1
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Courtney DK, Su Y, Jacobson T, Khana D, Ailiani A, Amador-Noguez D, Pfleger BF. Relative Activities of the β-ketoacyl-CoA and Acyl-CoA Reductases Influence Product Profile and Flux in a Reversed β-Oxidation Pathway. ACS Catal 2023; 13:5914-5925. [PMID: 38094510 PMCID: PMC10718561 DOI: 10.1021/acscatal.3c00379] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/21/2024]
Abstract
The β-Oxidation pathway, normally involved in the catabolism of fatty acids, can be functionally made to act as a fermentative, iterative, elongation pathway when driven by the activity of a trans-enoyl-CoA reductase. The terminal acyl-CoA reduction to alcohol can occur on substrates with varied chain lengths, leading to a broad distribution of fermentation products in vivo. Tight control of the average chain length and product profile is desirable as chain length greatly influences molecular properties and commercial value. Lacking a termination enzyme with a narrow chain length preference, we sought alternative factors that could influence the product profile and pathway flux in the iterative pathway. In this study, we reconstituted the reversed β-oxidation (R-βox) pathway in vitro with a purified tri-functional complex (FadBA) responsible for the thiolase, enoyl-CoA hydratase and hydroxyacyl-CoA dehydrogenase activities, a trans-enoyl-CoA reductase (TER), and an acyl-CoA reductase (ACR). Using this system, we determined the rate limiting step of the elongation cycle and demonstrated that by controlling the ratio of these three enzymes and the ratio of NADH and NADPH, we can influence the average chain length of the alcohol product profile.
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Affiliation(s)
- Dylan K. Courtney
- Department of Chemical and Biological Engineering, University of Wisconsin – Madison, Madison, WI, USA
| | - Yun Su
- Department of Chemical and Biological Engineering, University of Wisconsin – Madison, Madison, WI, USA
| | - Tyler Jacobson
- Department of Bacteriology, University of Wisconsin – Madison, Madison, WI, USA
| | - Daven Khana
- Department of Bacteriology, University of Wisconsin – Madison, Madison, WI, USA
| | - Aditya Ailiani
- Department of Biomedical Engineering, University of Wisconsin – Madison, Madison, WI, USA
| | | | - Brian F. Pfleger
- Department of Chemical and Biological Engineering, University of Wisconsin – Madison, Madison, WI, USA
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2
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Moxley WC, Brown RE, Eiteman MA. Escherichia coli aceE variants coding pyruvate dehydrogenase improve the generation of pyruvate-derived acetoin. Eng Life Sci 2023; 23:e2200054. [PMID: 36874610 PMCID: PMC9978916 DOI: 10.1002/elsc.202200054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 11/23/2022] [Accepted: 01/07/2023] [Indexed: 02/04/2023] Open
Abstract
Several chromosomally expressed AceE variants were constructed in Escherichia coli ΔldhA ΔpoxB ΔppsA and compared using glucose as the sole carbon source. These variants were examined in shake flask cultures for growth rate, pyruvate accumulation, and acetoin production via heterologous expression of the budA and budB genes from Enterobacter cloacae ssp. dissolvens. The best acetoin-producing strains were subsequently studied in controlled batch culture at the one-liter scale. PDH variant strains attained up to four-fold greater acetoin than the strain expressing the wild-type PDH. In a repeated batch process, the H106V PDH variant strain attained over 43 g/L of pyruvate-derived products, acetoin (38.5 g/L) and 2R,3R-butanediol (5.0 g/L), corresponding to an effective concentration of 59 g/L considering the dilution. The acetoin yield from glucose was 0.29 g/g with a volumetric productivity of 0.9 g/L·h (0.34 g/g and 1.0 g/L·h total products). The results demonstrate a new tool in pathway engineering, the modification of a key metabolic enzyme to improve the formation of a product via a kinetically slow, introduced pathway. Direct modification of the pathway enzyme offers an alternative to promoter engineering in cases where the promoter is involved in a complex regulatory network.
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Affiliation(s)
- W. Chris Moxley
- Department of MicrobiologyUniversity of GeorgiaAthensGeorgiaUSA
| | - Rachel E. Brown
- School of ChemicalMaterials and Biomedical EngineeringUniversity of GeorgiaAthensGeorgiaUSA
| | - Mark A. Eiteman
- Department of MicrobiologyUniversity of GeorgiaAthensGeorgiaUSA
- School of ChemicalMaterials and Biomedical EngineeringUniversity of GeorgiaAthensGeorgiaUSA
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3
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Antoniêto ACC, Nogueira KMV, Mendes V, Maués DB, Oshiquiri LH, Zenaide-Neto H, de Paula RG, Gaffey J, Tabatabaei M, Gupta VK, Silva RN. Use of carbohydrate-directed enzymes for the potential exploitation of sugarcane bagasse to obtain value-added biotechnological products. Int J Biol Macromol 2022; 221:456-471. [PMID: 36070819 DOI: 10.1016/j.ijbiomac.2022.08.186] [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: 04/12/2022] [Revised: 08/28/2022] [Accepted: 08/29/2022] [Indexed: 11/15/2022]
Abstract
Microorganisms, such as fungi and bacteria, are crucial players in the production of enzymatic cocktails for biomass hydrolysis or the bioconversion of plant biomass into products with industrial relevance. The biotechnology industry can exploit lignocellulosic biomass for the production of high-value chemicals. The generation of biotechnological products from lignocellulosic feedstock presents several bottlenecks, including low efficiency of enzymatic hydrolysis, high cost of enzymes, and limitations on microbe metabolic performance. Genetic engineering offers a route for developing improved microbial strains for biotechnological applications in high-value product biosynthesis. Sugarcane bagasse, for example, is an agro-industrial waste that is abundantly produced in sugar and first-generation processing plants. Here, we review the potential conversion of its feedstock into relevant industrial products via microbial production and discuss the advances that have been made in improving strains for biotechnological applications.
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Affiliation(s)
- Amanda Cristina Campos Antoniêto
- Department of Biochemistry and Immunology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, SP 14049-900, Brazil
| | - Karoline Maria Vieira Nogueira
- Department of Biochemistry and Immunology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, SP 14049-900, Brazil
| | - Vanessa Mendes
- Department of Biochemistry and Immunology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, SP 14049-900, Brazil
| | - David Batista Maués
- Department of Biochemistry and Immunology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, SP 14049-900, Brazil
| | - Letícia Harumi Oshiquiri
- Department of Biochemistry and Immunology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, SP 14049-900, Brazil
| | - Hermano Zenaide-Neto
- Department of Biochemistry and Immunology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, SP 14049-900, Brazil
| | - Renato Graciano de Paula
- Department of Physiological Sciences, Health Sciences Centre, Federal University of Espirito Santo, Vitória, ES 29047-105, Brazil
| | - James Gaffey
- Circular Bioeconomy Research Group, Shannon Applied Biotechnology Centre, Munster Technological University, Kerry, Ireland; BiOrbic, Bioeconomy Research Centre, University College Dublin, Belfield, Dublin, Ireland
| | - Meisam Tabatabaei
- Higher Institution Centre of Excellence (HICoE), Institute of Tropical Aquaculture and Fisheries (AKUATROP), Universiti Malaysia Terengganu, 21030 Kuala Nerus, Terengganu, Malaysia.
| | - Vijai Kumar Gupta
- Biorefining and Advanced Materials Research Center, SRUC, Kings Buildings, West Mains Road, Edinburgh EH9 3JG, UK; Center for Safe and Improved Food, SRUC, Kings Buildings, West Mains Road, Edinburgh EH9 3JG, UK.
| | - Roberto Nascimento Silva
- Department of Biochemistry and Immunology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, SP 14049-900, Brazil.
