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Maurya R, Gohil N, Nixon S, Kumar N, Noronha SB, Dhali D, Trabelsi H, Alzahrani KJ, Reshamwala SMS, Awasthi MK, Ramakrishna S, Singh V. Rewiring of metabolic pathways in yeasts for sustainable production of biofuels. BIORESOURCE TECHNOLOGY 2023; 372:128668. [PMID: 36693507 DOI: 10.1016/j.biortech.2023.128668] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 01/19/2023] [Accepted: 01/20/2023] [Indexed: 06/17/2023]
Abstract
The ever-increasing global energy demand has led world towards negative repercussions such as depletion of fossil fuels, pollution, global warming and climate change. Designing microbial cell factories for the sustainable production of biofuels is therefore an active area of research. Different yeast cells have been successfully engineered using synthetic biology and metabolic engineering approaches for the production of various biofuels. In the present article, recent advancements in genetic engineering strategies for production of bioalcohols, isoprenoid-based biofuels and biodiesels in different yeast chassis designs are reviewed, along with challenges that must be overcome for efficient and high titre production of biofuels.
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Affiliation(s)
- Rupesh Maurya
- Department of Biosciences, School of Science, Indrashil University, Rajpur, Mehsana 382715, Gujarat, India
| | - Nisarg Gohil
- Department of Biosciences, School of Science, Indrashil University, Rajpur, Mehsana 382715, Gujarat, India
| | - Snovia Nixon
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Mumbai, India
| | - Nilesh Kumar
- M.Tech. Programme in Bioprocess Engineering, Institute of Chemical Technology, Mumbai, India; DBT-ICT Centre for Energy Biosciences, Institute of Chemical Technology, Mumbai, India
| | - Santosh B Noronha
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Mumbai, India
| | - Debarun Dhali
- EV Biotech BV, Zernikelaan 8, 9747 AA Groningen, The Netherlands
| | - Heykel Trabelsi
- Carbocode GmbH, Byk-Gulden-Strasse 2, 78467 Konstanz, Germany
| | - Khalid J Alzahrani
- Department of Clinical Laboratories Sciences, College of Applied Medical Sciences, Taif University, P.O. Box 11099, Taif 21944, Saudi Arabia
| | | | - Mukesh Kumar Awasthi
- College of Natural Resources and Environment, Northwest A&F University, Yangling 712100, China
| | - Suresh Ramakrishna
- College of Medicine, Hanyang University, Seoul, South Korea; Graduate School of Biomedical Science and Engineering, Hanyang University, Seoul, South Korea
| | - Vijai Singh
- Department of Biosciences, School of Science, Indrashil University, Rajpur, Mehsana 382715, Gujarat, India.
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Jeung K, Kim S, Yeon Lee J, Yeol Jung G. Optimization of mevalonate production using acetate by precursor balancing and flux redistribution in Escherichia coli. J IND ENG CHEM 2023. [DOI: 10.1016/j.jiec.2022.12.049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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Wang X, Baidoo EEK, Kakumanu R, Xie S, Mukhopadhyay A, Lee TS. Engineering isoprenoids production in metabolically versatile microbial host Pseudomonas putida. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2022; 15:137. [PMID: 36510293 PMCID: PMC9743605 DOI: 10.1186/s13068-022-02235-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Accepted: 12/04/2022] [Indexed: 06/17/2023]
Abstract
With the increasing need for microbial bioproduction to replace petrochemicals, it is critical to develop a new industrial microbial workhorse that improves the conversion of lignocellulosic carbon to biofuels and bioproducts in an economically feasible manner. Pseudomonas putida KT2440 is a promising microbial host due to its capability to grow on a broad range of carbon sources and its high tolerance to xenobiotics. In this study, we engineered P. putida KT2440 to produce isoprenoids, a vast category of compounds that provide routes to many petrochemical replacements. A heterologous mevalonate (MVA) pathway was engineered to produce potential biofuels isoprenol (C5) and epi-isozizaene (C15) for the first time in P. putida. We compared the difference between three different isoprenoid pathways in P. putida on isoprenol production and achieved 104 mg/L of isoprenol production in a batch flask experiment through optimization of the strain. As P. putida can natively consume isoprenol, we investigated how to prevent this self-consumption. We discovered that supplementing L-glutamate in the medium can effectively prevent isoprenol consumption in P. putida and metabolomics analysis showed an insufficient energy availability and an imbalanced redox status during isoprenol degradation. We also showed that the engineered P. putida strain can produce isoprenol using aromatic substrates such as p-coumarate as the sole carbon source, and this result demonstrates that P. putida is a valuable microbial chassis for isoprenoids to achieve sustainable biofuel production from lignocellulosic biomass.
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Affiliation(s)
- Xi Wang
- Joint BioEnergy Institute (JBEI), 5885 Hollis St., Emeryville, CA, 94608, USA
- Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Edward E K Baidoo
- Joint BioEnergy Institute (JBEI), 5885 Hollis St., Emeryville, CA, 94608, USA
- Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Ramu Kakumanu
- Joint BioEnergy Institute (JBEI), 5885 Hollis St., Emeryville, CA, 94608, USA
- Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Silvia Xie
- Joint BioEnergy Institute (JBEI), 5885 Hollis St., Emeryville, CA, 94608, USA
- Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
- Department of Molecular & Cell Biology, University of California, Berkeley, CA, 94720, USA
| | - Aindrila Mukhopadhyay
- Joint BioEnergy Institute (JBEI), 5885 Hollis St., Emeryville, CA, 94608, USA
- Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Taek Soon Lee
- Joint BioEnergy Institute (JBEI), 5885 Hollis St., Emeryville, CA, 94608, USA.
- Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.
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Nirati Y, Purushotham N, Alagesan S. Quantitative insight into the metabolism of isoprene-producing Synechocystis sp. PCC 6803 using steady state 13C-MFA. PHOTOSYNTHESIS RESEARCH 2022; 154:195-206. [PMID: 36070060 DOI: 10.1007/s11120-022-00957-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Accepted: 08/24/2022] [Indexed: 06/15/2023]
Abstract
Cyanobacteria are photosynthetic bacteria, widely studied for the conversion of atmospheric carbon dioxide to useful platform chemicals. Isoprene is one such industrially important chemical, primarily used for production of synthetic rubber and biofuels. Synechocystis sp. PCC 6803, a genetically amenable cyanobacterium, produces isoprene on heterologous expression of isoprene synthase gene, albeit in very low quantities. Rationalized metabolic engineering to re-route the carbon flux for enhanced isoprene production requires in-dept knowledge of the metabolic flux distribution in the cell. Hence, in the present study, we undertook steady state 13C-metabolic flux analysis of glucose-tolerant wild-type (GTN) and isoprene-producing recombinant (ISP) Synechocystis sp. to understand and compare the carbon flux distribution in the two strains. The R-values for amino acids, flux analysis predictions and gene expression profiles emphasized predominance of Calvin cycle and glycogen metabolism in GTN. Alternatively, flux analysis predicted higher activity of the anaplerotic pathway through phosphoenolpyruvate carboxylase and malic enzyme in ISP. The striking difference in the Calvin cycle, glycogen metabolism and anaplerotic pathway activity in GTN and ISP suggested a possible role of energy molecules (ATP and NADPH) in regulating the carbon flux distribution in GTN and ISP. This claim was further supported by the transcript level of selected genes of the electron transport chain. This study provides the first quantitative insight into the carbon flux distribution of isoprene-producing cyanobacterium, information critical for developing Synechocystis sp. as a single cell factory for isoprenoid/terpenoid production.
