1
|
Dhingra S, Zhang Z, Lohans CT, Brewitz L, Schofield CJ. Substitution of 2-oxoglutarate alters reaction outcomes of the Pseudomonas savastanoi ethylene-forming enzyme. J Biol Chem 2024:107546. [PMID: 38992435 DOI: 10.1016/j.jbc.2024.107546] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2024] [Revised: 06/27/2024] [Accepted: 07/01/2024] [Indexed: 07/13/2024] Open
Abstract
In seeding plants, biosynthesis of the phytohormone ethylene, which regulates processes including fruit ripening and senescence, is catalyzed by 1-aminocyclopropyl-1-carboxylic acid (ACC) oxidase. The plant pathogen Pseudomonas savastanoi (previously classified as: P. syringae) employs a different type of ethylene-forming enzyme (psEFE), though from the same structural superfamily as ACC oxidase, to catalyze ethylene formation from 2-oxoglutarate (2OG) in an arginine dependent manner. psEFE also catalyzes the more typical oxidation of arginine to give L-Δ1-pyrroline-5-carboxylate (P5C), a reaction coupled to oxidative decarboxylation of 2OG giving succinate and CO2. We report on the effects of C3 and/or C4 substituted 2OG derivatives on the reaction modes of psEFE. 1H NMR assays, including using the pure shift method, reveal that, within our limits of detection, none of the tested 2OG derivatives is converted to an alkene; some are converted to the corresponding β-hydroxypropionate or succinate derivatives, with only the latter being coupled to arginine oxidation. The NMR results reveal that the nature of 2OG derivatization can affect the outcome of the bifurcating reaction, with some 2OG derivatives exclusively favoring the arginine oxidation pathway. Given that some of the tested 2OG derivatives are natural products, the results are of potential biological relevance. There are also opportunities for therapeutic or biocatalytic regulation of the outcomes of reactions catalyzed by 2OG-dependent oxygenases by the use of 2OG derivatives.
Collapse
Affiliation(s)
- Siddhant Dhingra
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford, 12 Mansfield Road, OX1 3TA, Oxford, United Kingdom
| | - Zhihong Zhang
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford, 12 Mansfield Road, OX1 3TA, Oxford, United Kingdom
| | - Christopher T Lohans
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford, 12 Mansfield Road, OX1 3TA, Oxford, United Kingdom
| | - Lennart Brewitz
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford, 12 Mansfield Road, OX1 3TA, Oxford, United Kingdom.
| | - Christopher J Schofield
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford, 12 Mansfield Road, OX1 3TA, Oxford, United Kingdom.
| |
Collapse
|
2
|
Kugler A, Stensjö K. Optimal energy and redox metabolism in the cyanobacterium Synechocystis sp. PCC 6803. NPJ Syst Biol Appl 2023; 9:47. [PMID: 37739963 PMCID: PMC10516873 DOI: 10.1038/s41540-023-00307-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2022] [Accepted: 09/01/2023] [Indexed: 09/24/2023] Open
Abstract
Understanding energy and redox homeostasis and carbon partitioning is crucial for systems metabolic engineering of cell factories. Carbon metabolism alone cannot achieve maximal accumulation of metabolites in production hosts, since an efficient production of target molecules requires energy and redox balance, in addition to carbon flow. The interplay between cofactor regeneration and heterologous production in photosynthetic microorganisms is not fully explored. To investigate the optimality of energy and redox metabolism, while overproducing alkenes-isobutene, isoprene, ethylene and 1-undecene, in the cyanobacterium Synechocystis sp. PCC 6803, we applied stoichiometric metabolic modelling. Our network-wide analysis indicates that the rate of NAD(P)H regeneration, rather than of ATP, controls ATP/NADPH ratio, and thereby bioproduction. The simulation also implies that energy and redox balance is interconnected with carbon and nitrogen metabolism. Furthermore, we show that an auxiliary pathway, composed of serine, one-carbon and glycine metabolism, supports cellular redox homeostasis and ATP cycling. The study revealed non-intuitive metabolic pathways required to enhance alkene production, which are mainly driven by a few key reactions carrying a high flux. We envision that the presented comparative in-silico metabolic analysis will guide the rational design of Synechocystis as a photobiological production platform of target chemicals.
