/s11274-021-03173-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2021] [Accepted: 10/13/2021] [Indexed: 11/26/2022]
Abstract
n-Butanol is an essential chemical intermediate produced through microbial fermentation. However, its toxicity to microbial cells has limited its production to a great extent. The anaerobe lactic acid bacteria (LAB) are the most resistant to n-butanol, so it should be the first choice for improving n-butanol production. The present article aims to review the following aspects of n-butanol production by LAB: (1) the tolerance of LAB to n-butanol, including its tolerance level and potential tolerance mechanisms; (2) genome editing tools in the n-butanol-resistant LAB; (3) methods of LAB modification for n-butanol production and the production levels after modification. This review will provide a theoretical basis for further research on n-butanol production by LAB.
Collapse
Affiliation(s)
- Qi Li
- College of Life Sciences, Sichuan Normal University, Chengdu, 610101, China
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai, 200032, China
| | - Jieze Zhang
- Department of Chemistry, University of Southern California, Los Angeles, CA, 90089, USA
| | - Junjie Yang
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai, 200032, China
| | - Yu Jiang
- Huzhou Center of Industrial Biotechnology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Huzhou, 313000, China
- Shanghai Taoyusheng Biotechnology Company Ltd, Shanghai, 200032, China
| | - Sheng Yang
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai, 200032, China.
- Huzhou Center of Industrial Biotechnology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Huzhou, 313000, China.
| |
Collapse
|
30
|
Neuendorf CS, Vignolle GA, Derntl C, Tomin T, Novak K, Mach RL, Birner-Grünberger R, Pflügl S. A quantitative metabolic analysis reveals Acetobacterium woodii as a flexible and robust host for formate-based bioproduction. Metab Eng 2021; 68:68-85. [PMID: 34537366 DOI: 10.1016/j.ymben.2021.09.004] [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] [Received: 06/14/2021] [Revised: 08/30/2021] [Accepted: 09/15/2021] [Indexed: 11/24/2022]
Abstract
Cheap and renewable feedstocks such as the one-carbon substrate formate are emerging for sustainable production in a growing chemical industry. We investigated the acetogen Acetobacterium woodii as a potential host for bioproduction from formate alone and together with autotrophic and heterotrophic co-substrates by quantitatively analyzing physiology, transcriptome, and proteome in chemostat cultivations in combination with computational analyses. Continuous cultivations with a specific growth rate of 0.05 h-1 on formate showed high specific substrate uptake rates (47 mmol g-1 h-1). Co-utilization of formate with H2, CO, CO2 or fructose was achieved without catabolite repression and with acetate as the sole metabolic product. A transcriptomic comparison of all growth conditions revealed a distinct adaptation of A. woodii to growth on formate as 570 genes were changed in their transcript level. Transcriptome and proteome showed higher expression of the Wood-Ljungdahl pathway during growth on formate and gaseous substrates, underlining its function during utilization of one-carbon substrates. Flux balance analysis showed varying flux levels for the WLP (0.7-16.4 mmol g-1 h-1) and major differences in redox and energy metabolism. Growth on formate, H2/CO2, and formate + H2/CO2 resulted in low energy availability (0.20-0.22 ATP/acetate) which was increased during co-utilization with CO or fructose (0.31 ATP/acetate for formate + H2/CO/CO2, 0.75 ATP/acetate for formate + fructose). Unitrophic and mixotrophic conversion of all substrates was further characterized by high energetic efficiencies. In silico analysis of bioproduction of ethanol and lactate from formate and autotrophic and heterotrophic co-substrates showed promising energetic efficiencies (70-92%). Collectively, our findings reveal A. woodii as a promising host for flexible and simultaneous bioconversion of multiple substrates, underline the potential of substrate co-utilization to improve the energy availability of acetogens and encourage metabolic engineering of acetogenic bacteria for the efficient synthesis of bulk chemicals and fuels from sustainable one carbon substrates.
Collapse
Affiliation(s)
- Christian Simon Neuendorf
- Technische Universität Wien, Institute for Chemical, Environmental and Bioscience Engineering, Research Area Biochemical Engineering, Gumpendorfer Straße 1a, 1060, Vienna, Austria.
| | - Gabriel A Vignolle
- Technische Universität Wien, Institute for Chemical, Environmental and Bioscience Engineering, Research Area Biochemical Engineering, Gumpendorfer Straße 1a, 1060, Vienna, Austria.
| | - Christian Derntl
- Technische Universität Wien, Institute for Chemical, Environmental and Bioscience Engineering, Research Area Biochemical Engineering, Gumpendorfer Straße 1a, 1060, Vienna, Austria.
| | - Tamara Tomin
- Technische Universität Wien, Institute for Chemical Technologies and Analytics, Research Group Bioanalytics, Getreidemarkt 9, 1060, Vienna, Austria.
| | - Katharina Novak
- Technische Universität Wien, Institute for Chemical, Environmental and Bioscience Engineering, Research Area Biochemical Engineering, Gumpendorfer Straße 1a, 1060, Vienna, Austria.
| | - Robert L Mach
- Technische Universität Wien, Institute for Chemical, Environmental and Bioscience Engineering, Research Area Biochemical Engineering, Gumpendorfer Straße 1a, 1060, Vienna, Austria.
| | - Ruth Birner-Grünberger
- Technische Universität Wien, Institute for Chemical Technologies and Analytics, Research Group Bioanalytics, Getreidemarkt 9, 1060, Vienna, Austria; Medical University of Graz, Diagnostic and Research Institute of Pathology, Center for Medical Research, Stiftingtalstrasse 24, 8036, Graz, Austria.
| | - Stefan Pflügl
- Technische Universität Wien, Institute for Chemical, Environmental and Bioscience Engineering, Research Area Biochemical Engineering, Gumpendorfer Straße 1a, 1060, Vienna, Austria.
| |
Collapse
|
31
|
Montaño López J, Duran L, Avalos JL. Physiological limitations and opportunities in microbial metabolic engineering. Nat Rev Microbiol 2021; 20:35-48. [PMID: 34341566 DOI: 10.1038/s41579-021-00600-0] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/22/2021] [Indexed: 11/10/2022]
Abstract
Metabolic engineering can have a pivotal role in increasing the environmental sustainability of the transportation and chemical manufacturing sectors. The field has already developed engineered microorganisms that are currently being used in industrial-scale processes. However, it is often challenging to achieve the titres, yields and productivities required for commercial viability. The efficiency of microbial chemical production is usually dependent on the physiological traits of the host organism, which may either impose limitations on engineered biosynthetic pathways or, conversely, boost their performance. In this Review, we discuss different aspects of microbial physiology that often create obstacles for metabolic engineering, and present solutions to overcome them. We also describe various instances in which natural or engineered physiological traits in host organisms have been harnessed to benefit engineered metabolic pathways for chemical production.