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4
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Seo H, Giannone RJ, Yang YH, Trinh CT. Proteome reallocation enables the selective de novo biosynthesis of non-linear, branched-chain acetate esters. Metab Eng 2022; 73:38-49. [PMID: 35561848 DOI: 10.1016/j.ymben.2022.05.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Revised: 04/21/2022] [Accepted: 05/06/2022] [Indexed: 10/25/2022]
Abstract
The one-carbon recursive ketoacid elongation pathway is responsible for making various branched-chain amino acids, aldehydes, alcohols, and acetate esters in living cells. Controlling selective microbial biosynthesis of these target molecules at high efficiency is challenging due to enzyme promiscuity, regulation, and metabolic burden. In this study, we present a systematic modular design approach to control proteome reallocation for selective microbial biosynthesis of branched-chain acetate esters. Through pathway modularization, we partitioned the branched-chain ester pathways into four submodules including keto-isovalerate submodule for converting pyruvate to keto-isovalerate, ketoacid elongation submodule for producing longer carbon-chain keto-acids, ketoacid decarboxylase submodule for converting ketoacids to alcohols, and alcohol acyltransferase submodule for producing branched-chain acetate esters by condensing alcohols and acetyl-CoA. By systematic manipulation of pathway gene replication and transcription, enzyme specificity of the first committed steps of these submodules, and downstream competing pathways, we demonstrated selective microbial production of isoamyl acetate over isobutyl acetate. We found that the optimized isoamyl acetate pathway globally redistributed the amino acid fractions in the proteomes and required up to 23-31% proteome reallocation at the expense of other cellular resources, such as those required to generate precursor metabolites and energy for growth and amino acid biosynthesis. From glucose fed-batch fermentation, the engineered strains produced isoamyl acetate up to a titer of 8.8 g/L (>0.25 g/L toxicity limit), a yield of 0.22 g/g (61% of maximal theoretical value), and 86% selectivity, achieving the highest titers, yields and selectivity of isoamyl acetate reported to date.
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Affiliation(s)
- Hyeongmin Seo
- Department of Chemical and Biomolecular Engineering, The University of Tennessee, Knoxville, TN, USA; Center of Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Richard J Giannone
- Center of Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, USA; Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37830, USA
| | - Yung-Hun Yang
- Department of Biological Engineering, Konkuk University, Seoul, South Korea
| | - Cong T Trinh
- Department of Chemical and Biomolecular Engineering, The University of Tennessee, Knoxville, TN, USA; Center of Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, USA.
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5
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Lou YR, Pichersky E, Last RL. Deep roots and many branches: Origins of plant-specialized metabolic enzymes in general metabolism. CURRENT OPINION IN PLANT BIOLOGY 2022; 66:102192. [PMID: 35217473 DOI: 10.1016/j.pbi.2022.102192] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 01/15/2022] [Accepted: 01/20/2022] [Indexed: 06/14/2023]
Abstract
Collectively, plants produce hundreds of thousands of specialized metabolites from simple building blocks such as amino acids, fatty acids, and isoprenoids. As additional specialized metabolic enzymes are described, there is increasing recognition of the importance of cooption of general metabolic enzymes to specialized metabolism by gene duplication, narrowing of expression, and alteration of enzymatic activities. Here, we examine how several classes of enzymes were each coopted multiple times. We demonstrate the simplicity of achieving the synthesis of analogous chemicals by coopting existing enzymes and summarize emerging insights that could inform rational metabolic engineering of both general and specialized metabolic enzymes.
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Affiliation(s)
- Yann-Ru Lou
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
| | - Eran Pichersky
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Robert L Last
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA; Department of Plant Biology, Michigan State University, East Lansing, MI 48824, USA.
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6
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Tarasava K, Lee SH, Chen J, Köpke M, Jewett MC, Gonzalez R. Reverse β-oxidation pathways for efficient chemical production. J Ind Microbiol Biotechnol 2022; 49:6537408. [PMID: 35218187 PMCID: PMC9118988 DOI: 10.1093/jimb/kuac003] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Accepted: 01/25/2022] [Indexed: 12/04/2022]
Abstract
Microbial production of fuels, chemicals, and materials has the potential to reduce greenhouse gas emissions and contribute to a sustainable bioeconomy. While synthetic biology allows readjusting of native metabolic pathways for the synthesis of desired products, often these native pathways do not support maximum efficiency and are affected by complex regulatory mechanisms. A synthetic or engineered pathway that allows modular synthesis of versatile bioproducts with minimal enzyme requirement and regulation while achieving high carbon and energy efficiency could be an alternative solution to address these issues. The reverse β-oxidation (rBOX) pathways enable iterative non-decarboxylative elongation of carbon molecules of varying chain lengths and functional groups with only four core enzymes and no ATP requirement. Here, we describe recent developments in rBOX pathway engineering to produce alcohols and carboxylic acids with diverse functional groups, along with other commercially important molecules such as polyketides. We discuss the application of rBOX beyond the pathway itself by its interfacing with various carbon-utilization pathways and deployment in different organisms, which allows feedstock diversification from sugars to glycerol, carbon dioxide, methane, and other substrates.
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Affiliation(s)
- Katia Tarasava
- Department of Chemical, Biological, and Materials Engineering, University of South Florida, Tampa, FL, USA
| | - Seung Hwan Lee
- Department of Chemical, Biological, and Materials Engineering, University of South Florida, Tampa, FL, USA
| | - Jing Chen
- Department of Chemical, Biological, and Materials Engineering, University of South Florida, Tampa, FL, USA
| | | | - Michael C Jewett
- Department of Chemical and Biological Engineering and Center for Synthetic Biology, Northwestern University, Evanston, IL, USA
| | - Ramon Gonzalez
- Department of Chemical, Biological, and Materials Engineering, University of South Florida, Tampa, FL, USA
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7
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Yunus IS, Wang Z, Sattayawat P, Muller J, Zemichael FW, Hellgardt K, Jones PR. Improved Bioproduction of 1-Octanol Using Engineered Synechocystis sp. PCC 6803. ACS Synth Biol 2021; 10:1417-1428. [PMID: 34003632 DOI: 10.1021/acssynbio.1c00029] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
1-Octanol has gained interest as a chemical precursor for both high and low value commodities including fuel, solvents, surfactants, and fragrances. By harnessing the power from sunlight and CO2 as carbon source, cyanobacteria has recently been engineered for renewable production of 1-octanol. The productivity, however, remained low. In the present work, we report efforts to further improve the 1-octanol productivity. Different N-terminal truncations were evaluated on three thioesterases from different plant species, resulting in several candidate thioesterases with improved activity and selectivity toward octanoyl-ACP. The structure/function trials suggest that current knowledge and/or state-of-the art computational tools are insufficient to determine the most appropriate cleavage site for thioesterases in Synechocystis. Additionally, by tuning the inducer concentration and light intensity, we further improved the 1-octanol productivity, reaching up to 35% (w/w) carbon partitioning and a titer of 526 ± 5 mg/L 1-octanol in 12 days. Long-term cultivation experiments demonstrated that the improved strain can be stably maintained for at least 30 days and/or over ten times serial dilution. Surprisingly, the improved strain was genetically stable in contrast to earlier strains having lower productivity (and hence a reduced chance of reaching toxic product concentrations). Altogether, improved enzymes and environmental conditions (e.g., inducer concentration and light intensity) substantially increased the 1-octanol productivity. When cultured under continuous conditions, the bioproduction system reached an accumulative titer of >3.5 g/L 1-octanol over close to 180 days.