Collapse
Affiliation(s)
- Amit Kugler
- Microbial Chemistry, Department of Chemistry-Ångström Laboratory, Uppsala University, Box 523, SE-751 20, Uppsala, Sweden
| | - Karin Stensjö
- Microbial Chemistry, Department of Chemistry-Ångström Laboratory, Uppsala University, Box 523, SE-751 20, Uppsala, Sweden.
| |
Collapse
|
3
|
Ye DY, Moon JH, Jung GY. Recent Progress in Metabolic Engineering of Escherichia coli for the Production of Various C4 and C5-Dicarboxylic Acids. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:10916-10931. [PMID: 37458388 DOI: 10.1021/acs.jafc.3c02156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/27/2023]
Abstract
As an alternative to petrochemical synthesis, well-established industrial microbes, such as Escherichia coli, are employed to produce a wide range of chemicals, including dicarboxylic acids (DCAs), which have significant potential in diverse areas including biodegradable polymers. The demand for biodegradable polymers has been steadily rising, prompting the development of efficient production pathways on four- (C4) and five-carbon (C5) DCAs derived from central carbon metabolism to meet the increased demand via the biosynthesis. In this context, E. coli is utilized to produce these DCAs through various metabolic engineering strategies, including the design or selection of metabolic pathways, pathway optimization, and enhancement of catalytic activity. This review aims to highlight the recent advancements in metabolic engineering techniques for the production of C4 and C5 DCAs in E. coli.
Collapse
Affiliation(s)
- Dae-Yeol Ye
- Department of Chemical Engineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk 37673, Republic of Korea
| | - Jo Hyun Moon
- Department of Chemical Engineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk 37673, Republic of Korea
| | - Gyoo Yeol Jung
- Department of Chemical Engineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk 37673, Republic of Korea
- School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk 37673, Republic of Korea
| |
Collapse
|
4
|
Vajravel S, Cid Gomes L, Rana A, Ottosson H. Toward combined photobiological-photochemical formation of kerosene-type biofuels: which small 1,3-diene photodimerizes most efficiently? Photochem Photobiol Sci 2023:10.1007/s43630-023-00418-0. [PMID: 37101106 DOI: 10.1007/s43630-023-00418-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Accepted: 04/03/2023] [Indexed: 04/28/2023]
Abstract
A transition from fossil- to bio-based hydrocarbon fuels is required to reduce greenhouse gas emissions; yet, traditional biomass cultivation for biofuel production competes with food production and impacts negatively on biodiversity. Recently, we reported a proof-of-principle study of a two-step photobiological-photochemical approach to kerosene biofuels in which a volatile hydrocarbon (isoprene) is produced by photosynthetic cyanobacteria, followed by its photochemical dimerization into C10 hydrocarbons. Both steps can utilize solar irradiation. Here, we report the triplet state (T1)-sensitized photodimerization of a broader set of small 1,3-dienes to identify which structural features lead to rapid photodimerization. Neat 1,3-cyclohexadiene gave the highest yield (93%) after 24 h of irradiation at 365 nm, followed by isoprene (66%). The long triplet lifetime of 1,3-cyclohexadiene, which is two orders of magnitude longer than those of acyclic dienes, is key to its high photoreactivity and stem from its planar T1 state structure. In contrast, while isoprene is conformationally flexible, it has both photochemical and photobiological advantages, as it is the most reactive among the volatile 1,3-dienes and it can be produced by cyanobacteria. Finally, we explored the influence of solvent viscosity, diene concentration, and triplet sensitizer loading on the photodimerization, with a focus on conditions that are amenable when the dienes are produced photobiologically. Our findings should be useful for the further development of the two-step photobiological-photochemical approach to kerosene biofuels.