Collapse
Affiliation(s)
- José Montaño López
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ, USA
| | - Lisset Duran
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - José L Avalos
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ, USA. .,Department of Molecular Biology, Princeton University, Princeton, NJ, USA. .,Andlinger Center for Energy and the Environment, Princeton University, Princeton, NJ, USA. .,Princeton Environmental Institute, Princeton University, Princeton, NJ, USA.
| |
Collapse
|
32
|
Bai SK, Hong Y, Wu YR. Emerging technologies for genetic modification of solventogenic clostridia: From tool to strategy development. BIORESOURCE TECHNOLOGY 2021; 334:125222. [PMID: 33951568 DOI: 10.1016/j.biortech.2021.125222] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Revised: 04/20/2021] [Accepted: 04/21/2021] [Indexed: 06/12/2023]
Abstract
Solventogenic clostridia has been considered as one of the most potential microbial cell factories for biofuel production in the biorefinery industry. However, the inherent shortcomings of clostridia strains such as low productivity, by-products formation and toxic tolerance still strongly restrict the large-scale application. Therefore, concerns regarding the genetic modification of solventogenic clostridia have spurred interests into the development of modern gene-editing tools. In this review, we summarize the latest advances of genetic tools involved in modifying solventogenic clostridia. Following a systematic comparison on their respective characteristics, we then review the corresponding strategies for overcoming the obstacles to the enhanced production. Discussing the progress of other microbial cell factories for solventogenesis, we finally describe the key challenges and trends with valuable recommendations for future large-scale biosolvent industrial application.
Collapse
Affiliation(s)
- Sheng-Kai Bai
- Department of Biology, Shantou University, Shantou, Guangdong 515063, China
| | - Ying Hong
- Department of Biology, Shantou University, Shantou, Guangdong 515063, China
| | - Yi-Rui Wu
- Department of Biology, Shantou University, Shantou, Guangdong 515063, China; Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou, Guangdong 515063, China; Institute of Marine Sciences, Shantou University, Shantou, Guangdong 515063, China.
| |
Collapse
|
33
|
Dai Z, Zhu Y, Dong H, Zhao C, Zhang Y, Li Y. Enforcing ATP hydrolysis enhanced anaerobic glycolysis and promoted solvent production in Clostridium acetobutylicum. Microb Cell Fact 2021; 20:149. [PMID: 34325704 PMCID: PMC8320212 DOI: 10.1186/s12934-021-01639-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Accepted: 07/19/2021] [Indexed: 12/25/2022] Open
Abstract
Background The intracellular ATP level is an indicator of cellular energy state and plays a critical role in regulating cellular metabolism. Depletion of intracellular ATP in (facultative) aerobes can enhance glycolysis, thereby promoting end product formation. In the present study, we examined this s trategy in anaerobic ABE (acetone-butanol-ethanol) fermentation using Clostridium acetobutylicum DSM 1731. Results Following overexpression of atpAGD encoding the subunits of water-soluble, ATP-hydrolyzing F1-ATPase, the intracellular ATP level of 1731(pITF1) was significantly reduced compared to control 1731(pIMP1) over the entire batch fermentation. The glucose uptake was markedly enhanced, achieving a 78.8% increase of volumetric glucose utilization rate during the first 18 h. In addition, an early onset of acid re-assimilation and solventogenesis in concomitant with the decreased intracellular ATP level was evident. Consequently, the total solvent production was significantly improved with remarkable increases in yield (14.5%), titer (9.9%) and productivity (5.3%). Further genome-scale metabolic modeling revealed that many metabolic fluxes in 1731(pITF1) were significantly elevated compared to 1731(pIMP1) in acidogenic phase, including those from glycolysis, tricarboxylic cycle, and pyruvate metabolism; this indicates significant metabolic changes in response to intracellular ATP depletion. Conclusions In C. acetobutylicum DSM 1731, depletion of intracellular ATP significantly increased glycolytic rate, enhanced solvent production, and resulted in a wide range of metabolic changes. Our findings provide a novel strategy for engineering solvent-producing C. acetobutylicum, and many other anaerobic microbial cell factories. Supplementary Information The online version contains supplementary material available at 10.1186/s12934-021-01639-7.
Collapse
Affiliation(s)
- Zongjie Dai
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, 1 Beichen West Road, Chaoyang District, Beijing, 100101, China.,CAS Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
| | - Yan Zhu
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, 1 Beichen West Road, Chaoyang District, Beijing, 100101, China.,Infection and Immunity Program and Department of Microbiology, Biomedicine Discovery Institute, Monash University, Melbourne, VIC, 3800, Australia
| | - Hongjun Dong
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, 1 Beichen West Road, Chaoyang District, Beijing, 100101, China.,CAS Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
| | - Chunhua Zhao
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, 1 Beichen West Road, Chaoyang District, Beijing, 100101, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yanping Zhang
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, 1 Beichen West Road, Chaoyang District, Beijing, 100101, China.