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Affiliation(s)
- Yasha Nirati
- Institute of Bioinformatics and Applied Biotechnology (IBAB), Bengaluru, 560100, India
| | - Nidhish Purushotham
- Institute of Bioinformatics and Applied Biotechnology (IBAB), Bengaluru, 560100, India
- Dayananda Sagar University, Bengaluru, India
| | - Swathi Alagesan
- Institute of Bioinformatics and Applied Biotechnology (IBAB), Bengaluru, 560100, India.
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Rinaldi MA, Tait S, Toogood HS, Scrutton NS. Bioproduction of Linalool From Paper Mill Waste. Front Bioeng Biotechnol 2022; 10:892896. [PMID: 35711639 PMCID: PMC9195575 DOI: 10.3389/fbioe.2022.892896] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Accepted: 05/09/2022] [Indexed: 11/18/2022] Open
Abstract
A key challenge in chemicals biomanufacturing is the maintenance of stable, highly productive microbial strains to enable cost-effective fermentation at scale. A “cookie-cutter” approach to microbial engineering is often used to optimize host stability and productivity. This can involve identifying potential limitations in strain characteristics followed by attempts to systematically optimize production strains by targeted engineering. Such targeted approaches however do not always lead to the desired traits. Here, we demonstrate both ‘hit and miss’ outcomes of targeted approaches in attempts to generate a stable Escherichia coli strain for the bioproduction of the monoterpenoid linalool, a fragrance molecule of industrial interest. First, we stabilized linalool production strains by eliminating repetitive sequences responsible for excision of pathway components in plasmid constructs that encode the pathway for linalool production. These optimized pathway constructs were then integrated within the genome of E. coli in three parts to eliminate a need for antibiotics to maintain linalool production. Additional strategies were also employed including: reduction in cytotoxicity of linalool by adaptive laboratory evolution and modification or homologous gene replacement of key bottleneck enzymes GPPS/LinS. Our study highlights that a major factor influencing linalool titres in E. coli is the stability of the genetic construct against excision or similar recombination events. Other factors, such as decreasing linalool cytotoxicity and changing pathway genes, did not lead to improvements in the stability or titres obtained. With the objective of reducing fermentation costs at scale, the use of minimal base medium containing paper mill wastewater secondary paper fiber as sole carbon source was also investigated. This involved simultaneous saccharification and fermentation using either supplemental cellulase blends or by co-expressing secretable cellulases in E. coli containing the stabilized linalool production pathway. Combined, this study has demonstrated a stable method for linalool production using an abundant and low-cost feedstock and improved production strains, providing an important proof-of-concept for chemicals production from paper mill waste streams. For scaled production, optimization will be required, using more holistic approaches that involve further rounds of microbial engineering and fermentation process development.
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Affiliation(s)
- Mauro A Rinaldi
- Future Biomanufacturing Research Hub, Manchester, United Kingdom.,Manchester Institute of Biotechnology, The University of Manchester, Manchester, United Kingdom
| | - Shirley Tait
- Manchester Institute of Biotechnology, The University of Manchester, Manchester, United Kingdom
| | - Helen S Toogood
- Future Biomanufacturing Research Hub, Manchester, United Kingdom.,Manchester Institute of Biotechnology, The University of Manchester, Manchester, United Kingdom
| | - Nigel S Scrutton
- Future Biomanufacturing Research Hub, Manchester, United Kingdom.,Manchester Institute of Biotechnology, The University of Manchester, Manchester, United Kingdom.,C3 Biotechnologies (Maritime and Aerospace) Ltd, Lancaster, United Kingdom
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Kothandaraman J, Cosimbescu L, Swita MS. Solvent-Induced Selectivity of Isoprene From Bio-Derived Prenol. Front Chem 2022; 10:879129. [PMID: 35655703 PMCID: PMC9152107 DOI: 10.3389/fchem.2022.879129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Accepted: 04/26/2022] [Indexed: 11/25/2022] Open
Abstract
In this work we demonstrate the selective catalytic conversion of prenol, which is an allylic alcohol that can be prepared from renewable resources to isoprene. The catalyst is an inexpensive molybdenum complex (Molyvan L) designed and used as an additive for lubricants. Isoprene is generated under relatively mild reaction parameters at 130–150°C, for 2 h, under vapor pressure conditions that do not exceed 50 psi. Two cases were studied: one in which Molyvan L was dissolved in a base oil at 1% concentration (weight/weight) and then mixed with a solvent and prenol and the other in which neat Molyvan L was introduced in the reaction and the base oil was replaced with the solvent and prenol. We investigated the selectivity of the reaction using the following solvents in both cases: dodecane, dodecanol, isododecane, octane, blendstock for oxygenate blending (BOB3), a fuel surrogate, a polyalphaolefin (PAO4), and methoxy polyethylene glycol (methoxy PEG350). Although conversion of prenol was above 94% in all experiments, isoprene was formed with various degrees of efficiency alongside a prenol isomeric alcohol, diprenyl ether and mixed ether via intramolecular and intermolecular dehydration reactions. Dodecane appeared to have the highest level of selectivity initially in base oil so we studied the effect of various dodecane-like solvents on isoprene yield and product profile. Surprisingly, octane (similar to dodecane) and isododecane (branched alkane) generated insignificant amounts of byproducts, essentially providing the highly desired isoprene with a very high selectivity. Branching of the solvent does not appear to have an effect on selectivity. Another advantage of this catalyst is the low loadings required to effect the transformation; that is, 0.25% (weight/volume) in the cases using neat Molyvan L and 0.5% (weight/volume) in the cases using Molyvan L dissolved in the base oil. Provided that prenol can be produced in large scale from bioresources, this work would enable the sustainable production of isoprene, in good yield, and with very high selectivity.
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Leferink NGH, Escorcia AM, Ouwersloot BR, Johanissen LO, Hay S, van der Kamp MW, Scrutton NS. Molecular Determinants of Carbocation Cyclisation in Bacterial Monoterpene Synthases. Chembiochem 2022; 23:e202100688. [PMID: 35005823 PMCID: PMC9303655 DOI: 10.1002/cbic.202100688] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 01/07/2022] [Indexed: 11/24/2022]
Abstract
Monoterpene synthases are often promiscuous enzymes, yielding product mixtures rather than pure compounds due to the nature of the branched reaction mechanism involving reactive carbocations. Two previously identified bacterial monoterpene synthases, a linalool synthase (bLinS) and a cineole synthase (bCinS), produce nearly pure linalool and cineole from geranyl diphosphate, respectively. We used a combined experimental and computational approach to identify critical residues involved in bacterial monoterpenoid synthesis. Phe77 is essential for bCinS activity, guiding the linear carbocation intermediate towards the formation of the cyclic α-terpinyl intermediate; removal of the aromatic ring results in variants that produce acyclic products only. Computational chemistry confirmed the importance of Phe77 in carbocation stabilisation. Phe74, Phe78 and Phe179 are involved in maintaining the active site shape in bCinS without a specific role for the aromatic ring. Phe295 in bLinS, and the equivalent Ala301 in bCinS, are essential for linalool and cineole formation, respectively. Where Phe295 places steric constraints on the carbocation intermediates, Ala301 is essential for bCinS initial cyclisation and activity. Our multidisciplinary approach gives unique insights into how carefully placed amino acid residues in the active site can direct carbocations down specific paths, by placing steric constraints or offering stabilisation via cation-π interactions.
