1
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Wu J, Wu J, He RL, Hu L, Liu DF, Li WW. Modularized Engineering of Shewanella oneidensis MR-1 for Efficient and Directional Synthesis of 5-Aminolevulinic Acid. Metab Eng 2024; 83:206-215. [PMID: 38710300 DOI: 10.1016/j.ymben.2024.05.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Revised: 04/13/2024] [Accepted: 05/03/2024] [Indexed: 05/08/2024]
Abstract
Shewanella oneidensis MR-1 has found widespread applications in pollutant transformation and bioenergy production, closely tied to its outstanding heme synthesis capabilities. However, this significant biosynthetic potential is still unexploited so far. Here, we turned this bacterium into a highly-efficient bio-factory for green synthesis of 5-Aminolevulinic Acid (5-ALA), an important chemical for broad applications in agriculture, medicine, and the food industries. The native C5 pathway genes of S. oneidensis was employed, together with the introduction of foreign anti-oxidation module, to establish the 5-ALA production module, resulting 87-fold higher 5-ALA yield and drastically enhanced tolerance than the wild type. Furthermore, the metabolic flux was regulated by using CRISPR interference and base editing techniques to suppress the competitive pathways to further improve the 5-ALA titer. The engineered strain exhibited 123-fold higher 5-ALA production capability than the wild type. This study not only provides an appealing new route for 5-ALA biosynthesis, but also presents a multi-dimensional modularized engineering strategy to broaden the application scope of S. oneidensis.
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Affiliation(s)
- Jie Wu
- CAS Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Engineering, University of Science & Technology of China, Hefei, 230026, China; Institute of Advanced Technology, University of Science and Technology of China, Hefei, 230000, China
| | - Jing Wu
- School of Life Sciences and Medical Center, University of Science and Technology of China, Hefei, 230026, China
| | - Ru-Li He
- CAS Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Engineering, University of Science & Technology of China, Hefei, 230026, China; Institute of Advanced Technology, University of Science and Technology of China, Hefei, 230000, China
| | - Lan Hu
- School of Life Sciences and Medical Center, University of Science and Technology of China, Hefei, 230026, China
| | - Dong-Feng Liu
- CAS Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Engineering, University of Science & Technology of China, Hefei, 230026, China.
| | - Wen-Wei Li
- CAS Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Engineering, University of Science & Technology of China, Hefei, 230026, China; Institute of Advanced Technology, University of Science and Technology of China, Hefei, 230000, China; School of Life Sciences and Medical Center, University of Science and Technology of China, Hefei, 230026, China.
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2
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Ma Y, Shang Y, Stephanopoulos G. Engineering peroxisomal biosynthetic pathways for maximization of triterpene production in Yarrowia lipolytica. Proc Natl Acad Sci U S A 2024; 121:e2314798121. [PMID: 38261612 PMCID: PMC10835042 DOI: 10.1073/pnas.2314798121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Accepted: 12/20/2023] [Indexed: 01/25/2024] Open
Abstract
Constructing efficient cell factories for product synthesis is frequently hampered by competing pathways and/or insufficient precursor supply. This is particularly evident in the case of triterpenoid biosynthesis in Yarrowia lipolytica, where squalene biosynthesis is tightly coupled to cytosolic biosynthesis of sterols essential for cell viability. Here, we addressed this problem by reconstructing the complete squalene biosynthetic pathway, starting from acetyl-CoA, in the peroxisome, thus harnessing peroxisomal acetyl-CoA pool and sequestering squalene synthesis in this organelle from competing cytosolic reactions. This strategy led to increasing the squalene levels by 1,300-fold relatively to native cytosolic synthesis. Subsequent enhancement of the peroxisomal acetyl-CoA supply by two independent approaches, 1) converting cellular lipid pool to peroxisomal acetyl-CoA and 2) establishing an orthogonal acetyl-CoA shortcut from CO2-derived acetate in the peroxisome, further significantly improved local squalene accumulation. Using these approaches, we constructed squalene-producing strains capable of yielding 32.8 g/L from glucose, and 31.6 g/L from acetate by employing a cofeeding strategy, in bioreactor fermentations. Our findings provide a feasible strategy for protecting intermediate metabolites that can be claimed by multiple reactions by engineering peroxisomes in Y. lipolytica as microfactories for the production of such intermediates and in particular acetyl-CoA-derived metabolites.
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Affiliation(s)
- Yongshuo Ma
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA02142
| | - Yi Shang
- Yunnan Key Laboratory of Potato Biology, Chinese Academy of Agricultural Sciences (CAAS)-Yunnan Normal University (YNNU)-YINMORE Joint Academy of Potato Sciences, Yunnan Normal University, Kunming650500, China
- Engineering Research Center of Sustainable Development and Utilization of Biomass Energy (Ministry of Education), Yunnan Normal University, Kunming650500, China
| | - Gregory Stephanopoulos
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA02142
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3
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Chin WC, Zhou YZ, Wang HY, Feng YT, Yang RY, Huang ZF, Yang YL. Bacterial polyynes uncovered: a journey through their bioactive properties, biosynthetic mechanisms, and sustainable production strategies. Nat Prod Rep 2024. [PMID: 38284321 DOI: 10.1039/d3np00059a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2024]
Abstract
Covering: up to 2023Conjugated polyynes are natural compounds characterized by alternating single and triple carbon-carbon bonds, endowing them with distinct physicochemical traits and a range of biological activities. While traditionally sourced mainly from plants, recent investigations have revealed many compounds originating from bacterial strains. This review synthesizes current research on bacterial-derived conjugated polyynes, delving into their biosynthetic routes, underscoring the variety in their molecular structures, and examining their potential applications in biotechnology. Additionally, we outline future directions for metabolic and protein engineering to establish more robust and stable platforms for their production.
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Affiliation(s)
- Wei-Chih Chin
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan.
- Biotechnology Center in Southern Taiwan, Academia Sinica, Tainan, Taiwan
| | - Yang-Zhi Zhou
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan.
- Biotechnology Center in Southern Taiwan, Academia Sinica, Tainan, Taiwan
| | - Hao-Yung Wang
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan.
- Biotechnology Center in Southern Taiwan, Academia Sinica, Tainan, Taiwan
- Department of Wood Based Materials and Design, National Chiayi University, Chiayi, Taiwan
| | - Yu-Ting Feng
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan.
- Biotechnology Center in Southern Taiwan, Academia Sinica, Tainan, Taiwan
| | - Ru-Yin Yang
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan.
- Biotechnology Center in Southern Taiwan, Academia Sinica, Tainan, Taiwan
| | - Zih-Fang Huang
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan.
- Biotechnology Center in Southern Taiwan, Academia Sinica, Tainan, Taiwan
| | - Yu-Liang Yang
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan.
- Biotechnology Center in Southern Taiwan, Academia Sinica, Tainan, Taiwan
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4
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Du H, Liang Y, Li J, Yuan X, Tao F, Dong C, Shen Z, Sui G, Wang P. Directed Evolution of 4-Hydroxyphenylpyruvate Biosensors Based on a Dual Selection System. Int J Mol Sci 2024; 25:1533. [PMID: 38338812 PMCID: PMC10855707 DOI: 10.3390/ijms25031533] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Revised: 01/12/2024] [Accepted: 01/23/2024] [Indexed: 02/12/2024] Open
Abstract
Biosensors based on allosteric transcription factors have been widely used in synthetic biology. In this study, we utilized the Acinetobacter ADP1 transcription factor PobR to develop a biosensor activating the PpobA promoter when bound to its natural ligand, 4-hydroxybenzoic acid (4HB). To screen for PobR mutants responsive to 4-hydroxyphenylpyruvate(HPP), we developed a dual selection system in E. coli. The positive selection of this system was used to enrich PobR mutants that identified the required ligands. The following negative selection eliminated or weakened PobR mutants that still responded to 4HB. Directed evolution of the PobR library resulted in a variant where PobRW177R was 5.1 times more reactive to 4-hydroxyphenylpyruvate than PobRWT. Overall, we developed an efficient dual selection system for directed evolution of biosensors.
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Affiliation(s)
- Hongxuan Du
- School of Life Science, Northeast Forestry University, Harbin 150040, China; (H.D.); (Y.L.); (J.L.); (F.T.)
- NEFU-China iGEM Team, Northeast Forestry University, Harbin 150040, China;
- Key Laboratory for Enzyme and Enzyme-Like Material Engineering of Heilongjiang, College of Life Science, Northeast Forestry University, Harbin 150040, China
| | - Yaoyao Liang
- School of Life Science, Northeast Forestry University, Harbin 150040, China; (H.D.); (Y.L.); (J.L.); (F.T.)
- NEFU-China iGEM Team, Northeast Forestry University, Harbin 150040, China;
- Key Laboratory for Enzyme and Enzyme-Like Material Engineering of Heilongjiang, College of Life Science, Northeast Forestry University, Harbin 150040, China
| | - Jianing Li
- School of Life Science, Northeast Forestry University, Harbin 150040, China; (H.D.); (Y.L.); (J.L.); (F.T.)
- NEFU-China iGEM Team, Northeast Forestry University, Harbin 150040, China;
| | - Xinyao Yuan
- School of Life Science, Northeast Forestry University, Harbin 150040, China; (H.D.); (Y.L.); (J.L.); (F.T.)
- NEFU-China iGEM Team, Northeast Forestry University, Harbin 150040, China;
| | - Fenglin Tao
- School of Life Science, Northeast Forestry University, Harbin 150040, China; (H.D.); (Y.L.); (J.L.); (F.T.)
- NEFU-China iGEM Team, Northeast Forestry University, Harbin 150040, China;
| | - Chengjie Dong
- NEFU-China iGEM Team, Northeast Forestry University, Harbin 150040, China;
- Aulin College, Northeast Forestry University, Harbin 150040, China
| | - Zekai Shen
- School of Pharmacology, China Pharmaceutical University, Nanjing 210009, China
| | - Guangchao Sui
- School of Life Science, Northeast Forestry University, Harbin 150040, China; (H.D.); (Y.L.); (J.L.); (F.T.)
- NEFU-China iGEM Team, Northeast Forestry University, Harbin 150040, China;
- Key Laboratory for Enzyme and Enzyme-Like Material Engineering of Heilongjiang, College of Life Science, Northeast Forestry University, Harbin 150040, China
- Aulin College, Northeast Forestry University, Harbin 150040, China
| | - Pengchao Wang
- School of Life Science, Northeast Forestry University, Harbin 150040, China; (H.D.); (Y.L.); (J.L.); (F.T.)
- NEFU-China iGEM Team, Northeast Forestry University, Harbin 150040, China;
- Key Laboratory for Enzyme and Enzyme-Like Material Engineering of Heilongjiang, College of Life Science, Northeast Forestry University, Harbin 150040, China
- Aulin College, Northeast Forestry University, Harbin 150040, China
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5
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Effendi SSW, Ng IS. Challenges and opportunities for engineered Escherichia coli as a pivotal chassis toward versatile tyrosine-derived chemicals production. Biotechnol Adv 2023; 69:108270. [PMID: 37852421 DOI: 10.1016/j.biotechadv.2023.108270] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 08/30/2023] [Accepted: 10/11/2023] [Indexed: 10/20/2023]
Abstract
Growing concerns over limited fossil resources and associated environmental problems are motivating the development of sustainable processes for the production of high-volume fuels and high-value-added compounds. The shikimate pathway, an imperative pathway in most microorganisms, is branched with tyrosine as the rate-limiting step precursor of valuable aromatic substances. Such occurrence suggests the shikimate pathway as a promising route in developing microbial cell factories with multiple applications in the nutraceutical, pharmaceutical, and chemical industries. Therefore, an increasing number of studies have focused on this pathway to enable the biotechnological manufacture of pivotal and versatile aromatic products. With advances in genome databases and synthetic biology tools, genetically programmed Escherichia coli strains are gaining immense interest in the sustainable synthesis of chemicals. Engineered E. coli is expected to be the next bio-successor of fossil fuels and plants in commercial aromatics synthesis. This review summarizes successful and applicable genetic and metabolic engineering strategies to generate new chassis and engineer the iterative pathway of the tyrosine route in E. coli, thus addressing the opportunities and current challenges toward the realization of sustainable tyrosine-derived aromatics.
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Affiliation(s)
| | - I-Son Ng
- Department of Chemical Engineering, National Cheng Kung University, Tainan 701, Taiwan.
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6
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Yi X, Rasor BJ, Boadi N, Louie K, Northen TR, Karim AS, Jewett MC, Alper HS. Establishing a versatile toolkit of flux enhanced strains and cell extracts for pathway prototyping. Metab Eng 2023; 80:241-253. [PMID: 37890611 DOI: 10.1016/j.ymben.2023.10.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Revised: 10/07/2023] [Accepted: 10/23/2023] [Indexed: 10/29/2023]
Abstract
Building and optimizing biosynthetic pathways in engineered cells holds promise to address societal needs in energy, materials, and medicine, but it is often time-consuming. Cell-free synthetic biology has emerged as a powerful tool to accelerate design-build-test-learn cycles for pathway engineering with increased tolerance to toxic compounds. However, most cell-free pathway prototyping to date has been performed in extracts from wildtype cells which often do not have sufficient flux towards the pathways of interest, which can be enhanced by engineering. Here, to address this gap, we create a set of engineered Escherichia coli and Saccharomyces cerevisiae strains rewired via CRISPR-dCas9 to achieve high-flux toward key metabolic precursors; namely, acetyl-CoA, shikimate, triose-phosphate, oxaloacetate, α-ketoglutarate, and glucose-6-phosphate. Cell-free extracts generated from these strains are used for targeted enzyme screening in vitro. As model systems, we assess in vivo and in vitro production of triacetic acid lactone from acetyl-CoA and muconic acid from the shikimate pathway. The need for these platforms is exemplified by the fact that muconic acid cannot be detected in wildtype extracts provided with the same biosynthetic enzymes. We also perform metabolomic comparison to understand biochemical differences between the cellular and cell-free muconic acid synthesis systems (E. coli and S. cerevisiae cells and cell extracts with and without metabolic rewiring). While any given pathway has different interfaces with metabolism, we anticipate that this set of pre-optimized, flux enhanced cell extracts will enable prototyping efforts for new biosynthetic pathways and the discovery of biochemical functions of enzymes.