| | - Yin Li
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, 1 Beichen West Road, Chaoyang District, Beijing, 100101, China
| |
Collapse
|
34
|
Joseph RC, Kelley SQ, Kim NM, Sandoval NR. Metabolic Engineering and the Synthetic Biology Toolbox for
Clostridium. Metab Eng 2021. [DOI: 10.1002/9783527823468.ch16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
|
35
|
Feng J, Zhang J, Ma Y, Feng Y, Wang S, Guo N, Wang H, Wang P, Jiménez-Bonilla P, Gu Y, Zhou J, Zhang ZT, Cao M, Jiang D, Wang S, Liu XW, Shao Z, Borovok I, Huang H, Wang Y. Renewable fatty acid ester production in Clostridium. Nat Commun 2021; 12:4368. [PMID: 34272383 PMCID: PMC8285483 DOI: 10.1038/s41467-021-24038-3] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Accepted: 05/26/2021] [Indexed: 11/25/2022] Open
Abstract
Bioproduction of renewable chemicals is considered as an urgent solution for fossil energy crisis. However, despite tremendous efforts, it is still challenging to generate microbial strains that can produce target biochemical to high levels. Here, we report an example of biosynthesis of high-value and easy-recoverable derivatives built upon natural microbial pathways, leading to improvement in bioproduction efficiency. By leveraging pathways in solventogenic clostridia for co-producing acyl-CoAs, acids and alcohols as precursors, through rational screening for host strains and enzymes, systematic metabolic engineering-including elimination of putative prophages, we develop strains that can produce 20.3 g/L butyl acetate and 1.6 g/L butyl butyrate. Techno-economic analysis results suggest the economic competitiveness of our developed bioprocess. Our principles of selecting the most appropriate host for specific bioproduction and engineering microbial chassis to produce high-value and easy-separable end products may be applicable to other bioprocesses. Esters can be used as fuels and specialty chemicals for food flavoring, cosmetic and pharmaceutical industries. Here, the authors systematically engineer clostridia, including discovery and deletion of prophages to increase strain stability, for the production of butyl acetate and butyl butyrate from corn stover at low cost.
Collapse
Affiliation(s)
- Jun Feng
- Department of Biosystems Engineering, Auburn University, Auburn, AL, USA.,Center for Bioenergy and Bioproducts, Auburn University, Auburn, AL, USA
| | - Jie Zhang
- Department of Biosystems Engineering, Auburn University, Auburn, AL, USA.,Center for Bioenergy and Bioproducts, Auburn University, Auburn, AL, USA
| | - Yuechao Ma
- Department of Biosystems Engineering, Auburn University, Auburn, AL, USA.,Center for Bioenergy and Bioproducts, Auburn University, Auburn, AL, USA
| | - Yiming Feng
- Department of Food Science and Technology, Virginia Tech, Blacksburg, VA, USA
| | - Shangjun Wang
- Department of Biosystems Engineering, Auburn University, Auburn, AL, USA.,Center for Bioenergy and Bioproducts, Auburn University, Auburn, AL, USA
| | - Na Guo
- Department of Biosystems Engineering, Auburn University, Auburn, AL, USA.,Center for Bioenergy and Bioproducts, Auburn University, Auburn, AL, USA
| | - Haijiao Wang
- Department of Biosystems Engineering, Auburn University, Auburn, AL, USA.,Center for Bioenergy and Bioproducts, Auburn University, Auburn, AL, USA
| | - Pixiang Wang
- Department of Biosystems Engineering, Auburn University, Auburn, AL, USA.,Center for Bioenergy and Bioproducts, Auburn University, Auburn, AL, USA
| | - Pablo Jiménez-Bonilla
- Department of Biosystems Engineering, Auburn University, Auburn, AL, USA.,Center for Bioenergy and Bioproducts, Auburn University, Auburn, AL, USA.,School of Chemistry, National University (UNA), Heredia, Costa Rica
| | - Yanyan Gu
- Department of Biosystems Engineering, Auburn University, Auburn, AL, USA.,Center for Bioenergy and Bioproducts, Auburn University, Auburn, AL, USA
| | - Junping Zhou
- Department of Biosystems Engineering, Auburn University, Auburn, AL, USA.,Center for Bioenergy and Bioproducts, Auburn University, Auburn, AL, USA
| | - Zhong-Tian Zhang
- Department of Biosystems Engineering, Auburn University, Auburn, AL, USA.,Center for Bioenergy and Bioproducts, Auburn University, Auburn, AL, USA
| | - Mingfeng Cao
- Department of Chemical and Biological Engineering, Iowa State University, Ames, IA, USA.,NSF Engineering Research Center for Biorenewable Chemicals, Iowa State University, Ames, IA, USA
| | - Di Jiang
- Department of Applied Chemistry, University of Science and Technology of China, Hefei, China
| | - Shuning Wang
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao, China
| | - Xian-Wei Liu
- Department of Applied Chemistry, University of Science and Technology of China, Hefei, China
| | - Zengyi Shao
- Department of Chemical and Biological Engineering, Iowa State University, Ames, IA, USA.,NSF Engineering Research Center for Biorenewable Chemicals, Iowa State University, Ames, IA, USA
| | - Ilya Borovok
- The Shmunis School of Biomedicine and Cancer Research, Faculty of Life Sciences, Tel Aviv University, Ramat Aviv, Tel Aviv, Israel
| | - Haibo Huang
- Department of Food Science and Technology, Virginia Tech, Blacksburg, VA, USA.
| | - Yi Wang
- Department of Biosystems Engineering, Auburn University, Auburn, AL, USA. .,Center for Bioenergy and Bioproducts, Auburn University, Auburn, AL, USA.
| |
Collapse
|
36
|
Zhu C, Du G, Zhang J, Xue C. A high-efficient strategy for combinatorial engineering paralogous gene family: A case study on histidine kinases in Clostridium. Biotechnol Bioeng 2021; 118:2770-2780. [PMID: 33871069 DOI: 10.1002/bit.27796] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 04/08/2021] [Accepted: 04/17/2021] [Indexed: 11/10/2022]
Abstract
Microorganisms harbor bulks of functionally similar or undefined genes, which belong to paralogous gene family. There is a necessity of exploring combinatorial or interactive functions of these genes, but conventional loss-of-function strategy with one-by-one rounds suffers extremely low efficiency for generating mutant libraries with all gene permutations. Here, taking histidine kinases (HKs) in Clostridium acetobutylicum as a proof-of-concept, we developed a multi-plasmid cotransformation strategy for generating all theoretical HKs combinations in one round. For five HKs with 31 theoretical combinations, the library containing 22 mutants within all the possible HKs-inactivated combinations was constructed with 11 days compared to 242 days by conventional strategy, while the other 9 combinations cannot survive. Six mutants with the enhanced butanol production and tolerance were obtained with changes of cell development during fermentation, one of which could produce 54.2% more butanol (56.4% more solvents), while the butanol production of other mutants was unchanged or decreased. The cotransformation strategy demonstrated potentials for fast exploring pleiotropic function of paralogous family genes in cell survival, cell development, and target product metabolism.