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Affiliation(s)
- Nicole G H Leferink
- Future Biomanufacturing Research Hub, Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK
- Manchester Institute of Biotechnology and Department of Chemistry, University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK
| | - Andrés M Escorcia
- School of Biochemistry, University of Bristol, University Walk, Bristol, BS8 1TD, UK
| | - Bodi R Ouwersloot
- Future Biomanufacturing Research Hub, Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK
- Manchester Institute of Biotechnology and Department of Chemistry, University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK
| | - Linus O Johanissen
- Manchester Institute of Biotechnology and Department of Chemistry, University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK
| | - Sam Hay
- Manchester Institute of Biotechnology and Department of Chemistry, University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK
| | - Marc W van der Kamp
- School of Biochemistry, University of Bristol, University Walk, Bristol, BS8 1TD, UK
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Cantock's Close, Bristol, BS8 1TS, UK
| | - Nigel S Scrutton
- Future Biomanufacturing Research Hub, Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK
- Manchester Institute of Biotechnology and Department of Chemistry, University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK
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Leferink NGH, Scrutton NS. Predictive Engineering of Class I Terpene Synthases Using Experimental and Computational Approaches. Chembiochem 2022; 23:e202100484. [PMID: 34669250 PMCID: PMC9298401 DOI: 10.1002/cbic.202100484] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 10/15/2021] [Indexed: 12/18/2022]
Abstract
Terpenoids are a highly diverse group of natural products with considerable industrial interest. Increasingly, engineered microbes are used for the production of terpenoids to replace natural extracts and chemical synthesis. Terpene synthases (TSs) show a high level of functional plasticity and are responsible for the vast structural diversity observed in natural terpenoids. Their relatively inert active sites guide intrinsically reactive linear carbocation intermediates along one of many cyclisation paths via exertion of subtle steric and electrostatic control. Due to the absence of a strong protein interaction with these intermediates, there is a remarkable lack of sequence-function relationship within the TS family, making product-outcome predictions from sequences alone challenging. This, in combination with the fact that many TSs produce multiple products from a single substrate hampers the design and use of TSs in the biomanufacturing of terpenoids. This review highlights recent advances in genome mining, computational modelling, high-throughput screening, and machine-learning that will allow more predictive engineering of these fascinating enzymes in the near future.
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Affiliation(s)
- Nicole G. H. Leferink
- Future Biomanufacturing Research HubManchester Institute of BiotechnologyDepartment of ChemistrySchool of Natural SciencesThe University of Manchester131 Princess StreetManchesterM1 7DNUK
| | - Nigel S. Scrutton
- Future Biomanufacturing Research HubManchester Institute of BiotechnologyDepartment of ChemistrySchool of Natural SciencesThe University of Manchester131 Princess StreetManchesterM1 7DNUK
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Recent Progress and Trends in the Development of Microbial Biofuels from Solid Waste—A Review. ENERGIES 2021. [DOI: 10.3390/en14196011] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
This review covers the recent progress in the design and application of microbial biofuels, assessing the advancement of genetic engineering undertakings and their marketability, and lignocellulosic biomass pretreatment issues. Municipal solid waste (MSW) is a promising sustainable biofuel feedstock due to its high content of lignocellulosic fiber. In this review, we compared the production of fatty alcohols, alkanes, and n-butanol from residual biogenic waste and the environmental/economic parameters to that of conventional biofuels. New synthetic biology tools can be used to engineer fermentation pathways within micro-organisms to produce long-chain alcohols, isoprenoids, long-chain fatty acids, and esters, along with alkanes, as substitutes to petroleum-derived fuels. Biotechnological advances have struggled to address problems with bioethanol, such as lower energy density compared to gasoline and high corrosive and hygroscopic qualities that restrict its application in present infrastructure. Biofuels derived from the organic fraction of municipal solid waste (OFMSW) may have less environmental impacts compared to traditional fuel production, with the added benefit of lower production costs. Unfortunately, current advanced biofuel production suffers low production rates, which hinders commercial scaling-up efforts. Microbial-produced biofuels can address low productivity while increasing the spectrum of produced bioenergy molecules.
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Shukla V, Runthala A, Rajput VS, Chandrasai PD, Tripathi A, Phulara SC. Computational and synthetic biology approaches for the biosynthesis of antiviral and anticancer terpenoids from Bacillus subtilis. Med Chem 2021; 18:307-322. [PMID: 34254925 DOI: 10.2174/1573406417666210712211557] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Revised: 04/18/2021] [Accepted: 04/25/2021] [Indexed: 11/22/2022]
Abstract
Recent advancements in medicinal research have identified several antiviral and anticancer terpenoids that are usually deployed as a source of flavor, fragrances and pharmaceuticals. Under the current COVID-19 pandemic conditions, natural therapeutics with least side effects are the need of the hour to save the patients, especially, which are pre-affected with other medical complications. Although, plants are the major sources of terpenoids; however, for the environmental concerns, the global interest has shifted to the biocatalytic production of molecules from microbial sources. The gram-positive bacterium Bacillus subtilis is a suitable host in this regard due to its GRAS (generally regarded as safe) status, ease in genetic manipulations and wide industrial acceptability. The B. subtilis synthesizes its terpenoid molecules from 1-deoxy-d-xylulose-5-phosphate (DXP) pathway, a common route in almost all microbial strains. Here, we summarize the computational and synthetic biology approaches to improve the production of terpenoid-based therapeutics from B. subtilis by utilizing DXP pathway. We focus on the in-silico approaches for screening the functionally improved enzyme-variants of the two crucial enzymes namely, the DXP synthase (DXS) and farnesyl pyrophosphate synthase (FPPS). The approaches for engineering the active sites are subsequently explained. It will be helpful to construct the functionally improved enzymes for the high-yield production of terpenoid-based anticancer and antiviral metabolites, which would help to reduce the cost and improve the availability of such therapeutics for the humankind.
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Affiliation(s)
- Vibha Shukla
- Food, Drug and Chemical Toxicology Group, CSIR-Indian Institute of Toxicology Research, Vishvigyan Bhawan, 31 Mahatma Gandhi Marg, Lucknow-226001, India
| | - Ashish Runthala
- Department of Biotechnology, Koneru Lakshmaiah Education Foundation, Vaddeswaram, Guntur-522502, Andhra Pradesh, India
| | | | - Potla Durthi Chandrasai
- Department of Biotechnology, National Institute of Technology Warangal, Warangal-506004, Telangana, India
| | - Anurag Tripathi
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad- 201002, India
| | - Suresh Chandra Phulara
- Department of Biotechnology, Koneru Lakshmaiah Education Foundation, Vaddeswaram, Guntur-522502, Andhra Pradesh, India
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Ferraz CA, Leferink NGH, Kosov I, Scrutton NS. Isopentenol Utilization Pathway for the Production of Linalool in Escherichia coli Using an Improved Bacterial Linalool/Nerolidol Synthase. Chembiochem 2021; 22:2325-2334. [PMID: 33938632 PMCID: PMC8362072 DOI: 10.1002/cbic.202100110] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Revised: 05/02/2021] [Indexed: 11/24/2022]
Abstract
Linalool is a monoterpenoid used as a fragrance ingredient, and is a promising source for alternative fuels. Synthetic biology offers attractive alternative production methods compared to extraction from natural sources and chemical synthesis. Linalool/nerolidol synthase (bLinS) from Streptomyces clavuligerus is a bifunctional enzyme, producing linalool as well as the sesquiterpenoid nerolidol when expressed in engineered Escherichia coli harbouring a precursor terpenoid pathway such as the mevalonate (MVA) pathway. Here we identified two residues important for substrate selection by bLinS, L72 and V214, where the introduction of bulkier residues results in variants with reduced nerolidol formation. Terpenoid production using canonical precursor pathways is usually limited by numerous and highly regulated enzymatic steps. Here we compared the canonical MVA pathway to the non-canonical isopentenol utilization (IU) pathway to produce linalool using the optimised bLinS variant. The IU pathway uses isoprenol and prenol to produce linalool in only five steps. Adjusting substrate, plasmid system, inducer concentration, and cell strain directs the flux towards monoterpenoids. Our integrated approach, combining enzyme engineering with flux control using the artificial IU pathway, resulted in high purity production of the commercially attractive monoterpenoid linalool, and will guide future efforts towards efficient optimisation of terpenoid production in engineered microbes.