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Affiliation(s)
- Ian Sofian Yunus
- Department of Life Sciences, Imperial College London, SW7 2AZ London, United Kingdom
| | - Zhixuan Wang
- Department of Chemical Engineering, Imperial College London, SW7 2AZ London, United Kingdom
| | - Pachara Sattayawat
- Department of Life Sciences, Imperial College London, SW7 2AZ London, United Kingdom
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai, 50200, Thailand
| | - Jonathan Muller
- Department of Life Sciences, Imperial College London, SW7 2AZ London, United Kingdom
| | - Fessehaye W. Zemichael
- Department of Chemical Engineering, Imperial College London, SW7 2AZ London, United Kingdom
| | - Klaus Hellgardt
- Department of Chemical Engineering, Imperial College London, SW7 2AZ London, United Kingdom
| | - Patrik R. Jones
- Department of Life Sciences, Imperial College London, SW7 2AZ London, United Kingdom
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8
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Sugimoto N, Engelgau P, Jones AD, Song J, Beaudry R. Citramalate synthase yields a biosynthetic pathway for isoleucine and straight- and branched-chain ester formation in ripening apple fruit. Proc Natl Acad Sci U S A 2021; 118:e2009988118. [PMID: 33431667 PMCID: PMC7826400 DOI: 10.1073/pnas.2009988118] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
A plant pathway that initiates with the formation of citramalate from pyruvate and acetyl-CoA by citramalate synthase (CMS) is shown to contribute to the synthesis of α-ketoacids and important odor-active esters in apple (Malus × domestica) fruit. Microarray screening led to the discovery of a gene with high amino acid similarity to 2-isopropylmalate synthase (IPMS). However, functional analysis of recombinant protein revealed its substrate preference differed substantially from IPMS and was more typical of CMS. MdCMS also lacked the regulatory region present in MdIPMS and was not sensitive to feedback inhibition. 13C-acetate feeding of apple tissue labeled citramalate and α-ketoacids in a manner consistent with the presence of the citramalate pathway, labeling both straight- and branched-chain esters. Analysis of genomic DNA (gDNA) revealed the presence of two nearly identical alleles in "Jonagold" fruit (MdCMS_1 and MdCMS_2), differing by two nonsynonymous single-nucleotide polymorphisms (SNPs). The mature proteins differed only at amino acid 387, possessing either glutamine387 (MdCMS_1) or glutamate387 (MdCMS_2). Glutamate387 was associated with near complete loss of activity. MdCMS expression was fruit-specific, increasing severalfold during ripening. The translated protein product was detected in ripe fruit. Transient expression of MdCMS_1 in Nicotiana benthamiana induced the accumulation of high levels of citramalate, whereas MdCMS_2 did not. Domesticated apple lines with MdCMS isozymes containing only glutamate387 produced a very low proportion of 2-methylbutanol- and 2-methylbutanoate (2MB) and 1-propanol and propanoate (PROP) esters. The citramalate pathway, previously only described in microorganisms, is shown to function in ripening apple and contribute to isoleucine and 2MB and PROP ester biosynthesis without feedback regulation.
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Affiliation(s)
- Nobuko Sugimoto
- Department of Horticulture, Michigan State University, East Lansing, MI 48824
| | - Philip Engelgau
- Department of Horticulture, Michigan State University, East Lansing, MI 48824
| | - A Daniel Jones
- Mass Spectrometry and Metabolomics Core, Research Technology Support Facility, Michigan State University, East Lansing, MI 48824
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824
- Department of Chemistry, Michigan State University, East Lansing, MI 48824
| | - Jun Song
- Kentville Research and Development Center, Agriculture and Agri-Food Canada, Kentville, NS B4N 1J5, Canada
| | - Randolph Beaudry
- Department of Horticulture, Michigan State University, East Lansing, MI 48824;
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9
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Hammer SK, Zhang Y, Avalos JL. Mitochondrial Compartmentalization Confers Specificity to the 2-Ketoacid Recursive Pathway: Increasing Isopentanol Production in Saccharomyces cerevisiae. ACS Synth Biol 2020; 9:546-555. [PMID: 32049515 DOI: 10.1021/acssynbio.9b00420] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Recursive elongation pathways produce compounds of increasing carbon-chain length with each iterative cycle. Of particular interest are 2-ketoacids derived from recursive elongation, which serve as precursors to a valuable class of advanced biofuels known as branched-chain higher alcohols (BCHAs). Protein engineering has been used to increase the number of iterative elongation cycles completed, yet specific production of longer-chain 2-ketoacids remains difficult to achieve. Here, we show that mitochondrial compartmentalization is an effective strategy to increase specificity of recursive pathways to favor longer-chain products. Using 2-ketoacid elongation as a proof of concept, we show that overexpression of the three elongation enzymes-LEU4, LEU1, and LEU2-in mitochondria of an isobutanol production strain results in a 2.3-fold increase in the isopentanol to isobutanol product ratio relative to overexpressing the same elongation enzymes in the cytosol, and a 31-fold increase relative to wild-type enzyme expression. Reducing the loss of intermediates allows us to further boost isopentanol production to 1.24 ± 0.06 g/L of isopentanol. In this strain, isopentanol accounts for 86% of the total BCHAs produced, while achieving the highest isopentanol titer reported for Saccharomyces cerevisiae. Localizing the elongation enzymes in mitochondria enables the development of strains in which isopentanol constitutes as much as 93% of BCHA production. This work establishes mitochondrial compartmentalization as a new approach to favor high titers and product specificities of larger products from recursive pathways.
