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Jo SY, Lim SH, Lee JY, Son J, Choi JI, Park SJ. Microbial production of poly(3-hydroxybutyrate-co-3-hydroxyvalerate), from lab to the shelf: A review. Int J Biol Macromol 2024; 274:133157. [PMID: 38901504 DOI: 10.1016/j.ijbiomac.2024.133157] [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: 02/09/2024] [Revised: 06/11/2024] [Accepted: 06/12/2024] [Indexed: 06/22/2024]
Abstract
Polyhydroxyalkanoates (PHAs) are natural biopolyesters produced by microorganisms that represent one of the most promising candidates for the replacement of conventional plastics due to their complete biodegradability and advantageous material properties which can be modulated by varying their monomer composition. Poly(3-hydroxybutyrate-co-3-hydroxyvalerate) [P(3HB-co-3HV)] has received particular research attention because it can be synthesized based on the same microbial platform developed for poly(3-hydroxybutyrate) [P(3HB)] without much modification, with as high productivity as P(3HB). It also offers more useful mechanical and thermal properties than P(3HB), which broaden its application as a biocompatible and biodegradable polyester. However, a significant commercial disadvantage of P(3HB-co-3HV) is its rather high production cost, thus many studies have investigated the economical synthesis of P(3HB-co-3HV) from structurally related and unrelated carbon sources in both wild-type and recombinant microbial strains. A large number of metabolic engineering strategies have also been proposed to tune the monomer composition of P(3HB-co-3HV) and thus its material properties. In this review, recent metabolic engineering strategies designed for enhanced production of P(3HB-co-3HV) are discussed, along with their current status, limitations, and future perspectives.
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Affiliation(s)
- Seo Young Jo
- Department of Chemical Engineering and Materials Science, Graduate Program in System Health Science and Engineering, Ewha Womans University, Seoul 03760, Republic of Korea
| | - Seo Hyun Lim
- Department of Chemical Engineering and Materials Science, Graduate Program in System Health Science and Engineering, Ewha Womans University, Seoul 03760, Republic of Korea
| | - Ji Yeon Lee
- Department of Chemical Engineering and Materials Science, Graduate Program in System Health Science and Engineering, Ewha Womans University, Seoul 03760, Republic of Korea
| | - Jina Son
- Department of Chemical Engineering and Materials Science, Graduate Program in System Health Science and Engineering, Ewha Womans University, Seoul 03760, Republic of Korea
| | - Jong-Il Choi
- Department of Biotechnology and Bioengineering, Chonnam National University, Gwangju 61186, Republic of Korea.
| | - Si Jae Park
- Department of Chemical Engineering and Materials Science, Graduate Program in System Health Science and Engineering, Ewha Womans University, Seoul 03760, Republic of Korea.
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Gu J, Qiu Q, Yu Y, Sun X, Tian K, Chang M, Wang Y, Zhang F, Huo H. Bacterial transformation of lignin: key enzymes and high-value products. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2024; 17:2. [PMID: 38172947 PMCID: PMC10765951 DOI: 10.1186/s13068-023-02447-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Accepted: 12/08/2023] [Indexed: 01/05/2024]
Abstract
Lignin, a natural organic polymer that is recyclable and inexpensive, serves as one of the most abundant green resources in nature. With the increasing consumption of fossil fuels and the deterioration of the environment, the development and utilization of renewable resources have attracted considerable attention. Therefore, the effective and comprehensive utilization of lignin has become an important global research topic, with the goal of environmental protection and economic development. This review focused on the bacteria and enzymes that can bio-transform lignin, focusing on the main ways that lignin can be utilized to produce high-value chemical products. Bacillus has demonstrated the most prominent effect on lignin degradation, with 89% lignin degradation by Bacillus cereus. Furthermore, several bacterial enzymes were discussed that can act on lignin, with the main enzymes consisting of dye-decolorizing peroxidases and laccase. Finally, low-molecular-weight lignin compounds were converted into value-added products through specific reaction pathways. These bacteria and enzymes may become potential candidates for efficient lignin degradation in the future, providing a method for lignin high-value conversion. In addition, the bacterial metabolic pathways convert lignin-derived aromatics into intermediates through the "biological funnel", achieving the biosynthesis of value-added products. The utilization of this "biological funnel" of aromatic compounds may address the heterogeneous issue of the aromatic products obtained via lignin depolymerization. This may also simplify the separation of downstream target products and provide avenues for the commercial application of lignin conversion into high-value products.
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Affiliation(s)
- Jinming Gu
- School of Environment, Northeast Normal University, No. 2555 Jingyue Avenue, Changchun, 130117, China
| | - Qing Qiu
- School of Environment, Northeast Normal University, No. 2555 Jingyue Avenue, Changchun, 130117, China
| | - Yue Yu
- School of Environment, Northeast Normal University, No. 2555 Jingyue Avenue, Changchun, 130117, China
| | - Xuejian Sun
- School of Environment, Northeast Normal University, No. 2555 Jingyue Avenue, Changchun, 130117, China
| | - Kejian Tian
- School of Environment, Northeast Normal University, No. 2555 Jingyue Avenue, Changchun, 130117, China
| | - Menghan Chang
- School of Environment, Northeast Normal University, No. 2555 Jingyue Avenue, Changchun, 130117, China
| | - Yibing Wang
- School of Environment, Northeast Normal University, No. 2555 Jingyue Avenue, Changchun, 130117, China
| | - Fenglin Zhang
- School of Environment, Northeast Normal University, No. 2555 Jingyue Avenue, Changchun, 130117, China
| | - Hongliang Huo
- School of Environment, Northeast Normal University, No. 2555 Jingyue Avenue, Changchun, 130117, China.
- Engineering Lab for Water Pollution Control and Resources Recovery of Jilin Province, Changchun, 130117, China.
- Engineering Research Center of Low-Carbon Treatment and Green Development of Polluted Water in Northeast China, Ministry of Education, Changchun, 130117, China.
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3
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Huang T, Ma Y. Advances in biosynthesis of higher alcohols in Escherichia coli. World J Microbiol Biotechnol 2023; 39:125. [PMID: 36941474 DOI: 10.1007/s11274-023-03580-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Accepted: 03/13/2023] [Indexed: 03/23/2023]
Abstract
In recent years, the development of green energy to replace fossil fuels has been the focus of research. Higher alcohols are important biofuels and chemicals. The production of higher alcohols in microbes has gained attention due to its environmentally friendly character. Higher alcohols have been synthesized in model microorganism Escherichia coli, and the production has reached the gram level through enhancement of metabolic flow, the balance of reducing power and the optimization of fermentation processes. Sustainable bio-higher alcohols production is expected to replace fossil fuels as a green and renewable energy source. Therefore, this review summarizes the latest developments in producing higher alcohols (C3-C6) by E. coli, elucidate the main bottlenecks limiting the biosynthesis of higher alcohols, and proposes potential engineering strategies of improving the production of biological higher alcohols. This review would provide a theoretical basis for further research on higher alcohols production by E. coli.
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Affiliation(s)
- Tong Huang
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, People's Republic of China
| | - Yuanyuan Ma
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, People's Republic of China.
- School of Marin Science and Technology, Tianjin University, Tianjin, 300072, China.
- R&D Center for Petrochemical Technology, Tianjin University, Tianjin, 300072, China.
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John J A, Samuel MS, Govarthanan M, Selvarajan E. A comprehensive review on strategic study of cellulase producing marine actinobacteria for biofuel applications. ENVIRONMENTAL RESEARCH 2022; 214:114018. [PMID: 35961544 DOI: 10.1016/j.envres.2022.114018] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 07/12/2022] [Accepted: 07/28/2022] [Indexed: 06/15/2023]
Abstract
Every year, 180 billion tonnes of cellulose are produced by plants as waste biomass after the cultivation of the desired product. One of the smart and effective ways to utilize this biomass rather than burn it is to utilize the biomass to adequately meet the energy needs with the help of microbial cellulase that can catalytically convert the cellulose into simple sugar units. Marine actinobacteria is one of the plentiful gram-positive bacteria known for its industrial application as it can produce multienzyme cellulase with high thermal tolerance, pH stability and high resistant towards metal ions and salt concentration, along with other antimicrobial properties. Highly stable cellulase obtained from marine actinobacteria will convert the cellulose biomass into glucose, which is the precursor for biofuel production. This review will provide a comprehensive outlook of various strategic applications of cellulase from marine actinobacteria which can facilitate the breakdown of lignocellulosic biomass to bioenergy with respect to its characteristics based on the location/environment that the organism was collected and its screening strategies followed by adopted methodologies to mine the novel cellulase genome and enhance the production, thereby increasing the activity of cellulase continued by effective immobilization on novel substrates for the multiple usage of cellulase along with the industrial applications.
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Affiliation(s)
- Ashwini John J
- Department of Genetic Engineering, School of Bioengineering, College of Engineering and Technology, SRM Institute of Science and Technology, Kattankulathur, Chengalpattu, 603 203, Tamil Nadu, India
| | - Melvin S Samuel
- Department of Material Science and Engineering, University of Winsconsin-Milwaukee, Milwaukee, WI, USA
| | - Muthusamy Govarthanan
- Department of Environmental Engineering, Kyungpook National University, Daegu, South Korea; Departrment of Biomaterials, Saveetha Dental College and Hospital, Saveetha Institute of Medical and Technical Sciences, Chennai, 600 077, India
| | - Ethiraj Selvarajan
- Department of Genetic Engineering, School of Bioengineering, College of Engineering and Technology, SRM Institute of Science and Technology, Kattankulathur, Chengalpattu, 603 203, Tamil Nadu, India.