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Affiliation(s)
- Xiunan Yi
- Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX, 78712, USA; McKetta Department of Chemical Engineering, The University of Texas at Austin, Austin, TX, 78712, USA
| | - Blake J Rasor
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, 60208, USA; Chemistry of Life Processes Institute, Northwestern University, Evanston, IL, 60208, USA; Center for Synthetic Biology, Northwestern University, Evanston, IL, 60208, USA
| | - Nathalie Boadi
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, 60208, USA; Chemistry of Life Processes Institute, Northwestern University, Evanston, IL, 60208, USA; Center for Synthetic Biology, Northwestern University, Evanston, IL, 60208, USA
| | - Katherine Louie
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Trent R Northen
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Ashty S Karim
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, 60208, USA; Chemistry of Life Processes Institute, Northwestern University, Evanston, IL, 60208, USA; Center for Synthetic Biology, Northwestern University, Evanston, IL, 60208, USA
| | - Michael C Jewett
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, 60208, USA; Chemistry of Life Processes Institute, Northwestern University, Evanston, IL, 60208, USA; Center for Synthetic Biology, Northwestern University, Evanston, IL, 60208, USA; Department of Bioengineering, Stanford University, Stanford, CA, 94305, USA.
| | - Hal S Alper
- Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX, 78712, USA; McKetta Department of Chemical Engineering, The University of Texas at Austin, Austin, TX, 78712, USA.
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7
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Wang Y, Demirer GS. Synthetic biology for plant genetic engineering and molecular farming. Trends Biotechnol 2023; 41:1182-1198. [PMID: 37012119 DOI: 10.1016/j.tibtech.2023.03.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Revised: 03/03/2023] [Accepted: 03/09/2023] [Indexed: 04/03/2023]
Abstract
Many efforts have been put into engineering plants to improve crop yields and stress tolerance and boost the bioproduction of valuable molecules. Yet, our capabilities are still limited due to the lack of well-characterized genetic building blocks and resources for precise manipulation and given the inherently challenging properties of plant tissues. Advancements in plant synthetic biology can overcome these bottlenecks and release the full potential of engineered plants. In this review, we first discuss the recently developed plant synthetic elements from single parts to advanced circuits, software, and hardware tools expediting the engineering cycle. Next, we survey the advancements in plant biotechnology enabled by these recent resources. We conclude the review with outstanding challenges and future directions of plant synthetic biology.
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Affiliation(s)
- Yunqing Wang
- Department of Bioengineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Gozde S Demirer
- Department of Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA.
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8
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Peña-Castro JM, Muñoz-Páez KM, Robledo-Narvaez PN, Vázquez-Núñez E. Engineering the Metabolic Landscape of Microorganisms for Lignocellulosic Conversion. Microorganisms 2023; 11:2197. [PMID: 37764041 PMCID: PMC10535843 DOI: 10.3390/microorganisms11092197] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Revised: 08/16/2023] [Accepted: 08/18/2023] [Indexed: 09/29/2023] Open
Abstract
Bacteria and yeast are being intensively used to produce biofuels and high-added-value products by using plant biomass derivatives as substrates. The number of microorganisms available for industrial processes is increasing thanks to biotechnological improvements to enhance their productivity and yield through microbial metabolic engineering and laboratory evolution. This is allowing the traditional industrial processes for biofuel production, which included multiple steps, to be improved through the consolidation of single-step processes, reducing the time of the global process, and increasing the yield and operational conditions in terms of the desired products. Engineered microorganisms are now capable of using feedstocks that they were unable to process before their modification, opening broader possibilities for establishing new markets in places where biomass is available. This review discusses metabolic engineering approaches that have been used to improve the microbial processing of biomass to convert the plant feedstock into fuels. Metabolically engineered microorganisms (MEMs) such as bacteria, yeasts, and microalgae are described, highlighting their performance and the biotechnological tools that were used to modify them. Finally, some examples of patents related to the MEMs are mentioned in order to contextualize their current industrial use.
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Affiliation(s)
- Julián Mario Peña-Castro
- Centro de Investigaciones Científicas, Instituto de Biotecnología, Universidad del Papaloapan, Tuxtepec 68301, Oaxaca, Mexico;
| | - Karla M. Muñoz-Páez
- CONAHCYT—Instituto de Ingeniería, Unidad Académica Juriquilla, Universidad Nacional Autónoma de México, Queretaro 76230, Queretaro, Mexico;
| | | | - Edgar Vázquez-Núñez
- Grupo de Investigación Sobre Aplicaciones Nano y Bio Tecnológicas para la Sostenibilidad (NanoBioTS), Departamento de Ingenierías Química, Electrónica y Biomédica, División de Ciencias e Ingenierías, Universidad de Guanajuato, Lomas del Bosque 103, Lomas del Campestre, León 37150, Guanajuato, Mexico
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9
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Sajid S, Mashkoor M, Jørgensen MG, Christensen LP, Hansen PR, Franzyk H, Mirza O, Prabhala BK. The Y-ome Conundrum: Insights into Uncharacterized Genes and Approaches for Functional Annotation. Mol Cell Biochem 2023:10.1007/s11010-023-04827-8. [PMID: 37610616 DOI: 10.1007/s11010-023-04827-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Accepted: 08/09/2023] [Indexed: 08/24/2023]
Abstract
The ever-increasing availability of genome sequencing data has revealed a substantial number of uncharacterized genes without known functions across various organisms. The first comprehensive genome sequencing of E. coli K12 revealed that more than 50% of its open reading frames corresponded to transcripts with no known functions. The group of protein-coding genes without a functional description and/or a recognized pathway, beginning with the letter "Y", is classified as the "y-ome". Several efforts have been made to elucidate the functions of these genes and to recognize their role in biological processes. This review provides a brief update on various strategies employed when studying the y-ome, such as high-throughput experimental approaches, comparative omics, metabolic engineering, gene expression analysis, and data integration techniques. Additionally, we highlight recent advancements in functional annotation methods, including the use of machine learning, network analysis, and functional genomics approaches. Novel approaches are required to produce more precise functional annotations across the genome to reduce the number of genes with unknown functions.
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Affiliation(s)
- Salvia Sajid
- Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, 2100, Copenhagen Ø, Denmark
- Department of Physics, Chemistry, and Pharmacy, University of Southern Denmark, Campusvej 55, 5230, Odense M, Denmark
| | - Maliha Mashkoor
- Department of Surgery, Center for Surgical Sciences, Zealand University Hospital, Lykkebækvej 1, 4600, Køge, Denmark
| | - Mikkel Girke Jørgensen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, 5230, Odense M, Denmark
| | - Lars Porskjær Christensen
- Department of Physics, Chemistry, and Pharmacy, University of Southern Denmark, Campusvej 55, 5230, Odense M, Denmark
| | - Paul Robert Hansen
- Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, 2100, Copenhagen Ø, Denmark
| | - Henrik Franzyk
- Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, 2100, Copenhagen Ø, Denmark
| | - Osman Mirza
- Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, 2100, Copenhagen Ø, Denmark
| | - Bala Krishna Prabhala
- Department of Physics, Chemistry, and Pharmacy, University of Southern Denmark, Campusvej 55, 5230, Odense M, Denmark.
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10
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Sugianto W, Altin-Yavuzarslan G, Tickman BI, Kiattisewee C, Yuan SF, Brooks SM, Wong J, Alper HS, Nelson A, Carothers JM. Gene expression dynamics in input-responsive engineered living materials programmed for bioproduction. Mater Today Bio 2023; 20:100677. [PMID: 37273790 PMCID: PMC10239009 DOI: 10.1016/j.mtbio.2023.100677] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Revised: 05/14/2023] [Accepted: 05/19/2023] [Indexed: 06/06/2023] Open
Abstract
Engineered living materials (ELMs) fabricated by encapsulating microbes in hydrogels have great potential as bioreactors for sustained bioproduction. While long-term metabolic activity has been demonstrated in these systems, the capacity and dynamics of gene expression over time is not well understood. Thus, we investigate the long-term gene expression dynamics in microbial ELMs constructed using different microbes and hydrogel matrices. Through direct gene expression measurements of engineered E. coli in F127-bisurethane methacrylate (F127-BUM) hydrogels, we show that inducible, input-responsive genetic programs in ELMs can be activated multiple times and maintained for multiple weeks. Interestingly, the encapsulated bacteria sustain inducible gene expression almost 10 times longer than free-floating, planktonic cells. These ELMs exhibit dynamic responsiveness to repeated induction cycles, with up to 97% of the initial gene expression capacity retained following a subsequent induction event. We demonstrate multi-week bioproduction cycling by implementing inducible CRISPR transcriptional activation (CRISPRa) programs that regulate the expression of enzymes in a pteridine biosynthesis pathway. ELMs fabricated from engineered S. cerevisiae in bovine serum albumin (BSA) - polyethylene glycol diacrylate (PEGDA) hydrogels were programmed to express two different proteins, each under the control of a different chemical inducer. We observed scheduled bioproduction switching between betaxanthin pigment molecules and proteinase A in S. cerevisiae ELMs over the course of 27 days under continuous cultivation. Overall, these results suggest that the capacity for long-term genetic expression may be a general property of microbial ELMs. This work establishes approaches for implementing dynamic, input-responsive genetic programs to tailor ELM functions for a wide range of advanced applications.
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Affiliation(s)
- Widianti Sugianto
- Department of Chemical Engineering, University of Washington, Seattle, WA, 98195, United States
- Molecular Engineering & Sciences Institute, University of Washington, Seattle, WA, 98195, United States
- Center for Synthetic Biology, University of Washington, Seattle, WA, 98195, United States
| | - Gokce Altin-Yavuzarslan
- Molecular Engineering & Sciences Institute, University of Washington, Seattle, WA, 98195, United States
- Department of Chemistry, University of Washington, Seattle, WA, 98195, United States
| | - Benjamin I. Tickman
- Department of Chemical Engineering, University of Washington, Seattle, WA, 98195, United States
- Molecular Engineering & Sciences Institute, University of Washington, Seattle, WA, 98195, United States
- Center for Synthetic Biology, University of Washington, Seattle, WA, 98195, United States
| | - Cholpisit Kiattisewee
- Molecular Engineering & Sciences Institute, University of Washington, Seattle, WA, 98195, United States
- Center for Synthetic Biology, University of Washington, Seattle, WA, 98195, United States
| | - Shuo-Fu Yuan
- Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX, 78712, United States
| | - Sierra M. Brooks
- McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, TX, 78712, United States
| | - Jitkanya Wong
- Department of Chemistry, University of Washington, Seattle, WA, 98195, United States
| | - Hal S. Alper
- Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX, 78712, United States
- McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, TX, 78712, United States
| | - Alshakim Nelson
- Molecular Engineering & Sciences Institute, University of Washington, Seattle, WA, 98195, United States
- Department of Chemistry, University of Washington, Seattle, WA, 98195, United States
| | - James M. Carothers
- Department of Chemical Engineering, University of Washington, Seattle, WA, 98195, United States
- Molecular Engineering & Sciences Institute, University of Washington, Seattle, WA, 98195, United States
- Center for Synthetic Biology, University of Washington, Seattle, WA, 98195, United States
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11
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Zhu J, Wang S, Wang C, Wang Z, Luo G, Li J, Zhan Y, Cai D, Chen S. Microbial synthesis of bacitracin: Recent progress, challenges, and prospects. Synth Syst Biotechnol 2023; 8:314-322. [PMID: 37122958 PMCID: PMC10130698 DOI: 10.1016/j.synbio.2023.03.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2023] [Revised: 03/12/2023] [Accepted: 03/23/2023] [Indexed: 05/02/2023] Open
Abstract
Microorganisms are important sources of various natural products that have been commercialized for human medicine and animal healthcare. Bacitracin is an important antibacterial natural product predominantly produced by Bacillus licheniformis and Bacillus subtilis, and it is characterized by a broad antimicrobial spectrum, strong activity and low resistance, thus bacitracin is extensively applied in animal feed and veterinary medicine industries. In recent years, various strategies have been proposed to improve bacitracin production. Herein, we systematically describe the regulation of bacitracin biosynthesis in genus Bacillus and its associated mechanism, to provide a theoretical basis for bacitracin overproduction. The metabolic engineering strategies applied for bacitracin production are explored, including improving substrate utilization, using an enlarged precursor amino acid pool, increasing ATP supply and NADPH generation, and engineering transcription regulators. We also present several approaches of fermentation process optimization to facilitate the industrial large-scale production of bacitracin. Finally, the challenges and prospects associated with microbial bacitracin synthesis are discussed to facilitate the establishment of high-yield and low-cost biological factories.