Collapse
Affiliation(s)
- Chao Zhu
- School of Bioengineering, Engineering Research Center of Application and Transformation for Synthetic Biology, Dalian University of Technology, Dalian, China.,Ningbo Institute of Dalian University of Technology, Ningbo, China
| | - Guangqing Du
- School of Bioengineering, Engineering Research Center of Application and Transformation for Synthetic Biology, Dalian University of Technology, Dalian, China.,Ningbo Institute of Dalian University of Technology, Ningbo, China
| | - Jie Zhang
- School of Bioengineering, Engineering Research Center of Application and Transformation for Synthetic Biology, Dalian University of Technology, Dalian, China
| | - Chuang Xue
- School of Bioengineering, Engineering Research Center of Application and Transformation for Synthetic Biology, Dalian University of Technology, Dalian, China.,Ningbo Institute of Dalian University of Technology, Ningbo, China
| |
Collapse
|
37
|
Bao T, Hou W, Wu X, Lu L, Zhang X, Yang ST. Engineering Clostridium cellulovorans for highly selective n-butanol production from cellulose in consolidated bioprocessing. Biotechnol Bioeng 2021; 118:2703-2718. [PMID: 33844271 DOI: 10.1002/bit.27789] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 03/06/2021] [Accepted: 04/09/2021] [Indexed: 01/05/2023]
Abstract
Cellulosic n-butanol from renewable lignocellulosic biomass has gained increased interest. Previously, we have engineered Clostridium cellulovorans, a cellulolytic acidogen, to overexpress the bifunctional butyraldehyde/butanol dehydrogenase gene adhE2 from C. acetobutylicum for n-butanol production from crystalline cellulose. However, butanol production by this engineered strain had a relatively low yield of approximately 0.22 g/g cellulose due to the coproduction of ethanol and acids. We hypothesized that strengthening the carbon flux through the central butyryl-CoA biosynthesis pathway and increasing intracellular NADH availability in C. cellulovorans adhE2 would enhance n-butanol production. In this study, thiolase (thlACA ) from C. acetobutylicum and 3-hydroxybutyryl-CoA dehydrogenase (hbdCT ) from C. tyrobutyricum were overexpressed in C. cellulovorans adhE2 to increase the flux from acetyl-CoA to butyryl-CoA. In addition, ferredoxin-NAD(P)+ oxidoreductase (fnr), which can regenerate the intracellular NAD(P)H and thus increase butanol biosynthesis, was also overexpressed. Metabolic flux analyses showed that mutants overexpressing these genes had a significantly increased carbon flux toward butyryl-CoA, which resulted in increased production of butyrate and butanol. The addition of methyl viologen as an electron carrier in batch fermentation further directed more carbon flux towards n-butanol biosynthesis due to increased reducing equivalent or NADH. The engineered strain C. cellulovorans adhE2-fnrCA -thlACA -hbdCT produced n-butanol from cellulose at a 50% higher yield (0.34 g/g), the highest ever obtained in batch fermentation by any known bacterial strain. The engineered C. cellulovorans is thus a promising host for n-butanol production from cellulosic biomass in consolidated bioprocessing.
Collapse
Affiliation(s)
- Teng Bao
- William G. Lowrie Department of Chemical and Biomolecular Engineering, The Ohio State University, Columbus, Ohio, USA
| | - Wenjie Hou
- William G. Lowrie Department of Chemical and Biomolecular Engineering, The Ohio State University, Columbus, Ohio, USA.,College of Life Sciences, Northwest A&F University, Yangling, Shanxi, China
| | - Xuefeng Wu
- William G. Lowrie Department of Chemical and Biomolecular Engineering, The Ohio State University, Columbus, Ohio, USA.,School of Food and Biological Engineering, Hefei University of Technology, Hefei, China
| | - Li Lu
- William G. Lowrie Department of Chemical and Biomolecular Engineering, The Ohio State University, Columbus, Ohio, USA
| | - Xian Zhang
- William G. Lowrie Department of Chemical and Biomolecular Engineering, The Ohio State University, Columbus, Ohio, USA.,School of Biotechnology, Jiangnan University, Wuxi, China
| | - Shang-Tian Yang
- William G. Lowrie Department of Chemical and Biomolecular Engineering, The Ohio State University, Columbus, Ohio, USA
| |
Collapse
|
38
|
Wilding-Steele T, Ramette Q, Jacottin P, Soucaille P. Improved CRISPR/Cas9 Tools for the Rapid Metabolic Engineering of Clostridium acetobutylicum. Int J Mol Sci 2021; 22:ijms22073704. [PMID: 33918190 PMCID: PMC8037352 DOI: 10.3390/ijms22073704] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Revised: 03/24/2021] [Accepted: 03/31/2021] [Indexed: 11/16/2022] Open
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPR)/Cas (CRISPR-associated proteins)9 tools have revolutionized biology-several highly efficient tools have been constructed that have resulted in the ability to quickly engineer model bacteria, for example, Escherichia coli. However, the use of CRISPR/Cas9 tools has lagged behind in non-model bacteria, hampering engineering efforts. Here, we developed improved CRISPR/Cas9 tools to enable efficient rapid metabolic engineering of the industrially relevant bacterium Clostridium acetobutylicum. Previous efforts to implement a CRISPR/Cas9 system in C. acetobutylicum have been hampered by the lack of tightly controlled inducible systems along with large plasmids resulting in low transformation efficiencies. We successfully integrated the cas9 gene from Streptococcuspyogenes into the genome under control of the xylose inducible system from Clostridium difficile, which we then showed resulted in a tightly controlled system. We then optimized the length of the editing cassette, resulting in a small editing plasmid, which also contained the upp gene in order to rapidly lose the plasmid using the upp/5-fluorouracil counter-selection system. We used this system to perform individual and sequential deletions of ldhA and the ptb-buk operon.
Collapse
Affiliation(s)
- Tom Wilding-Steele
- INP, TBI, INSA, UPS, Université de Toulouse, 31400 Toulouse, France; wilding-@insa-toulouse.fr (T.W.-S.); (Q.R.); (P.J.)