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5
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Fang H, Deng Y, Pan Y, Li C, Yu L. Distributive and collaborative push‐and‐pull in an artificial microbial consortium for improved consolidated bioprocessing. AIChE J 2022. [DOI: 10.1002/aic.17844] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Hao Fang
- ZJU‐Hangzhou Global Scientific and Technological Innovation Center, No.733 Jianshe San Road Hangzhou Zhejiang China
- College of Life Sciences, Northwest A&F University, No.22 Xinong Road Yangling Shaanxi China
- College of Chemical and Biological Engineering, Zhejiang University, No.38 Zheda Road Hangzhou Zhejiang China
| | - Yuntao Deng
- College of Life Sciences, Northwest A&F University, No.22 Xinong Road Yangling Shaanxi China
| | - Yingjie Pan
- ZJU‐Hangzhou Global Scientific and Technological Innovation Center, No.733 Jianshe San Road Hangzhou Zhejiang China
| | - Chaofeng Li
- College of Life Sciences, Northwest A&F University, No.22 Xinong Road Yangling Shaanxi China
| | - Liang Yu
- Department of Biological Systems Engineering Washington State University Pullman Washington United States of America
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Zhou B, Song F, Ma X, Wang L. Batch and Continuous-Flow Preparation of Biomass-Derived Furfural Acetals over a TiO 2 Nanoparticle-Exfoliated Montmorillonite Composite Catalyst. CHEMSUSCHEM 2021; 14:2341-2351. [PMID: 33831278 DOI: 10.1002/cssc.202100303] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 03/24/2021] [Indexed: 06/12/2023]
Abstract
Furfural acetals with high octane value, high calorific value and high oxidation resistance are considered promising biofuels or fuel precursors with huge potential demand. However, there are few studies on efficient scalable catalyst systems, including continuous-flow catalyst systems, for their preparation. In this work, TiO2 nanoparticles supported on exfoliated montmorillonite, with strong Lewis acid sites and abundant accessible Brønsted acid sites, is used to catalyze the acetalization reactions of biomass-derived furfural and alcohols. Low dosage of the catalyst made the reaction reach equilibrium in a very short time (TOF=690-1305 min-1 ) at room temperature with the acetal as the only product. In continuous-flow reactions, the catalyst showed a stable product output with conversion close to that for the batch reaction with a short catalyst-reactant contact time of 150 s. Contrast experiments revealed that both Lewis and Brønsted acid sites on the catalyst were indispensable for maximizing the catalytic performance, and simultaneously activating both furfural and alcohol on the adjacent Lewis and Brønsted acid sites was proposed to be responsible for the high catalytic performance.
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Affiliation(s)
- Bo Zhou
- School of Chemistry and Chemical Engineering, Shaoxing University, Huanchengxi Road 508, Shaoxing, 312000, P. R. China
- School of Civil Engineering, Shaoxing University, Huanchengxi Road 508, Shaoxing, 312000, P. R. China
| | - Fan Song
- School of Chemistry and Chemical Engineering, Shaoxing University, Huanchengxi Road 508, Shaoxing, 312000, P. R. China
| | - Xinyue Ma
- School of Chemistry and Chemical Engineering, Shaoxing University, Huanchengxi Road 508, Shaoxing, 312000, P. R. China
| | - Lijun Wang
- School of Chemistry and Chemical Engineering, Shaoxing University, Huanchengxi Road 508, Shaoxing, 312000, P. R. China
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Zhang X, Liu Y, Wang J, Zhao Y, Deng Y. Biosynthesis of adipic acid in metabolically engineered Saccharomyces cerevisiae. J Microbiol 2020; 58:1065-1075. [PMID: 33095385 DOI: 10.1007/s12275-020-0261-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Revised: 07/27/2020] [Accepted: 08/12/2020] [Indexed: 11/26/2022]
Abstract
Adipic Acid (AA) is a valued platform chemical compound, which can be used as a precursor of nylon-6,6. Due to the generation of an enormous amount of nitric oxide metabolites and the growing depletion of oil resources as a result of AA production from a mixture of cyclohexanol and cyclohexanone, the microbial methods for synthesizing AA have attracted significant attention. Of the several AA-producing pathways, the reverse adipate degradation pathway in Thermobifida fusca (Tfu RADP) is reported to be the most efficient, which has been confirmed in Escherichia coli. In this study, the heterologous Tfu RADP was constructed for producing AA in S. cerevisiae by co-expressing genes of Tfu_0875, Tfu_2399, Tfu_0067, Tfu_1647, Tfu_2576, and Tfu_2576. The AA titer combined with biomass, cofactors and other by-products was all determined after fermentation. During batch fermentation in a shake flask, the maximum AA titer was 3.83 mg/L, while the titer increased to 10.09 mg/L during fed-batch fermentation in a 5-L bioreactor after fermentation modification.
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Affiliation(s)
- Xi Zhang
- National Engineering Laboratory for Cereal Fermentation Technology (NELCF), School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, P. R. China
- School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, P. R. China
| | - Yingli Liu
- China-Canada Joint Lab of Food Nutrition and Health (Beijing), Beijing Technology & Business University, Beijing, 100048, P. R. China
| | - Jing Wang
- China-Canada Joint Lab of Food Nutrition and Health (Beijing), Beijing Technology & Business University, Beijing, 100048, P. R. China
| | - Yunying Zhao
- National Engineering Laboratory for Cereal Fermentation Technology (NELCF), School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, P. R. China.
- Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, P. R. China.
| | - Yu Deng
- National Engineering Laboratory for Cereal Fermentation Technology (NELCF), School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, P. R. China.
- School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, P. R. China.
- Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, P. R. China.
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8
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Zhong Y, Zhou B, Wang L. Fe/FeOx embedded in LDH catalyzing C-C bond forming reactions of furfural with alcohols in the absence of a homogeneous base. MOLECULAR CATALYSIS 2020. [DOI: 10.1016/j.mcat.2020.111056] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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9
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Characterization of a Novel Thermobifida fusca Bacteriophage P318. Viruses 2019; 11:v11111042. [PMID: 31717440 PMCID: PMC6893835 DOI: 10.3390/v11111042] [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: 10/11/2019] [Revised: 11/07/2019] [Accepted: 11/07/2019] [Indexed: 11/16/2022] Open
Abstract
Thermobifida fusca is of biotechnological interest due to its ability to produce an array of plant cell wall hydrolytic enzymes. Nonetheless, only one T. fusca bacteriophage with genome information has been reported to date. This study was aimed at discovering more relevant bacteriophages to expand the existing knowledge of phage diversity for this host species. With this end in view, a thermostable T. fusca bacteriophage P318, which belongs to the Siphoviridae family, was isolated and characterized. P318 has a double-stranded DNA genome of 48,045 base pairs with 3′-extended COS ends, on which 52 putative ORFs are organized into clusters responsible for the order of genome replication, virion morphogenesis, and the regulation of the lytic/lysogenic cycle. In comparison with T. fusca and the previously discovered bacteriophage P1312, P318 has a much lower G+C content in its genome except at the region encompassing ORF42, which produced a protein with unknown function. P1312 and P318 share very few similarities in their genomes except for the regions encompassing ORF42 of P318 and ORF51 of P1312 that are homologous. Thus, acquisition of ORF42 by lateral gene transfer might be an important step in the evolution of P318.
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Lee S, Kang M, Bae JH, Sohn JH, Sung BH. Bacterial Valorization of Lignin: Strains, Enzymes, Conversion Pathways, Biosensors, and Perspectives. Front Bioeng Biotechnol 2019; 7:209. [PMID: 31552235 PMCID: PMC6733911 DOI: 10.3389/fbioe.2019.00209] [Citation(s) in RCA: 64] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Accepted: 08/19/2019] [Indexed: 12/17/2022] Open
Abstract
Lignin, an aromatic polymer found in plants, has been studied for years in many biological fields. Initially, when biofuel was produced from lignocellulosic biomass, lignin was regarded as waste generated by the biorefinery and had to be removed, because of its inhibitory effects on fermentative bacteria. Although it has since proven to be a natural resource for bio-products with considerable potential, its utilization is confined by its complex structure. Hence, the microbial degradation of lignin has attracted researchers' interest to overcome this problem. From this perspective, the studies have primarily focused on fungal systems, such as extracellular peroxidase and laccase from white- and brown-rot fungi. However, recent reports have suggested that bacteria play an increasing role in breaking down lignin. This paper, therefore, reviews the role of bacteria in lignin and lignin-related research. Several reports on bacterial species in soil that can degrade lignin and their enzymes are included. In addition, a cellulolytic anaerobic bacterium capable of solubilizing lignin and carbohydrate simultaneously has recently been identified, even though the enzyme involved has not been discovered yet. The assimilation of lignin-derived small molecules and their conversion to renewable chemicals by bacteria, such as muconic acid and polyhydroxyalkanoates, including genetic modification to enhance their capability was discussed. This review also covers the indirect use of bacteria for lignin degradation, which is concerned with whole-cell biosensors designed to detect the aromatic chemicals released from lignin transformation.