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Affiliation(s)
- Jiang Zhu
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Environmental Microbial Technology Center of Hubei Province, College of Life Sciences, Hubei University, Wuhan, 430062, PR China
| | - Shiyi Wang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Environmental Microbial Technology Center of Hubei Province, College of Life Sciences, Hubei University, Wuhan, 430062, PR China
| | - Cheng Wang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Environmental Microbial Technology Center of Hubei Province, College of Life Sciences, Hubei University, Wuhan, 430062, PR China
| | - Zhi Wang
- Hubei Provincial Key Laboratory of Industrial Microbiology, Key Laboratory of Fermentation Engineering (Ministry of Education), School of Food and Biological Engineering, Hubei University of Technology, Wuhan, 430068, Hubei, PR China
| | - Gan Luo
- Lifecome Biochemistry Co. Ltd, Nanping, 353400, PR China
| | - Junhui Li
- Lifecome Biochemistry Co. Ltd, Nanping, 353400, PR China
| | - Yangyang Zhan
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Environmental Microbial Technology Center of Hubei Province, College of Life Sciences, Hubei University, Wuhan, 430062, PR China
| | - Dongbo Cai
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Environmental Microbial Technology Center of Hubei Province, College of Life Sciences, Hubei University, Wuhan, 430062, PR China
- Corresponding author.
| | - Shouwen Chen
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Environmental Microbial Technology Center of Hubei Province, College of Life Sciences, Hubei University, Wuhan, 430062, PR China
- Corresponding author. 368 Youyi Avenue, Wuchang District, Wuhan, 430062, Hubei, PR China.
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12
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Sun J, Zhu Z, Lin Q, Qi S, Li Q, Zhou Y, Li R. Metabolic Engineering of Escherichia coli for the Biosynthesis of 3-Phenylpropionic Acid and 3-Phenylpropyl Acetate. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:7451-7458. [PMID: 37146254 DOI: 10.1021/acs.jafc.3c00330] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
3-Phenylpropionic acid (3PPA) and its derivative 3-phenylpropyl acetate (3PPAAc) are important aromatic compounds with broad applications in the cosmetics and food industries. In this study, we constructed a plasmid-free 3PPA-producing Escherichia coli strain and designed a novel 3PPAAc biosynthetic pathway. A module containing tyrosine ammonia lyase and enoate reductase, evaluated under the control of different promoters, was combined with phenylalanine-overproducing strain E. coli ATCC31884, enabling the plasmid-free de novo production of 218.16 ± 43.62 mg L-1 3PPA. The feasibility of the pathway was proved by screening four heterologous alcohol acetyltransferases, which catalyzed the transformation of 3-phenylpropyl alcohol into 3PPAAc. Afterward, 94.59 ± 16.25 mg L-1 3PPAAc was achieved in the engineered E. coli strain. Overall, we have not only demonstrated the potential of de novo synthesis of 3PPAAc in microbes for the first time but also provided a platform for the future of biosynthesis of other aromatic compounds.
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Affiliation(s)
- Jing Sun
- The Key Laboratory of Biotechnology for Medicinal Plants of Jiangsu Province, School of Life Sciences, Jiangsu Normal University, Xuzhou 221116, China
| | - Zhi Zhu
- The Key Laboratory of Biotechnology for Medicinal Plants of Jiangsu Province, School of Life Sciences, Jiangsu Normal University, Xuzhou 221116, China
| | - Qingfang Lin
- The Key Laboratory of Biotechnology for Medicinal Plants of Jiangsu Province, School of Life Sciences, Jiangsu Normal University, Xuzhou 221116, China
| | - Shilian Qi
- The Key Laboratory of Biotechnology for Medicinal Plants of Jiangsu Province, School of Life Sciences, Jiangsu Normal University, Xuzhou 221116, China
| | - Qianqian Li
- The Key Laboratory of Biotechnology for Medicinal Plants of Jiangsu Province, School of Life Sciences, Jiangsu Normal University, Xuzhou 221116, China
| | - Yang Zhou
- The Key Laboratory of Biotechnology for Medicinal Plants of Jiangsu Province, School of Life Sciences, Jiangsu Normal University, Xuzhou 221116, China
| | - Rongpeng Li
- The Key Laboratory of Biotechnology for Medicinal Plants of Jiangsu Province, School of Life Sciences, Jiangsu Normal University, Xuzhou 221116, China
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13
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Bowman EK, Nguyen Hoang PT, Gordillo Sierra AR, Vieira Nogueira KM, Alper HS. Temporal sorting of microdroplets can identify productivity differences of itaconic acid from libraries of Yarrowia lipolytica. LAB ON A CHIP 2023; 23:2249-2256. [PMID: 37013836 DOI: 10.1039/d3lc00020f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Microdroplet screening of microorganisms can improve the rate of strain selection and characterization within the canonical design-build-test paradigm. However, a full analysis of the microdroplet environment and how well these conditions translate to culturing conditions and techniques is lacking in the field. Quantification of three different biosensor/analyte combinations at 12 hour timepoints reveals the potential for extended dose-response ranges as compared to traditional in vitro conditions. Using these dynamics, we present an application and analysis of microfluidic droplet screening utilizing whole-cell biosensors, ultimately identifying an altered productivity profile of itaconic acid in a Yarrowia lipolytica-based piggyBac transposon library. Specifically, we demonstrate that the timepoint for microdroplet selection can influence the outcome of the selection and thus shift the identified strain productivity and final titer. In this case, strains selected at earlier timepoints showed increased early productivity in flask scale, with the converse true as well. Differences in response indicate microdroplet assays require tailored development to more accurately sort for phenotypes that are scalable to larger incubation volumes. Likewise, these results further highlight that screening conditions are critical parameters for success in high-throughput applications.
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Affiliation(s)
- Emily K Bowman
- Interdisciplinary Life Sciences Graduate Program, The University of Texas at Austin, Austin, TX 78712, USA.
| | | | - Angela R Gordillo Sierra
- McKetta Department of Chemical Engineering, The University of Texas at Austin, Austin, TX 78712, USA
| | - Karoline M Vieira Nogueira
- Molecular Biotechnology Laboratory, Department of Biochemistry and Immunology, Ribeirao Preto Medical School (FMRP), University of Sao Paulo, Ribeirao Preto, SP, Brazil
| | - Hal S Alper
- Interdisciplinary Life Sciences Graduate Program, The University of Texas at Austin, Austin, TX 78712, USA.
- McKetta Department of Chemical Engineering, The University of Texas at Austin, Austin, TX 78712, USA
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14
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Yuan Q, Wu M, Liao Y, Liang S, Lu Y, Lin Y. Rapid prototyping enzyme homologs to improve titer of nicotinamide mononucleotide using a strategy combining cell-free protein synthesis with split GFP. Biotechnol Bioeng 2023; 120:1133-1146. [PMID: 36585353 DOI: 10.1002/bit.28326] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2022] [Revised: 12/18/2022] [Accepted: 12/29/2022] [Indexed: 01/01/2023]
Abstract
Engineering biological systems to test new pathway variants containing different enzyme homologs is laborious and time-consuming. To tackle this challenge, a strategy was developed for rapidly prototyping enzyme homologs by combining cell-free protein synthesis (CFPS) with split green fluorescent protein (GFP). This strategy featured two main advantages: (1) dozens of enzyme homologs were parallelly produced by CFPS within hours, and (2) the expression level and activity of each homolog was determined simultaneously by using the split GFP assay. As a model, this strategy was applied to optimize a 3-step pathway for nicotinamide mononucleotide (NMN) synthesis. Ten enzyme homologs from different organisms were selected for each step. Here, the most productive homolog of each step was identified within 24 h rather than weeks or months. Finally, the titer of NMN was increased to 1213 mg/L by improving physiochemical conditions, tuning enzyme ratios and cofactor concentrations, and decreasing the feedback inhibition, which was a more than 12-fold improvement over the initial setup. This strategy would provide a promising way to accelerate design-build-test cycles for metabolic engineering to improve the production of desired products.
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Affiliation(s)
- Qingyan Yuan
- Guangdong Key Laboratory of Fermentation and Enzyme Engineering, Guangdong Research Center of Industrial Enzyme and Green Manufacturing Technology, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| | - Minhui Wu
- Guangdong Key Laboratory of Fermentation and Enzyme Engineering, Guangdong Research Center of Industrial Enzyme and Green Manufacturing Technology, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| | - Yibo Liao
- Guangdong Key Laboratory of Fermentation and Enzyme Engineering, Guangdong Research Center of Industrial Enzyme and Green Manufacturing Technology, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| | - Shuli Liang
- Guangdong Key Laboratory of Fermentation and Enzyme Engineering, Guangdong Research Center of Industrial Enzyme and Green Manufacturing Technology, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| | - Yuan Lu
- Key Laboratory of Industrial Biocatalysis, Ministry of Education, Department of Chemical Engineering, Tsinghua University, Beijing, China
| | - Ying Lin
- Guangdong Key Laboratory of Fermentation and Enzyme Engineering, Guangdong Research Center of Industrial Enzyme and Green Manufacturing Technology, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
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15
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Cheng Y, Bi X, Xu Y, Liu Y, Li J, Du G, Lv X, Liu L. Machine learning for metabolic pathway optimization: A review. Comput Struct Biotechnol J 2023; 21:2381-2393. [PMID: 38213889 PMCID: PMC10781721 DOI: 10.1016/j.csbj.2023.03.045] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 03/24/2023] [Accepted: 03/25/2023] [Indexed: 03/29/2023] Open
Abstract
Optimizing the metabolic pathways of microbial cell factories is essential for establishing viable biotechnological production processes. However, due to the limited understanding of the complex setup of cellular machinery, building efficient microbial cell factories remains tedious and time-consuming. Machine learning (ML), a powerful tool capable of identifying patterns within large datasets, has been used to analyze biological datasets generated using various high-throughput technologies to build data-driven models for complex bioprocesses. In addition, ML can also be integrated with Design-Build-Test-Learn to accelerate development. This review focuses on recent ML applications in genome-scale metabolic model construction, multistep pathway optimization, rate-limiting enzyme engineering, and gene regulatory element designing. In addition, we have discussed some limitations of these methods as well as potential solutions.
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Affiliation(s)
- Yang Cheng
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
- Science Center for Future Foods, Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Xinyu Bi
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
- Science Center for Future Foods, Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Yameng Xu
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
- Science Center for Future Foods, Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Yanfeng Liu
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
- Science Center for Future Foods, Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Jianghua Li
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
- Science Center for Future Foods, Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Guocheng Du
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
- Science Center for Future Foods, Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Xueqin Lv
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
- Science Center for Future Foods, Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Long Liu
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
- Science Center for Future Foods, Ministry of Education, Jiangnan University, Wuxi 214122, China
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16
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Santos-Merino M, Yun L, Ducat DC. Cyanobacteria as cell factories for the photosynthetic production of sucrose. Front Microbiol 2023; 14:1126032. [PMID: 36865782 PMCID: PMC9971976 DOI: 10.3389/fmicb.2023.1126032] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2022] [Accepted: 01/24/2023] [Indexed: 02/16/2023] Open
Abstract
Biofuels and other biologically manufactured sustainable goods are growing in popularity and demand. Carbohydrate feedstocks required for industrial fermentation processes have traditionally been supplied by plant biomass, but the large quantities required to produce replacement commodity products may prevent the long-term feasibility of this approach without alternative strategies to produce sugar feedstocks. Cyanobacteria are under consideration as potential candidates for sustainable production of carbohydrate feedstocks, with potentially lower land and water requirements relative to plants. Several cyanobacterial strains have been genetically engineered to export significant quantities of sugars, especially sucrose. Sucrose is not only naturally synthesized and accumulated by cyanobacteria as a compatible solute to tolerate high salt environments, but also an easily fermentable disaccharide used by many heterotrophic bacteria as a carbon source. In this review, we provide a comprehensive summary of the current knowledge of the endogenous cyanobacterial sucrose synthesis and degradation pathways. We also summarize genetic modifications that have been found to increase sucrose production and secretion. Finally, we consider the current state of synthetic microbial consortia that rely on sugar-secreting cyanobacterial strains, which are co-cultivated alongside heterotrophic microbes able to directly convert the sugars into higher-value compounds (e.g., polyhydroxybutyrates, 3-hydroxypropionic acid, or dyes) in a single-pot reaction. We summarize recent advances reported in such cyanobacteria/heterotroph co-cultivation strategies and provide a perspective on future developments that are likely required to realize their bioindustrial potential.
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Affiliation(s)
- María Santos-Merino
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, MI, United States
| | - Lisa Yun
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, MI, United States
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, United States
| | - Daniel C. Ducat
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, MI, United States
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, United States
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17
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Kang CK, Shin J, Cha Y, Kim MS, Choi MS, Kim T, Park YK, Choi YJ. Machine learning-guided prediction of potential engineering targets for microbial production of lycopene. BIORESOURCE TECHNOLOGY 2023; 369:128455. [PMID: 36503092 DOI: 10.1016/j.biortech.2022.128455] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Revised: 12/02/2022] [Accepted: 12/04/2022] [Indexed: 06/17/2023]
Abstract
The process of designing streamlined workflows for developing microbial strains using classical methods from vast amounts of biological big data has reached its limits. With the continuous increase in the amount of biological big data, data-driven machine learning approaches are being used to overcome the limits of classical approaches for strain development. Here, machine learning-guided engineering of Deinococcus radiodurans R1 for high-yield production of lycopene was demonstrated. The multilayer perceptron models were first trained using the mRNA expression levels of the key genes along with lycopene titers and yields obtained from 17 strains. Then, the potential overexpression targets from 2,047 possible combinations were predicted by the multilayer perceptron combined with a genetic algorithm. Through the machine learning-aided fine-tuning of the predicted genes, the final-engineered LY04 strain resulted in an 8-fold increase in the lycopene production, up to 1.25 g/L from glycerol, and a 6-fold increase in the lycopene yield.