- Institut National de la Recherche Agronomique (INRA), UMR 792, 31077 Toulouse, France
- Centre National de la Recherche Scientifique (CNRS), UMR 5504, 31400 Toulouse, France
| | - Quentin Ramette
- INP, TBI, INSA, UPS, Université de Toulouse, 31400 Toulouse, France; wilding-@insa-toulouse.fr (T.W.-S.); (Q.R.); (P.J.)
- Institut National de la Recherche Agronomique (INRA), UMR 792, 31077 Toulouse, France
- Centre National de la Recherche Scientifique (CNRS), UMR 5504, 31400 Toulouse, France
| | - Paul Jacottin
- INP, TBI, INSA, UPS, Université de Toulouse, 31400 Toulouse, France; wilding-@insa-toulouse.fr (T.W.-S.); (Q.R.); (P.J.)
- Institut National de la Recherche Agronomique (INRA), UMR 792, 31077 Toulouse, France
- Centre National de la Recherche Scientifique (CNRS), UMR 5504, 31400 Toulouse, France
| | - Philippe Soucaille
- INP, TBI, INSA, UPS, Université de Toulouse, 31400 Toulouse, France; wilding-@insa-toulouse.fr (T.W.-S.); (Q.R.); (P.J.)
- Institut National de la Recherche Agronomique (INRA), UMR 792, 31077 Toulouse, France
- Centre National de la Recherche Scientifique (CNRS), UMR 5504, 31400 Toulouse, France
- BBSRC/EPSRC Synthetic Biology Research Centre (SBRC), School of Life Sciences, The University of Nottingham, University Park, Nottingham NG7 2RD, UK
- Correspondence:
| |
Collapse
|
39
|
Amador-Castro F, García-Cayuela T, Alper HS, Rodriguez-Martinez V, Carrillo-Nieves D. Valorization of pelagic sargassum biomass into sustainable applications: Current trends and challenges. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2021; 283:112013. [PMID: 33508553 DOI: 10.1016/j.jenvman.2021.112013] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Revised: 01/15/2021] [Accepted: 01/16/2021] [Indexed: 06/12/2023]
Abstract
Since long ago, pelagic Sargassum mats have been known to be abundant in the Sargasso Sea, where they provide habitat to diverse organisms. However, over the last few years, massive amounts of pelagic Sargassum have reached the coast of several countries in the Caribbean and West Africa, causing economic and environmental problems. Aiming for lessening the impacts of the blooms, governments and private companies remove the seaweeds from the shore, but this process results expensive. The valorization of this abundant biomass can render Sargassum tides into an economic opportunity and concurrently solve their associated environmental problems. Despite the diverse fields where algae have found applications and the relevance of this recurrent situation, Sargassum biomass remains without large scale applications. Therefore, this review aims to present the potential uses of these algae, identifying the limitations that must be assessed to effectively valorize this bioresource. Due to the constraints identified for each of the presented applications, it is concluded that a biorefinery approach should be developed to effectively valorize this abundant biomass. However, there is an urgent need for investigations focusing on holopelagic Sargassum to be able to truly valorize this seaweed.
Collapse
Affiliation(s)
- Fernando Amador-Castro
- Tecnologico de Monterrey, Escuela de Ingenieria y Ciencias, Av. General Ramon Corona No. 2514, 45201, Zapopan, Jal., Mexico
| | - Tomás García-Cayuela
- Tecnologico de Monterrey, Escuela de Ingenieria y Ciencias, Av. General Ramon Corona No. 2514, 45201, Zapopan, Jal., Mexico
| | - Hal S Alper
- Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX, USA
| | - Verónica Rodriguez-Martinez
- Tecnologico de Monterrey, Escuela de Ingenieria y Ciencias, Av. General Ramon Corona No. 2514, 45201, Zapopan, Jal., Mexico
| | - Danay Carrillo-Nieves
- Tecnologico de Monterrey, Escuela de Ingenieria y Ciencias, Av. General Ramon Corona No. 2514, 45201, Zapopan, Jal., Mexico.
| |
Collapse
|
40
|
Li Q, Wu M, Wen Z, Jiang Y, Wang X, Zhao Y, Liu J, Yang J, Jiang Y, Yang S. Optimization of n-butanol synthesis in Lactobacillus brevis via the functional expression of thl, hbd, crt and ter. ACTA ACUST UNITED AC 2020; 47:1099-1108. [DOI: 10.1007/s10295-020-02331-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Accepted: 11/02/2020] [Indexed: 12/15/2022]
Abstract
Abstract
N-butanol is an important chemical and can be naturally synthesized by Clostridium species; however, the poor n-butanol tolerance of Clostridium impedes the further improvement in titer. In this study, Lactobacillus brevis, which possesses a higher butanol tolerance, was selected as host for heterologous butanol production. The Clostridium acetobutylicum genes thl, hbd, and crt which encode thiolase, β-hydroxybutyryl-CoA dehydrogenase, and crotonase, and the Treponema denticola gene ter, which encodes trans-enoyl-CoA reductase were cloned into a single plasmid to express the butanol synthesis pathway in L. brevis. A titer of 40 mg/L n-butanol was initially achieved with plasmid pLY15-opt, in which all pathway genes are codon-optimized. A titer of 450 mg/L of n-butanol was then synthesized when ter was further overexpressed in this pathway. The role of metabolic flux was reinforced with pLY15, in which only the ter gene was codon-optimized, which greatly increased the n-butanol titer to 817 mg/L. Our strategy significantly improved n-butanol synthesis in L. brevis and the final titer is the highest achieved amongst butanol-tolerant lactic acid bacteria.