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Affiliation(s)
- Siseon Lee
- Synthetic Biology and Bioengineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, South Korea
| | - Minsik Kang
- Synthetic Biology and Bioengineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, South Korea
- Department of Biosystems and Bioengineering, Korea University of Science and Technology, Daejeon, South Korea
| | - Jung-Hoon Bae
- Synthetic Biology and Bioengineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, South Korea
| | - Jung-Hoon Sohn
- Synthetic Biology and Bioengineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, South Korea
- Department of Biosystems and Bioengineering, Korea University of Science and Technology, Daejeon, South Korea
| | - Bong Hyun Sung
- Synthetic Biology and Bioengineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, South Korea
- Department of Biosystems and Bioengineering, Korea University of Science and Technology, Daejeon, South Korea
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Yan Q, Robert S, Brooks JP, Fong SS. Metabolic characterization of the chitinolytic bacterium Serratia marcescens using a genome-scale metabolic model. BMC Bioinformatics 2019; 20:227. [PMID: 31060515 PMCID: PMC6501404 DOI: 10.1186/s12859-019-2826-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Accepted: 04/17/2019] [Indexed: 12/31/2022] Open
Abstract
Background Serratia marcescens is a chitinolytic bacterium that can potentially be used for consolidated bioprocessing to convert chitin to value-added chemicals. Currently, S. marcescens is poorly characterized and studies on intracellular metabolic and regulatory mechanisms would expedite development of bioprocessing applications. Results In this study, our goal was to characterize the metabolic profile of S. marcescens to provide insight for metabolic engineering applications and fundamental biological studies. Hereby, we constructed a constraint-based genome-scale metabolic model (iSR929) including 929 genes, 1185 reactions and 1164 metabolites based on genomic annotation of S. marcescens Db11. The model was tested by comparing model predictions with experimental data and analyzed to identify essential aspects of the metabolic network (e.g. 138 essential genes predicted). The model iSR929 was refined by integrating RNAseq data of S. marcescens growth on three different carbon sources (glucose, N-acetylglucosamine, and glycerol). Significant differences in TCA cycle utilization were found for growth on the different carbon substrates, For example, for growth on N-acetylglucosamine, S. marcescens exhibits high pentose phosphate pathway activity and nucleotide synthesis but low activity of the TCA cycle. Conclusions Our results show that S. marcescens model iSR929 can provide reasonable predictions and can be constrained to fit with experimental values. Thus, our model may be used to guide strain designs for metabolic engineering to produce chemicals such as 2,3-butanediol, N-acetylneuraminic acid, and n-butanol using S. marcescens. Electronic supplementary material The online version of this article (10.1186/s12859-019-2826-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Qiang Yan
- Department of Chemical and Life Science Engineering, School of Engineering, Virginia Commonwealth University, West Hall, Room 422, 601 West Main Street, P.O. Box 843028, Richmond, VA, 23284-3028, USA.
| | - Seth Robert
- Department of Chemical and Life Science Engineering, School of Engineering, Virginia Commonwealth University, West Hall, Room 422, 601 West Main Street, P.O. Box 843028, Richmond, VA, 23284-3028, USA
| | - J Paul Brooks
- Department of Statistical Sciences and Operations Research, Virginia Commonwealth University, P.O. Box 843083, Richmond, VA, 23284, USA.,Center for the study of Biological Complexity, Virginia Commonwealth University, Richmond, VA, 23284, USA
| | - Stephen S Fong
- Department of Chemical and Life Science Engineering, School of Engineering, Virginia Commonwealth University, West Hall, Room 422, 601 West Main Street, P.O. Box 843028, Richmond, VA, 23284-3028, USA. .,Center for the study of Biological Complexity, Virginia Commonwealth University, Richmond, VA, 23284, USA.
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12
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Anteneh YS, Franco CMM. Whole Cell Actinobacteria as Biocatalysts. Front Microbiol 2019; 10:77. [PMID: 30833932 PMCID: PMC6387938 DOI: 10.3389/fmicb.2019.00077] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2018] [Accepted: 01/15/2019] [Indexed: 12/25/2022] Open
Abstract
Production of fuels, therapeutic drugs, chemicals, and biomaterials using sustainable biological processes have received renewed attention due to increasing environmental concerns. Despite having high industrial output, most of the current chemical processes are associated with environmentally undesirable by-products which escalate the cost of downstream processing. Compared to chemical processes, whole cell biocatalysts offer several advantages including high selectivity, catalytic efficiency, milder operational conditions and low impact on the environment, making this approach the current choice for synthesis and manufacturing of different industrial products. In this review, we present the application of whole cell actinobacteria for the synthesis of biologically active compounds, biofuel production and conversion of harmful compounds to less toxic by-products. Actinobacteria alone are responsible for the production of nearly half of the documented biologically active metabolites and many enzymes; with the involvement of various species of whole cell actinobacteria such as Rhodococcus, Streptomyces, Nocardia and Corynebacterium for the production of useful industrial commodities.
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Affiliation(s)
- Yitayal Shiferaw Anteneh
- College of Medicine and Public Health, Medical Biotechnology, Flinders University, Bedford Park, SA, Australia
- Department of Medical Microbiology, College of Medicine, Addis Ababa University, Addis Ababa, Ethiopia
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13
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Fu Y, Yeom SJ, Kwon KK, Hwang J, Kim H, Woo EJ, Lee DH, Lee SG. Structural and functional analyses of the cellulase transcription regulator CelR. FEBS Lett 2018; 592:2776-2785. [PMID: 30062758 DOI: 10.1002/1873-3468.13206] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2018] [Revised: 07/05/2018] [Accepted: 07/19/2018] [Indexed: 11/10/2022]
Abstract
CelR is a transcriptional regulator that controls the expression of cellulases catalyzing cellulose hydrolysis. However, the structural mechanism of its regulation has remained unclear. Here, we report the first structure of CelR, in this case with cellobiose bound. CelR consists of a DNA-binding domain (DBD) and a regulatory domain (RD), and homodimerizes with each monomer bound to cellobiose. A hinge region (HR) in CelR connects the DBD with the RD, and Leu59 in the HR acts as a 'leucine lever' that transduces a transcriptional activation signal. Furthermore, an α4 helix mediates the ligand-binding signal for transcriptional activation. Tyr84 and Gln301 can potentially alter the ligand specificity of CelR. This study provides a pivotal step toward understanding transcription of the cellulases.
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Affiliation(s)
- Yaoyao Fu
- Synthetic Biology and Bioengineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, Korea.,The Key Laboratory of Biotechnology for Medicinal Plant of Jiangsu Province, Jiangsu Normal University, China
| | - Soo-Jin Yeom
- Synthetic Biology and Bioengineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, Korea
| | - Kil Koang Kwon
- Synthetic Biology and Bioengineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, Korea
| | - Jungwon Hwang
- Infection and Immunity Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, Korea
| | - Haseong Kim
- Synthetic Biology and Bioengineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, Korea.,Department of Biosystems and Bioengineering, KRIBB School of Biotechnology, University of Science and Technology (UST), Daejeon, Korea
| | - Eui-Jeon Woo
- Disease Target Structure Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, Korea.,Department of Bio-Analytical Science, KRIBB School of Bioscience, University of Science and Technology (UST), Daejeon, Korea
| | - Dae-Hee Lee
- Synthetic Biology and Bioengineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, Korea.,Department of Biosystems and Bioengineering, KRIBB School of Biotechnology, University of Science and Technology (UST), Daejeon, Korea
| | - Seung-Goo Lee
- Synthetic Biology and Bioengineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, Korea.,Department of Biosystems and Bioengineering, KRIBB School of Biotechnology, University of Science and Technology (UST), Daejeon, Korea
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14
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Kashiwagi N, Ogino C, Kondo A. Production of chemicals and proteins using biomass-derived substrates from a Streptomyces host. BIORESOURCE TECHNOLOGY 2017; 245:1655-1663. [PMID: 28651868 DOI: 10.1016/j.biortech.2017.06.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Revised: 05/31/2017] [Accepted: 06/01/2017] [Indexed: 06/07/2023]
Abstract
Bioproduction using microbes from biomass feedstocks is of interest in regards to environmental problems and cost reduction. Streptomyces as an industrial microorganism plays an important role in the production of useful secondary metabolites for various applications. This strain also secretes a wide range of extracellular enzymes which degrade various biopolymers in nature, and it consumes these degrading substrates as nutrients. Hence, Streptomyces can be employed as a cell factory for the conversion of biomass-derived substrates into various products. This review focuses on the following two points: (1) Streptomyces as a producer of enzymes for degrading biomass-derived polysaccharides and polymers; and, (2) wild-type and engineered strains of Streptomyces as a host for chemical production from biomass-derived substrates.