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Affiliation(s)
- Sarah K. Hammer
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544, United States
| | - Yanfei Zhang
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544, United States
| | - José L. Avalos
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544, United States
- Andlinger Center for Energy and the Environment, Princeton University, Princeton, New Jersey 08544, United States
- Department of Molecular Biology, Princeton University, Princeton, New Jersey 08544, United States
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10
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Lee JW, Trinh CT. Towards renewable flavors, fragrances, and beyond. Curr Opin Biotechnol 2020; 61:168-180. [PMID: 31986468 DOI: 10.1016/j.copbio.2019.12.017] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2019] [Revised: 12/01/2019] [Accepted: 12/17/2019] [Indexed: 02/08/2023]
Abstract
Esters constitute a large space of unique molecules with broad range of applications as flavors, fragrances, pharmaceuticals, cosmetics, green solvents, and advanced biofuels. Global demand of natural esters in food, household cleaner, personal care, and perfume industries is increasing while the ester supply from natural sources has been limited. Development of novel microbial cell factories for ester production from renewable feedstocks can potentially provide an alternative and sustainable source of natural esters and hence help fulfill growing demand. Here, we highlight recent advances in microbial production of esters and provide perspectives for improving its economic feasibility. As the field matures, microbial ester production platforms will enable renewable and sustainable production of flavors and fragrances, and open new market opportunities beyond what nature can offer.
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Affiliation(s)
- Jong-Won Lee
- Bredesen Center for Interdisciplinary Research and Graduate Education, The University of Tennessee, Knoxville, TN, USA; Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Cong T Trinh
- Bredesen Center for Interdisciplinary Research and Graduate Education, The University of Tennessee, Knoxville, TN, USA; Department of Chemical and Biomolecular Engineering, The University of Tennessee, Knoxville, TN, USA; Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, USA.
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11
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Recent trends in metabolic engineering of microbial chemical factories. Curr Opin Biotechnol 2019; 60:188-197. [DOI: 10.1016/j.copbio.2019.05.010] [Citation(s) in RCA: 62] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Accepted: 05/09/2019] [Indexed: 11/24/2022]
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12
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Derrington SR, Turner NJ, France SP. Carboxylic acid reductases (CARs): An industrial perspective. J Biotechnol 2019; 304:78-88. [DOI: 10.1016/j.jbiotec.2019.08.010] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Revised: 08/14/2019] [Accepted: 08/14/2019] [Indexed: 01/09/2023]
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13
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Production of nonnatural straight-chain amino acid 6-aminocaproate via an artificial iterative carbon-chain-extension cycle. Metab Eng 2019; 55:23-32. [DOI: 10.1016/j.ymben.2019.06.009] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Revised: 06/13/2019] [Accepted: 06/15/2019] [Indexed: 12/23/2022]
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14
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Distinct mechanisms of substrate selectivity in the DRE-TIM metallolyase superfamily: A role for the LeuA dimer regulatory domain. Arch Biochem Biophys 2019; 664:1-8. [DOI: 10.1016/j.abb.2019.01.021] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Revised: 01/14/2019] [Accepted: 01/16/2019] [Indexed: 11/20/2022]
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15
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Boock JT, Freedman AJE, Tompsett GA, Muse SK, Allen AJ, Jackson LA, Castro-Dominguez B, Timko MT, Prather KLJ, Thompson JR. Engineered microbial biofuel production and recovery under supercritical carbon dioxide. Nat Commun 2019; 10:587. [PMID: 30718495 PMCID: PMC6361901 DOI: 10.1038/s41467-019-08486-6] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Accepted: 01/11/2019] [Indexed: 12/16/2022] Open
Abstract
Culture contamination, end-product toxicity, and energy efficient product recovery are long-standing bioprocess challenges. To solve these problems, we propose a high-pressure fermentation strategy, coupled with in situ extraction using the abundant and renewable solvent supercritical carbon dioxide (scCO2), which is also known for its broad microbial lethality. Towards this goal, we report the domestication and engineering of a scCO2-tolerant strain of Bacillus megaterium, previously isolated from formation waters from the McElmo Dome CO2 field, to produce branched alcohols that have potential use as biofuels. After establishing induced-expression under scCO2, isobutanol production from 2-ketoisovalerate is observed with greater than 40% yield with co-produced isopentanol. Finally, we present a process model to compare the energy required for our process to other in situ extraction methods, such as gas stripping, finding scCO2 extraction to be potentially competitive, if not superior. End-product toxicity, culture contamination, and energy efficient product recovery are long-standing issues in bioprocessing. Here, the authors address these problems using a fermentation strategy that combines microbial production of branched alcohols with supercritical carbon dioxide extraction.
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Affiliation(s)
- Jason T Boock
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.,Department of Chemical, Paper, and Biomedical Engineering, Miami University, Oxford, OH, 45056, USA
| | - Adam J E Freedman
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.,Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Geoffrey A Tompsett
- Department of Chemical Engineering, Worcester Polytechnic Institute, Worcester, MA, 01609, USA
| | - Sarah K Muse
- Department of Chemical Engineering, Worcester Polytechnic Institute, Worcester, MA, 01609, USA
| | - Audrey J Allen
- Department of Chemical Engineering, Worcester Polytechnic Institute, Worcester, MA, 01609, USA
| | - Luke A Jackson
- Department of Chemical Engineering, Worcester Polytechnic Institute, Worcester, MA, 01609, USA
| | - Bernardo Castro-Dominguez
- Department of Chemical Engineering, Worcester Polytechnic Institute, Worcester, MA, 01609, USA.,Department of Chemical Engineering, University of Bath, Bath, BA2 7AY, UK
| | - Michael T Timko
- Department of Chemical Engineering, Worcester Polytechnic Institute, Worcester, MA, 01609, USA
| | - Kristala L J Prather
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
| | - Janelle R Thompson
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
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16
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Black WB, King E, Wang Y, Jenic A, Rowley AT, Seki K, Luo R, Li H. Engineering a Coenzyme A Detour To Expand the Product Scope and Enhance the Selectivity of the Ehrlich Pathway. ACS Synth Biol 2018; 7:2758-2764. [PMID: 30433765 DOI: 10.1021/acssynbio.8b00358] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The Ehrlich pathway is a major route for the renewable production of higher alcohols. However, the product scope of the Ehrlich pathway is restricted, and the product selectivity is suboptimal. Here, we demonstrate that a Coenzyme A (CoA) detour, which involves conversion of the 2-keto acids into acyl-CoAs, expands the biological toolkit of reaction chemistries available in the Ehrlich pathway to include the gamut of CoA-dependent enzymes. As a proof-of-concept, we demonstrated the first biosynthesis of a tertiary branched-alcohol, pivalcohol, at a level of ∼10 mg/L from glucose in Escherichia coli, using a pivalyl-CoA mutase from Xanthobacter autotrophicus. Furthermore, engineering an enzyme in the CoA detour, the Lactobacillus brevis CoA-acylating aldehyde dehydrogenase, allowed stringent product selectivity. Targeted production of 3-methyl-1-butanol (3-MB) in E. coli mediated by the CoA detour showed a 3-MB:side-product (isobutanol) ratio of >20, an increase over the ratios previously achieved using the conventional Ehrlich pathway.