Graphic abstract
Collapse
Affiliation(s)
- Qi Li
- grid.412600.1 0000 0000 9479 9538 College of Life Sciences Sichuan Normal University 610101 Chengdu China
- grid.9227.e 0000000119573309 Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences Chinese Academy of Sciences 200032 Shanghai China
| | - Meixian Wu
- grid.9227.e 0000000119573309 Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences Chinese Academy of Sciences 200032 Shanghai China
| | - Zhiqiang Wen
- grid.9227.e 0000000119573309 Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences Chinese Academy of Sciences 200032 Shanghai China
| | - Yuan Jiang
- grid.9227.e 0000000119573309 Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences Chinese Academy of Sciences 200032 Shanghai China
| | - Xin Wang
- grid.9227.e 0000000119573309 Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences Chinese Academy of Sciences 200032 Shanghai China
| | - Yawei Zhao
- grid.9227.e 0000000119573309 Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences Chinese Academy of Sciences 200032 Shanghai China
| | - Jinle Liu
- grid.9227.e 0000000119573309 Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences Chinese Academy of Sciences 200032 Shanghai China
| | - Junjie Yang
- grid.9227.e 0000000119573309 Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences Chinese Academy of Sciences 200032 Shanghai China
| | - Yu Jiang
- grid.419092.7 0000 0004 0467 2285 Huzhou Center of Industrial Biotechnology Shanghai Institutes for Biological Sciences 313000 Huzhou China
| | - Sheng Yang
- grid.9227.e 0000000119573309 Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences Chinese Academy of Sciences 200032 Shanghai China
- grid.419092.7 0000 0004 0467 2285 Huzhou Center of Industrial Biotechnology Shanghai Institutes for Biological Sciences 313000 Huzhou China
| |
Collapse
|
41
|
How to outwit nature: Omics insight into butanol tolerance. Biotechnol Adv 2020; 46:107658. [PMID: 33220435 DOI: 10.1016/j.biotechadv.2020.107658] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Revised: 11/10/2020] [Accepted: 11/13/2020] [Indexed: 12/16/2022]
Abstract
The energy crisis, depletion of oil reserves, and global climate changes are pressing problems of developed societies. One possibility to counteract that is microbial production of butanol, a promising new fuel and alternative to many petrochemical reagents. However, the high butanol toxicity to all known microbial species is the main obstacle to its industrial implementation. The present state of the art review aims to expound the recent advances in modern omics approaches to resolving this insurmountable to date problem of low butanol tolerance. Genomics, transcriptomics, and proteomics show that butanol tolerance is a complex phenomenon affecting multiple genes and their expression. Efflux pumps, stress and multidrug response, membrane transport, and redox-related genes are indicated as being most important during butanol challenge, in addition to fine-tuning of global regulators of transcription (Spo0A, GntR), which may further improve tolerance. Lipidomics shows that the alterations in membrane composition (saturated lipids and plasmalogen increase) are very much species-specific and butanol-related. Glycomics discloses the pleiotropic effect of CcpA, the role of alternative sugar transport, and the production of exopolysaccharides as alternative routes to overcoming butanol stress. Unfortunately, the strain that simultaneously syntheses and tolerates butanol in concentrations that allow its commercialization has not yet been discovered or produced. Omics insight will allow the purposeful increase of butanol tolerance in natural and engineered producers and the effective heterologous expression of synthetic butanol pathways in strains hereditary butanol-resistant up to 3.2 - 4.9% (w/v). Future breakthrough can be achieved by a detailed study of the membrane proteome, of which 21% are proteins with unknown functions.
Collapse
|
42
|
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: 27] [Impact Index Per Article: 6.8] [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.
Collapse
|
43
|
Vees CA, Neuendorf CS, Pflügl S. Towards continuous industrial bioprocessing with solventogenic and acetogenic clostridia: challenges, progress and perspectives. J Ind Microbiol Biotechnol 2020; 47:753-787. [PMID: 32894379 PMCID: PMC7658081 DOI: 10.1007/s10295-020-02296-2] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Accepted: 07/20/2020] [Indexed: 12/11/2022]
Abstract
The sustainable production of solvents from above ground carbon is highly desired. Several clostridia naturally produce solvents and use a variety of renewable and waste-derived substrates such as lignocellulosic biomass and gas mixtures containing H2/CO2 or CO. To enable economically viable production of solvents and biofuels such as ethanol and butanol, the high productivity of continuous bioprocesses is needed. While the first industrial-scale gas fermentation facility operates continuously, the acetone-butanol-ethanol (ABE) fermentation is traditionally operated in batch mode. This review highlights the benefits of continuous bioprocessing for solvent production and underlines the progress made towards its establishment. Based on metabolic capabilities of solvent producing clostridia, we discuss recent advances in systems-level understanding and genome engineering. On the process side, we focus on innovative fermentation methods and integrated product recovery to overcome the limitations of the classical one-stage chemostat and give an overview of the current industrial bioproduction of solvents.
Collapse
Affiliation(s)
- Charlotte Anne Vees
- Institute of Chemical, Environmental and Bioscience Engineering, Research Area Biochemical Engineering, Technische Universität Wien, Gumpendorfer Straße 1a, 1060 Vienna, Austria
| | - Christian Simon Neuendorf
- Institute of Chemical, Environmental and Bioscience Engineering, Research Area Biochemical Engineering, Technische Universität Wien, Gumpendorfer Straße 1a, 1060 Vienna, Austria
| | - Stefan Pflügl
- Institute of Chemical, Environmental and Bioscience Engineering, Research Area Biochemical Engineering, Technische Universität Wien, Gumpendorfer Straße 1a, 1060 Vienna, Austria
| |
Collapse
|
44
|
Liu L, Zhou S, Deng Y. The 3-ketoacyl-CoA thiolase: an engineered enzyme for carbon chain elongation of chemical compounds. Appl Microbiol Biotechnol 2020; 104:8117-8129. [PMID: 32830293 DOI: 10.1007/s00253-020-10848-w] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Revised: 08/09/2020] [Accepted: 08/17/2020] [Indexed: 01/03/2023]
Abstract
Because of their function of catalyzing the rearrangement of the carbon chains, thiolases have attracted increasing attentions over the past decades. The 3-ketoacyl-CoA thiolase (KAT) is a member of the thiolase, which is capable of catalyzing the Claisen condensation reaction between the two acyl-CoAs, thereby achieving carbon chain elongation. In this way, diverse value-added compounds might be synthesized starting from simple small CoA thioesters. However, most KATs are hampered by low stability and poor substrate specificity, which has hindered the development of large-scale biosynthesis. In this review, the common characteristics in the three-dimensional structure of KATs from different sources are summarized. Moreover, structure-guided rational engineering is discussed as a strategy for enhancing the performance of KATs. Finally, we reviewed the metabolic engineering applications of KATs for producing various energy-storage molecules, such as n-butanol, fatty acids, dicarboxylic acids, and polyhydroxyalkanoates. KEY POINTS: • Summarize the structural characteristics and catalyzation mechanisms of KATs. • Review on the rational engineering to enhance the performance of KATs. • Discuss the applications of KATs for producing energy-storage molecules.