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Affiliation(s)
- Norimasa Kashiwagi
- Graduate School of Science, Technology and Innovation, Kobe University, 1-1 Rokkodaicho, Nada-ku, Kobe, Hyogo 657-8501, Japan
| | - Chiaki Ogino
- Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, 1-1 Rokkodaicho, Nada-ku, Kobe, Hyogo 657-8501, Japan.
| | - Akihiko Kondo
- Graduate School of Science, Technology and Innovation, Kobe University, 1-1 Rokkodaicho, Nada-ku, Kobe, Hyogo 657-8501, Japan; RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
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15
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Metabolic Profile of the Cellulolytic Industrial Actinomycete Thermobifida fusca. Metabolites 2017; 7:metabo7040057. [PMID: 29137138 PMCID: PMC5746737 DOI: 10.3390/metabo7040057] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2017] [Revised: 11/03/2017] [Accepted: 11/08/2017] [Indexed: 11/17/2022] Open
Abstract
Actinomycetes have a long history of being the source of numerous valuable natural products and medicinals. To expedite product discovery and optimization of biochemical production, high-throughput technologies can now be used to screen the library of compounds present (or produced) at a given time in an organism. This not only facilitates chemical product screening, but also provides a comprehensive methodology to the study cellular metabolic networks to inform cellular engineering. Here, we present some of the first metabolomic data of the industrial cellulolytic actinomycete Thermobifida fusca generated using LC-MS/MS. The underlying objective of conducting global metabolite profiling was to gain better insight on the innate capabilities of T. fusca, with a long-term goal of facilitating T. fusca-based bioprocesses. The T. fusca metabolome was characterized for growth on two cellulose-relevant carbon sources, cellobiose and Avicel. Furthermore, the comprehensive list of measured metabolites was computationally integrated into a metabolic model of T. fusca, to study metabolic shifts in the network flux associated with carbohydrate and amino acid metabolism.
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16
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Lewin GR, Carlos C, Chevrette MG, Horn HA, McDonald BR, Stankey RJ, Fox BG, Currie CR. Evolution and Ecology of Actinobacteria and Their Bioenergy Applications. Annu Rev Microbiol 2017; 70:235-54. [PMID: 27607553 DOI: 10.1146/annurev-micro-102215-095748] [Citation(s) in RCA: 146] [Impact Index Per Article: 20.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The ancient phylum Actinobacteria is composed of phylogenetically and physiologically diverse bacteria that help Earth's ecosystems function. As free-living organisms and symbionts of herbivorous animals, Actinobacteria contribute to the global carbon cycle through the breakdown of plant biomass. In addition, they mediate community dynamics as producers of small molecules with diverse biological activities. Together, the evolution of high cellulolytic ability and diverse chemistry, shaped by their ecological roles in nature, make Actinobacteria a promising group for the bioenergy industry. Specifically, their enzymes can contribute to industrial-scale breakdown of cellulosic plant biomass into simple sugars that can then be converted into biofuels. Furthermore, harnessing their ability to biosynthesize a range of small molecules has potential for the production of specialty biofuels.
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Affiliation(s)
- Gina R Lewin
- Department of Bacteriology, University of Wisconsin-Madison, Wisconsin 53706; .,Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Wisconsin 53726
| | - Camila Carlos
- Department of Bacteriology, University of Wisconsin-Madison, Wisconsin 53706; .,Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Wisconsin 53726
| | - Marc G Chevrette
- Department of Bacteriology, University of Wisconsin-Madison, Wisconsin 53706; .,Department of Genetics, University of Wisconsin-Madison, Wisconsin 53706
| | - Heidi A Horn
- Department of Bacteriology, University of Wisconsin-Madison, Wisconsin 53706;
| | - Bradon R McDonald
- Department of Bacteriology, University of Wisconsin-Madison, Wisconsin 53706; .,Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Wisconsin 53726
| | - Robert J Stankey
- Department of Bacteriology, University of Wisconsin-Madison, Wisconsin 53706; .,Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Wisconsin 53726
| | - Brian G Fox
- Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Wisconsin 53726.,Department of Biochemistry, University of Wisconsin-Madison, Wisconsin 53706
| | - Cameron R Currie
- Department of Bacteriology, University of Wisconsin-Madison, Wisconsin 53706; .,Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Wisconsin 53726
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17
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Thillainayagam M, Venkatesan K, Dipak R, Subramani S, Sethuramasamyraja B, Babu RK. Diesel reformulation using bio-derived propanol to control toxic emissions from a light-duty agricultural diesel engine. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2017; 24:16725-16734. [PMID: 28567673 DOI: 10.1007/s11356-017-9161-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Accepted: 05/01/2017] [Indexed: 06/07/2023]
Abstract
In the Indian agricultural sector, millions of diesel-driven pump-sets were used for irrigation purposes. These engines produce carcinogenic diesel particulates, toxic nitrogen oxides (NOx), and carbon monoxide (CO) emissions which threaten the livelihood of large population of farmers in India. The present study investigates the use of n-propanol, a less-explored high carbon bio-alcohol that can be produced by sustainable pathways from industrial and crop wastes that has an attractive opportunity for powering stationary diesel engines meant for irrigation and rural electrification. This study evaluates the use of n-propanol addition in fossil diesel by up to 30% by vol. and concurrently reports the effects of exhaust gas recirculation (EGR) on emissions of an agricultural DI diesel engine. Three blends PR10, PR20, and PR30 were prepared by mixing 10, 20, and 30% by vol. of n-propanol with fossil diesel. Results when compared to baseline diesel case indicated that smoke density reduced with increasing n-propanol fraction in the blends. PR10, PR20, and PR30 reduced smoke density by 13.33, 33.33, and 60%, respectively. NOx emissions increased with increasing n-propanol fraction in the blends. Later, three EGR rates (10, 20, and 30%) were employed. At any particular EGR rate, smoke density remained lower with increasing n-propanol content in the blends under increasing EGR rates. NOx reduced gradually with EGR. At 30% EGR, the blends PR10, PR20, and PR30 reduced NOx emissions by 43.04, 37.98, and 34.86%, respectively when compared to baseline diesel. CO emissions remained low but hydrocarbon (HC) emissions were high for n-propanol/diesel blends under EGR. Study confirmed that n-propanol could be used by up to 30% by vol. with diesel and the blends delivered lower soot density, NOx, and CO emissions under EGR.
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Affiliation(s)
- Muthukkumar Thillainayagam
- Centre for Research, Sathyabama University, Chennai, TN, India.
- Department of Mechanical Engineering, Jeppiaar Maamallan Engineering College, Chennai, TN, India.
| | | | - Rana Dipak
- Department of Chemical and Biological Engineering, University of Ottawa, Ottawa, ON, K1N 6N5, Canada
| | - Saravanan Subramani
- Research centre, Department of Mechanical Engineering, Sri Venkateswara College of Engineering, Chennai, TN, India
| | | | - Rajesh Kumar Babu
- Research centre, Department of Mechanical Engineering, Sri Venkateswara College of Engineering, Chennai, TN, India.
- Department of Industrial Technology, California State University, Fresno, CA, 93740-8002, USA.
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18
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Lepore AW, Li Z, Davison BH, Foo GS, Wu Z, Narula CK. Catalytic Dehydration of Biomass Derived 1-Propanol to Propene over M-ZSM-5 (M = H, V, Cu, or Zn). Ind Eng Chem Res 2017. [DOI: 10.1021/acs.iecr.7b00592] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- A. W. Lepore
- Bredesen
Center for Interdisciplinary Research, University of Tennessee, 821 Volunteer
Blvd, Knoxville, Tennessee 37996, United States
| | | | | | | | | | - C. K. Narula
- Bredesen
Center for Interdisciplinary Research, University of Tennessee, 821 Volunteer
Blvd, Knoxville, Tennessee 37996, United States
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19
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Recent advances in genetic modification systems for Actinobacteria. Appl Microbiol Biotechnol 2017; 101:2217-2226. [PMID: 28184986 DOI: 10.1007/s00253-017-8156-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2016] [Revised: 01/19/2017] [Accepted: 01/24/2017] [Indexed: 01/08/2023]
Abstract
Actinobacteria are extremely important to human health, agriculture, and forests. Because of the vast differences of the characteristics of Actinobacteria, a lot of genetic tools have been developed for efficiently manipulating the genetics. Although there are a lot of successful examples of engineering Actinobacteria, they are still more difficult to be genetically manipulated than other model microorganisms such as Saccharomyces cerevisiae, Escherichia coli, and Bacillus subtilis etc. due to the diverse genomics and biochemical machinery. Here, we review the methods to introduce heterologous DNA into Actinobacteria and the available genetic modification tools. The trends and problems existing in engineering Actinobacteria are also covered.
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20
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Ábrego U, Chen Z, Wan C. Consolidated Bioprocessing Systems for Cellulosic Biofuel Production. ADVANCES IN BIOENERGY 2017. [DOI: 10.1016/bs.aibe.2017.01.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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21
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Genome-Scale Modeling of Thermophilic Microorganisms. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2016. [PMID: 27913830 DOI: 10.1007/10_2016_45] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register]
Abstract
Thermophilic microorganisms are of increasing interest for many industries as their enzymes and metabolisms are highly efficient at elevated temperatures. However, their metabolic processes are often largely different from their mesophilic counterparts. These differences can lead to metabolic engineering strategies that are doomed to fail. Genome-scale metabolic modeling is an effective and highly utilized way to investigate cellular phenotypes and to test metabolic engineering strategies. In this review we chronicle a number of thermophilic organisms that have recently been studied with genome-scale models. The microorganisms spread across archaea and bacteria domains, and their study gives insights that can be applied in a broader context than just the species they describe. We end with a perspective on the future development and applications of genome-scale models of thermophilic organisms.