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17
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Escherichia coli as a host for metabolic engineering. Metab Eng 2018; 50:16-46. [DOI: 10.1016/j.ymben.2018.04.008] [Citation(s) in RCA: 181] [Impact Index Per Article: 30.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2018] [Revised: 04/11/2018] [Accepted: 04/12/2018] [Indexed: 12/21/2022]
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18
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Expanding lysine industry: industrial biomanufacturing of lysine and its derivatives. ACTA ACUST UNITED AC 2018; 45:719-734. [DOI: 10.1007/s10295-018-2030-8] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2017] [Accepted: 03/22/2018] [Indexed: 12/12/2022]
Abstract
Abstract
l-Lysine is widely used as a nutrition supplement in feed, food, and beverage industries as well as a chemical intermediate. At present, great efforts are made to further decrease the cost of lysine to make it more competitive in the markets. Furthermore, lysine also shows potential as a feedstock to produce other high-value chemicals for active pharmaceutical ingredients, drugs, or materials. In this review, the current biomanufacturing of lysine is first presented. Second, the production of novel derivatives from lysine is discussed. Some chemicals like l-pipecolic acid, cadaverine, and 5-aminovalerate already have been obtained at a lab scale. Others like 6-aminocaproic acid, valerolactam, and caprolactam could be produced through a biological and chemical coupling pathway or be synthesized by a hypothetical pathway. This review demonstrates an active and expansive lysine industry, and these green biomanufacturing strategies could also be applied to enhance the competitiveness of other amino acid industry.
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19
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Yu JL, Qian ZG, Zhong JJ. Advances in bio-based production of dicarboxylic acids longer than C4. Eng Life Sci 2018; 18:668-681. [PMID: 32624947 DOI: 10.1002/elsc.201800023] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Revised: 05/18/2018] [Accepted: 06/13/2018] [Indexed: 12/15/2022] Open
Abstract
Growing concerns of environmental pollution and fossil resource shortage are major driving forces for bio-based production of chemicals traditionally from petrochemical industry. Dicarboxylic acids (DCAs) are important platform chemicals with large market and wide applications, and here the recent advances in bio-based production of straight-chain DCAs longer than C4 from biological approaches, especially by synthetic biology, are reviewed. A couple of pathways were recently designed and demonstrated for producing DCAs, even those ranging from C5 to C15, by employing respective starting units, extending units, and appropriate enzymes. Furthermore, in order to achieve higher production of DCAs, enormous efforts were made in engineering microbial hosts that harbored the biosynthetic pathways and in improving properties of biocatalytic elements to enhance metabolic fluxes toward target DCAs. Here we summarize and discuss the current advantages and limitations of related pathways, and also provide perspectives on synthetic pathway design and optimization for hyper-production of DCAs.
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Affiliation(s)
- Jia-Le Yu
- State Key Laboratory of Microbial Metabolism Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology Shanghai Jiao Tong University Shanghai P. R. China.,State Key Laboratory of Bioreactor Engineering, School of Biotechnology East China University of Science and Technology Shanghai P. R. China
| | - Zhi-Gang Qian
- State Key Laboratory of Microbial Metabolism Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology Shanghai Jiao Tong University Shanghai P. R. China.,Shanghai Collaborative Innovation Center for Biomanufacturing Technology (SCICBT) East China University of Science and Technology Shanghai P. R. China
| | - Jian-Jiang Zhong
- State Key Laboratory of Microbial Metabolism Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology Shanghai Jiao Tong University Shanghai P. R. China.,State Key Laboratory of Bioreactor Engineering, School of Biotechnology East China University of Science and Technology Shanghai P. R. China.,Shanghai Collaborative Innovation Center for Biomanufacturing Technology (SCICBT) East China University of Science and Technology Shanghai P. R. China
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20
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Noda-Garcia L, Liebermeister W, Tawfik DS. Metabolite–Enzyme Coevolution: From Single Enzymes to Metabolic Pathways and Networks. Annu Rev Biochem 2018; 87:187-216. [DOI: 10.1146/annurev-biochem-062917-012023] [Citation(s) in RCA: 75] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
How individual enzymes evolved is relatively well understood. However, individual enzymes rarely confer a physiological advantage on their own. Judging by its current state, the emergence of metabolism seemingly demanded the simultaneous emergence of many enzymes. Indeed, how multicomponent interlocked systems, like metabolic pathways, evolved is largely an open question. This complexity can be unlocked if we assume that survival of the fittest applies not only to genes and enzymes but also to the metabolites they produce. This review develops our current knowledge of enzyme evolution into a wider hypothesis of pathway and network evolution. We describe the current models for pathway evolution and offer an integrative metabolite–enzyme coevolution hypothesis. Our hypothesis addresses the origins of new metabolites and of new enzymes and the order of their recruitment. We aim to not only survey established knowledge but also present open questions and potential ways of addressing them.
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Affiliation(s)
- Lianet Noda-Garcia
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot 76100, Israel;,
| | - Wolfram Liebermeister
- INRA, Unité MaIAGE, 78352 Jouy en Josas, France
- Institute of Biochemistry, Charité Universitätsmedizin, Berlin, 10117 Berlin, Germany
| | - Dan S. Tawfik
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot 76100, Israel;,
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21
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Henritzi S, Fischer M, Grininger M, Oreb M, Boles E. An engineered fatty acid synthase combined with a carboxylic acid reductase enables de novo production of 1-octanol in Saccharomyces cerevisiae. BIOTECHNOLOGY FOR BIOFUELS 2018; 11:150. [PMID: 29881455 PMCID: PMC5984327 DOI: 10.1186/s13068-018-1149-1] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Accepted: 05/23/2018] [Indexed: 05/05/2023]
Abstract
BACKGROUND The ideal biofuel should not only be a regenerative fuel from renewable feedstocks, but should also be compatible with the existing fuel distribution infrastructure and with normal car engines. As the so-called drop-in biofuel, the fatty alcohol 1-octanol has been described as a valuable substitute for diesel and jet fuels and has already been produced fermentatively from sugars in small amounts with engineered bacteria via reduction of thioesterase-mediated premature release of octanoic acid from fatty acid synthase or via a reversal of the β-oxidation pathway. RESULTS The previously engineered short-chain acyl-CoA producing yeast Fas1R1834K/Fas2 fatty acid synthase variant was expressed together with carboxylic acid reductase from Mycobacterium marinum and phosphopantetheinyl transferase Sfp from Bacillus subtilis in a Saccharomyces cerevisiae Δfas1 Δfas2 Δfaa2 mutant strain. With the involvement of endogenous thioesterases, alcohol dehydrogenases, and aldehyde reductases, the synthesized octanoyl-CoA was converted to 1-octanol up to a titer of 26.0 mg L-1 in a 72-h fermentation. The additional accumulation of 90 mg L-1 octanoic acid in the medium indicated a bottleneck in 1-octanol production. When octanoic acid was supplied externally to the yeast cells, it could be efficiently converted to 1-octanol indicating that re-uptake of octanoic acid across the plasma membrane is not limiting. Additional overexpression of aldehyde reductase Ahr from Escherichia coli nearly completely prevented accumulation of octanoic acid and increased 1-octanol titers up to 49.5 mg L-1. However, in growth tests concentrations even lower than 50.0 mg L-1 turned out to be inhibitory to yeast growth. In situ extraction in a two-phase fermentation with dodecane as second phase did not improve growth, indicating that 1-octanol acts inhibitive before secretion. Furthermore, 1-octanol production was even reduced, which results from extraction of the intermediate octanoic acid to the organic phase, preventing its re-uptake. CONCLUSIONS By providing chain length control via an engineered octanoyl-CoA producing fatty acid synthase, we were able to specifically produce 1-octanol with S. cerevisiae. Before metabolic engineering can be used to further increase product titers and yields, strategies must be developed that cope with the toxic effects of 1-octanol on the yeast cells.