Collapse
Affiliation(s)
- Lixia Liu
- National Engineering Laboratory for Cereal Fermentation Technology (NELCF), Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, People's Republic of China.,Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, People's Republic of China
| | - Shenghu Zhou
- National Engineering Laboratory for Cereal Fermentation Technology (NELCF), Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, People's Republic of China.,Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, People's Republic of China
| | - Yu Deng
- National Engineering Laboratory for Cereal Fermentation Technology (NELCF), Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, People's Republic of China. .,Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, People's Republic of China.
| |
Collapse
|
45
|
Recent advances in n-butanol and butyrate production using engineered Clostridium tyrobutyricum. World J Microbiol Biotechnol 2020; 36:138. [PMID: 32794091 DOI: 10.1007/s11274-020-02914-2] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2020] [Accepted: 08/08/2020] [Indexed: 12/12/2022]
Abstract
Acidogenic clostridia naturally producing acetic and butyric acids has attracted high interest as a novel host for butyrate and n-butanol production. Among them, Clostridium tyrobutyricum is a hyper butyrate-producing bacterium, which re-assimilates acetate for butyrate biosynthesis by butyryl-CoA/acetate CoA transferase (CoAT), rather than the phosphotransbutyrylase-butyrate kinase (PTB-BK) pathway widely found in clostridia and other microbial species. To date, C. tyrobutyricum has been engineered to overexpress a heterologous alcohol/aldehyde dehydrogenase, which converts butyryl-CoA to n-butanol. Compared to conventional solventogenic clostridia, which produce acetone, ethanol, and butanol in a biphasic fermentation process, the engineered C. tyrobutyricum with a high metabolic flux toward butyryl-CoA produced n-butanol at a high yield of > 0.30 g/g and titer of > 20 g/L in glucose fermentation. With no acetone production and a high C4/C2 ratio, butanol was the only major fermentation product by the recombinant C. tyrobutyricum, allowing simplified downstream processing for product purification. In this review, novel metabolic engineering strategies to improve n-butanol and butyrate production by C. tyrobutyricum from various substrates, including glucose, xylose, galactose, sucrose, and cellulosic hydrolysates containing the mixture of glucose and xylose, are discussed. Compared to other recombinant hosts such as Clostridium acetobutylicum and Escherichia coli, the engineered C. tyrobutyricum strains with higher butyrate and butanol titers, yields and productivities are the most promising hosts for potential industrial applications.
Collapse
|
46
|
Liu J, Jiang Y, Chen J, Yang J, Jiang W, Zhuang W, Ying H, Yang S. Metabolic Engineering and Adaptive Evolution of Clostridium beijerinckii To Increase Solvent Production from Corn Stover Hydrolysate. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2020; 68:7916-7925. [PMID: 32614183 DOI: 10.1021/acs.jafc.0c03048] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
The production of acetone-butanol-ethanol by solventogenic Clostridium using lignocellulosic biomass can be a potential alternative to petroleum-based butanol. However, previous studies on nondetoxified lignocellulose hydrolysate could not provide better results when compared to those in synthetic medium. In this study, we engineered the pentose pathway of Clostridium beijerinckii NCIMB 8052, which was then subjected to adaptive laboratory evolution in the gradient mixture of synthetic medium and pretreated corn stover enzymatic hydrolysate (CSH) prepared according to the National Renewable Energy Laboratory (NREL) standard. The final resultant strain CIBTS1274A produced 20.7 g/L of total solvents in NREL CSH diluted to 6% initial total sugars, supplemented with ammonium acetate. This performance was comparable with that of corn-based butanol. In addition, this strain was successfully used in the scale-up operation using nondetoxified corn stover and corncob hydrolysate at Lignicell Refining Biotechnologies Ltd., which once was the only commercial biobutanol industry in the world.
Collapse
Affiliation(s)
- Jinle Liu
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Yu Jiang
- Huzhou Center of Industrial Biotechnology, Shanghai Institutes of Biological Sciences, Chinese Academy of Sciences, Huzhou 313000, China
| | - Jun Chen
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Junjie Yang
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Weihong Jiang
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Wei Zhuang
- School of Chemical Engineering and Energy, Zhengzhou University, Zhengzhou 450001, China
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211816, China
| | - Hanjie Ying
- School of Chemical Engineering and Energy, Zhengzhou University, Zhengzhou 450001, China
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211816, China
| | - Sheng Yang
- Huzhou Center of Industrial Biotechnology, Shanghai Institutes of Biological Sciences, Chinese Academy of Sciences, Huzhou 313000, China
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| |
Collapse
|
47
|
Cuellar MC, Straathof AJJ. Downstream of the bioreactor: advancements in recovering fuels and commodity chemicals. Curr Opin Biotechnol 2020; 62:189-195. [DOI: 10.1016/j.copbio.2019.11.012] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Revised: 10/13/2019] [Accepted: 11/13/2019] [Indexed: 12/15/2022]
|
48
|
Luo H, Zheng P, Bilal M, Xie F, Zeng Q, Zhu C, Yang R, Wang Z. Efficient bio-butanol production from lignocellulosic waste by elucidating the mechanisms of Clostridium acetobutylicum response to phenolic inhibitors. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 710:136399. [PMID: 31923698 DOI: 10.1016/j.scitotenv.2019.136399] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Revised: 12/24/2019] [Accepted: 12/27/2019] [Indexed: 05/12/2023]
Abstract
Lignocellulosic biomass is considered abundant renewable feedstock to constitute a green and environmentally friendly approach for biofuels (bio-butanol) production as an effective substitute for fossil resources. However, a variety of fermentable inhibitors can be generated in hydrolysates during the biomass pretreatment process. Among them, phenolics including phenolic acids and phenolic aldehydes are the most toxic inhibitors to solventogenic clostridia for bio-butanol production. This study elucidates the physiological mechanism of Clostridium acetobutylicum ATCC 824 response to phenolic inhibitors by the integration of kinetics and transcriptional analysis. Butanol fermentations were stressed by 0.4 g/L phenolic acids or 0.4 g/L phenolic aldehydes at 12 h at the beginning of solventogenesis. With post-stress for 12 h, butanol titer was 7.01 g/L in fermentation with phenolic acid stress, while only 5.82 g/L butanol was produced in the case of phenolic aldehydes stress. Reductions in the two fermentations were 27.6% and 40.0% in comparison with the control (without stress), indicated that phenolic aldehydes had a stronger inhibitory effect on solvents synthesis in C. acetobutylicum than phenolic acids. Additionally, the transcriptional analysis revealed that phenolics altered the gene expression profiles related to membrane transporters such as ATP-binding cassette (ABC)-transporter and phosphotransferase system (PTS), glycolysis, and heat shock proteins. The lower expression levels of PTS-related genes might result in reduced glucose consumption and finally inhibited solvents synthesis under phenolic aldehydes stress. Some genes encoding histidine kinase (CA_C0323, CA_C0903, and CA_C3319) were also affected by phenolics, which might inhibit sporulation. In conclusion, our results provide valuable guidance for the construction of robust strain to efficiently produce bio-butanol from lignocellulosic biomass.