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22
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Srirangan K, Bruder M, Akawi L, Miscevic D, Kilpatrick S, Moo-Young M, Chou CP. Recent advances in engineering propionyl-CoA metabolism for microbial production of value-added chemicals and biofuels. Crit Rev Biotechnol 2016; 37:701-722. [PMID: 27557613 DOI: 10.1080/07388551.2016.1216391] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Diminishing fossil fuel reserves and mounting environmental concerns associated with petrochemical manufacturing practices have generated significant interests in developing whole-cell biocatalytic systems for the production of value-added chemicals and biofuels. Although acetyl-CoA is a common natural biogenic precursor for the biosynthesis of numerous metabolites, propionyl-CoA is unpopular and non-native to most organisms. Nevertheless, with its C3-acyl moiety as a discrete building block, propionyl-CoA can serve as another key biogenic precursor to several biological products of industrial importance. As a result, engineering propionyl-CoA metabolism, particularly in genetically tractable hosts with the use of inexpensive feedstocks, has paved an avenue for novel biomanufacturing. Herein, we present a systematic review on manipulation of propionyl-CoA metabolism as well as relevant genetic and metabolic engineering strategies for microbial production of value-added chemicals and biofuels, including odd-chain alcohols and organic acids, bio(co)polymers and polyketides. [Formula: see text].
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Affiliation(s)
| | - Mark Bruder
- a Department of Chemical Engineering , University of Waterloo , Waterloo , ON , Canada
| | - Lamees Akawi
- a Department of Chemical Engineering , University of Waterloo , Waterloo , ON , Canada
| | - Dragan Miscevic
- a Department of Chemical Engineering , University of Waterloo , Waterloo , ON , Canada
| | - Shane Kilpatrick
- a Department of Chemical Engineering , University of Waterloo , Waterloo , ON , Canada
| | - Murray Moo-Young
- a Department of Chemical Engineering , University of Waterloo , Waterloo , ON , Canada
| | - C Perry Chou
- a Department of Chemical Engineering , University of Waterloo , Waterloo , ON , Canada
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23
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Deng Y, Lin J, Mao Y, Zhang X. Systematic analysis of an evolved Thermobifida fusca muC producing malic acid on organic and inorganic nitrogen sources. Sci Rep 2016; 6:30025. [PMID: 27424527 PMCID: PMC4948018 DOI: 10.1038/srep30025] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2016] [Accepted: 06/27/2016] [Indexed: 12/21/2022] Open
Abstract
Thermobifida fusca is a thermophilic actinobacterium. T. fusca muC obtained by adaptive evolution preferred yeast extract to ammonium sulfate for accumulating malic acid and ammonium sulfate for cell growth. We did transcriptome analysis of T. fusca muC on Avicel and cellobiose with addition of ammonium sulfate or yeast extract, respectively by RNAseq. The transcriptional results indicate that ammonium sulfate induced the transcriptions of the genes related to carbohydrate metabolisms significantly more than yeast extract. Importantly, Tfu_2487, encoding histidine-containing protein (HPr), didn’t transcribe on yeast extract at all, while it transcribed highly on ammonium sulfate. In order to understand the impact of HPr on malate production and cell growth of the muC strain, we deleted Tfu_2487 to get a mutant strain: muCΔ2487, which had 1.33 mole/mole-glucose equivalent malate yield, much higher than that on yeast extract. We then developed an E. coli-T. fusca shuttle plasmid for over-expressing HPr in muCΔ2487, a strain without HPr background, forming the muCΔ2487S strain. The muCΔ2487S strain had a much lower malate yield but faster cell growth than the muC strain. The results of both mutant strains confirmed that HPr was the key regulatory protein for T. fusca’s metabolisms on nitrogen sources.
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Affiliation(s)
- Yu Deng
- National Engineering Laboratory for Cereal Fermentation Technology (NELCF), Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China.,The Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Jia Lin
- College of Life Science, North China University of Science and Technology, Tangshan 063000, China
| | - Yin Mao
- National Engineering Laboratory for Cereal Fermentation Technology (NELCF), Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China.,The Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Xiaojuan Zhang
- School of pharmaceutical science, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
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24
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Walther T, François JM. Microbial production of propanol. Biotechnol Adv 2016; 34:984-996. [PMID: 27262999 DOI: 10.1016/j.biotechadv.2016.05.011] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2016] [Revised: 04/08/2016] [Accepted: 05/31/2016] [Indexed: 11/19/2022]
Abstract
Both, n-propanol and isopropanol are industrially attractive value-added molecules that can be produced by microbes from renewable resources. The development of cost-effective fermentation processes may allow using these alcohols as a biofuel component, or as a precursor for the chemical synthesis of propylene. This review reports and discusses the recent progress which has been made in the biochemical production of propanol. Several synthetic propanol-producing pathways were developed that vary with respect to stoichiometry and metabolic entry point. These pathways were expressed in different host organisms and enabled propanol production from various renewable feedstocks. Furthermore, it was shown that the optimization of fermentation conditions greatly improved process performance, in particular, when continuous product removal prevented accumulation of toxic propanol levels. Although these advanced metabolic engineering and fermentation strategies have facilitated significant progress in the biochemical production of propanol, the currently achieved propanol yields and productivities appear to be insufficient to compete with chemical propanol synthesis. The development of biosynthetic pathways with improved propanol yields, the breeding or identification of microorganisms with higher propanol tolerance, and the engineering of propanol producer strains that efficiently utilize low-cost feedstocks are the major challenges on the way to industrially relevant microbial propanol production processes.
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Affiliation(s)
- Thomas Walther
- Université de Toulouse, INSA, UPS, INP, LISBP, 135 Avenue de Rangueil, 31077 Toulouse, France; INRA, UMR792 Ingénierie des Systèmes Biologiques et des Procédés, 31400 Toulouse, France; CNRS, UMR5504, 31400 Toulouse, France; Toulouse White Biotechnology (TWB) Center, 3 rue Ariane, Canal Biotech Building 2, 31520 Ramonville - St. Agne, France.
| | - Jean Marie François
- Université de Toulouse, INSA, UPS, INP, LISBP, 135 Avenue de Rangueil, 31077 Toulouse, France; INRA, UMR792 Ingénierie des Systèmes Biologiques et des Procédés, 31400 Toulouse, France; CNRS, UMR5504, 31400 Toulouse, France
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25
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Zhang X, Tervo CJ, Reed JL. Metabolic assessment of E. coli as a Biofactory for commercial products. Metab Eng 2016; 35:64-74. [DOI: 10.1016/j.ymben.2016.01.007] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2015] [Revised: 01/11/2016] [Accepted: 01/25/2016] [Indexed: 11/24/2022]
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26
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Yim SS, Choi JW, Lee SH, Jeong KJ. Modular Optimization of a Hemicellulose-Utilizing Pathway in Corynebacterium glutamicum for Consolidated Bioprocessing of Hemicellulosic Biomass. ACS Synth Biol 2016; 5:334-43. [PMID: 26808593 DOI: 10.1021/acssynbio.5b00228] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Hemicellulose, which is the second most abundant polysaccharide in nature after cellulose, has the potential to become a major feedstock for microbial fermentation to produce various biofuels and chemicals. To utilize hemicellulose economically, it is necessary to develop a consolidated bioprocess (CBP), in which all processes from biomass degradation to the production of target products occur in a single bioreactor. Here, we report a modularly engineered Corynebacterium glutamicum strain suitable for CBP using hemicellulosic biomass (xylan) as a feedstock. The hemicellulose-utilizing pathway was divided into three distinct modules, and each module was separately optimized. In the module for xylose utilization, the expression level of the xylose isomerase (xylA) and xylulokinase (xylB) genes was optimized with synthetic promoters of different strengths. Then, the module for xylose transport was engineered with combinatorial sets of synthetic promoters and heterologous transporters to achieve the fastest cell growth rate on xylose (0.372 h(-1)). Next, the module for the enzymatic degradation of xylan to xylose was also engineered with different combinations of promoters and signal peptides to efficiently secrete both endoxylanase and xylosidase into the extracellular medium. Finally, each optimized module was integrated into a single plasmid to construct a highly efficient xylan-utilizing pathway. Subsequently, the direct production of lysine from xylan was successfully demonstrated with the engineered pathway. To the best of our knowledge, this is the first report of the development of a consolidated bioprocessing C. glutamicum strain for hemicellulosic biomass.
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Affiliation(s)
- Sung Sun Yim
- Department of Chemical and Biomolecular Engineering, BK21 Plus Program, ‡Institute for the BioCentury, KAIST, 291 Daehak-ro,
Yuseong-gu, Daejeon 34141, Republic of Korea
| | - Jae Woong Choi
- Department of Chemical and Biomolecular Engineering, BK21 Plus Program, ‡Institute for the BioCentury, KAIST, 291 Daehak-ro,
Yuseong-gu, Daejeon 34141, Republic of Korea
| | - Se Hwa Lee
- Department of Chemical and Biomolecular Engineering, BK21 Plus Program, ‡Institute for the BioCentury, KAIST, 291 Daehak-ro,
Yuseong-gu, Daejeon 34141, Republic of Korea
| | - Ki Jun Jeong
- Department of Chemical and Biomolecular Engineering, BK21 Plus Program, ‡Institute for the BioCentury, KAIST, 291 Daehak-ro,
Yuseong-gu, Daejeon 34141, Republic of Korea
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27
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Sun X, Shen X, Jain R, Lin Y, Wang J, Sun J, Wang J, Yan Y, Yuan Q. Synthesis of chemicals by metabolic engineering of microbes. Chem Soc Rev 2016; 44:3760-85. [PMID: 25940754 DOI: 10.1039/c5cs00159e] [Citation(s) in RCA: 75] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Metabolic engineering is a powerful tool for the sustainable production of chemicals. Over the years, the exploration of microbial, animal and plant metabolism has generated a wealth of valuable genetic information. The prudent application of this knowledge on cellular metabolism and biochemistry has enabled the construction of novel metabolic pathways that do not exist in nature or enhance existing ones. The hand in hand development of computational technology, protein science and genetic manipulation tools has formed the basis of powerful emerging technologies that make the production of green chemicals and fuels a reality. Microbial production of chemicals is more feasible compared to plant and animal systems, due to simpler genetic make-up and amenable growth rates. Here, we summarize the recent progress in the synthesis of biofuels, value added chemicals, pharmaceuticals and nutraceuticals via metabolic engineering of microbes.