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Affiliation(s)
- Clara A. Ferraz
- Manchester Institute of Biotechnology, Department of ChemistrySchool of Natural SciencesUniversity of Manchester131 Princess StreetManchesterM1 7DNUK
| | - Nicole G. H. Leferink
- Manchester Institute of Biotechnology, Department of ChemistrySchool of Natural SciencesUniversity of Manchester131 Princess StreetManchesterM1 7DNUK
- Future Biomanufacturing Research HubManchester Institute of Biotechnology, Department of ChemistrySchool of Natural SciencesUniversity of Manchester131 Princess StreetManchesterM1 7DNUK
| | - Iaroslav Kosov
- Manchester Institute of Biotechnology, Department of ChemistrySchool of Natural SciencesUniversity of Manchester131 Princess StreetManchesterM1 7DNUK
| | - Nigel S. Scrutton
- Manchester Institute of Biotechnology, Department of ChemistrySchool of Natural SciencesUniversity of Manchester131 Princess StreetManchesterM1 7DNUK
- Future Biomanufacturing Research HubManchester Institute of Biotechnology, Department of ChemistrySchool of Natural SciencesUniversity of Manchester131 Princess StreetManchesterM1 7DNUK
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Shukla V, Phulara SC. Impact of culture condition modulation on the high-yield, high-specificity and cost-effective production of terpenoids from microbial sources: A review. Appl Environ Microbiol 2021; 87:AEM.02369-20. [PMID: 33257314 PMCID: PMC7851692 DOI: 10.1128/aem.02369-20] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Recent years have seen a remarkable increase in the non-natural production of terpenoids from microbial route. This is due to the advancements in synthetic biology tools and techniques, which have overcome the challenges associated with the non-native production of terpenoids from microbial hosts. Although, microbes in their native form have ability to grow in wide range of physicochemical parameters such as, pH, temperature, agitation, aeration etc; however, after genetic modifications, culture conditions need to be optimized in order to achieve improved titers of desired terpenoids from engineered microbes. The physicochemical parameters together with medium supplements, such as, inducer, carbon and nitrogen source, and cofactor supply not only play an important role in high-yield production of target terpenoids from engineered host, but also reduce the accumulation of undesired metabolites in fermentation medium, thus facilitate product recovery. Further, for the economic production of terpenoids, the biomass derived sugars can be utilized together with the optimized culture conditions. In the present mini-review, we have highlighted the impact of culture conditions modulation on the high-yield and high-specificity production of terpenoids from engineered microbes. Lastly, utilization of economic feedstock has also been discussed for the cost-effective and sustainable production of terpenoids.
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Affiliation(s)
- Vibha Shukla
- Food, Drug and Chemical Toxicology Group, CSIR-Indian Institute of Toxicology Research, Vishvigyan Bhawan, 31 Mahatma Gandhi Marg, Lucknow-226001, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad-201002, India
| | - Suresh Chandra Phulara
- Department of Biotechnology, Koneru Lakshmaiah Education Foundation, Vaddeswaram, Guntur-522502, Andhra Pradesh, India
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Schalck T, den Bergh BV, Michiels J. Increasing Solvent Tolerance to Improve Microbial Production of Alcohols, Terpenoids and Aromatics. Microorganisms 2021; 9:249. [PMID: 33530454 PMCID: PMC7912173 DOI: 10.3390/microorganisms9020249] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Revised: 01/14/2021] [Accepted: 01/20/2021] [Indexed: 12/16/2022] Open
Abstract
Fuels and polymer precursors are widely used in daily life and in many industrial processes. Although these compounds are mainly derived from petrol, bacteria and yeast can produce them in an environment-friendly way. However, these molecules exhibit toxic solvent properties and reduce cell viability of the microbial producer which inevitably impedes high product titers. Hence, studying how product accumulation affects microbes and understanding how microbial adaptive responses counteract these harmful defects helps to maximize yields. Here, we specifically focus on the mode of toxicity of industry-relevant alcohols, terpenoids and aromatics and the associated stress-response mechanisms, encountered in several relevant bacterial and yeast producers. In practice, integrating heterologous defense mechanisms, overexpressing native stress responses or triggering multiple protection pathways by modifying the transcription machinery or small RNAs (sRNAs) are suitable strategies to improve solvent tolerance. Therefore, tolerance engineering, in combination with metabolic pathway optimization, shows high potential in developing superior microbial producers.
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Affiliation(s)
- Thomas Schalck
- VIB Center for Microbiology, Flanders Institute for Biotechnology, B-3001 Leuven, Belgium; (T.S.); (B.V.d.B.)
- Centre of Microbial and Plant Genetics, KU Leuven, Kasteelpark Arenberg 20, B-3001 Leuven, Belgium
| | - Bram Van den Bergh
- VIB Center for Microbiology, Flanders Institute for Biotechnology, B-3001 Leuven, Belgium; (T.S.); (B.V.d.B.)
- Centre of Microbial and Plant Genetics, KU Leuven, Kasteelpark Arenberg 20, B-3001 Leuven, Belgium
| | - Jan Michiels
- VIB Center for Microbiology, Flanders Institute for Biotechnology, B-3001 Leuven, Belgium; (T.S.); (B.V.d.B.)