Collapse
Affiliation(s)
- Sindhujaa Vajravel
- Department of Chemistry-Ångström Laboratory, Uppsala University, Box 523, 751 20, Uppsala, Sweden
| | - Leandro Cid Gomes
- Department of Chemistry-Ångström Laboratory, Uppsala University, Box 523, 751 20, Uppsala, Sweden
| | - Anup Rana
- Department of Chemistry-Ångström Laboratory, Uppsala University, Box 523, 751 20, Uppsala, Sweden
| | - Henrik Ottosson
- Department of Chemistry-Ångström Laboratory, Uppsala University, Box 523, 751 20, Uppsala, Sweden.
| |
Collapse
|
5
|
Klaehn JR, Orme CJ, Ginosar DM. Separation of isoprene from biologically-derived gas streams. SEP SCI TECHNOL 2022. [DOI: 10.1080/01496395.2022.2050756] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- John R. Klaehn
- Biological and Chemical Processing and Engineering Department, Idaho National Laboratory, Idaho Falls, Idaho, United States
| | - Christopher J. Orme
- Biological and Chemical Processing and Engineering Department, Idaho National Laboratory, Idaho Falls, Idaho, United States
| | - Daniel M. Ginosar
- Biological and Chemical Processing and Engineering Department, Idaho National Laboratory, Idaho Falls, Idaho, United States
| |
Collapse
|
6
|
Sawant KR, Savvashe P, Pal D, Sarnaik A, Lali A, Pandit R. Progressive transitional studies of engineered Synechococcus from laboratory to outdoor pilot-scale cultivation for production of ethylene. BIORESOURCE TECHNOLOGY 2021; 341:125852. [PMID: 34479144 DOI: 10.1016/j.biortech.2021.125852] [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: 06/29/2021] [Revised: 08/21/2021] [Accepted: 08/24/2021] [Indexed: 06/13/2023]
Abstract
Cyanobacterial research is impeded by the substantial discrepancies between laboratory studies and outdoor performances, despite successful demonstrations of genetically engineered strains for array of compounds. Therefore, evaluation of adaptive responses is necessary to achieve outdoor scale-up cultivation of cyanobacteria. Under current study, cyanobacterium Synechococcus elongatusPCC7942 engineered for ethylene biosynthesis, was gradually acclimatised, ensuring sustained and progressive transition from laboratory to outdoor conditions. Bubble size of 4.9 ± 0.2 mm and air-flow rate of 0.05 vvm in BG11 supplemented with 5 g/L bicarbonate giving mass transfer coefficient (KLa) of 10.48 h-1 yielded highest specific growth rate (0.24 h-1) with the transformants. At the 100 L photobioreactor scale, ethylene productivity of 1.5 mL.L-1.h-1 was achieved. A comprehensive investigation on photosynthetic responses of the transformants adapted to the outdoor conditions exhibited interesting photosynthetic electron transport regulations, involving antenna density modulation in response to diurnal and dynamic light transitions, indicating successful transition.
Collapse
Affiliation(s)
- Kaustubh R Sawant
- DBT-ICT Centre for Energy Biosciences, Institute of Chemical Technology, Matunga, Mumbai, 400019, India
| | - Prashant Savvashe
- DBT-ICT Centre for Energy Biosciences, Institute of Chemical Technology, Matunga, Mumbai, 400019, India; Department of Chemical Engineering, Institute of Chemical Technology, Matunga, Mumbai, 400019, India
| | - Divyani Pal
- DBT-ICT Centre for Energy Biosciences, Institute of Chemical Technology, Matunga, Mumbai, 400019, India
| | - Aditya Sarnaik
- DBT-ICT Centre for Energy Biosciences, Institute of Chemical Technology, Matunga, Mumbai, 400019, India; Chemical Engineering Department, School for Engineering of Matter, Transport and Energy, Arizona State University, Tempe, AZ, USA
| | - Arvind Lali
- Department of Chemical Engineering, Institute of Chemical Technology, Matunga, Mumbai, 400019, India
| | - Reena Pandit
- DBT-ICT Centre for Energy Biosciences, Institute of Chemical Technology, Matunga, Mumbai, 400019, India.