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Affiliation(s)
- Xinxiao Sun
- State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, 15#, Beisanhuan East Road, Chaoyang District, Beijing 100029, China.
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28
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Deng Y, Mao Y, Zhang X. Metabolic engineering of a laboratory-evolvedThermobifida fuscamuC strain for malic acid production on cellulose and minimal treated lignocellulosic biomass. Biotechnol Prog 2016; 32:14-20. [DOI: 10.1002/btpr.2180] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2015] [Revised: 09/23/2015] [Indexed: 11/08/2022]
Affiliation(s)
- Yu Deng
- National Engineering Laboratory for Cereal Fermentation Technology (NELCF); Jiangnan University; Wuxi Jiangsu 214122 China
- School of pharmaceutical science; Jiangnan University; Wuxi Jiangsu 214122 China
| | - Yin Mao
- National Engineering Laboratory for Cereal Fermentation Technology (NELCF); Jiangnan University; Wuxi Jiangsu 214122 China
- School of pharmaceutical science; Jiangnan University; Wuxi Jiangsu 214122 China
| | - Xiaojuan Zhang
- School of pharmaceutical science; Jiangnan University; Wuxi Jiangsu 214122 China
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29
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Deng Y, Ma L, Mao Y. Biological production of adipic acid from renewable substrates: Current and future methods. Biochem Eng J 2016. [DOI: 10.1016/j.bej.2015.08.015] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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30
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Recent advances in microbial production of fuels and chemicals using tools and strategies of systems metabolic engineering. Biotechnol Adv 2015; 33:1455-66. [DOI: 10.1016/j.biotechadv.2014.11.006] [Citation(s) in RCA: 84] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2014] [Revised: 10/23/2014] [Accepted: 11/09/2014] [Indexed: 11/22/2022]
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31
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Deng Y, Mao Y, Zhang X. Driving carbon flux through exogenous butyryl-CoA: Acetate CoA-transferase to produce butyric acid at high titer in Thermobifida fusca. J Biotechnol 2015; 216:151-7. [PMID: 26535965 DOI: 10.1016/j.jbiotec.2015.10.022] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2015] [Revised: 10/07/2015] [Accepted: 10/29/2015] [Indexed: 12/31/2022]
Abstract
Butyric acid, a 4-carbon short chain fatty acid, is widely used in chemical, food, and pharmaceutical industries. The low activity of butyryl-CoA: acetate CoA-transferase in Thermobifida fusca muS, a thermophilic actinobacterium whose optimal temperature was 55°C, was found to hinder the accumulation of high yield of butyric acid. In order to solve this problem, an exogenous butyryl-CoA: acetate CoA-transferase gene (actA) from Thermoanaerobacterium thermosaccharolyticum DSM571 was integrated into the chromosome of T. fusca muS by replacing celR gene, forming T. fusca muS-1. We demonstrated that on 5g/L cellulose, the yield of butyric acid by the engineered muS-1 strain was increased by 42.9 % compared to the muS strain. On 100g/L of cellulose, the muS-1 strain could consume 90.5% of total cellulose in 144h, with 33.2g/L butyric acid produced. Furthermore, on the mix substrates including the major components of biomass: cellulose, xylose, mannose and galactose, 70.4g/L butyric acid was produced in 168h by fed-batch fermentation. To validate the ability of fermenting biomass, the muS-1 strain was grown on the milled corn stover ranging from 200 to 250μm. The muS-1 strain had the highest butyrate titer 17.1g/L on 90g/L corn stover.
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Affiliation(s)
- Yu Deng
- National Engineering Laboratory for Cereal Fermentation Technology (NELCF), Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; The Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China.
| | - Yin Mao
- National Engineering Laboratory for Cereal Fermentation Technology (NELCF), Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; The Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Xiaojuan Zhang
- School of Pharmaceutical Science, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China.
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Deng Y, Mao Y, Zhang X. Metabolic engineering of E. coli for efficient production of glycolic acid from glucose. Biochem Eng J 2015. [DOI: 10.1016/j.bej.2015.08.008] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Shivlata L, Satyanarayana T. Thermophilic and alkaliphilic Actinobacteria: biology and potential applications. Front Microbiol 2015; 6:1014. [PMID: 26441937 PMCID: PMC4585250 DOI: 10.3389/fmicb.2015.01014] [Citation(s) in RCA: 103] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2015] [Accepted: 09/07/2015] [Indexed: 11/13/2022] Open
Abstract
Microbes belonging to the phylum Actinobacteria are prolific sources of antibiotics, clinically useful bioactive compounds and industrially important enzymes. The focus of the current review is on the diversity and potential applications of thermophilic and alkaliphilic actinobacteria, which are highly diverse in their taxonomy and morphology with a variety of adaptations for surviving and thriving in hostile environments. The specific metabolic pathways in these actinobacteria are activated for elaborating pharmaceutically, agriculturally, and biotechnologically relevant biomolecules/bioactive compounds, which find multifarious applications.
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Cheepudom J, Lee CC, Cai B, Meng M. Isolation, characterization, and complete genome analysis of P1312, a thermostable bacteriophage that infects Thermobifida fusca. Front Microbiol 2015; 6:959. [PMID: 26441893 PMCID: PMC4569894 DOI: 10.3389/fmicb.2015.00959] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2015] [Accepted: 08/31/2015] [Indexed: 11/13/2022] Open
Abstract
Thermobifida fusca is a moderately thermophilic and cellulolytic actinobacterium. It is of particular interest due to its ability to not only produce a variety of biotechnologically relevant enzymes but also serve as an alternative host for metabolic engineering for the production of valuable chemicals from lignocellulosic agricultural wastes. No bacteriophage that infects T. fusca has been reported, despite its potential impacts on the utilization of T. fusca. In this study, an extremely thermostable bacteriophage P1312 that infects T. fusca was isolated from manure compost. Electron microscopy showed that P1312 has an icosahedral head and a long flexible non-contractile tail, a characteristic of the family Siphoviridae. P1312 has a double-stranded DNA genome of 60,284 bp with 93 potential ORFs. Thirty-one ORFs encode proteins having putative biological functions. The genes involved in phage particle formation cluster together in a region of approximately 16 kb, followed by a segment containing genes presumably for DNA degradation/modification and cell wall disruption. The genes required for DNA replication and transcriptional control are dispersed within the rest of the genome. Phylogenetic analysis of large terminase subunit suggests that P1312 is a headful packaging phage containing a chromosome with circularly permuted direct terminal repeats.
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Affiliation(s)
- Jatuporn Cheepudom
- Graduate Institute of Biotechnology, National Chung Hsing University Taichung, Taiwan
| | - Cheng-Cheng Lee
- Graduate Institute of Biotechnology, National Chung Hsing University Taichung, Taiwan
| | - Bingfu Cai
- Graduate Institute of Biotechnology, National Chung Hsing University Taichung, Taiwan
| | - Menghsiao Meng
- Graduate Institute of Biotechnology, National Chung Hsing University Taichung, Taiwan
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Deng Y, Mao Y. Production of adipic acid by the native-occurring pathway in Thermobifida fusca
B6. J Appl Microbiol 2015; 119:1057-63. [DOI: 10.1111/jam.12905] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2015] [Revised: 07/02/2015] [Accepted: 07/10/2015] [Indexed: 11/28/2022]
Affiliation(s)
- Y. Deng
- National Engineering Laboratory for Cereal Fermentation Technology (NELCF); Jiangnan University; Wuxi Jiangsu China
- The Key Laboratory of Industrial Biotechnology; Ministry of Education; Jiangnan University; 1800 Lihu Road Wuxi Jiangsu China
| | - Y. Mao
- National Engineering Laboratory for Cereal Fermentation Technology (NELCF); Jiangnan University; Wuxi Jiangsu China
- The Key Laboratory of Industrial Biotechnology; Ministry of Education; Jiangnan University; 1800 Lihu Road Wuxi Jiangsu China
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Systematic analysis of intracellular mechanisms of propanol production in the engineered Thermobifida fusca B6 strain. Appl Microbiol Biotechnol 2015; 99:8089-100. [PMID: 26227414 DOI: 10.1007/s00253-015-6850-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2015] [Revised: 06/30/2015] [Accepted: 07/15/2015] [Indexed: 10/23/2022]
Abstract
Thermobifida fusca is a moderately thermophilic actinobacterium naturally capable of utilizing lignocellulosic biomass. The B6 strain of T. fusca was previously engineered to produce 1-propanol directly on lignocellulosic biomass by expressing a bifunctional butyraldehyde/alcohol dehydrogenase (adhE2). To characterize the intracellular mechanisms related to the accumulation of 1-propanol, the engineered B6 and wild-type (WT) strains were systematically compared by analysis of the transcriptome and intracellular metabolome during exponential growth on glucose, cellobiose, and Avicel. Of the 18 known cellulases in T. fusca, 10 cellulase genes were transcriptionally expressed on all three substrates along with three hemicellulases. Transcriptomic analysis of cellodextrin and cellulose transport revealed that Tfu_0936 (multiple sugar transport system permease) was the key enzyme regulating the uptake of sugars in T. fusca. For both WT and B6 strains, it was found that growth in oxygen-limited conditions resulted in a blocked tricarboxylic acid (TCA) cycle caused by repressed expression of Tfu_1925 (aconitate hydratase). Further, the transcriptome suggested a pathway for synthesizing succinyl-CoA: oxaloacetate to malate (by malate dehydrogenase), malate to fumarate (by fumarate hydratase), and fumarate to succinate (by succinate dehydrogenase/fumarate reductase) which was ultimately converted to succinyl-CoA by succinyl-CoA synthetase. Both the transcriptome and the intracellular metabolome confirmed that 1-propanol was produced through succinyl-CoA, L-methylmalonyl-CoA, D-methylmalonyl-CoA, and propionyl-CoA in the B6 strain.