- Centre of Microbial and Plant Genetics, KU Leuven, Kasteelpark Arenberg 20, B-3001 Leuven, Belgium
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Improved linalool production in Saccharomyces cerevisiae by combining directed evolution of linalool synthase and overexpression of the complete mevalonate pathway. Biochem Eng J 2020. [DOI: 10.1016/j.bej.2020.107655] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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15
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Khatua A, Pal S, Bisai V. Formal Total Syntheses of (+)- and (-)- ar
-Macrocarpene via Rh (I)
-BINAP Catalyzed Conjugate Addition. European J Org Chem 2020. [DOI: 10.1002/ejoc.202000100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Arindam Khatua
- Department of Chemistry; Indian Institute of Science Education and Research Bhopal; Bhopal Bypass Road, Bhauri 462 066 Bhopal - Madhya Pradesh India
| | - Souvik Pal
- Department of Chemistry; Indian Institute of Science Education and Research Bhopal; Bhopal Bypass Road, Bhauri 462 066 Bhopal - Madhya Pradesh India
| | - Vishnumaya Bisai
- Department of Chemistry; Indian Institute of Science Education and Research Bhopal; Bhopal Bypass Road, Bhauri 462 066 Bhopal - Madhya Pradesh India
- Department of Chemistry; Indian Institute of Science Education and Research Tirupati; Transit Campus, Mangalam, Karkambadi Road 517 507 Tirupati - Andhra Pradesh India
- Department of Chemical Sciences; Indian Institute of Science Education and Research Berhampur; Transit Campus, Engg. School Junction (Govt. ITI Building) 760 010 Berhampur - Odisha India
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Khatua A, Roy A, Bisai V. Catalytic asymmetric total syntheses of sesquiterpenoids, (+)- and ( )-ar-macrocarpene. Tetrahedron 2020. [DOI: 10.1016/j.tet.2019.130918] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Microbiological Advances in Bioactives from High Altitude. MICROBIOLOGICAL ADVANCEMENTS FOR HIGHER ALTITUDE AGRO-ECOSYSTEMS & SUSTAINABILITY 2020. [DOI: 10.1007/978-981-15-1902-4_17] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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Advances in the Metabolic Engineering of Escherichia coli for the Manufacture of Monoterpenes. Catalysts 2019. [DOI: 10.3390/catal9050433] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Monoterpenes are commonly applied as pharmaceuticals and valuable chemicals in various areas. The bioproduction of valuable monoterpenes in prokaryotic microbial hosts, such as E. coli, has progressed considerably thanks to the development of different outstanding approaches. However, the large-scale production of monoterpenes still presents considerable limitations. Thus, process development warrants further investigations. This review discusses the endogenous methylerythritol-4-phosphate-dependent pathway engineering and the exogenous mevalonate-dependent isoprenoid pathway introduction, as well as the accompanied optimization of rate-limiting enzymes, metabolic flux, and product toxicity tolerance. We suggest further studies to focus on the development of systematical, integrational, and synthetic biological strategies in light of the inter disciplines at the cutting edge. Our review provides insights into the current advances of monoterpene bioengineering and serves as a reference for future studies to promote the industrial production of valuable monoterpenes.
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Phulara SC, Chaturvedi P, Chaurasia D, Diwan B, Gupta P. Modulation of culture medium confers high-specificity production of isopentenol in Bacillus subtilis. J Biosci Bioeng 2019; 127:458-464. [DOI: 10.1016/j.jbiosc.2018.10.002] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2018] [Revised: 09/27/2018] [Accepted: 10/03/2018] [Indexed: 11/25/2022]
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22
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Xie SS, Qiu XY, Zhu LY, Zhu CS, Liu CY, Wu XM, Zhu L, Zhang DY. Assembly of TALE-based DNA scaffold for the enhancement of exogenous multi-enzymatic pathway. J Biotechnol 2019; 296:69-74. [DOI: 10.1016/j.jbiotec.2019.03.008] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Revised: 03/11/2019] [Accepted: 03/14/2019] [Indexed: 10/27/2022]
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McClory J, Lin JT, Timson DJ, Zhang J, Huang M. Catalytic mechanism of mevalonate kinase revisited, a QM/MM study. Org Biomol Chem 2019; 17:2423-2431. [PMID: 30735219 DOI: 10.1039/c8ob03197e] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Mevalonate Kinase (MVK) catalyses the ATP-Mg2+ mediated phosphate transfer of mevalonate to produce mevalonate 5-phosphate and is a key kinase in the mevalonate pathway in the biosynthesis of isopentenyl diphosphate, the precursor of isoprenoid-based biofuels. However, the crystal structure in complex with the native substrate mevalonate, ATP and Mg2+ has not been resolved, which has limited the understanding of its reaction mechanism and therefore its application in the production of isoprenoid-based biofuels. Here using molecular docking, molecular dynamics (MD) simulations and a hybrid QM/MM study, we revisited the location of Mg2+ resolved in the crystal structure of MVK and determined a catalytically competent MVK structure in complex with the native substrate mevalonate and ATP. We demonstrated that significant conformational change on a flexible loop connecting the α6 and α7 helix is induced by the substrate binding. Further, we found that Asp204 is coordinated to the Mg2+ ion. Arg241 plays a crucial role in organizing the triphosphoryl tail of ATP for in-line phosphate transfer and stabilizing the negative charge that accumulates at the β,γ-bridging oxygen of ATP upon bond cleavage. Remarkably, we revealed that the phosphorylation of mevalonate catalyzed by MVK occurs via a direct phosphorylation mechanism, instead of the conventionally postulated catalytic base mechanism. The catalytically competent complex structure of MVK as well as the mechanism of reaction will pave the way for the rational engineering of MVK to exploit its applications in the production of biofuels.
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Affiliation(s)
- James McClory
- School of Chemistry and Chemical Engineering, Queen's University Belfast, David Keir Building, Stranmillis Road, Belfast, BT9 5AG, Northern Ireland, UK.
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Tian T, Kang JW, Kang A, Lee TS. Redirecting Metabolic Flux via Combinatorial Multiplex CRISPRi-Mediated Repression for Isopentenol Production in Escherichia coli. ACS Synth Biol 2019; 8:391-402. [PMID: 30681833 DOI: 10.1021/acssynbio.8b00429] [Citation(s) in RCA: 62] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
CRISPR interference (CRISPRi) via target guide RNA (gRNA) arrays and a deactivated Cas9 (dCas9) protein has been shown to simultaneously repress expression of multiple genomic DNA loci. By knocking down endogenous genes in competing pathways, CRISPRi technology can be utilized to redirect metabolic flux toward target metabolite. In this study, we constructed a CRISPRi-mediated multiplex repression system to silence transcription of several endogenous genes to increase precursor availability in a heterologous isopentenol biosynthesis pathway. To identify genomic knockdown targets in competing pathways, we first designed a single-gRNA library with 15 individual targets, where 3 gRNA cassettes targeting gene asnA, prpE, and gldA increased isopentenol titer by 18-24%. We then combined the 3 single-gRNA cassettes into a two- or three-gRNA array and observed up to 98% enhancement in production by fine-tuning the repression level through titrating dCas9 expression. Our strategy shows that multiplex combinatorial knockdown of competing genes using CRISPRi can increase production of the target metabolite, while the repression level needs to be adjusted to balance the metabolic network and achieve the maximum titer improvement.