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Affiliation(s)
- Chang Keun Kang
- School of Environmental Engineering, University of Seoul, Seoul 02504, Republic of Korea
| | - Jihoon Shin
- School of Environmental Engineering, University of Seoul, Seoul 02504, Republic of Korea
| | - YoonKyung Cha
- School of Environmental Engineering, University of Seoul, Seoul 02504, Republic of Korea
| | - Min Sun Kim
- School of Environmental Engineering, University of Seoul, Seoul 02504, Republic of Korea
| | - Min Sun Choi
- School of Environmental Engineering, University of Seoul, Seoul 02504, Republic of Korea
| | - TaeHo Kim
- School of Environmental Engineering, University of Seoul, Seoul 02504, Republic of Korea
| | - Young-Kwon Park
- School of Environmental Engineering, University of Seoul, Seoul 02504, Republic of Korea
| | - Yong Jun Choi
- School of Environmental Engineering, University of Seoul, Seoul 02504, Republic of Korea.
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18
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Lu YA, Brien CMO, Mashek DG, Hu WS, Zhang Q. Kinetic-model-based pathway optimization with application to reverse glycolysis in mammalian cells. Biotechnol Bioeng 2023; 120:216-229. [PMID: 36184902 DOI: 10.1002/bit.28249] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2022] [Revised: 09/19/2022] [Accepted: 09/28/2022] [Indexed: 12/13/2022]
Abstract
Over the last two decades, model-based metabolic pathway optimization tools have been developed for the design of microorganisms to produce desired metabolites. However, few have considered more complex cellular systems such as mammalian cells, which requires the use of nonlinear kinetic models to capture the effects of concentration changes and cross-regulatory interactions. In this study, we develop a new two-stage pathway optimization framework based on kinetic models that incorporate detailed kinetics and regulation information. In Stage 1, a set of optimization problems are solved to identify and rank the enzymes that contribute the most to achieving the metabolic objective. Stage 2 then determines the optimal enzyme interventions for specified desired numbers of enzyme adjustments. It also incorporates multi-scenario optimization, which allows the simultaneous consideration of multiple physiological conditions. We apply the proposed framework to find enzyme adjustments that enable a reverse glucose flow in cultured mammalian cells, thereby eliminating the need for glucose feed in the late culture stage and enhancing process robustness. The computational results demonstrate the efficacy of the proposed approach; it not only captures the important regulations and key enzymes for reverse glycolysis but also identifies differences and commonalities in the metabolic requirements for different carbon sources.
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Affiliation(s)
- Yen-An Lu
- Department of Chemical Engineering and Materials Science, University of Minnesota, Minneapolis, Minnesota, USA
| | - Conor M O' Brien
- Department of Chemical Engineering and Materials Science, University of Minnesota, Minneapolis, Minnesota, USA
| | - Douglas G Mashek
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota, USA
| | - Wei-Shou Hu
- Department of Chemical Engineering and Materials Science, University of Minnesota, Minneapolis, Minnesota, USA
| | - Qi Zhang
- Department of Chemical Engineering and Materials Science, University of Minnesota, Minneapolis, Minnesota, USA
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19
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Metabolic engineering of Rhodotorula toruloides for resveratrol production. Microb Cell Fact 2022; 21:270. [PMID: 36566171 PMCID: PMC9789595 DOI: 10.1186/s12934-022-02006-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Accepted: 12/17/2022] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND Resveratrol is a plant-derived phenylpropanoid with diverse biological activities and pharmacological applications. Plant-based extraction could not satisfy ever-increasing market demand, while chemical synthesis is impeded by the existence of toxic impurities. Microbial production of resveratrol offers a promising alternative to plant- and chemical-based processes. The non-conventional oleaginous yeast Rhodotorula toruloides is a potential workhorse for the production of resveratrol that endowed with an efficient and intrinsic bifunctional phenylalanine/tyrosine ammonia-lyase (RtPAL) and malonyl-CoA pool, which may facilitate the resveratrol synthesis when properly rewired. RESULTS Resveratrol showed substantial stability and would not affect the R. toruloides growth during the yeast cultivation in flasks. The heterologus resveratrol biosynthesis pathway was established by introducing the 4-coumaroyl-CoA ligase (At4CL), and the stilbene synthase (VlSTS) from Arabidopsis thaliana and Vitis labrusca, respectively. Next, The resveratrol production was increased by 634% through employing the cinnamate-4-hydroxylase from A. thaliana (AtC4H), the fused protein At4CL::VlSTS, the cytochrome P450 reductase 2 from A. thaliana (AtATR2) and the endogenous cytochrome B5 of R. toruloides (RtCYB5). Then, the related endogenous pathways were optimized to affect a further 60% increase. Finally, the engineered strain produced a maximum titer of 125.2 mg/L resveratrol in YPD medium. CONCLUSION The non-conventional oleaginous yeast R. toruloides was engineered for the first time to produce resveratrol. Protein fusion, co-factor channeling, and ARO4 and ARO7 overexpression were efficient for improving resveratrol production. The results demonstrated the potential of R. toruloides for resveratrol and other phenylpropanoids production.
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20
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Kozaeva E, Nieto-Domínguez M, Hernández AD, Nikel PI. Synthetic metabolism for in vitro acetone biosynthesis driven by ATP regeneration. RSC Chem Biol 2022; 3:1331-1341. [PMID: 36349222 PMCID: PMC9627730 DOI: 10.1039/d2cb00170e] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Accepted: 09/15/2022] [Indexed: 05/14/2024] Open
Abstract
In vitro ketone production continues to be a challenge due to the biochemical features of the enzymes involved-even when some of them have been extensively characterized (e.g. thiolase from Clostridium acetobutylicum), the assembly of synthetic enzyme cascades still face significant limitations (including issues with protein aggregation and multimerization). Here, we designed and assembled a self-sustaining enzyme cascade with acetone yields close to the theoretical maximum using acetate as the only carbon input. The efficiency of this system was further boosted by coupling the enzymatic sequence to a two-step ATP-regeneration system that enables continuous, cost-effective acetone biosynthesis. Furthermore, simple methods were implemented for purifying the enzymes necessary for this synthetic metabolism, including a first-case example on the isolation of a heterotetrameric acetate:coenzyme A transferase by affinity chromatography.
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Affiliation(s)
- Ekaterina Kozaeva
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark 2800 Kongens Lyngby Denmark +93 51 19 18
| | - Manuel Nieto-Domínguez
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark 2800 Kongens Lyngby Denmark +93 51 19 18
| | - Abril D Hernández
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark 2800 Kongens Lyngby Denmark +93 51 19 18
| | - Pablo I Nikel
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark 2800 Kongens Lyngby Denmark +93 51 19 18
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21
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Chen S, Lu Y, Wang W, Hu Y, Wang J, Tang S, Lin CSK, Yang X. Efficient production of the β-ionone aroma compound from organic waste hydrolysates using an engineered Yarrowia lipolytica strain. Front Microbiol 2022; 13:960558. [PMID: 36212878 PMCID: PMC9532697 DOI: 10.3389/fmicb.2022.960558] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Accepted: 09/07/2022] [Indexed: 11/16/2022] Open
Abstract
This study demonstrates the feasibility of establishing a natural compound supply chain in a biorefinery. The process starts with the biological or chemical hydrolysis of food and agricultural waste into simple and fermentative sugars, followed by their fermentation into more complex molecules. The yeast strain, Yarrowia lipolytica, was modified by introducing high membrane affinity variants of the carotenoid cleavage dioxygenase enzyme, PhCCD1, to increase the production of the aroma compound, β-ionone. The initial hydrolysis process converted food waste or sugarcane bagasse into nutrient-rich hydrolysates containing 78.4 g/L glucose and 8.3 g/L fructose, or 34.7 g/L glucose and 20.1 g/L xylose, respectively. During the next step, engineered Y. lipolytica strains were used to produce β-ionone from these feedstocks. The yeast strain YLBI3120, carrying a modified PhCCD1 gene was able to produce 4 g/L of β-ionone with a productivity of 13.9 mg/L/h from food waste hydrolysate. This is the highest yield reported for the fermentation of this compound to date. The integrated process described in this study could be scaled up to achieve economical large-scale conversion of inedible food and agricultural waste into valuable aroma compounds for a wide range of potential applications.
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Affiliation(s)
- Shuyi Chen
- Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, Guangdong, China
| | - Yanping Lu
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, Guangdong, China
- Technology Research Center, Wuliangye Yibin Company Limited, Yibin, Sichuan, China
- Postdoctoral Research Workstation, Sichuan Yibin Wuliangye Group Company Limited, Yibin, Sichuan, China
| | - Wen Wang
- Guangzhou Institute of Energy Conversion, Chinese Academy of Sciences (CAS), Guangzhou, Guangdong, China
| | - Yunzi Hu
- Guangzhou Institute of Energy Conversion, Chinese Academy of Sciences (CAS), Guangzhou, Guangdong, China
| | - Jufang Wang
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, Guangdong, China
| | - Shixing Tang
- Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, Guangdong, China
| | - Carol Sze Ki Lin
- School of Energy and Environment, City University of Hong Kong, Kowloon, Hong Kong SAR, China
| | - Xiaofeng Yang
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, Guangdong, China
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22
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Luo Z, Pan F, Zhu Y, Du S, Yan Y, Wang R, Li S, Xu H. Synergistic Improvement of 5-Aminolevulinic Acid Production with Synthetic Scaffolds and System Pathway Engineering. ACS Synth Biol 2022; 11:2766-2778. [PMID: 35939037 DOI: 10.1021/acssynbio.2c00157] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Engineered synthetic scaffolds to organize metabolic pathway enzymes and system pathway engineering to fine-tune metabolic fluxes play essential roles in microbial production. Here, we first obtained the most favorable combination of key enzymes for 5-aminolevulinic acid (5-ALA) synthesis through the C5 pathway by screening enzymes from different sources and optimizing their combination in different pathways. Second, we successfully constructed a multienzyme complex assembly system with PduA*, which spatially recruits the above three key enzymes for 5-ALA synthesis in a designable manner. By further optimizing the ratio of these key enzymes in synthetic scaffolds, the efficiency of 5-ALA synthesis through the C5 pathway was significantly improved. Then, the competitive metabolism pathway was fine-tuned by rationally designing different antisense RNAs, further significantly increasing 5-ALA titers. Furthermore, for efficient 5-ALA synthesis, obstacles of NADH and NADPH imbalances and feedback inhibition of the synthesis pathway were also overcome through engineering the NADPH regeneration pathway and transport pathway, respectively. Finally, combining these strategies with further fermentation optimization, we achieved a final 5-ALA titer of 11.4 g/L. These results highlight the importance of synthetic scaffolds and system pathway engineering to improve the microbial cell factory production performance.
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Affiliation(s)
- Zhengshan Luo
- State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing Tech University, Nanjing 211816, China.,College of Food Science and Light Industry, Nanjing Tech University, Nanjing 211816, China
| | - Fei Pan
- State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing Tech University, Nanjing 211816, China.,College of Food Science and Light Industry, Nanjing Tech University, Nanjing 211816, China
| | - Yifan Zhu
- State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing Tech University, Nanjing 211816, China.,College of Food Science and Light Industry, Nanjing Tech University, Nanjing 211816, China
| | - Shanshan Du
- State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing Tech University, Nanjing 211816, China.,College of Food Science and Light Industry, Nanjing Tech University, Nanjing 211816, China
| | - Yifan Yan
- State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing Tech University, Nanjing 211816, China.,College of Food Science and Light Industry, Nanjing Tech University, Nanjing 211816, China
| | - Rui Wang
- State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing Tech University, Nanjing 211816, China.,College of Food Science and Light Industry, Nanjing Tech University, Nanjing 211816, China
| | - Sha Li
- State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing Tech University, Nanjing 211816, China.,College of Food Science and Light Industry, Nanjing Tech University, Nanjing 211816, China
| | - Hong Xu
- State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing Tech University, Nanjing 211816, China.,College of Food Science and Light Industry, Nanjing Tech University, Nanjing 211816, China
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23
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Fenton DA, Kiniry SJ, Yordanova MM, Baranov PV, Morrissey JP. Development of a ribosome profiling protocol to study translation in Kluyveromyces marxianus. FEMS Yeast Res 2022; 22:foac024. [PMID: 35521744 PMCID: PMC9246280 DOI: 10.1093/femsyr/foac024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 04/17/2022] [Accepted: 05/04/2022] [Indexed: 11/27/2022] Open
Abstract
Kluyveromyces marxianus is an interesting and important yeast because of particular traits such as thermotolerance and rapid growth, and for applications in food and industrial biotechnology. For both understanding its biology and developing bioprocesses, it is important to understand how K. marxianus responds and adapts to changing environments. For this, a full suite of omics tools to measure and compare global patterns of gene expression and protein synthesis is needed. We report here the development of a ribosome profiling method for K. marxianus, which allows codon resolution of translation on a genome-wide scale by deep sequencing of ribosome locations on mRNAs. To aid in the analysis and sharing of ribosome profiling data, we added the K. marxianus genome as well as transcriptome and ribosome profiling data to the publicly accessible GWIPS-viz and Trips-Viz browsers. Users are able to upload custom ribosome profiling and RNA-Seq data to both browsers, therefore allowing easy analysis and sharing of data. We also provide a set of step-by-step protocols for the experimental and bioinformatic methods that we developed.