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Sun J, Alper HS. Metabolic engineering of strains: from industrial-scale to lab-scale chemical production. ACTA ACUST UNITED AC 2015; 42:423-36. [DOI: 10.1007/s10295-014-1539-8] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2014] [Accepted: 11/06/2014] [Indexed: 12/11/2022]
Abstract
Abstract
A plethora of successful metabolic engineering case studies have been published over the past several decades. Here, we highlight a collection of microbially produced chemicals using a historical framework, starting with titers ranging from industrial scale (more than 50 g/L), to medium-scale (5–50 g/L), and lab-scale (0–5 g/L). Although engineered Escherichia coli and Saccharomyces cerevisiae emerge as prominent hosts in the literature as a result of well-developed genetic engineering tools, several novel native-producing strains are gaining attention. This review catalogs the current progress of metabolic engineering towards production of compounds such as acids, alcohols, amino acids, natural organic compounds, and others.
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Affiliation(s)
- Jie Sun
- grid.89336.37 0000000419369924 McKetta Department of Chemical Engineering The University of Texas at Austin 200 E Dean Keeton St. Stop C0400 78712 Austin TX USA
| | - Hal S Alper
- grid.89336.37 0000000419369924 McKetta Department of Chemical Engineering The University of Texas at Austin 200 E Dean Keeton St. Stop C0400 78712 Austin TX USA
- grid.89336.37 0000000419369924 Institute for Cellular and Molecular Biology The University of Texas at Austin 2500 Speedway Avenue 78712 Austin TX USA
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Lee S, J. Mitchell R. Perspectives on the use of transcriptomics to advance biofuels. AIMS BIOENGINEERING 2015. [DOI: 10.3934/bioeng.2015.4.487] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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39
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Isikgor FH, Becer CR. Lignocellulosic biomass: a sustainable platform for the production of bio-based chemicals and polymers. Polym Chem 2015. [DOI: 10.1039/c5py00263j] [Citation(s) in RCA: 1492] [Impact Index Per Article: 165.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
The ongoing research activities in the field of lignocellulosic biomass for production of value-added chemicals and polymers that can be utilized to replace petroleum-based materials are reviewed.
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Affiliation(s)
| | - C. Remzi Becer
- School of Engineering and Materials Science
- Queen Mary University of London
- E1 4NS London
- UK
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Wang Z, Ammar EM, Zhang A, Wang L, Lin M, Yang ST. Engineering Propionibacterium freudenreichii subsp. shermanii for enhanced propionic acid fermentation: effects of overexpressing propionyl-CoA:Succinate CoA transferase. Metab Eng 2014; 27:46-56. [PMID: 25447642 DOI: 10.1016/j.ymben.2014.10.005] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2014] [Revised: 09/19/2014] [Accepted: 10/20/2014] [Indexed: 11/25/2022]
Abstract
Propionibacterium freudenreichii subsp. shermanii naturally forms propionic acid as the main fermentation product with acetate and succinate as two major by-products. In this study, overexpressing the native propionyl-CoA:succinate CoA transferase (CoAT) in P. shermanii was investigated to evaluate its effects on propionic acid fermentation with glucose, glycerol, and their mixtures as carbon source. In general, the mutant produced more propionic acid, with up to 10% increase in yield (0.62 vs. 0.56g/g) and 46% increase in productivity (0.41 vs. 0.28g/Lh), depending on the fermentation conditions. The mutant also produced less acetate and succinate, with the ratios of propionate to acetate (P/A) and succinate (P/S) in the final product increased 50% and 23%, respectively, in the co-fermentation of glucose/glycerol. Metabolic flux analysis elucidated that CoAT overexpression diverted more carbon fluxes toward propionic acid, resulting in higher propionic acid purity and a preference for glycerol over glucose as carbon source.
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Affiliation(s)
- Zhongqiang Wang
- William G. Lowrie Department of Chemical and Biomolecular Engineering, The Ohio State University, 140 W 19th Avenue, Columbus, OH 43210, USA
| | - Ehab M Ammar
- William G. Lowrie Department of Chemical and Biomolecular Engineering, The Ohio State University, 140 W 19th Avenue, Columbus, OH 43210, USA
| | - An Zhang
- William G. Lowrie Department of Chemical and Biomolecular Engineering, The Ohio State University, 140 W 19th Avenue, Columbus, OH 43210, USA
| | - Liqun Wang
- William G. Lowrie Department of Chemical and Biomolecular Engineering, The Ohio State University, 140 W 19th Avenue, Columbus, OH 43210, USA; School of Pharmaceutical Engineering and Life Sciences, Changzhou University, 1 Ge Hu Road, Jiangsu 213164, China
| | - Meng Lin
- William G. Lowrie Department of Chemical and Biomolecular Engineering, The Ohio State University, 140 W 19th Avenue, Columbus, OH 43210, USA
| | - Shang-Tian Yang
- William G. Lowrie Department of Chemical and Biomolecular Engineering, The Ohio State University, 140 W 19th Avenue, Columbus, OH 43210, USA.
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Tian JH, Pourcher AM, Bouchez T, Gelhaye E, Peu P. Occurrence of lignin degradation genotypes and phenotypes among prokaryotes. Appl Microbiol Biotechnol 2014; 98:9527-44. [PMID: 25343973 DOI: 10.1007/s00253-014-6142-4] [Citation(s) in RCA: 75] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2014] [Revised: 10/06/2014] [Accepted: 10/07/2014] [Indexed: 11/24/2022]
Abstract
A number of prokaryotes actively contribute to lignin degradation in nature and their activity could be of interest for many applications including the production of biogas/biofuel from lignocellulosic biomass and biopulping. This review compares the reliability and efficiency of the culture-dependent screening methods currently used for the isolation of ligninolytic prokaryotes. Isolated prokaryotes exhibiting lignin-degrading potential are presented according to their phylogenetic groups. With the development of bioinformatics, culture-independent techniques are emerging that allow larger-scale data mining for ligninolytic prokaryotic functions but today, these techniques still have some limits. In this work, two phylogenetic affiliations of isolated prokaryotes exhibiting ligninolytic potential and laccase-encoding prokaryotes were determined on the basis of 16S rDNA sequences, providing a comparative view of results obtained by the two types of screening techniques. The combination of laboratory culture and bioinformatics approaches is a promising way to explore lignin-degrading prokaryotes.
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Affiliation(s)
- Jiang-Hao Tian
- IRSTEA, UR GERE, 17 avenue de Cucillé, CS 64427, 35044, Rennes, France
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Biochemical, genetic, and metabolic engineering strategies to enhance coproduction of 1-propanol and ethanol in engineered Escherichia coli. Appl Microbiol Biotechnol 2014; 98:9499-515. [DOI: 10.1007/s00253-014-6093-9] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2014] [Revised: 09/08/2014] [Accepted: 09/10/2014] [Indexed: 12/14/2022]
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Lin H, Wang Q, Shen Q, Ma J, Fu J, Zhao Y. Engineering Aspergillus oryzae A-4 through the chromosomal insertion of foreign cellulase expression cassette to improve conversion of cellulosic biomass into lipids. PLoS One 2014; 9:e108442. [PMID: 25251435 PMCID: PMC4177402 DOI: 10.1371/journal.pone.0108442] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2014] [Accepted: 08/29/2014] [Indexed: 11/18/2022] Open
Abstract
A genetic modification scheme was designed for Aspergillus oryzae A-4, a natural cellulosic lipids producer, to enhance its lipid production from biomass by putting the spotlight on improving cellulase secretion. Four cellulase genes were separately expressed in A-4 under the control of hlyA promoter, with the help of the successful development of a chromosomal genetic manipulation system. Comparison of cellulase activities of PCR-positive transformants showed that these transformants integrated with celA gene and with celC gene had significantly (p<0.05) higher average FPAase activities than those strains integrated with celB gene and with celD gene. Through the assessment of cellulosic lipids accumulating abilities, celA transformant A2-2 and celC transformant D1-B1 were isolated as promising candidates, which could yield 101%-133% and 35.22%-59.57% higher amount of lipids than the reference strain A-4 (WT) under submerged (SmF) conditions and solid-state (SSF) conditions, respectively. Variability in metabolism associated to the introduction of cellulase gene in A2-2 and D1-B1 was subsequently investigated. It was noted that cellulase expression repressed biomass formation but enhanced lipid accumulation; whereas the inhibitory effect on cell growth would be shielded during cellulosic lipids production owing to the essential role of cellulase in substrate utilization. Different metabolic profiles also existed between A2-2 and D1-B1, which could be attributed to not only different transgene but also biological impacts of different integration. Overall, both simultaneous saccharification and lipid accumulation were enhanced in A2-2 and D1-B1, resulting in efficient conversion of cellulose into lipids. A regulation of cellulase secretion in natural cellulosic lipids producers could be a possible strategy to enhance its lipid production from lignocellulosic biomass.