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Affiliation(s)
- Tian Tian
- Joint BioEnergy Institute, 5885 Hollis Street, Emeryville, California 94608, United States
- Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Jing Wei Kang
- Joint BioEnergy Institute, 5885 Hollis Street, Emeryville, California 94608, United States
- Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
- Department of Chemical Engineering, University of California, Berkeley, California 94720, United States
| | - Aram Kang
- Joint BioEnergy Institute, 5885 Hollis Street, Emeryville, California 94608, United States
- Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Taek Soon Lee
- Joint BioEnergy Institute, 5885 Hollis Street, Emeryville, California 94608, United States
- Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
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Li M, Chen H, Liu C, Guo J, Xu X, Zhang H, Nian R, Xian M. Improvement of isoprene production in Escherichia coli by rational optimization of RBSs and key enzymes screening. Microb Cell Fact 2019; 18:4. [PMID: 30626394 PMCID: PMC6327615 DOI: 10.1186/s12934-018-1051-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Accepted: 12/26/2018] [Indexed: 01/13/2023] Open
Abstract
Background As an essential platform chemical mostly used for rubber synthesis, isoprene is produced in industry through chemical methods, derived from petroleum. As an alternative, bio-production of isoprene has attracted much attention in recent years. Previous researches were mostly focused on key enzymes to improve isoprene production. In this research, besides screening of key enzymes, we also paid attention to expression intensity of non-key enzymes. Results Firstly, screening of key enzymes, IDI, MK and IspS, from other organisms and then RBS optimization of the key enzymes were carried out. The strain utilized IDIsa was firstly detected to produce more isoprene than other IDIs. IDIsa expression was improved after RBS modification, leading to 1610-fold increase of isoprene production. Secondly, RBS sequence optimization was performed to reduce translation initiation rate value of non-key enzymes, ERG19 and MvaE. Decreased ERG19 and MvaE expression and increased isoprene production were detected. The final strain showed 2.6-fold increase in isoprene production relative to the original strain. Furthermore, for the first time, increased key enzyme expression and decreased non-key enzyme expression after RBS sequence optimization were obviously detected through SDS-PAGE analysis. Conclusions This study prove that desired enzyme expression and increased isoprene production were obtained after RBS sequence optimization. RBS optimization of genes could be a powerful strategy for metabolic engineering of strain. Moreover, to increase the production of engineered strain, attention should not only be focused on the key enzymes, but also on the non-key enzymes. Electronic supplementary material The online version of this article (10.1186/s12934-018-1051-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Meijie Li
- Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No.135 Songlin Road, Qingdao, 266101, People's Republic of China.,University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
| | - Hailin Chen
- Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No.135 Songlin Road, Qingdao, 266101, People's Republic of China
| | - Changqing Liu
- Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No.135 Songlin Road, Qingdao, 266101, People's Republic of China
| | - Jing Guo
- Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No.135 Songlin Road, Qingdao, 266101, People's Republic of China
| | - Xin Xu
- Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No.135 Songlin Road, Qingdao, 266101, People's Republic of China
| | - Haibo Zhang
- Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No.135 Songlin Road, Qingdao, 266101, People's Republic of China.
| | - Rui Nian
- Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No.135 Songlin Road, Qingdao, 266101, People's Republic of China.
| | - Mo Xian
- Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No.135 Songlin Road, Qingdao, 266101, People's Republic of China.
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Pandey S, Phulara SC, Jha A, Chauhan PS, Gupta P, Shukla V. 3-Methyl-3-buten-1-ol (isoprenol) confers longevity and stress tolerance in Caenorhabditis elegans. Int J Food Sci Nutr 2019; 70:595-602. [PMID: 30624146 DOI: 10.1080/09637486.2018.1554031] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The present investigation demonstrates the longevity-promoting effects of 3-methyl-3-buten-1-ol (isoprenol) in the animal model Caenorhabditis elegans that might be served as a lead nutraceutical in geriatric research. Our results showed that 0.5 mM isoprenol extended the mean lifespan of worms by 25% in comparison to control worms. Isoprenol also significantly enhanced survival of the worms under various stress conditions. It was found that the longevity-promoting effects of isoprenol were associated with improved age-associated physiological behaviour and reduced intracellular reactive oxygen species (ROS) accumulation. Finally, studies with gene-specific mutants revealed the involvement of pro-longevity transcription factors (TFs) DAF-16 and SKN-1 with simultaneous over-expression of GST-4 and SOD-3 in isoprenol treated worms. In silico analysis revealed the binding affinity of isoprenol with DAF-16 and SKN-1 TFs. Together, the findings suggest that isoprenol is able to enhance the lifespan of C. elegans and embarks its potential in the developments of formulations for age-related ailments.
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Affiliation(s)
- Swapnil Pandey
- a Department of Microbial Technology , CSIR-National Botanical Research Institute , Lucknow , India.,b Academy of Scientific and Innovative Research (AcSIR) , Ghaziabad , India
| | - Suresh Chandra Phulara
- c Department of Biotechnology , National Institute of Technology Raipur , Raipur , India
| | - Anubhuti Jha
- c Department of Biotechnology , National Institute of Technology Raipur , Raipur , India
| | - Puneet Singh Chauhan
- a Department of Microbial Technology , CSIR-National Botanical Research Institute , Lucknow , India.,b Academy of Scientific and Innovative Research (AcSIR) , Ghaziabad , India
| | - Pratima Gupta
- c Department of Biotechnology , National Institute of Technology Raipur , Raipur , India
| | - Virendra Shukla
- d School of Bio-science and Biotechnology , Babasaheb Bhimrao Ambedker University (A Central University) , Lucknow , India
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Wu C, Lan L, Li Y, Nie Z, Zeng R. The relationship between latex metabolism gene expression with rubber yield and related traits in Hevea brasiliensis. BMC Genomics 2018; 19:897. [PMID: 30526485 PMCID: PMC6288877 DOI: 10.1186/s12864-018-5242-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Accepted: 11/12/2018] [Indexed: 11/20/2022] Open
Abstract
Background Expression patterns of many laticifer-specific gens are closely correlative with rubber yield of Hevea brasiliensis (para rubber tree). To unveil the mechanisms underlying the rubber yield, transcript levels of nine major latex metabolism-related genes, i.e., HMG-CoA synthase (HMGS), HMG-CoA reductase (HMGR), diphosphomevalonate decarboxylase (PMD), farnesyl diphosphate synthase (FPS), cis-prenyltransferase (CPT), rubber elongation factor (REF), small rubber particle protein (SRPP), dihydroxyacid dehydratase (DHAD) and actin depolymerizing factor (ADF), were dertermined, and the relationship between rubber yield with their expression levels was analysed. Results Except HbHMGR1, HbPMD and HbDHAD, most of these genes were predominantly expressed in latex, and bark tapping markedly elevated the transcript abundance of the analyzed genes, with the 7th tapping producing the greatest expression levels. Both ethephon (ETH) and methyl jasmonate (MeJA) stimulation greatly induced the expression levels of the examined genes, at least at one time point, except HbDHAD, which was unresponsive to MeJA. The genes’ expression levels, as well as the rubber yields and two yield characteristics differed significantly among the different genotypes examined. Additionally, the latex and dry rubber yields increased gradually but the dry rubber content did not. Rubber yields and/or yield characteristics were significantly positively correlated with HbCPT, HbFPS, HbHMGS, HbHMGR1 and HbDHAD expression levels, negatively correlated with that of HbREF, but not significantly correlated with HbPMD, HbSRPP and HbADF expression levels. In addition, during rubber production, significantly positive correlations existed between the expression level of HbPMD and the levels of HbREF and HbHMGR1, between HbSRPP and the levels of HbHMGS and HbHMGR1, and between HbADF and HbFPS. Conclusions The up-regulation of these genes might be related to the latex production of rubber trees under the stress of bark tapping and latex metabolism. The various correlations among the genes implied that there are differences in their synergic interactions. Thus, these nine genes might be related to rubber yield and yield-related traits in H. brasiliensis, and this work increases our understanding of their complex functions and how they are expressed in both high-and medium-yield rubber tree varieties and low-yield wild rubber tree germplasm. Electronic supplementary material The online version of this article (10.1186/s12864-018-5242-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Chuntai Wu
- Ministry of Agriculture Key Laboratory of Biology and Genetic Resources of Rubber Tree, Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences (CATAS), Danzhou, Hainan, 571737, People's Republic of China
| | - Li Lan
- Ministry of Agriculture Key Laboratory of Biology and Genetic Resources of Rubber Tree, Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences (CATAS), Danzhou, Hainan, 571737, People's Republic of China.,College of Agriculture, Hainan University, Haikou, 570228, China
| | - Yu Li
- Ministry of Agriculture Key Laboratory of Biology and Genetic Resources of Rubber Tree, Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences (CATAS), Danzhou, Hainan, 571737, People's Republic of China
| | - Zhiyi Nie
- Ministry of Agriculture Key Laboratory of Biology and Genetic Resources of Rubber Tree, Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences (CATAS), Danzhou, Hainan, 571737, People's Republic of China
| | - Rizhong Zeng
- Ministry of Agriculture Key Laboratory of Biology and Genetic Resources of Rubber Tree, Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences (CATAS), Danzhou, Hainan, 571737, People's Republic of China.