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Affiliation(s)
- Sandra Henritzi
- Faculty of Biological Sciences, Institute of Molecular Bioscience, Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt, Germany
| | - Manuel Fischer
- Institute of Organic Chemistry and Chemical Biology, Buchmann Institute for Molecular Life Sciences, Cluster of Excellence “Macromolecular Complexes”, Goethe University Frankfurt, Max-von-Laue-Str. 15, 60438 Frankfurt, Germany
| | - Martin Grininger
- Institute of Organic Chemistry and Chemical Biology, Buchmann Institute for Molecular Life Sciences, Cluster of Excellence “Macromolecular Complexes”, Goethe University Frankfurt, Max-von-Laue-Str. 15, 60438 Frankfurt, Germany
| | - Mislav Oreb
- Faculty of Biological Sciences, Institute of Molecular Bioscience, Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt, Germany
| | - Eckhard Boles
- Faculty of Biological Sciences, Institute of Molecular Bioscience, Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt, Germany
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22
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Steps towards 'drop-in' biofuels: focusing on metabolic pathways. Curr Opin Biotechnol 2017; 53:26-32. [PMID: 29207330 DOI: 10.1016/j.copbio.2017.10.010] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2017] [Revised: 10/27/2017] [Accepted: 10/30/2017] [Indexed: 12/20/2022]
Abstract
The past decade has witnessed rapid advance in microbial production of 'drop-in' biofuels from renewable resources. Various biosynthetic pathways have been constructed to produce biofuels with diverse structures, and multiple metabolic engineering strategies have been developed to increase biofuel titers, yields, productivities and system robustness. In this review, we intend to give a brief but comprehensive overview of the most recent progresses on four essential pathways leading to 'drop-in' biofuel production, with an emphasis on the metabolic pathway efficiencies and biofuel structures. Furthermore, we also provide an insightful discussion on optimization strategies to improve the robustness of the microbial platforms for biofuel production.
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23
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Miao R, Liu X, Englund E, Lindberg P, Lindblad P. Isobutanol production in Synechocystis PCC 6803 using heterologous and endogenous alcohol dehydrogenases. Metab Eng Commun 2017; 5:45-53. [PMID: 29188183 PMCID: PMC5699533 DOI: 10.1016/j.meteno.2017.07.003] [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: 06/13/2017] [Revised: 07/18/2017] [Accepted: 07/27/2017] [Indexed: 12/24/2022] Open
Abstract
Isobutanol is a flammable compound that can be used as a biofuel due to its high energy density and suitable physical and chemical properties. In this study, we examined the capacity of engineered strains of Synechocystis PCC 6803 containing the α-ketoisovalerate decarboxylase from Lactococcus lactis and different heterologous and endogenous alcohol dehydrogenases (ADH) for isobutanol production. A strain expressing an introduced kivd without any additional copy of ADH produced 3 mg L-1 OD750-1 isobutanol in 6 days. After the cultures were supplemented with external addition of isobutyraldehyde, the substrate for ADH, 60.8 mg L-1 isobutanol was produced after 24 h when OD750 was 0.8. The in vivo activities of four different ADHs, two heterologous and two putative endogenous in Synechocystis, were examined and the Synechocystis endogenous ADH encoded by slr1192 showed the highest efficiency for isobutanol production. Furthermore, the strain overexpressing the isobutanol pathway on a self-replicating vector with the strong Ptrc promoter showed significantly higher gene expression and isobutanol production compared to the corresponding strains expressing the same operon introduced on the genome. Hence, this study demonstrates that Synechocystis endogenous AHDs have a high capacity for isobutanol production, and identifies kivd encoded α-ketoisovalerate decarboxylase as one of the likely bottlenecks for further isobutanol production.
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Affiliation(s)
| | | | | | | | - Peter Lindblad
- Microbial chemistry, Department of Chemistry-Ångström Laboratory, Uppsala University, Box 523, SE-751 20 Uppsala, Sweden
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24
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Abstract
Systems metabolic engineering, which recently emerged as metabolic engineering integrated with systems biology, synthetic biology, and evolutionary engineering, allows engineering of microorganisms on a systemic level for the production of valuable chemicals far beyond its native capabilities. Here, we review the strategies for systems metabolic engineering and particularly its applications in Escherichia coli. First, we cover the various tools developed for genetic manipulation in E. coli to increase the production titers of desired chemicals. Next, we detail the strategies for systems metabolic engineering in E. coli, covering the engineering of the native metabolism, the expansion of metabolism with synthetic pathways, and the process engineering aspects undertaken to achieve higher production titers of desired chemicals. Finally, we examine a couple of notable products as case studies produced in E. coli strains developed by systems metabolic engineering. The large portfolio of chemical products successfully produced by engineered E. coli listed here demonstrates the sheer capacity of what can be envisioned and achieved with respect to microbial production of chemicals. Systems metabolic engineering is no longer in its infancy; it is now widely employed and is also positioned to further embrace next-generation interdisciplinary principles and innovation for its upgrade. Systems metabolic engineering will play increasingly important roles in developing industrial strains including E. coli that are capable of efficiently producing natural and nonnatural chemicals and materials from renewable nonfood biomass.
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25
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Wang J, Wu Y, Sun X, Yuan Q, Yan Y. De Novo Biosynthesis of Glutarate via α-Keto Acid Carbon Chain Extension and Decarboxylation Pathway in Escherichia coli. ACS Synth Biol 2017; 6:1922-1930. [PMID: 28618222 DOI: 10.1021/acssynbio.7b00136] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Microbial based bioplastics are promising alternatives to petroleum based synthetic plastics due to their renewability and economic feasibility. Glutarate is one of the most potential building blocks for bioplastics. The recent biosynthetic routes for glutarate were mostly based on the l-lysine degradation pathway from Pseudomonas putida that required lysine either by feeding or lysine overproduction via genetic manipulations. Herein, we established a novel glutarate biosynthetic pathway by incorporation of a "+1" carbon chain extension pathway from α-ketoglutarate (α-KG) in combination with α-keto acid decarboxylation pathway in Escherichia coli. Introduction of homocitrate synthase (HCS), homoaconitase (HA) and homoisocitrate dehydrogenase (HICDH) from Saccharomyces cerevisiae into E. coli enabled "+1" carbon extension from α-KG to α-ketoadipate (α-KA), which was subsequently converted into glutarate by a promiscuous α-keto acid decarboxylase (KivD) and a succinate semialdehyde dehydrogenase (GabD). The recombinant E. coli coexpressing all five genes produced 0.3 g/L glutarate from glucose. To further improve the titers, α-KG was rechanneled into carbon chain extension pathway via the clustered regularly interspersed palindromic repeats system mediated interference (CRISPRi) of essential genes sucA and sucB in tricarboxylic acid (TCA) cycle. The final strain could produce 0.42 g/L glutarate, which was increased by 40% compared with the parental strain.