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Affiliation(s)
- Hui Lin
- Institute of Environment Resource and Soil Fertilizer, Zhejiang Academy of Agriculture Science, Hangzhou, China
| | - Qun Wang
- Institute of Microbiology, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Qi Shen
- Institute of Microbiology, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Junwei Ma
- Institute of Environment Resource and Soil Fertilizer, Zhejiang Academy of Agriculture Science, Hangzhou, China
| | - Jianrong Fu
- Institute of Environment Resource and Soil Fertilizer, Zhejiang Academy of Agriculture Science, Hangzhou, China
- * E-mail: (YZ); (JF)
| | - Yuhua Zhao
- Institute of Microbiology, College of Life Sciences, Zhejiang University, Hangzhou, China
- * E-mail: (YZ); (JF)
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44
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Production of butyric acid by a cellulolytic actinobacterium Thermobifida fusca on cellulose. Biochem Eng J 2014. [DOI: 10.1016/j.bej.2014.06.012] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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45
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Vanee N, Brooks JP, Spicer V, Shamshurin D, Krokhin O, Wilkins JA, Deng Y, Fong SS. Proteomics-based metabolic modeling and characterization of the cellulolytic bacterium Thermobifida fusca. BMC SYSTEMS BIOLOGY 2014; 8:86. [PMID: 25115351 PMCID: PMC4236713 DOI: 10.1186/s12918-014-0086-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/24/2014] [Accepted: 07/14/2014] [Indexed: 12/31/2022]
Abstract
Background Thermobifida fusca is a cellulolytic bacterium with potential to be used as a platform organism for sustainable industrial production of biofuels, pharmaceutical ingredients and other bioprocesses due to its capability of potential to convert plant biomass to value-added chemicals. To best develop T. fusca as a bioprocess organism, it is important to understand its native cellular processes. In the current study, we characterize the metabolic network of T. fusca through reconstruction of a genome-scale metabolic model and proteomics data. The overall goal of this study was to use multiple metabolic models generated by different methods and comparison to experimental data to gain a high-confidence understanding of the T. fusca metabolic network. Results We report the generation of three versions of a metabolic model of Thermobifida fusca sp. XY developed using three different approaches (automated, semi-automated, and proteomics-derived). The model closest to in vivo growth was the proteomics-derived model that consists of 975 reactions involving 1382 metabolites and account for 316 EC numbers (296 genes). The model was optimized for biomass production with the optimal flux of 0.48 doublings per hour when grown on cellobiose with a substrate uptake rate of 0.25 mmole/h. In vivo activity of the DXP pathway for terpenoid biosynthesis was also confirmed using real-time PCR. Conclusions iTfu296 provides a platform to understand and explore the metabolic capabilities of the actinomycete T. fusca for the potential use in bioprocess industries for the production of biofuel and pharmaceutical ingredients. By comparing different model reconstruction methods, the use of high-throughput proteomics data as a starting point proved to be the most accurate to in vivo growth.
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Parisutham V, Kim TH, Lee SK. Feasibilities of consolidated bioprocessing microbes: from pretreatment to biofuel production. BIORESOURCE TECHNOLOGY 2014; 161:431-40. [PMID: 24745899 DOI: 10.1016/j.biortech.2014.03.114] [Citation(s) in RCA: 81] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2014] [Revised: 03/20/2014] [Accepted: 03/21/2014] [Indexed: 05/03/2023]
Abstract
Lignocelluloses are rich sugar treasures, which can be converted to useful commodities such as biofuel with the help of efficient combination of enzymes and microbes. Although several bioprocessing approaches have been proposed, biofuel production from lignocelluloses is limited because of economically infeasible technologies for pretreatment, saccharification and fermentation. Use of consolidated bioprocessing (CBP) microbes is the most promising method for the cost-effective production of biofuels. However, lignocelluloses are obtained from highly diverse environment and hence are heterogeneous in nature. Therefore, it is necessary to develop and integrate tailor-designed pretreatment processes and efficient microbes that can thrive on many different kinds of biomass. In this review, the progress towards the construction of consolidated bioprocessing microbes, which can efficiently convert heterogeneous lignocellulosic biomass to bioenergy, has been discussed; in addition, the potential and constraints of current bioprocessing technologies for cellulosic biofuel production have been discussed.
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Affiliation(s)
- Vinuselvi Parisutham
- School of Life Sciences, Ulsan National Institute of Science and Technology, Republic of Korea.
| | - Tae Hyun Kim
- Department of Environmental Engineering, Kongju National University, Republic of Korea.
| | - Sung Kuk Lee
- School of Life Sciences, Ulsan National Institute of Science and Technology, Republic of Korea; School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology, Republic of Korea.
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Blumer-Schuette SE, Brown SD, Sander KB, Bayer EA, Kataeva I, Zurawski JV, Conway JM, Adams MWW, Kelly RM. Thermophilic lignocellulose deconstruction. FEMS Microbiol Rev 2014; 38:393-448. [DOI: 10.1111/1574-6976.12044] [Citation(s) in RCA: 128] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2012] [Revised: 08/20/2013] [Accepted: 08/28/2013] [Indexed: 11/28/2022] Open
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Srirangan K, Akawi L, Liu X, Westbrook A, Blondeel EJM, Aucoin MG, Moo-Young M, Chou CP. Manipulating the sleeping beauty mutase operon for the production of 1-propanol in engineered Escherichia coli. BIOTECHNOLOGY FOR BIOFUELS 2013; 6:139. [PMID: 24074355 PMCID: PMC3850637 DOI: 10.1186/1754-6834-6-139] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/06/2013] [Accepted: 09/24/2013] [Indexed: 06/02/2023]
Abstract
BACKGROUND While most resources in biofuels were directed towards implementing bioethanol programs, 1-propanol has recently received attention as a promising alternative biofuel. Nevertheless, no microorganism has been identified as a natural 1-propanol producer. In this study, we manipulated a novel metabolic pathway for the synthesis of 1-propanol in the genetically tractable bacterium Escherichia coli. RESULTS E. coli strains capable of producing heterologous 1-propanol were engineered by extending the dissimilation of succinate via propionyl-CoA. This was accomplished by expressing a selection of key genes, i.e. (1) three native genes in the sleeping beauty mutase (Sbm) operon, i.e. sbm-ygfD-ygfG from E. coli, (2) the genes encoding bifunctional aldehyde/alcohol dehydrogenases (ADHs) from several microbial sources, and (3) the sucCD gene encoding succinyl-CoA synthetase from E. coli. Using the developed whole-cell biocatalyst under anaerobic conditions, production titers up to 150 mg/L of 1-propanol were obtained. In addition, several genetic and chemical effects on the production of 1-propanol were investigated, indicating that certain host-gene deletions could abolish 1-propanol production as well as that the expression of a putative protein kinase (encoded by ygfD/argK) was crucial for 1-propanol biosynthesis. CONCLUSIONS The study has provided a novel route for 1-propanol production in E. coli, which is subjected to further improvement by identifying limiting conversion steps, shifting major carbon flux to the productive pathway, and optimizing gene expression and culture conditions.
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Affiliation(s)
- Kajan Srirangan
- Department of Chemical Engineering, University of Waterloo, 200 University Avenue West, Waterloo, ON N2L 3G1, Canada
| | - Lamees Akawi
- Department of Chemical Engineering, University of Waterloo, 200 University Avenue West, Waterloo, ON N2L 3G1, Canada
| | - Xuejia Liu
- Department of Chemical Engineering, University of Waterloo, 200 University Avenue West, Waterloo, ON N2L 3G1, Canada
| | - Adam Westbrook
- Department of Chemical Engineering, University of Waterloo, 200 University Avenue West, Waterloo, ON N2L 3G1, Canada
| | - Eric JM Blondeel
- Department of Chemical Engineering, University of Waterloo, 200 University Avenue West, Waterloo, ON N2L 3G1, Canada
| | - Marc G Aucoin
- Department of Chemical Engineering, University of Waterloo, 200 University Avenue West, Waterloo, ON N2L 3G1, Canada
| | - Murray Moo-Young
- Department of Chemical Engineering, University of Waterloo, 200 University Avenue West, Waterloo, ON N2L 3G1, Canada
| | - C Perry Chou
- Department of Chemical Engineering, University of Waterloo, 200 University Avenue West, Waterloo, ON N2L 3G1, Canada
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50
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Noda S, Kawai Y, Miyazaki T, Tanaka T, Kondo A. Creation of endoglucanase-secreting Streptomyces lividans for enzyme production using cellulose as the carbon source. Appl Microbiol Biotechnol 2013; 97:5711-20. [DOI: 10.1007/s00253-013-4880-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2013] [Revised: 03/22/2013] [Accepted: 03/22/2013] [Indexed: 10/26/2022]
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