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Li M, Nian R, Xian M, Zhang H. Metabolic engineering for the production of isoprene and isopentenol by Escherichia coli. Appl Microbiol Biotechnol 2018; 102:7725-7738. [PMID: 30006784 PMCID: PMC6132537 DOI: 10.1007/s00253-018-9200-5] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2018] [Revised: 06/23/2018] [Accepted: 06/25/2018] [Indexed: 12/12/2022]
Abstract
The biotechnological production of isoprene and isopentenol has recently been studied. Isoprene, which is currently made mainly from petroleum, is an important platform chemical for synthesizing pesticides, medicines, oil additives, fragrances, and more and is especially important in the rubber production industry. Isopentenols, which have better combustion properties than well-known biofuels (ethanol), have recently received more attention. Supplies of petroleum, the conventional source of isoprene and isopentenols, are unsustainable, and chemical synthesis processes could cause serious environmental problems. As an alternative, the biosynthesis of isoprene and isopentenols in cell factories is more sustainable and environmentally friendly. With a number of advantages over other microorganisms, Escherichia coli is considered to be a powerful workhorse organism for producing these compounds. This review will highlight the recent advances in metabolic engineering for isoprene and isopentenol production, especially using E. coli cell factories.
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Affiliation(s)
- Meijie Li
- Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No. 135 Songling Road, Qingdao, 266101, People's Republic of China.,University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
| | - Rui Nian
- Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No. 135 Songling Road, Qingdao, 266101, People's Republic of China
| | - Mo Xian
- Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No. 135 Songling Road, Qingdao, 266101, People's Republic of China.
| | - Haibo Zhang
- Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No. 135 Songling Road, Qingdao, 266101, People's Republic of China.
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30
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In situ biomolecule production by bacteria; a synthetic biology approach to medicine. J Control Release 2018; 275:217-228. [DOI: 10.1016/j.jconrel.2018.02.023] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Revised: 02/14/2018] [Accepted: 02/15/2018] [Indexed: 02/06/2023]
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Thapa HR, Tang S, Sacchettini JC, Devarenne TP. Tetraterpene Synthase Substrate and Product Specificity in the Green Microalga Botryococcus braunii Race L. ACS Chem Biol 2017; 12:2408-2416. [PMID: 28813599 DOI: 10.1021/acschembio.7b00457] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Recently, the biosynthetic pathway for lycopadiene, a C40 tetraterpenoid hydrocarbon, was deciphered from the L race of Botryococcus braunii, an alga that produces hydrocarbon oils capable of being converted into combustible fuels. The lycopadiene pathway is initiated by the squalene synthase (SS)-like enzyme lycopaoctaene synthase (LOS), which catalyzes the head-to-head condensation of two C20 geranylgeranyl diphosphate (GGPP) molecules to produce C40 lycopaoctaene. LOS shows unusual substrate promiscuity for SS or SS-like enzymes by utilizing C15 farnesyl diphosphate (FPP) and C20 phytyl diphosphate in addition to GGPP as substrates. These three substrates can be combined by LOS individually or in combinations to produce six different hydrocarbons of C30, C35, and C40 chain lengths. To understand LOS substrate and product specificity, rational mutagenesis experiments were conducted based on sequence alignment with several SS proteins as well as a structural comparison with the human SS (HSS) crystal structure. Characterization of the LOS mutants in vitro identified Ser276 and Ala288 in the LOS active site as key amino acids responsible for controlling substrate binding, and thus the promiscuity of this enzyme. Mutating these residues to those found in HSS largely converted LOS from lycopaoctaene production to C30 squalene production. Furthermore, these studies were confirmed in vivo by expressing LOS in E. coli cells metabolically engineered to produce high FPP and GGPP levels. These studies also offer insights into tetraterpene hydrocarbon metabolism in B. braunii and provide a foundation for engineering LOS for robust production of specific hydrocarbons of a desired chain length.
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Affiliation(s)
- Hem R. Thapa
- Department of Biochemistry & Biophysics, Texas A&M University, College Station, Texas 77843, United States
| | - Su Tang
- Department of Biochemistry & Biophysics, Texas A&M University, College Station, Texas 77843, United States
| | - James C. Sacchettini
- Department of Biochemistry & Biophysics, Texas A&M University, College Station, Texas 77843, United States
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Timothy P. Devarenne
- Department of Biochemistry & Biophysics, Texas A&M University, College Station, Texas 77843, United States
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Niu FX, Lu Q, Bu YF, Liu JZ. Metabolic engineering for the microbial production of isoprenoids: Carotenoids and isoprenoid-based biofuels. Synth Syst Biotechnol 2017; 2:167-175. [PMID: 29318197 PMCID: PMC5655344 DOI: 10.1016/j.synbio.2017.08.001] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Revised: 08/03/2017] [Accepted: 08/09/2017] [Indexed: 12/22/2022] Open
Abstract
Isoprenoids are the most abundant and highly diverse group of natural products. Many isoprenoids have been used for pharmaceuticals, nutraceuticals, flavors, cosmetics, food additives and biofuels. Carotenoids and isoprenoid-based biofuels are two classes of important isoprenoids. These isoprenoids have been produced microbially through metabolic engineering and synthetic biology efforts. Herein, we briefly review the engineered biosynthetic pathways in well-characterized microbial systems for the production of carotenoids and several isoprenoid-based biofuels.
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Affiliation(s)
- Fu-Xing Niu
- Biotechnology Research Center and Biomedical Center, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China.,South China Sea Bio-Resource Exploitation and Utilization Collaborative Innovation Center, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Qian Lu
- Biotechnology Research Center and Biomedical Center, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China.,South China Sea Bio-Resource Exploitation and Utilization Collaborative Innovation Center, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Yi-Fan Bu
- Biotechnology Research Center and Biomedical Center, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China.,South China Sea Bio-Resource Exploitation and Utilization Collaborative Innovation Center, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Jian-Zhong Liu
- Biotechnology Research Center and Biomedical Center, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China.,South China Sea Bio-Resource Exploitation and Utilization Collaborative Innovation Center, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
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Mendez-Perez D, Alonso-Gutierrez J, Hu Q, Molinas M, Baidoo EEK, Wang G, Chan LJG, Adams PD, Petzold CJ, Keasling JD, Lee TS. Production of jet fuel precursor monoterpenoids from engineered Escherichia coli. Biotechnol Bioeng 2017; 114:1703-1712. [PMID: 28369701 DOI: 10.1002/bit.26296] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2016] [Revised: 02/04/2017] [Accepted: 03/24/2017] [Indexed: 12/27/2022]
Abstract
Monoterpenes (C10 isoprenoids) are the main components of essential oils and are possible precursors for many commodity chemicals and high energy density fuels. Monoterpenes are synthesized from geranyl diphosphate (GPP), which is also the precursor for the biosynthesis of farnesyl diphosphate (FPP). FPP biosynthesis diverts the carbon flux from monoterpene production to C15 products and quinone biosynthesis. In this study, we tested a chromosomal mutation of Escherichia coli's native FPP synthase (IspA) to improve GPP availability for the production of monoterpenes using a heterologous mevalonate pathway. Monoterpene production at high levels required not only optimization of GPP production but also a basal level of FPP to maintain growth. The optimized strains produced two jet fuel precursor monoterpenoids 1,8-cineole and linalool at the titer of 653 mg/L and 505 mg/L, respectively, in batch cultures with 1% glucose. The engineered strains developed in this work provide useful resources for the production of high-value monoterpenes. Biotechnol. Bioeng. 2017;114: 1703-1712. © 2017 Wiley Periodicals, Inc.