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Affiliation(s)
- Darren A Fenton
- School of Biochemistry and Cell Biology, University College Cork, Cork, T12 XF62, Ireland
- School of Microbiology, Environmental Research Institute, APC Microbiome Institute, SUSFERM Fermentation Science Centre, University College Cork, Cork T12 K8AF, Ireland
| | - Stephen J Kiniry
- School of Biochemistry and Cell Biology, University College Cork, Cork, T12 XF62, Ireland
| | - Martina M Yordanova
- School of Biochemistry and Cell Biology, University College Cork, Cork, T12 XF62, Ireland
| | - Pavel V Baranov
- School of Biochemistry and Cell Biology, University College Cork, Cork, T12 XF62, Ireland
| | - John P Morrissey
- School of Microbiology, Environmental Research Institute, APC Microbiome Institute, SUSFERM Fermentation Science Centre, University College Cork, Cork T12 K8AF, Ireland
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24
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Woodley JM. Ensuring the Sustainability of Biocatalysis. CHEMSUSCHEM 2022; 15:e202102683. [PMID: 35084801 DOI: 10.1002/cssc.202102683] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 01/20/2022] [Indexed: 06/14/2023]
Abstract
Biocatalysis offers many attractive features for the synthetic chemist. In many cases, the high selectivity and ability to tailor specific enzyme features via protein engineering already make it the catalyst of choice. From the perspective of sustainability, several features such as catalysis under mild conditions and use of a renewable and biodegradable catalyst also look attractive. Nevertheless, to be sustainable at a larger scale it will be essential to develop processes operating at far higher concentrations of product, and which make better use of the enzyme via improved stability. In this Concept, it is argued that a particular emphasis on these specific metrics is of particular importance for the future implementation of biocatalysis in industry, at a level that fulfills its true potential.
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Affiliation(s)
- John M Woodley
- Department of Chemical and Biochemical Engineering, Technical University of Denmark, 2800, Kgs Lyngby, Denmark
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25
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Design of stable and self-regulated microbial consortia for chemical synthesis. Nat Commun 2022; 13:1554. [PMID: 35322005 PMCID: PMC8943006 DOI: 10.1038/s41467-022-29215-6] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Accepted: 03/04/2022] [Indexed: 12/16/2022] Open
Abstract
Microbial coculture engineering has emerged as a promising strategy for biomanufacturing. Stability and self-regulation pose a significant challenge for the generation of intrinsically robust cocultures for large-scale applications. Here, we introduce the use of multi-metabolite cross-feeding (MMCF) to establish a close correlation between the strains and the design rules for selecting the appropriate metabolic branches. This leads to an intrinicially stable two-strain coculture where the population composition and the product titer are insensitive to the initial inoculation ratios. With an intermediate-responsive biosensor, the population of the microbial coculture is autonomously balanced to minimize intermediate accumulation. This static-dynamic strategy is extendable to three-strain cocultures, as demonstrated with de novo biosynthesis of silybin/isosilybin. This strategy is generally applicable, paving the way to the industrial application of microbial cocultures. Stability and tunability are two desirable properties of microbial consortia-based bioproduction. Here, the authors integrate a caffeate-responsive biosensor into two and three strains coculture system to achieve autonomous regulation of strain ratios for coniferol and silybin/isosiltbin production, respectively.
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26
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Choi BH, Kang HJ, Kim SC, Lee PC. Organelle Engineering in Yeast: Enhanced Production of Protopanaxadiol through Manipulation of Peroxisome Proliferation in Saccharomyces cerevisiae. Microorganisms 2022; 10:microorganisms10030650. [PMID: 35336225 PMCID: PMC8950469 DOI: 10.3390/microorganisms10030650] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Revised: 03/13/2022] [Accepted: 03/14/2022] [Indexed: 12/15/2022] Open
Abstract
Isoprenoids, which are natural compounds with diverse structures, possess several biological activities that are beneficial to humans. A major consideration in isoprenoid production in microbial hosts is that the accumulation of biosynthesized isoprenoid within intracellular membranes may impede balanced cell growth, which may consequently reduce the desired yield of the target isoprenoid. As a strategy to overcome this suggested limitation, we selected peroxisome membranes as depots for the additional storage of biosynthesized isoprenoids to facilitate increased isoprenoid production in Saccharomyces cerevisiae. To maximize the peroxisome membrane storage capacity of S.cerevisiae, the copy number and size of peroxisomes were increased through genetic engineering of the expression of three peroxisome biogenesis-related peroxins (Pex11p, Pex34p, and Atg36p). The genetically enlarged and high copied peroxisomes in S.cerevisiae were stably maintained under a bioreactor fermentation condition. The peroxisome-engineered S.cerevisiae strains were then utilized as host strains for metabolic engineering of heterologous protopanaxadiol pathway. The yields of protopanaxadiol from the engineered peroxisome strains were ca 78% higher than those of the parent strain, which strongly supports the rationale for harnessing the storage capacity of the peroxisome membrane to accommodate the biosynthesized compounds. Consequently, this study presents in-depth knowledge on peroxisome biogenesis engineering in S.cerevisiae and could serve as basic information for improvement in ginsenosides production and as a potential platform to be utilized for other isoprenoids.
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Affiliation(s)
- Bo Hyun Choi
- Department of Molecular Science and Technology, Ajou University, World Cup-ro, Yeongtong-gu, Suwon 16499, Korea; (B.H.C.); (H.J.K.)
| | - Hyun Joon Kang
- Department of Molecular Science and Technology, Ajou University, World Cup-ro, Yeongtong-gu, Suwon 16499, Korea; (B.H.C.); (H.J.K.)
| | - Sun Chang Kim
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Korea;
| | - Pyung Cheon Lee
- Department of Molecular Science and Technology, Ajou University, World Cup-ro, Yeongtong-gu, Suwon 16499, Korea; (B.H.C.); (H.J.K.)
- Correspondence: ; Tel.: +82-31-219-2461
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27
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Ma Y, Liu N, Greisen P, Li J, Qiao K, Huang S, Stephanopoulos G. Removal of lycopene substrate inhibition enables high carotenoid productivity in Yarrowia lipolytica. Nat Commun 2022; 13:572. [PMID: 35102143 PMCID: PMC8803881 DOI: 10.1038/s41467-022-28277-w] [Citation(s) in RCA: 47] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2021] [Accepted: 01/11/2022] [Indexed: 01/28/2023] Open
Abstract
Substrate inhibition of enzymes can be a major obstacle to the production of valuable chemicals in engineered microorganisms. Here, we show substrate inhibition of lycopene cyclase as the main limitation in carotenoid biosynthesis in Yarrowia lipolytica. To overcome this bottleneck, we exploit two independent approaches. Structure-guided protein engineering yields a variant, Y27R, characterized by complete loss of substrate inhibition without reduction of enzymatic activity. Alternatively, establishing a geranylgeranyl pyrophosphate synthase-mediated flux flow restrictor also prevents the onset of substrate inhibition by diverting metabolic flux away from the inhibitory metabolite while maintaining sufficient flux towards product formation. Both approaches result in high levels of near-exclusive β-carotene production. Ultimately, we construct strains capable of producing 39.5 g/L β-carotene at a productivity of 0.165 g/L/h in bioreactor fermentations (a 1441-fold improvement over the initial strain). Our findings provide effective approaches for removing substrate inhibition in engineering pathways for efficient synthesis of natural products. Substrate inhibition has not been widely studied in the context of synthetic biology and metabolic engineering. Here, the authors report removal of lycopene substrate inhibition by two different strategies and enable high carotenoid productivity in Yarrowia lipolytica.
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28
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Optogenetic approaches in biotechnology and biomaterials. Trends Biotechnol 2022; 40:858-874. [PMID: 35031132 DOI: 10.1016/j.tibtech.2021.12.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2021] [Revised: 12/13/2021] [Accepted: 12/13/2021] [Indexed: 11/21/2022]
Abstract
Advances in genetic engineering, combined with the development of optical technologies, have allowed optogenetics to broaden its area of possible applications in recent years. However, the application of optogenetic tools in industry, including biotechnology and the production of biomaterials, is still limited, because each practical task requires the engineering of a specific optogenetic system. In this review, we discuss recent advances in the use of optogenetic tools in the production of biofuels and valuable chemicals, the synthesis of biomedical and polymer materials, and plant agrobiology. We also offer a comprehensive analysis of the properties and industrial applicability of light-controlled and other smart biomaterials. These data allow us to outline the prospects for the future use of optogenetics in bioindustry.
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29
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Xu S, Wu S, Li Y. Investigating Plant Biosynthetic Pathways Using Heterologous Gene Expression: Yeast as a Heterologous Host. Methods Mol Biol 2022; 2489:369-393. [PMID: 35524060 DOI: 10.1007/978-1-0716-2273-5_19] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Plant natural products (PNPs) are valuable resources for the development of pharmaceuticals and agrochemicals, yet the biosynthesis and metabolism of PNPs are largely unknown. Heterologous pathway reconstitution is a heavily adopted strategy in secondary metabolism characterization. Yeast systems have been broadly utilized in the heterologous production of PNPs and have been considered as a promising platform to investigate plant biosynthetic pathways. Here, we describe the reconstitution and verification of the upstream part of brassinolide biosynthesis in S. cerevisiae using this method.
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Affiliation(s)
- Shanhui Xu
- Department of Chemical and Environmental Engineering, University of California, Riverside, CA, USA
| | - Sheng Wu
- Department of Chemical and Environmental Engineering, University of California, Riverside, CA, USA
| | - Yanran Li
- Department of Chemical and Environmental Engineering, University of California, Riverside, CA, USA.
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30
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Li C, Jiang T, Li M, Zou Y, Yan Y. Fine-tuning gene expression for improved biosynthesis of natural products: From transcriptional to post-translational regulation. Biotechnol Adv 2022; 54:107853. [PMID: 34637919 PMCID: PMC8724446 DOI: 10.1016/j.biotechadv.2021.107853] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 10/04/2021] [Accepted: 10/05/2021] [Indexed: 02/08/2023]
Abstract
Microbial production of natural compounds has attracted extensive attention due to their high value in pharmaceutical, cosmetic, and food industries. Constructing efficient microbial cell factories for biosynthesis of natural products requires the fine-tuning of gene expressions to minimize the accumulation of toxic metabolites, reduce the competition between cell growth and product generation, as well as achieve the balance of redox or co-factors. In this review, we focus on recent advances in fine-tuning gene expression at the DNA, RNA, and protein levels to improve the microbial biosynthesis of natural products. Commonly used regulatory toolsets in each level are discussed, and perspectives for future direction in this area are provided.
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Affiliation(s)
- Chenyi Li
- School of Chemical, Materials and Biomedical Engineering, College of Engineering, The University of Georgia, Athens, GA 30602, USA
| | - Tian Jiang
- School of Chemical, Materials and Biomedical Engineering, College of Engineering, The University of Georgia, Athens, GA 30602, USA
| | - Michelle Li
- North Oconee High School, Bogart, GA 30622, USA
| | - Yusong Zou
- School of Chemical, Materials and Biomedical Engineering, College of Engineering, The University of Georgia, Athens, GA 30602, USA
| | - Yajun Yan
- School of Chemical, Materials and Biomedical Engineering, College of Engineering, The University of Georgia, Athens, GA 30602, USA.
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31
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Wirth NT, Nikel PI. Combinatorial pathway balancing provides biosynthetic access to 2-fluoro- cis, cis-muconate in engineered Pseudomonas putida. CHEM CATALYSIS 2021; 1:1234-1259. [PMID: 34977847 PMCID: PMC8711041 DOI: 10.1016/j.checat.2021.09.002] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/13/2021] [Revised: 08/15/2021] [Accepted: 08/31/2021] [Indexed: 12/18/2022]
Abstract
The wealth of bio-based building blocks produced by engineered microorganisms seldom include halogen atoms. Muconate is a platform chemical with a number of industrial applications that could be broadened by introducing fluorine atoms to tune its physicochemical properties. The soil bacterium Pseudomonas putida naturally assimilates benzoate via the ortho-cleavage pathway with cis,cis-muconate as intermediate. Here, we harnessed the native enzymatic machinery (encoded within the ben and cat gene clusters) to provide catalytic access to 2-fluoro-cis,cis-muconate (2-FMA) from fluorinated benzoates. The reactions in this pathway are highly imbalanced, leading to accumulation of toxic intermediates and limited substrate conversion. By disentangling regulatory patterns of ben and cat in response to fluorinated effectors, metabolic activities were adjusted to favor 2-FMA biosynthesis. After implementing this combinatorial approach, engineered P. putida converted 3-fluorobenzoate to 2-FMA at the maximum theoretical yield. Hence, this study illustrates how synthetic biology can expand the diversity of nature's biochemical catalysis.
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Affiliation(s)
- Nicolas T Wirth
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Pablo I Nikel
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
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32
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Bahls MO, Platz L, Morgado G, Schmidt GW, Panke S. Directed evolution of biofuel-responsive biosensors for automated optimization of branched-chain alcohol biosynthesis. Metab Eng 2021; 69:98-111. [PMID: 34767976 DOI: 10.1016/j.ymben.2021.10.014] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Revised: 10/21/2021] [Accepted: 10/31/2021] [Indexed: 12/18/2022]
Abstract
The biosynthesis of short-chain alcohols is a carbon-neutral alternative to petroleum-derived production, but strain screening operations are encumbered by laborious analytics. Here, we built, characterized and applied whole cell biosensors by directed evolution of the transcription factor AlkS for screening microbial strain libraries producing industrially relevant alcohols. A selected AlkS variant was applied for in situ product detection in two screening applications concerning key steps in alcohol production. Further, the biosensor strains enabled the implementation of an automated, robotic platform-based workflow with data clustering, which readily allowed the identification of significantly improved strain variants for isopentanol production.
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Affiliation(s)
- Maximilian O Bahls
- Department of Biosystems Science and Engineering, ETH Zurich, Switzerland
| | - Lukas Platz
- Department of Biosystems Science and Engineering, ETH Zurich, Switzerland
| | - Gaspar Morgado
- Department of Biosystems Science and Engineering, ETH Zurich, Switzerland
| | - Gregor W Schmidt
- Department of Biosystems Science and Engineering, ETH Zurich, Switzerland
| | - Sven Panke
- Department of Biosystems Science and Engineering, ETH Zurich, Switzerland.