Collapse
Affiliation(s)
- Hongzhen Luo
- School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huaian 223003, China.
| | - Panli Zheng
- School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huaian 223003, China
| | - Muhammad Bilal
- School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huaian 223003, China
| | - Fang Xie
- School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huaian 223003, China
| | - Qingwei Zeng
- School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huaian 223003, China
| | - Chun Zhu
- School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huaian 223003, China
| | - Rongling Yang
- School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huaian 223003, China
| | - Zhaoyu Wang
- School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huaian 223003, China
| |
Collapse
|
49
|
Wen Z, Li Q, Liu J, Jin M, Yang S. Consolidated bioprocessing for butanol production of cellulolytic Clostridia: development and optimization. Microb Biotechnol 2020; 13:410-422. [PMID: 31448546 PMCID: PMC7017829 DOI: 10.1111/1751-7915.13478] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Revised: 08/02/2019] [Accepted: 08/04/2019] [Indexed: 12/20/2022] Open
Abstract
Butanol is an important bulk chemical, as well as a promising renewable gasoline substitute, that is commonly produced by solventogenic Clostridia. The main cost of cellulosic butanol fermentation is caused by cellulases that are required to saccharify lignocellulose, since solventogenic Clostridia cannot efficiently secrete cellulases. However, cellulolytic Clostridia can natively degrade lignocellulose and produce ethanol, acetate, butyrate and even butanol. Therefore, cellulolytic Clostridia offer an alternative to develop consolidated bioprocessing (CBP), which combines cellulase production, lignocellulose hydrolysis and co-fermentation of hexose/pentose into butanol in one step. This review focuses on CBP advances for butanol production of cellulolytic Clostridia and various synthetic biotechnologies that drive these advances. Moreover, the efforts to optimize the CBP-enabling cellulolytic Clostridia chassis are also discussed. These include the development of genetic tools, pentose metabolic engineering and the improvement of butanol tolerance. Designer cellulolytic Clostridia or consortium provide a promising approach and resource to accelerate future CBP for butanol production.
Collapse
Affiliation(s)
- Zhiqiang Wen
- School of Environmental and Biological EngineeringNanjing University of Science and TechnologyNanjing210094China
| | - Qi Li
- College of Life SciencesSichuan Normal UniversityLongquan, Chengdu610101China
| | - Jinle Liu
- Key Laboratory of Synthetic BiologyCAS Center for Excellence in Molecular Plant SciencesShanghai Institute of Plant Physiology and EcologyChinese Academy of SciencesShanghai200032China
| | - Mingjie Jin
- School of Environmental and Biological EngineeringNanjing University of Science and TechnologyNanjing210094China
| | - Sheng Yang
- Key Laboratory of Synthetic BiologyCAS Center for Excellence in Molecular Plant SciencesShanghai Institute of Plant Physiology and EcologyChinese Academy of SciencesShanghai200032China
- Huzhou Center of Industrial BiotechnologyShanghai Institutes of Biological SciencesChinese Academy of SciencesShanghai200032China
| |
Collapse
|
50
|
Wen Z, Ledesma-Amaro R, Lu M, Jin M, Yang S. Metabolic Engineering of Clostridium cellulovorans to Improve Butanol Production by Consolidated Bioprocessing. ACS Synth Biol 2020; 9:304-315. [PMID: 31940438 DOI: 10.1021/acssynbio.9b00331] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Clostridium cellulovorans DSM 743B can produce butyrate when grown on lignocellulose, but it can hardly synthesize butanol. In a previous study, C. cellulovorans was successfully engineered to switch the metabolism from butyryl-CoA to butanol by overexpressing an alcohol aldehyde dehydrogenase gene adhE1 from Clostridium acetobutylicum ATCC 824; however, its full potential in butanol production is still unexplored. In the study, a metabolic engineering approach based on a push-pull strategy was developed to further enhance cellulosic butanol production. In order to accomplish this, the carbon flux from acetyl-CoA to butyryl-CoA was pulled by overexpressing a trans-enoyl-coenzyme A reductase gene (ter), which can irreversibly catalyze crotonyl-CoA to butyryl-CoA. Then an acid reassimilation pathway uncoupled with acetone production was introduced to redirect the carbon flow from butyrate and acetate toward butyryl-CoA. Finally, xylose metabolism engineering was implemented by inactivating xylR (Clocel_0594) and araR (Clocel_1253), as well as overexpressing xylT (CA_C1345), which is expected to supply additional carbon and reducing power for CoA and butanol synthesis pathways. The final engineered strain produced 4.96 g/L of n-butanol from alkali extracted corn cobs (AECC), increasing by 235-fold compared to that of the wild type. It serves as a promising butanol producer by consolidated bioprocessing.
Collapse
Affiliation(s)
- Zhiqiang Wen
- School of Environmental and Biological Engineering, Nanjing University of Science & Technology, Nanjing 210094, China
| | | | - Minrui Lu
- School of Environmental and Biological Engineering, Nanjing University of Science & Technology, Nanjing 210094, China
| | - Mingjie Jin
- School of Environmental and Biological Engineering, Nanjing University of Science & Technology, Nanjing 210094, China
| | - Sheng Yang
- 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
- Huzhou Center of Industrial Biotechnology, Shanghai Institutes of Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| |
Collapse
|