| |
Collapse
|
7
|
Saaret A, Villiers B, Stricher F, Anissimova M, Cadillon M, Spiess R, Hay S, Leys D. Directed evolution of prenylated FMN-dependent Fdc supports efficient in vivo isobutene production. Nat Commun 2021; 12:5300. [PMID: 34489427 PMCID: PMC8421414 DOI: 10.1038/s41467-021-25598-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Accepted: 07/29/2021] [Indexed: 11/30/2022] Open
Abstract
Isobutene is a high value gaseous alkene used as fuel additive and a chemical building block. As an alternative to fossil fuel derived isobutene, we here develop a modified mevalonate pathway for the production of isobutene from glucose in vivo. The final step in the pathway consists of the decarboxylation of 3-methylcrotonic acid, catalysed by an evolved ferulic acid decarboxylase (Fdc) enzyme. Fdc belongs to the prFMN-dependent UbiD enzyme family that catalyses reversible decarboxylation of (hetero)aromatic acids or acrylic acids with extended conjugation. Following a screen of an Fdc library for inherent 3-methylcrotonic acid decarboxylase activity, directed evolution yields variants with up to an 80-fold increase in activity. Crystal structures of the evolved variants reveal that changes in the substrate binding pocket are responsible for increased selectivity. Solution and computational studies suggest that isobutene cycloelimination is rate limiting and strictly dependent on presence of the 3-methyl group. Isobutene is a high value gaseous alkene that is widely used as fuel additive and a chemical building block. Here, the authors report an alternative pathway for isobutene bioproduction by directed evolution of prenylated FMN-dependent ferulic acid decarboxylase.
Collapse
Affiliation(s)
- Annica Saaret
- Department of Chemistry, Manchester Institute for Biotechnology, University of Manchester, Manchester, UK
| | | | | | | | | | - Reynard Spiess
- Department of Chemistry, Manchester Institute for Biotechnology, University of Manchester, Manchester, UK
| | - Sam Hay
- Department of Chemistry, Manchester Institute for Biotechnology, University of Manchester, Manchester, UK
| | - David Leys
- Department of Chemistry, Manchester Institute for Biotechnology, University of Manchester, Manchester, UK.
| |
Collapse
|
8
|
Fouilloux H, Thomas CM. Production and Polymerization of Biobased Acrylates and Analogs. Macromol Rapid Commun 2021; 42:e2000530. [DOI: 10.1002/marc.202000530] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Revised: 11/23/2020] [Indexed: 12/13/2022]
Affiliation(s)
- Hugo Fouilloux
- PSL University Chimie ParisTech CNRS Institut de Recherche de Chimie Paris Paris 75005 France
| | - Christophe M. Thomas
- PSL University Chimie ParisTech CNRS Institut de Recherche de Chimie Paris Paris 75005 France
| |
Collapse
|
9
|
Wang Z, Zhang R, Yang Q, Zhang J, Zhao Y, Zheng Y, Yang J. Recent advances in the biosynthesis of isoprenoids in engineered Saccharomyces cerevisiae. ADVANCES IN APPLIED MICROBIOLOGY 2020; 114:1-35. [PMID: 33934850 DOI: 10.1016/bs.aambs.2020.11.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Isoprenoids, as the largest group of chemicals in the domains of life, constitute more than 50,000 members. These compounds consist of different numbers of isoprene units (C5H8), by which they are typically classified into hemiterpenoids (C5), monoterpenoids (C10), sesquiterpenoids (C15), diterpenoids (C20), triterpenoids (C30), and tetraterpenoids (C40). In recent years, isoprenoids have been employed as food additives, in the pharmaceutical industry, as advanced biofuels, and so on. To realize the sufficient and efficient production of valuable isoprenoids on an industrial scale, fermentation using engineered microorganisms is a promising strategy compared to traditional plant extraction and chemical synthesis. Due to the advantages of mature genetic manipulation, robustness and applicability to industrial bioprocesses, Saccharomyces cerevisiae has become an attractive microbial host for biochemical production, including that of various isoprenoids. In this review, we summarized the advances in the biosynthesis of isoprenoids in engineered S. cerevisiae over several decades, including synthetic pathway engineering, microbial host engineering, and central carbon pathway engineering. Furthermore, the challenges and corresponding strategies towards improving isoprenoid production in engineered S. cerevisiae were also summarized. Finally, suggestions and directions for isoprenoid production in engineered S. cerevisiae in the future are discussed.