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33
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Tong T, Chen X, Hu G, Wang XL, Liu GQ, Liu L. Engineering microbial metabolic energy homeostasis for improved bioproduction. Biotechnol Adv 2021; 53:107841. [PMID: 34610353 DOI: 10.1016/j.biotechadv.2021.107841] [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: 06/16/2021] [Revised: 08/25/2021] [Accepted: 09/28/2021] [Indexed: 10/20/2022]
Abstract
Metabolic energy (ME) homeostasis is essential for the survival and proper functioning of microbial cell factories. However, it is often disrupted during bioproduction because of inefficient ME supply and excessive ME consumption. In this review, we propose strategies, including reinforcement of the capacity of ME-harvesting systems in autotrophic microorganisms; enhancement of the efficiency of ME-supplying pathways in heterotrophic microorganisms; and reduction of unessential ME consumption by microbial cells, to address these issues. This review highlights the potential of biotechnology in the engineering of microbial ME homeostasis and provides guidance for the higher efficient bioproduction of microbial cell factories.
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Affiliation(s)
- Tian Tong
- Hunan Provincial Key Laboratory for Forestry Biotechnology, Central South University of Forestry and Technology, Changsha 410004, China; International Cooperation Base of Science and Technology Innovation on Forest Resource Biotechnology of Hunan Province, Central South University of Forestry and Technology, Changsha 410004, China
| | - Xiulai Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China; International Joint Laboratory on Food Safety, Jiangnan University, Wuxi 214122, China
| | - Guipeng Hu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China; International Joint Laboratory on Food Safety, Jiangnan University, Wuxi 214122, China
| | - Xiao-Ling Wang
- Hunan Provincial Key Laboratory for Forestry Biotechnology, Central South University of Forestry and Technology, Changsha 410004, China; International Cooperation Base of Science and Technology Innovation on Forest Resource Biotechnology of Hunan Province, Central South University of Forestry and Technology, Changsha 410004, China
| | - Gao-Qiang Liu
- Hunan Provincial Key Laboratory for Forestry Biotechnology, Central South University of Forestry and Technology, Changsha 410004, China; International Cooperation Base of Science and Technology Innovation on Forest Resource Biotechnology of Hunan Province, Central South University of Forestry and Technology, Changsha 410004, China.
| | - Liming Liu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China; International Joint Laboratory on Food Safety, Jiangnan University, Wuxi 214122, China.
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34
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Aamer Mehmood M, Shahid A, Malik S, Wang N, Rizwan Javed M, Nabeel Haider M, Verma P, Umer Farooq Ashraf M, Habib N, Syafiuddin A, Boopathy R. Advances in developing metabolically engineered microbial platforms to produce fourth-generation biofuels and high-value biochemicals. BIORESOURCE TECHNOLOGY 2021; 337:125510. [PMID: 34320777 DOI: 10.1016/j.biortech.2021.125510] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Revised: 07/01/2021] [Accepted: 07/02/2021] [Indexed: 06/13/2023]
Abstract
Producing bio-based chemicals is imperative to establish an eco-friendly circular bioeconomy. However, the compromised titer of these biochemicals hampers their commercial implementation. Advances in genetic engineering tools have enabled researchers to develop robust strains producing desired titers of the next-generation biofuels and biochemicals. The native and non-native pathways have been extensively engineered in various host strains via pathway reconstruction and metabolic flux redirection of lipid metabolism and central carbon metabolism to produce myriad biomolecules including alcohols, isoprenoids, hydrocarbons, fatty-acids, and their derivatives. This review has briefly covered the research efforts made during the previous decade to produce advanced biofuels and biochemicals through engineered microbial platforms along with the engineering approaches employed. The efficiency of the various techniques along with their shortcomings is also covered to provide a comprehensive overview of the progress and future directions to achieve higher titer of fourth-generation biofuels and biochemicals while keeping environmental sustainability intact.
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Affiliation(s)
- Muhammad Aamer Mehmood
- School of Bioengineering, Sichuan University of Science and Engineering, Zigong, China; Bioenergy Research Centre, Department of Bioinformatics & Biotechnology, Government College University Faisalabad, Faisalabad, Pakistan
| | - Ayesha Shahid
- Bioenergy Research Centre, Department of Bioinformatics & Biotechnology, Government College University Faisalabad, Faisalabad, Pakistan
| | - Sana Malik
- Bioenergy Research Centre, Department of Bioinformatics & Biotechnology, Government College University Faisalabad, Faisalabad, Pakistan
| | - Ning Wang
- School of Bioengineering, Sichuan University of Science and Engineering, Zigong, China
| | - Muhammad Rizwan Javed
- Bioenergy Research Centre, Department of Bioinformatics & Biotechnology, Government College University Faisalabad, Faisalabad, Pakistan
| | - Muhammad Nabeel Haider
- Bioenergy Research Centre, Department of Bioinformatics & Biotechnology, Government College University Faisalabad, Faisalabad, Pakistan
| | - Pradeep Verma
- Department of Microbiology, Central University of Rajasthan, Bandarsindri, Kishangarh, Ajmer-305801, Rajasthan, India
| | - Muhammad Umer Farooq Ashraf
- Bioenergy Research Centre, Department of Bioinformatics & Biotechnology, Government College University Faisalabad, Faisalabad, Pakistan
| | - Nida Habib
- Bioenergy Research Centre, Department of Bioinformatics & Biotechnology, Government College University Faisalabad, Faisalabad, Pakistan
| | - Achmad Syafiuddin
- Department of Public Health, Universitas Nahdlatul Ulama Surabaya, 60237 Surabaya, East Java, Indonesia
| | - Raj Boopathy
- Department of Biological Sciences, Nicholls State University, Thibodaux, LA 70310, USA.
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35
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Kang S, Lumactud R, Li N, Bell TH, Kim HS, Park SY, Lee YH. Harnessing Chemical Ecology for Environment-Friendly Crop Protection. PHYTOPATHOLOGY 2021; 111:1697-1710. [PMID: 33908803 DOI: 10.1094/phyto-01-21-0035-rvw] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Heavy reliance on synthetic pesticides for crop protection has become increasingly unsustainable, calling for robust alternative strategies that do not degrade the environment and vital ecosystem services. There are numerous reports of successful disease control by various microbes used in small-scale trials. However, inconsistent efficacy has hampered their large-scale application. A better understanding of how beneficial microbes interact with plants, other microbes, and the environment and which factors affect disease control efficacy is crucial to deploy microbial agents as effective and reliable pesticide alternatives. Diverse metabolites produced by plants and microbes participate in pathogenesis and defense, regulate the growth and development of themselves and neighboring organisms, help maintain cellular homeostasis under various environmental conditions, and affect the assembly and activity of plant and soil microbiomes. However, research on the metabolites associated with plant health-related processes, except antibiotics, has not received adequate attention. This review highlights several classes of metabolites known or suspected to affect plant health, focusing on those associated with biocontrol and belowground plant-microbe and microbe-microbe interactions. The review also describes how new insights from systematic explorations of the diversity and mechanism of action of bioactive metabolites can be harnessed to develop novel crop protection strategies.
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Affiliation(s)
- Seogchan Kang
- Department of Plant Pathology and Environmental Microbiology, Pennsylvania State University, University Park, PA 16802, U.S.A
| | - Rhea Lumactud
- Department of Plant Pathology and Environmental Microbiology, Pennsylvania State University, University Park, PA 16802, U.S.A
| | - Ningxiao Li
- Department of Plant Pathology and Environmental Microbiology, Pennsylvania State University, University Park, PA 16802, U.S.A
| | - Terrence H Bell
- Department of Plant Pathology and Environmental Microbiology, Pennsylvania State University, University Park, PA 16802, U.S.A
| | - Hye-Seon Kim
- USDA, Agricultural Research Service, National Center for Agricultural Utilization Research, Mycotoxin Prevention and Applied Microbiology Research Unit, Peoria, IL 61604, U.S.A
| | - Sook-Young Park
- Department of Agricultural Life Science, Sunchon National University, Suncheon 57922, Korea
| | - Yong-Hwan Lee
- Department of Agricultural Biotechnology, Seoul National University, Seoul 151-921, Korea
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Raihan T, Rabbee MF, Roy P, Choudhury S, Baek KH, Azad AK. Microbial Metabolites: The Emerging Hotspot of Antiviral Compounds as Potential Candidates to Avert Viral Pandemic Alike COVID-19. Front Mol Biosci 2021; 8:732256. [PMID: 34557521 PMCID: PMC8452873 DOI: 10.3389/fmolb.2021.732256] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Accepted: 08/23/2021] [Indexed: 12/15/2022] Open
Abstract
The present global COVID-19 pandemic caused by the noble pleomorphic severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has created a vulnerable situation in the global healthcare and economy. In this pandemic situation, researchers all around the world are trying their level best to find suitable therapeutics from various sources to combat against the SARS-CoV-2. To date, numerous bioactive compounds from different sources have been tested to control many viral diseases. However, microbial metabolites are advantageous for drug development over metabolites from other sources. We herein retrieved and reviewed literatures from PubMed, Scopus and Google relevant to antiviral microbial metabolites by searching with the keywords "antiviral microbial metabolites," "microbial metabolite against virus," "microorganism with antiviral activity," "antiviral medicine from microbial metabolite," "antiviral bacterial metabolites," "antiviral fungal metabolites," "antiviral metabolites from microscopic algae' and so on. For the same purpose, the keywords "microbial metabolites against COVID-19 and SARS-CoV-2" and "plant metabolites against COVID-19 and SARS-CoV-2" were used. Only the full text literatures available in English and pertinent to the topic have been included and those which are not available as full text in English and pertinent to antiviral or anti-SARS-CoV-2 activity were excluded. In this review, we have accumulated microbial metabolites that can be used as antiviral agents against a broad range of viruses including SARS-CoV-2. Based on this concept, we have included 330 antiviral microbial metabolites so far available to date in the data bases and were previously isolated from fungi, bacteria and microalgae. The microbial source, chemical nature, targeted viruses, mechanism of actions and IC50/EC50 values of these metabolites are discussed although mechanisms of actions of many of them are not yet elucidated. Among these antiviral microbial metabolites, some compounds might be very potential against many other viruses including coronaviruses. However, these potential microbial metabolites need further research to be developed as effective antiviral drugs. This paper may provide the scientific community with the possible secret of microbial metabolites that could be an effective source of novel antiviral drugs to fight against many viruses including SARS-CoV-2 as well as the future viral pandemics.
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Affiliation(s)
- Topu Raihan
- Department of Genetic Engineering and Biotechnology, Shahjalal University of Science and Technology, Sylhet, Bangladesh
| | | | - Puja Roy
- Department of Genetic Engineering and Biotechnology, Shahjalal University of Science and Technology, Sylhet, Bangladesh
| | - Swapnila Choudhury
- Department of Genetic Engineering and Biotechnology, Jagannath University, Dhaka, Bangladesh
| | - Kwang-Hyun Baek
- Department of Biotechnology, Yeungnam University, Gyeongsan, South Korea
| | - Abul Kalam Azad
- Department of Genetic Engineering and Biotechnology, Shahjalal University of Science and Technology, Sylhet, Bangladesh
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Heath RS, Ruscoe RE, Turner NJ. The beauty of biocatalysis: sustainable synthesis of ingredients in cosmetics. Nat Prod Rep 2021; 39:335-388. [PMID: 34879125 DOI: 10.1039/d1np00027f] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Covering: 2015 up to July 2021The market for cosmetics is consumer driven and the desire for green, sustainable and natural ingredients is increasing. The use of isolated enzymes and whole-cell organisms to synthesise these products is congruent with these values, especially when combined with the use of renewable, recyclable or waste feedstocks. The literature of biocatalysis for the synthesis of ingredients in cosmetics in the past five years is herein reviewed.
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Affiliation(s)
- Rachel S Heath
- Manchester Institute of Biotechnology, Department of Chemistry, University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK.
| | - Rebecca E Ruscoe
- Manchester Institute of Biotechnology, Department of Chemistry, University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK.
| | - Nicholas J Turner
- Manchester Institute of Biotechnology, Department of Chemistry, University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK.
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Myers KS, Noguera DR, Donohue TJ. Promoter Architecture Differences among Alphaproteobacteria and Other Bacterial Taxa. mSystems 2021; 6:e0052621. [PMID: 34254822 PMCID: PMC8407463 DOI: 10.1128/msystems.00526-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Accepted: 06/17/2021] [Indexed: 11/20/2022] Open
Abstract
Much of our knowledge of bacterial transcription initiation has been derived from studying the promoters of Escherichia coli and Bacillus subtilis. Given the expansive diversity across the bacterial phylogeny, it is unclear how much of this knowledge can be applied to other organisms. Here, we report on bioinformatic analyses of promoter sequences of the primary σ factor (σ70) by leveraging publicly available transcription start site (TSS) sequencing data sets for nine bacterial species spanning five phyla. This analysis identifies previously unreported differences in the -35 and -10 elements of σ70-dependent promoters in several groups of bacteria. We found that Actinobacteria and Betaproteobacteria σ70-dependent promoters lack the TTG triad in their -35 element, which is predicted to be conserved across the bacterial phyla. In addition, the majority of the Alphaproteobacteria σ70-dependent promoters analyzed lacked the thymine at position -7 that is highly conserved in other phyla. Bioinformatic examination of the Alphaproteobacteria σ70-dependent promoters identifies a significant overrepresentation of essential genes and ones encoding proteins with common cellular functions downstream of promoters containing an A, C, or G at position -7. We propose that transcription of many σ70-dependent promoters in Alphaproteobacteria depends on the transcription factor CarD, which is an essential protein in several members of this phylum. Our analysis expands the knowledge of promoter architecture across the bacterial phylogeny and provides new information that can be used to engineer bacteria for use in medical, environmental, agricultural, and biotechnological processes. IMPORTANCE Transcription of DNA to RNA by RNA polymerase is essential for cells to grow, develop, and respond to stress. Understanding the process and control of transcription is important for health, disease, the environment, and biotechnology. Decades of research on a few bacteria have identified promoter DNA sequences that are recognized by the σ subunit of RNA polymerase. We used bioinformatic analyses to reveal previously unreported differences in promoter DNA sequences across the bacterial phylogeny. We found that many Actinobacteria and Betaproteobacteria promoters lack a sequence in their -35 DNA recognition element that was previously assumed to be conserved and that Alphaproteobacteria lack a thymine residue at position -7, also previously assumed to be conserved. Our work reports important new information about bacterial transcription, illustrates the benefits of studying bacteria across the phylogenetic tree, and proposes new lines of future investigation.