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Affiliation(s)
- Daniel Mendez-Perez
- Joint BioEnergy Institute (JBEI), 5885 Hollis Street, 4th floor, Emeryville, California, 94608, USA.,Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California
| | - Jorge Alonso-Gutierrez
- Joint BioEnergy Institute (JBEI), 5885 Hollis Street, 4th floor, Emeryville, California, 94608, USA.,Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California
| | - Qijun Hu
- Joint BioEnergy Institute (JBEI), 5885 Hollis Street, 4th floor, Emeryville, California, 94608, USA.,Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California
| | - Margaux Molinas
- Joint BioEnergy Institute (JBEI), 5885 Hollis Street, 4th floor, Emeryville, California, 94608, USA.,Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California
| | - Edward E K Baidoo
- Joint BioEnergy Institute (JBEI), 5885 Hollis Street, 4th floor, Emeryville, California, 94608, USA.,Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California
| | - George Wang
- Joint BioEnergy Institute (JBEI), 5885 Hollis Street, 4th floor, Emeryville, California, 94608, USA.,Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California
| | - Leanne J G Chan
- Joint BioEnergy Institute (JBEI), 5885 Hollis Street, 4th floor, Emeryville, California, 94608, USA.,Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California
| | - Paul D Adams
- Joint BioEnergy Institute (JBEI), 5885 Hollis Street, 4th floor, Emeryville, California, 94608, USA.,Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California
| | - Christopher J Petzold
- Joint BioEnergy Institute (JBEI), 5885 Hollis Street, 4th floor, Emeryville, California, 94608, USA.,Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California
| | - Jay D Keasling
- Joint BioEnergy Institute (JBEI), 5885 Hollis Street, 4th floor, Emeryville, California, 94608, USA.,Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California.,The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Horsholm, Denmark.,Department of Chemical & Biomolecular Engineering, University of California, Berkeley, California.,Department of Bioengineering, University of California, Berkeley, California
| | - Taek S Lee
- Joint BioEnergy Institute (JBEI), 5885 Hollis Street, 4th floor, Emeryville, California, 94608, USA.,Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California
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Huang M, Wei K, Li X, McClory J, Hu G, Zou JW, Timson D. Phosphorylation Mechanism of Phosphomevalonate Kinase: Implications for Rational Engineering of Isoprenoid Biosynthetic Pathway Enzymes. J Phys Chem B 2016; 120:10714-10722. [DOI: 10.1021/acs.jpcb.6b08480] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Meilan Huang
- School
of Chemistry and Chemical Engineering, Queen’s University Belfast, David
Keir Building, Stranmillis Road, Belfast, BT9 5AG, Northern Ireland, United Kingdom
| | - Kexin Wei
- School
of Chemistry and Chemical Engineering, Queen’s University Belfast, David
Keir Building, Stranmillis Road, Belfast, BT9 5AG, Northern Ireland, United Kingdom
| | - Xiao Li
- School
of Chemistry and Chemical Engineering, Queen’s University Belfast, David
Keir Building, Stranmillis Road, Belfast, BT9 5AG, Northern Ireland, United Kingdom
| | - James McClory
- School
of Chemistry and Chemical Engineering, Queen’s University Belfast, David
Keir Building, Stranmillis Road, Belfast, BT9 5AG, Northern Ireland, United Kingdom
| | - Guixiang Hu
- School
of Biotechnology and Chemical Engineering, Ningbo Institute of Technology, Zhejiang University, Ningbo 315100, China
| | - Jian-Wei Zou
- School
of Biotechnology and Chemical Engineering, Ningbo Institute of Technology, Zhejiang University, Ningbo 315100, China
| | - David Timson
- School
of Pharmacy and Biomolecular Sciences, The University of Brighton, Huxley Building, Lewes Road, Brighton, BN2 4GJ, United Kingdom
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Jiménez-Díaz L, Caballero A, Pérez-Hernández N, Segura A. Microbial alkane production for jet fuel industry: motivation, state of the art and perspectives. Microb Biotechnol 2016; 10:103-124. [PMID: 27723249 PMCID: PMC5270751 DOI: 10.1111/1751-7915.12423] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2016] [Revised: 09/09/2016] [Accepted: 09/15/2016] [Indexed: 11/27/2022] Open
Abstract
Bio‐jet fuel has attracted a lot of interest in recent years and has become a focus for aircraft and engine manufacturers, oil companies, governments and researchers. Given the global concern about environmental issues and the instability of oil market, bio‐jet fuel has been identified as a promising way to reduce the greenhouse gas emissions from the aviation industry, while also promoting energy security. Although a number of bio‐jet fuel sources have been approved for manufacture, their commercialization and entry into the market is still a far way away. In this review, we provide an overview of the drivers for intensified research into bio‐jet fuel technologies, the type of chemical compounds found in bio‐jet fuel preparations and the current state of related pre‐commercial technologies. The biosynthesis of hydrocarbons is one of the most promising approaches for bio‐jet fuel production, and thus we provide a detailed analysis of recent advances in the microbial biosynthesis of hydrocarbons (with a focus on alkanes). Finally, we explore the latest developments and their implications for the future of research into bio‐jet fuel technologies.
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Affiliation(s)
- Lorena Jiménez-Díaz
- Abengoa Research, Campus Palmas Altas, C/Energía Solar, 41014, Sevilla, Spain
| | - Antonio Caballero
- Abengoa Research, Campus Palmas Altas, C/Energía Solar, 41014, Sevilla, Spain
| | | | - Ana Segura
- Abengoa Research, Campus Palmas Altas, C/Energía Solar, 41014, Sevilla, Spain.,Estación Experimental del Zaidín-CSIC, C/Profesor Albareda s/n, 18008, Granada, Spain
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Isoprenoid-Based Biofuels: Homologous Expression and Heterologous Expression in Prokaryotes. Appl Environ Microbiol 2016; 82:5730-40. [PMID: 27422837 DOI: 10.1128/aem.01192-16] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Enthusiasm for mining advanced biofuels from microbial hosts has increased remarkably in recent years. Isoprenoids are one of the highly diverse groups of secondary metabolites and are foreseen as an alternative to petroleum-based fuels. Most of the prokaryotes synthesize their isoprenoid backbone via the deoxyxylulose-5-phosphate pathway from glyceraldehyde-3-phosphate and pyruvate, whereas eukaryotes synthesize isoprenoids via the mevalonate pathway from acetyl coenzyme A (acetyl-CoA). Microorganisms do not accumulate isoprenoids in large quantities naturally, which restricts their application for fuel purposes. Various metabolic engineering efforts have been utilized to overcome the limitations associated with their natural and nonnatural production. The introduction of heterologous pathways/genes and overexpression of endogenous/homologous genes have shown a remarkable increase in isoprenoid yield and substrate utilization in microbial hosts. Such modifications in the hosts' genomes have enabled researchers to develop commercially competent microbial strains for isoprenoid-based biofuel production utilizing a vast array of substrates. The present minireview briefly discusses the recent advancement in metabolic engineering efforts in prokaryotic hosts for the production of isoprenoid-based biofuels, with an emphasis on endogenous, homologous, and heterologous expression strategies.
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