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Affiliation(s)
- Jian Wang
- College
of Engineering, The University of Georgia, Athens, Georgia 30602, United States
| | - Yifei Wu
- State
Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, Beijing 100029, China
- Beijing
Advanced Innovation Center for Soft Matter Science and Engineering, Beijing University of Chemical Technology, Beijing 100029, China
| | - Xinxiao Sun
- State
Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, Beijing 100029, China
- Beijing
Advanced Innovation Center for Soft Matter Science and Engineering, Beijing University of Chemical Technology, Beijing 100029, China
| | - Qipeng Yuan
- State
Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, Beijing 100029, China
- Beijing
Advanced Innovation Center for Soft Matter Science and Engineering, Beijing University of Chemical Technology, Beijing 100029, China
| | - Yajun Yan
- College
of Engineering, The University of Georgia, Athens, Georgia 30602, United States
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26
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Saturated mutagenesis of ketoisovalerate decarboxylase V461 enabled specific synthesis of 1-pentanol via the ketoacid elongation cycle. Sci Rep 2017; 7:11284. [PMID: 28900255 PMCID: PMC5595793 DOI: 10.1038/s41598-017-11624-z] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2017] [Accepted: 08/25/2017] [Indexed: 11/25/2022] Open
Abstract
Iterative ketoacid elongation has been an essential tool in engineering artificial metabolism, in particular the synthetic alcohols. However, precise control of product specificity is still greatly challenged by the substrate promiscuity of the ketoacid decarboxylase, which unselectively hijacks ketoacid intermediates from the elongation cycle along with the target ketoacid. In this work, preferential tuning of the Lactococcus lactis ketoisovalerate decarboxylase (Kivd) specificity toward 1-pentanol synthesis was achieved via saturated mutagenesis of the key residue V461 followed by screening of the resulting alcohol spectrum. Substitution of V461 with the small and polar amino acid glycine or serine significantly improved the Kivd selectivity toward the 1-pentanol precursor 2-ketocaproate by lowering its catalytic efficiency for the upstream ketoacid 2-ketobutyrate and 2-ketovalerate. Conversely, replacing V461 with bulky or charged side chains displayed severely adverse effect. Increasing supply of the iterative addition unit acetyl-CoA by acetate feeding further drove 2-ketoacid flux into the elongation cycle and enhanced 1-pentanol productivity. The Kivd V461G variant enabled a 1-pentanol production specificity around 90% of the total alcohol content with or without oleyl alcohol extraction. This work adds insight to the selectivity of Kivd active site.
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27
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Meadows CW, Kang A, Lee TS. Metabolic Engineering for Advanced Biofuels Production and Recent Advances Toward Commercialization. Biotechnol J 2017; 13. [DOI: 10.1002/biot.201600433] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2017] [Revised: 06/13/2017] [Indexed: 12/27/2022]
Affiliation(s)
- Corey W. Meadows
- Joint BioEnergy Institute5885 Hollis StreetEmeryvilleCA94608USA
- Biological Systems & Engineering DivisionLawrence Berkeley National LaboratoryBerkeleyCA94720USA
| | - Aram Kang
- Joint BioEnergy Institute5885 Hollis StreetEmeryvilleCA94608USA
- Biological Systems & Engineering DivisionLawrence Berkeley National LaboratoryBerkeleyCA94720USA
| | - Taek S. Lee
- Joint BioEnergy Institute5885 Hollis StreetEmeryvilleCA94608USA
- Biological Systems & Engineering DivisionLawrence Berkeley National LaboratoryBerkeleyCA94720USA
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28
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Taniguchi H, Okano K, Honda K. Modules for in vitro metabolic engineering: Pathway assembly for bio-based production of value-added chemicals. Synth Syst Biotechnol 2017; 2:65-74. [PMID: 29062963 PMCID: PMC5636945 DOI: 10.1016/j.synbio.2017.06.002] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2017] [Accepted: 06/02/2017] [Indexed: 11/17/2022] Open
Abstract
Bio-based chemical production has drawn attention regarding the realization of a sustainable society. In vitro metabolic engineering is one of the methods used for the bio-based production of value-added chemicals. This method involves the reconstitution of natural or artificial metabolic pathways by assembling purified/semi-purified enzymes in vitro. Enzymes from distinct sources can be combined to construct desired reaction cascades with fewer biological constraints in one vessel, enabling easier pathway design with high modularity. Multiple modules have been designed, built, tested, and improved by different groups for different purpose. In this review, we focus on these in vitro metabolic engineering modules, especially focusing on the carbon metabolism, and present an overview of input modules, output modules, and other modules related to cofactor management.
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29
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Wang C, Pfleger BF, Kim SW. Reassessing Escherichia coli as a cell factory for biofuel production. Curr Opin Biotechnol 2017; 45:92-103. [DOI: 10.1016/j.copbio.2017.02.010] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2016] [Revised: 02/05/2017] [Accepted: 02/09/2017] [Indexed: 11/29/2022]
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30
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Arai S, Hayashihara K, Kanamoto Y, Shimizu K, Hirokawa Y, Hanai T, Murakami A, Honda H. Alcohol‐tolerant mutants of cyanobacterium
Synechococcus elongatus
PCC 7942 obtained by single‐cell mutant screening system. Biotechnol Bioeng 2017; 114:1771-1778. [DOI: 10.1002/bit.26307] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Revised: 04/02/2017] [Accepted: 04/04/2017] [Indexed: 11/10/2022]
Affiliation(s)
- Sayuri Arai
- Department of BiotechnologyGraduate School of EngineeringNagoya UniversityFuro‐choChikusa‐kuNagoyaAichi464‐8603Japan
| | | | - Yuki Kanamoto
- Kobe University Research Center for Inland SeasAwajiHyogoJapan
| | - Kazunori Shimizu
- Department of BiotechnologyGraduate School of EngineeringNagoya UniversityFuro‐choChikusa‐kuNagoyaAichi464‐8603Japan
| | - Yasutaka Hirokawa
- Laboratory for BioinformaticsGraduate School of Systems Life SciencesKyushu UniversityHigashi‐kuFukuokaJapan
| | - Taizo Hanai
- Laboratory for BioinformaticsGraduate School of Systems Life SciencesKyushu UniversityHigashi‐kuFukuokaJapan
| | - Akio Murakami
- Kobe University Research Center for Inland SeasAwajiHyogoJapan
| | - Hiroyuki Honda
- Department of BiotechnologyGraduate School of EngineeringNagoya UniversityFuro‐choChikusa‐kuNagoyaAichi464‐8603Japan
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31
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Leitner W, Klankermayer J, Pischinger S, Pitsch H, Kohse-Höinghaus K. Advanced Biofuels and Beyond: Chemistry Solutions for Propulsion and Production. Angew Chem Int Ed Engl 2017; 56:5412-5452. [DOI: 10.1002/anie.201607257] [Citation(s) in RCA: 187] [Impact Index Per Article: 26.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2016] [Revised: 11/18/2016] [Indexed: 12/12/2022]