Collapse
Affiliation(s)
- Zhaobao Wang
- Energy-Rich Compounds Production by Photosynthetic Carbon Fixation Research Center, Shandong Key Lab of Applied Mycology, College of Life Sciences, Qingdao Agricultural University, Qingdao, China
| | - Rubing Zhang
- CAS Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
| | - Qun Yang
- Energy-Rich Compounds Production by Photosynthetic Carbon Fixation Research Center, Shandong Key Lab of Applied Mycology, College of Life Sciences, Qingdao Agricultural University, Qingdao, China
| | - Jintian Zhang
- College of Biochemical Engineering, Beijing Union University, Beijing, China
| | - Youxi Zhao
- College of Biochemical Engineering, Beijing Union University, Beijing, China
| | - Yanning Zheng
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Jianming Yang
- Energy-Rich Compounds Production by Photosynthetic Carbon Fixation Research Center, Shandong Key Lab of Applied Mycology, College of Life Sciences, Qingdao Agricultural University, Qingdao, China.
| |
Collapse
|
10
|
Nitschel R, Ankenbauer A, Welsch I, Wirth NT, Massner C, Ahmad N, McColm S, Borges F, Fotheringham I, Takors R, Blombach B. Engineering Pseudomonas putida KT2440 for the production of isobutanol. Eng Life Sci 2020; 20:148-159. [PMID: 32874178 PMCID: PMC7447888 DOI: 10.1002/elsc.201900151] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Revised: 12/08/2019] [Accepted: 12/10/2019] [Indexed: 11/06/2022] Open
Abstract
We engineered P. putida for the production of isobutanol from glucose by preventing product and precursor degradation, inactivation of the soluble transhydrogenase SthA, overexpression of the native ilvC and ilvD genes, and implementation of the feedback-resistant acetolactate synthase AlsS from Bacillus subtilis, ketoacid decarboxylase KivD from Lactococcus lactis, and aldehyde dehydrogenase YqhD from Escherichia coli. The resulting strain P. putida Iso2 produced isobutanol with a substrate specific product yield (Y Iso/S) of 22 ± 2 mg per gram of glucose under aerobic conditions. Furthermore, we identified the ketoacid decarboxylase from Carnobacterium maltaromaticum to be a suitable alternative for isobutanol production, since replacement of kivD from L. lactis in P. putida Iso2 by the variant from C. maltaromaticum yielded an identical YIso/S. Although P. putida is regarded as obligate aerobic, we show that under oxygen deprivation conditions this bacterium does not grow, remains metabolically active, and that engineered producer strains secreted isobutanol also under the non-growing conditions.
Collapse
Affiliation(s)
- Robert Nitschel
- Institute of Biochemical EngineeringUniversity of StuttgartStuttgartGermany
| | - Andreas Ankenbauer
- Institute of Biochemical EngineeringUniversity of StuttgartStuttgartGermany
| | - Ilona Welsch
- Institute of Biochemical EngineeringUniversity of StuttgartStuttgartGermany
| | - Nicolas T. Wirth
- Institute of Biochemical EngineeringUniversity of StuttgartStuttgartGermany
| | - Christoph Massner
- Institute of Biochemical EngineeringUniversity of StuttgartStuttgartGermany
| | - Naveed Ahmad
- Ingenza Ltd., Roslin Innovation CentreCharnock Bradley Building, Easter Bush CampusRoslinUK
| | - Stephen McColm
- Ingenza Ltd., Roslin Innovation CentreCharnock Bradley Building, Easter Bush CampusRoslinUK
| | - Frédéric Borges
- Laboratoire d'Ingénierie des Biomolécules (LIBio)Université de LorraineNancyFrance
| | - Ian Fotheringham
- Ingenza Ltd., Roslin Innovation CentreCharnock Bradley Building, Easter Bush CampusRoslinUK
| | - Ralf Takors
- Institute of Biochemical EngineeringUniversity of StuttgartStuttgartGermany
| | - Bastian Blombach
- Institute of Biochemical EngineeringUniversity of StuttgartStuttgartGermany
- Microbial Biotechnology, Campus Straubing for Biotechnology and SustainabilityTechnical University of MunichStraubingGermany
| |
Collapse
|
11
|
Wang Z, Ganewatta MS, Tang C. Sustainable polymers from biomass: Bridging chemistry with materials and processing. Prog Polym Sci 2020. [DOI: 10.1016/j.progpolymsci.2019.101197] [Citation(s) in RCA: 63] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
|