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Affiliation(s)
- Kevin S. Myers
- Wisconsin Energy Institute and Great Lakes Bioenergy Research Center, University of Wisconsin—Madison, Madison, Wisconsin, USA
| | - Daniel R. Noguera
- Wisconsin Energy Institute and Great Lakes Bioenergy Research Center, University of Wisconsin—Madison, Madison, Wisconsin, USA
- Department of Civil & Environmental Engineering, University of Wisconsin—Madison, Madison, Wisconsin, USA
| | - Timothy J. Donohue
- Wisconsin Energy Institute and Great Lakes Bioenergy Research Center, University of Wisconsin—Madison, Madison, Wisconsin, USA
- Department of Bacteriology, University of Wisconsin—Madison, Madison, Wisconsin, USA
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Godoy P, García-Franco A, Recio MI, Ramos JL, Duque E. Synthesis of aromatic amino acids from 2G lignocellulosic substrates. Microb Biotechnol 2021; 14:1931-1943. [PMID: 34403199 PMCID: PMC8449653 DOI: 10.1111/1751-7915.13844] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Revised: 05/04/2021] [Accepted: 05/13/2021] [Indexed: 11/29/2022] Open
Abstract
Pseudomonas putida is a highly solvent‐resistant microorganism and useful chassis for the production of value‐added compounds from lignocellulosic residues, in particular aromatic compounds that are made from phenylalanine. The use of these agricultural residues requires a two‐step treatment to release the components of the polysaccharides of cellulose and hemicellulose as monomeric sugars, the most abundant monomers being glucose and xylose. Pan‐genomic studies have shown that Pseudomonas putida metabolizes glucose through three convergent pathways to yield 6‐phosphogluconate and subsequently metabolizes it through the Entner–Doudoroff pathway, but the strains do not degrade xylose. The valorization of both sugars is critical from the point of view of economic viability of the process. For this reason, a P. putida strain was endowed with the ability to metabolize xylose via the xylose isomerase pathway, by incorporating heterologous catabolic genes that convert this C5 sugar into intermediates of the pentose phosphate cycle. In addition, the open reading frame T1E_2822, encoding glucose dehydrogenase, was knocked‐out to avoid the production of the dead‐end product xylonate. We generated a set of DOT‐T1E‐derived strains that metabolized glucose and xylose simultaneously in culture medium and that reached high cell density with generation times of around 100 min with glucose and around 300 min with xylose. The strains grew in 2G hydrolysates from diluted acid and steam explosion pretreated corn stover and sugarcane straw. During growth, the strains metabolized > 98% of glucose, > 96% xylose and > 85% acetic acid. In 2G hydrolysates P. putida 5PL, a DOT‐T1E derivative strain that carries up to five independent mutations to avoid phenylalanine metabolism, accumulated this amino acid in the medium. We constructed P. putida 5PLΔgcd (xylABE) that produced up to 250 mg l−1 of phenylalanine when grown in 2G pretreated corn stover or sugarcane straw. These results support as a proof of concept the potential of P. putida as a chassis for 2G processes.
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Affiliation(s)
- Patricia Godoy
- Consejo Superior de Investigaciones Científicas, Estación Experimental del Zaidín, c/Profesor Albareda 1, Granada, 18008, Spain
| | - Ana García-Franco
- Consejo Superior de Investigaciones Científicas, Estación Experimental del Zaidín, c/Profesor Albareda 1, Granada, 18008, Spain
| | - María-Isabel Recio
- Consejo Superior de Investigaciones Científicas, Estación Experimental del Zaidín, c/Profesor Albareda 1, Granada, 18008, Spain.,BioEnterprise Master Program, School of Pharmacy, University of Granada, Granada, Spain
| | - Juan-Luis Ramos
- Consejo Superior de Investigaciones Científicas, Estación Experimental del Zaidín, c/Profesor Albareda 1, Granada, 18008, Spain
| | - Estrella Duque
- Consejo Superior de Investigaciones Científicas, Estación Experimental del Zaidín, c/Profesor Albareda 1, Granada, 18008, Spain
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Deng C, Lv X, Li J, Zhang H, Liu Y, Du G, Amaro RL, Liu L. Synergistic improvement of N-acetylglucosamine production by engineering transcription factors and balancing redox cofactors. Metab Eng 2021; 67:330-346. [PMID: 34329707 DOI: 10.1016/j.ymben.2021.07.012] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 06/29/2021] [Accepted: 07/26/2021] [Indexed: 12/17/2022]
Abstract
The regulation of single gene transcription level in the metabolic pathway is often failed to significantly improve the titer of the target product, and even leads to the imbalance of carbon/nitrogen metabolic network and cofactor network. Global transcription machinery engineering (gTME) can activate or inhibit the synergistic expression of multiple genes in specific metabolic pathways, so transcription factors with specific functions can be expressed according to different metabolic regulation requirements, thus effectively increasing the synthesis of target metabolites. In addition, maintaining intracellular redox balance through cofactor engineering can realize the self-balance of cofactors and promote the efficient synthesis of target products. In this study, we rebalanced the central carbon/nitrogen metabolism and redox metabolism of Corynebacterium glutamicum S9114 by gTME and redox cofactors engineering to promote the production of the nutraceutical N-acetylglucosamine (GlcNAc). Firstly, it was found that the overexpression of the transcription factor RamA can promote GlcNAc synthesis, and the titer was further improved to 16 g/L in shake flask by using a mutant RamA (RamAM). Secondly, a CRISPR interference (CRISPRi) system based on dCpf1 was developed and used to inhibit the expression of global negative transcriptional regulators of GlcNAc synthesis, which promoted the GlcNAc titer to 27.5 g/L. Thirdly, the cofactor specificity of the key enzymes in GlcNAc synthesis pathway was changed by rational protein engineering, and the titer of GlcNAc in shake flask was increased to 36.9 g/L. Finally, the production of GlcNAc was scaled up in a 50-L fermentor, and the titer reached 117.1 ± 1.9 g/L, which was 6.62 times that of the control group (17.7 ± 0.4 g/L), and the yield was increased from 0.19 g/g to 0.31 g/g glucose. The results obtained here highlight the importance of engineering the global regulation of central carbon/nitrogen metabolism and redox metabolism to improve the production performance of microbial cell factories.
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Affiliation(s)
- Chen Deng
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China; Science Center for Future Foods, Ministry of Education, Jiangnan University, Wuxi, 214122, China
| | - Xueqin Lv
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China; Science Center for Future Foods, Ministry of Education, Jiangnan University, Wuxi, 214122, China
| | - Jianghua Li
- Science Center for Future Foods, Ministry of Education, Jiangnan University, Wuxi, 214122, China
| | - Hongzhi Zhang
- Shandong Runde Biotechnology Co, Ltd, Tai'an, 271000, China
| | - Yanfeng Liu
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China; Science Center for Future Foods, Ministry of Education, Jiangnan University, Wuxi, 214122, China
| | - Guocheng Du
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China
| | - Rodrigo Ledesma Amaro
- Department of Bioengineering and Imperial College Centre for Synthetic Biology, Imperial College London, London, SW72AZ, UK
| | - Long Liu
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China; Science Center for Future Foods, Ministry of Education, Jiangnan University, Wuxi, 214122, China.
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41
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Pereira R, Ishchuk OP, Li X, Liu Q, Liu Y, Otto M, Chen Y, Siewers V, Nielsen J. Metabolic Engineering of Yeast. Metab Eng 2021. [DOI: 10.1002/9783527823468.ch18] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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42
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Mori Y, Noda S, Shirai T, Kondo A. Direct 1,3-butadiene biosynthesis in Escherichia coli via a tailored ferulic acid decarboxylase mutant. Nat Commun 2021; 12:2195. [PMID: 33850144 PMCID: PMC8044207 DOI: 10.1038/s41467-021-22504-6] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Accepted: 03/18/2021] [Indexed: 12/11/2022] Open
Abstract
The C4 unsaturated compound 1,3-butadiene is an important monomer in synthetic rubber and engineering plastic production. However, microorganisms cannot directly produce 1,3-butadiene when glucose is used as a renewable carbon source via biological processes. In this study, we construct an artificial metabolic pathway for 1,3-butadiene production from glucose in Escherichia coli by combining the cis,cis-muconic acid (ccMA)-producing pathway together with tailored ferulic acid decarboxylase mutations. The rational design of the substrate-binding site of the enzyme by computational simulations improves ccMA decarboxylation and thus 1,3-butadiene production. We find that changing dissolved oxygen (DO) levels and controlling the pH are important factors for 1,3-butadiene production. Using DO-stat fed-batch fermentation, we produce 2.13 ± 0.17 g L-1 1,3-butadiene. The results indicate that we can produce unnatural/nonbiological compounds from glucose as a renewable carbon source via a rational enzyme design strategy.
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Affiliation(s)
- Yutaro Mori
- Center for Sustainable Resource Science, RIKEN, Yokohama, Japan
| | - Shuhei Noda
- Center for Sustainable Resource Science, RIKEN, Yokohama, Japan
| | - Tomokazu Shirai
- Center for Sustainable Resource Science, RIKEN, Yokohama, Japan.
| | - Akihiko Kondo
- Center for Sustainable Resource Science, RIKEN, Yokohama, Japan
- Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, Kobe, Japan
- Graduate School of Science, Technology and Innovation, Kobe University, Kobe, Japan
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43
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β-Ionone: Its Occurrence and Biological Function and Metabolic Engineering. PLANTS 2021; 10:plants10040754. [PMID: 33921545 PMCID: PMC8069406 DOI: 10.3390/plants10040754] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Revised: 04/04/2021] [Accepted: 04/11/2021] [Indexed: 12/03/2022]
Abstract
β-Ionone is a natural plant volatile compound, and it is the 9,10 and 9′,10′ cleavage product of β-carotene by the carotenoid cleavage dioxygenase. β-Ionone is widely distributed in flowers, fruits, and vegetables. β-Ionone and other apocarotenoids comprise flavors, aromas, pigments, growth regulators, and defense compounds; serve as ecological cues; have roles as insect attractants or repellants, and have antibacterial and fungicidal properties. In recent years, β-ionone has also received increased attention from the biomedical community for its potential as an anticancer treatment and for other human health benefits. However, β-ionone is typically produced at relatively low levels in plants. Thus, expressing plant biosynthetic pathway genes in microbial hosts and engineering the metabolic pathway/host to increase metabolite production is an appealing alternative. In the present review, we discuss β-ionone occurrence, the biological activities of β-ionone, emphasizing insect attractant/repellant activities, and the current strategies and achievements used to reconstruct enzyme pathways in microorganisms in an effort to to attain higher amounts of the desired β-ionone.
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44
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Chang C, Liu B, Bao Y, Tao Y, Liu W. Efficient bioconversion of raspberry ketone in Escherichia coli using fatty acids feedstocks. Microb Cell Fact 2021; 20:68. [PMID: 33706766 PMCID: PMC7953670 DOI: 10.1186/s12934-021-01551-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Accepted: 02/21/2021] [Indexed: 02/02/2023] Open
Abstract
Background Phenylpropanoid including raspberry ketone, is a kind of important natural plant product and widely used in pharmaceuticals, chemicals, cosmetics, and healthcare products. Bioproduction of phenylpropanoid in Escherichia coli and other microbial cell factories is an attractive approach considering the low phenylpropanoid contents in plants. However, it is usually difficult to produce high titer phenylpropanoid production when fermentation using glucose as carbon source. Developing novel bioprocess using alternative sources might provide a solution to this problem. In this study, typical phenylpropanoid raspberry ketone was used as the target product to develop a biosynthesis pathway for phenylpropanoid production from fatty acids, a promising alternative low-cost feedstock. Results A raspberry ketone biosynthesis module was developed and optimized by introducing 4-coumarate-CoA ligase (4CL), benzalacetone synthase (BAS), and raspberry ketone reductase (RZS) in Escherichia coli strains CR1–CR4. Then strain CR5 was developed by introducing raspberry ketone biosynthesis module into a fatty acids-utilization chassis FA09 to achieve production of raspberry ketone from fatty acids feedstock. However, the production of raspberry ketone was still limited by the low biomass and unable to substantiate whole-cell bioconversion process. Thus, a process by coordinately using fatty-acids and glycerol was developed. In addition, we systematically screened and optimized fatty acids-response promoters. The optimized promoter Pfrd3 was then successfully used for the efficient expression of key enzymes of raspberry ketone biosynthesis module during bioconversion from fatty acids. The final engineered strain CR8 could efficiently produce raspberry ketone repeatedly using bioconversion from fatty acids feedstock strategy, and was able to produce raspberry ketone to a concentration of 180.94 mg/L from soybean oil in a 1-L fermentation process. Conclusion Metabolically engineered Escherichia coli strains were successfully developed for raspberry ketone production from fatty acids using several strategies, including optimization of bioconversion process and fine-tuning key enzyme expression. This study provides an essential reference to establish the low-cost biological manufacture of phenylpropanoids compounds. Supplementary Information The online version contains supplementary material available at 10.1186/s12934-021-01551-0.
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Affiliation(s)
- Chen Chang
- College of Forestry, Northeast Forestry University, No. 26 Hexing Road, Harbin, Heilongjiang Province, 150040, PR China.,CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, NO. 1 Beichen West Road, Chaoyang District, Beijing, 100101, PR China
| | - Bo Liu
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, NO. 1 Beichen West Road, Chaoyang District, Beijing, 100101, PR China
| | - Yihong Bao
- College of Forestry, Northeast Forestry University, No. 26 Hexing Road, Harbin, Heilongjiang Province, 150040, PR China. .,Heilongjiang Key Laboratory of Forest Food Resources Utilization, No. 26 Hexing Road, Harbin, Heilongjiang Province, 150040, PR China.
| | - Yong Tao
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, NO. 1 Beichen West Road, Chaoyang District, Beijing, 100101, PR China. .,University of Chinese Academy of Sciences, Shijingshan District, NO. 19A Yuquan Road, Beijing, 100049, PR China.
| | - Weifeng Liu
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, NO. 1 Beichen West Road, Chaoyang District, Beijing, 100101, PR China. .,University of Chinese Academy of Sciences, Shijingshan District, NO. 19A Yuquan Road, Beijing, 100049, PR China.
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Yocum HC, Pham A, Da Silva NA. Successful Enzyme Colocalization Strategies in Yeast for Increased Synthesis of Non-native Products. Front Bioeng Biotechnol 2021; 9:606795. [PMID: 33634084 PMCID: PMC7901933 DOI: 10.3389/fbioe.2021.606795] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Accepted: 01/11/2021] [Indexed: 11/13/2022] Open
Abstract
Yeast cell factories, particularly Saccharomyces cerevisiae, have proven valuable for the synthesis of non-native compounds, ranging from commodity chemicals to complex natural products. One significant challenge has been ensuring sufficient carbon flux to the desired product. Traditionally, this has been addressed by strategies involving "pushing" and "pulling" the carbon flux toward the products by overexpression while "blocking" competing pathways via downregulation or gene deletion. Colocalization of enzymes is an alternate and complementary metabolic engineering strategy to control flux and increase pathway efficiency toward the synthesis of non-native products. Spatially controlling the pathway enzymes of interest, and thus positioning them in close proximity, increases the likelihood of reaction along that pathway. This mini-review focuses on the recent developments and applications of colocalization strategies, including enzyme scaffolding, construction of synthetic organelles, and organelle targeting, in both S. cerevisiae and non-conventional yeast hosts. Challenges with these techniques and future directions will also be discussed.
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Affiliation(s)
- Hannah C Yocum
- Department of Chemical and Biomolecular Engineering, University of California, Irvine, CA, United States
| | - Anhuy Pham
- Department of Chemical and Biomolecular Engineering, University of California, Irvine, CA, United States
| | - Nancy A Da Silva
- Department of Chemical and Biomolecular Engineering, University of California, Irvine, CA, United States
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Amer B, Baidoo EEK. Omics-Driven Biotechnology for Industrial Applications. Front Bioeng Biotechnol 2021; 9:613307. [PMID: 33708762 PMCID: PMC7940536 DOI: 10.3389/fbioe.2021.613307] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Accepted: 01/11/2021] [Indexed: 12/11/2022] Open
Abstract
Biomanufacturing is a key component of biotechnology that uses biological systems to produce bioproducts of commercial relevance, which are of great interest to the energy, material, pharmaceutical, food, and agriculture industries. Biotechnology-based approaches, such as synthetic biology and metabolic engineering are heavily reliant on "omics" driven systems biology to characterize and understand metabolic networks. Knowledge gained from systems biology experiments aid the development of synthetic biology tools and the advancement of metabolic engineering studies toward establishing robust industrial biomanufacturing platforms. In this review, we discuss recent advances in "omics" technologies, compare the pros and cons of the different "omics" technologies, and discuss the necessary requirements for carrying out multi-omics experiments. We highlight the influence of "omics" technologies on the production of biofuels and bioproducts by metabolic engineering. Finally, we discuss the application of "omics" technologies to agricultural and food biotechnology, and review the impact of "omics" on current COVID-19 research.
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Affiliation(s)
- Bashar Amer
- Lawrence Berkeley National Laboratory, Joint BioEnergy Institute, Emeryville, CA, United States
- Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Edward E. K. Baidoo
- Lawrence Berkeley National Laboratory, Joint BioEnergy Institute, Emeryville, CA, United States
- Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
- U.S. Department of Energy, Agile BioFoundry, Emeryville, CA, United States
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Liu Y, Benitez MG, Chen J, Harrison E, Khusnutdinova AN, Mahadevan R. Opportunities and Challenges for Microbial Synthesis of Fatty Acid-Derived Chemicals (FACs). Front Bioeng Biotechnol 2021; 9:613322. [PMID: 33575251 PMCID: PMC7870715 DOI: 10.3389/fbioe.2021.613322] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Accepted: 01/04/2021] [Indexed: 11/13/2022] Open
Abstract
Global warming and uneven distribution of fossil fuels worldwide concerns have spurred the development of alternative, renewable, sustainable, and environmentally friendly resources. From an engineering perspective, biosynthesis of fatty acid-derived chemicals (FACs) is an attractive and promising solution to produce chemicals from abundant renewable feedstocks and carbon dioxide in microbial chassis. However, several factors limit the viability of this process. This review first summarizes the types of FACs and their widely applications. Next, we take a deep look into the microbial platform to produce FACs, give an outlook for the platform development. Then we discuss the bottlenecks in metabolic pathways and supply possible solutions correspondingly. Finally, we highlight the most recent advances in the fast-growing model-based strain design for FACs biosynthesis.
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Affiliation(s)
- Yilan Liu
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, ON, Canada
| | - Mauricio Garcia Benitez
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, ON, Canada
| | - Jinjin Chen
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, ON, Canada
| | - Emma Harrison
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, ON, Canada
| | - Anna N. Khusnutdinova
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, ON, Canada
| | - Radhakrishnan Mahadevan
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, ON, Canada
- Institute of Biomedical Engineering, University of Toronto, Toronto, ON, Canada
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Katsimpouras C, Stephanopoulos G. Enzymes in biotechnology: Critical platform technologies for bioprocess development. Curr Opin Biotechnol 2021; 69:91-102. [PMID: 33422914 DOI: 10.1016/j.copbio.2020.12.003] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Revised: 11/09/2020] [Accepted: 12/08/2020] [Indexed: 01/02/2023]
Abstract
Enzymes are core elements of biosynthetic pathways employed in the synthesis of numerous bioproducts. Here, we review enzyme promiscuity, enzyme engineering, enzyme immobilization, and cell-free systems as fundamental strategies of bioprocess development. Initially, promiscuous enzymes are the first candidates in the quest for new activities to power new, artificial, or bypass pathways that expand substrate range and catalyze the production of new products. If the activity or regulation of available enzymes is unsuitable for a process, protein engineering can be applied to improve them to the required level. When cell toxicity and low productivity cannot be engineered away, cell-free systems are an attractive option, especially in combination with enzyme immobilization that allows extended enzyme use. Overall, the above methods support powerful platforms for bioprocess development and optimization.
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Affiliation(s)
- Constantinos Katsimpouras
- Department of Chemical Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, 02139 MA, USA
| | - Gregory Stephanopoulos
- Department of Chemical Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, 02139 MA, USA.
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Li Y, Yang S, Ma D, Song W, Gao C, Liu L, Chen X. Microbial engineering for the production of C 2-C 6 organic acids. Nat Prod Rep 2021; 38:1518-1546. [PMID: 33410446 DOI: 10.1039/d0np00062k] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Covering: up to the end of 2020Organic acids, as building block compounds, have been widely used in food, pharmaceutical, plastic, and chemical industries. Until now, chemical synthesis is still the primary method for industrial-scale organic acid production. However, this process encounters some inevitable challenges, such as depletable petroleum resources, harsh reaction conditions and complex downstream processes. To solve these problems, microbial cell factories provide a promising approach for achieving the sustainable production of organic acids. However, some key metabolites in central carbon metabolism are strictly regulated by the network of cellular metabolism, resulting in the low productivity of organic acids. Thus, multiple metabolic engineering strategies have been developed to reprogram microbial cell factories to produce organic acids, including monocarboxylic acids, hydroxy carboxylic acids, amino carboxylic acids, dicarboxylic acids and monomeric units for polymers. These strategies mainly center on improving the catalytic efficiency of the enzymes to increase the conversion rate, balancing the multi-gene biosynthetic pathways to reduce the byproduct formation, strengthening the metabolic flux to promote the product biosynthesis, optimizing the metabolic network to adapt the environmental conditions and enhancing substrate utilization to broaden the substrate spectrum. Here, we describe the recent advances in producing C2-C6 organic acids by metabolic engineering strategies. In addition, we provide new insights as to when, what and how these strategies should be taken. Future challenges are also discussed in further advancing microbial engineering and establishing efficient biorefineries.
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Affiliation(s)
- Yang Li
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Road, Wuxi 214122, China.
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Goris T, Pérez‐Valero Á, Martínez I, Yi D, Fernández‐Calleja L, San León D, Bornscheuer UT, Magadán‐Corpas P, Lombó F, Nogales J. Repositioning microbial biotechnology against COVID-19: the case of microbial production of flavonoids. Microb Biotechnol 2021; 14:94-110. [PMID: 33047877 PMCID: PMC7675739 DOI: 10.1111/1751-7915.13675] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Revised: 09/17/2020] [Accepted: 09/18/2020] [Indexed: 12/19/2022] Open
Abstract
Coronavirus-related disease 2019 (COVID-19) became a pandemic in February 2020, and worldwide researchers try to tackle the disease with approved drugs of all kinds, or to develop novel compounds inhibiting viral spreading. Flavonoids, already investigated as antivirals in general, also might bear activities specific for the viral agent causing COVID-19, SARS-CoV-2. Microbial biotechnology and especially synthetic biology may help to produce flavonoids, which are exclusive plant secondary metabolites, at a larger scale or indeed to find novel pharmaceutically active flavonoids. Here, we review the state of the art in (i) antiviral activity of flavonoids specific for coronaviruses and (ii) results derived from computational studies, mostly docking studies mainly inhibiting specific coronaviral proteins such as the 3CL (main) protease, the spike protein or the RNA-dependent RNA polymerase. In the end, we strive towards a synthetic biology pipeline making the fast and tailored production of valuable antiviral flavonoids possible by applying the last concepts of division of labour through co-cultivation/microbial community approaches to the DBTL (Design, Build, Test, Learn) principle.
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Affiliation(s)
- Tobias Goris
- Department of Molecular Toxicology, Research Group Intestinal MicrobiologyGerman Institute of Human Nutrition Potsdam‐RehbrueckeArthur‐Scheunert‐Allee 114‐116NuthetalBrandenburg14558Germany
| | - Álvaro Pérez‐Valero
- Research Unit “Biotechnology in Nutraceuticals and Bioactive Compounds‐BIONUC”Departamento de Biología Funcional, Área de MicrobiologíaUniversidad de OviedoOviedoSpain
- Instituto Universitario de Oncología del Principado de AsturiasOviedoSpain
- Instituto de Investigación Sanitaria del Principado de AsturiasOviedoSpain
| | - Igor Martínez
- Department of Systems BiologyCentro Nacional de BiotecnologíaCSICMadridSpain
| | - Dong Yi
- Department of Biotechnology & Enzyme CatalysisInstitute of BiochemistryUniversity GreifswaldFelix‐Hausdorff‐Str. 4GreifswaldD‐17487Germany
| | - Luis Fernández‐Calleja
- Research Unit “Biotechnology in Nutraceuticals and Bioactive Compounds‐BIONUC”Departamento de Biología Funcional, Área de MicrobiologíaUniversidad de OviedoOviedoSpain
- Instituto Universitario de Oncología del Principado de AsturiasOviedoSpain
- Instituto de Investigación Sanitaria del Principado de AsturiasOviedoSpain
| | - David San León
- Department of Systems BiologyCentro Nacional de BiotecnologíaCSICMadridSpain
| | - Uwe T. Bornscheuer
- Department of Biotechnology & Enzyme CatalysisInstitute of BiochemistryUniversity GreifswaldFelix‐Hausdorff‐Str. 4GreifswaldD‐17487Germany
| | - Patricia Magadán‐Corpas
- Research Unit “Biotechnology in Nutraceuticals and Bioactive Compounds‐BIONUC”Departamento de Biología Funcional, Área de MicrobiologíaUniversidad de OviedoOviedoSpain
- Instituto Universitario de Oncología del Principado de AsturiasOviedoSpain
- Instituto de Investigación Sanitaria del Principado de AsturiasOviedoSpain
| | - Felipe Lombó
- Research Unit “Biotechnology in Nutraceuticals and Bioactive Compounds‐BIONUC”Departamento de Biología Funcional, Área de MicrobiologíaUniversidad de OviedoOviedoSpain
- Instituto Universitario de Oncología del Principado de AsturiasOviedoSpain
- Instituto de Investigación Sanitaria del Principado de AsturiasOviedoSpain
| | - Juan Nogales
- Department of Systems BiologyCentro Nacional de BiotecnologíaCSICMadridSpain
- Interdisciplinary Platform for Sustainable Plastics towards a Circular Economy‐Spanish National Research Council (SusPlast‐CSIC)MadridSpain
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