Affiliation(s)
- Walter Leitner
- Institut für Technische und Makromolekulare Chemie; RWTH Aachen University; Worringerweg 1 52074 Aachen Germany
| | - Jürgen Klankermayer
- Institut für Technische und Makromolekulare Chemie; RWTH Aachen University; Worringerweg 1 52074 Aachen Germany
| | - Stefan Pischinger
- Lehrstuhl für Verbrennungskraftmaschinen und Institut für Thermodynamik; RWTH Aachen University; Forckenbeckstrasse 4 52074 Aachen Germany
| | - Heinz Pitsch
- Institut für Technische Verbrennung; RWTH Aachen University; Templergraben 64 52056 Aachen Germany
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32
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Leitner W, Klankermayer J, Pischinger S, Pitsch H, Kohse-Höinghaus K. Synthese, motorische Verbrennung, Emissionen: Chemische Aspekte des Kraftstoffdesigns. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201607257] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Affiliation(s)
- Walter Leitner
- Institut für Technische und Makromolekulare Chemie; RWTH Aachen University; Worringerweg 1 52074 Aachen Deutschland
| | - Jürgen Klankermayer
- Institut für Technische und Makromolekulare Chemie; RWTH Aachen University; Worringerweg 1 52074 Aachen Deutschland
| | - Stefan Pischinger
- Lehrstuhl für Verbrennungskraftmaschinen und Institut für Thermodynamik; RWTH Aachen University; Forckenbeckstraße 4, 5 2074 Aachen Deutschland
| | - Heinz Pitsch
- Institut für Technische Verbrennung; RWTH Aachen University; Templergraben 64 52056 Aachen Deutschland
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33
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Jiang W, Qiao JB, Bentley GJ, Liu D, Zhang F. Modular pathway engineering for the microbial production of branched-chain fatty alcohols. BIOTECHNOLOGY FOR BIOFUELS 2017; 10:244. [PMID: 29090017 PMCID: PMC5658922 DOI: 10.1186/s13068-017-0936-4] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2017] [Accepted: 10/19/2017] [Indexed: 05/08/2023]
Abstract
The intrinsic structural properties of branched long-chain fatty alcohols (BLFLs) in the range of C12 to C18 make them more suitable as diesel fuel replacements and for other industrial applications than their straight-chain counterparts. While microbial production of straight long-chain fatty alcohols has been achieved, biosynthesis of BLFLs has never been reported. In this work, we engineered four different biosynthetic pathways in Escherichia coli to produce BLFLs. We then employed a modular engineering approach to optimize the supply of α-keto acid precursors and produced either odd-chain or even-chain BLFLs with high selectivity, reaching 70 and 75% of total fatty alcohols, respectively. The acyl-ACP and alcohol-producing modules were also extensively optimized to balance enzyme expression level and ratio, resulting in a 6.5-fold improvement in BLFL titers. The best performing strain overexpressed 14 genes from 6 engineered operons and produced 350 mg/L of BLFLs in fed-batch fermenter. The modular engineering strategy successfully facilitated microbial production of BLFLs and allowed us to quickly optimize new BLFL pathway with high titers and product specificity. More generally, this work provides pathways and knowledge for the production of BLFLs and BLFL-related, industry-relevant chemicals in high titers and yields.
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Affiliation(s)
- Wen Jiang
- Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, 1 Brookings Drive, Campus Box 1180, Saint Louis, MO 63130 USA
| | - James B. Qiao
- Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, 1 Brookings Drive, Campus Box 1180, Saint Louis, MO 63130 USA
| | - Gayle J. Bentley
- Division of Biological & Biomedical Sciences, Washington University in St. Louis, Saint Louis, MO 63130 USA
- Present Address: National Bioenergy Center, National Renewable Energy Laboratory, Golden, CO 80401 USA
| | - Di Liu
- Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, 1 Brookings Drive, Campus Box 1180, Saint Louis, MO 63130 USA
| | - Fuzhong Zhang
- Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, 1 Brookings Drive, Campus Box 1180, Saint Louis, MO 63130 USA
- Division of Biological & Biomedical Sciences, Washington University in St. Louis, Saint Louis, MO 63130 USA
- Institute of Materials Science & Engineering, Washington University in St. Louis, Saint Louis, MO 63130 USA
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Cheon S, Kim HM, Gustavsson M, Lee SY. Recent trends in metabolic engineering of microorganisms for the production of advanced biofuels. Curr Opin Chem Biol 2016; 35:10-21. [DOI: 10.1016/j.cbpa.2016.08.003] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2016] [Revised: 07/14/2016] [Accepted: 08/07/2016] [Indexed: 10/21/2022]
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Loder AJ, Zeldes BM, Conway JM, Counts JA, Straub CT, Khatibi PA, Lee LL, Vitko NP, Keller MW, Rhaesa AM, Rubinstein GM, Scott IM, Lipscomb GL, Adams MW, Kelly RM. Extreme Thermophiles as Metabolic Engineering Platforms: Strategies and Current Perspective. Ind Biotechnol (New Rochelle N Y) 2016. [DOI: 10.1002/9783527807796.ch14] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Affiliation(s)
- Andrew J. Loder
- North Carolina State University; Department of Chemical and Biomolecular Engineering; EB-1, 911 Partners Way Raleigh NC 27695-7905 USA
| | - Benjamin M. Zeldes
- North Carolina State University; Department of Chemical and Biomolecular Engineering; EB-1, 911 Partners Way Raleigh NC 27695-7905 USA
| | - Jonathan M. Conway
- North Carolina State University; Department of Chemical and Biomolecular Engineering; EB-1, 911 Partners Way Raleigh NC 27695-7905 USA
| | - James A. Counts
- North Carolina State University; Department of Chemical and Biomolecular Engineering; EB-1, 911 Partners Way Raleigh NC 27695-7905 USA
| | - Christopher T. Straub
- North Carolina State University; Department of Chemical and Biomolecular Engineering; EB-1, 911 Partners Way Raleigh NC 27695-7905 USA
| | - Piyum A. Khatibi
- North Carolina State University; Department of Chemical and Biomolecular Engineering; EB-1, 911 Partners Way Raleigh NC 27695-7905 USA
| | - Laura L. Lee
- North Carolina State University; Department of Chemical and Biomolecular Engineering; EB-1, 911 Partners Way Raleigh NC 27695-7905 USA
| | - Nicholas P. Vitko
- North Carolina State University; Department of Chemical and Biomolecular Engineering; EB-1, 911 Partners Way Raleigh NC 27695-7905 USA
| | - Matthew W. Keller
- University of Georgia; Department of Biochemistry and Molecular Biology; Life Sciences Bldg., University of Georgia, Athens GA 30602-7229, USA
| | - Amanda M. Rhaesa
- University of Georgia; Department of Biochemistry and Molecular Biology; Life Sciences Bldg., University of Georgia, Athens GA 30602-7229, USA
| | - Gabe M. Rubinstein
- University of Georgia; Department of Biochemistry and Molecular Biology; Life Sciences Bldg., University of Georgia, Athens GA 30602-7229, USA
| | - Israel M. Scott
- University of Georgia; Department of Biochemistry and Molecular Biology; Life Sciences Bldg., University of Georgia, Athens GA 30602-7229, USA
| | - Gina L. Lipscomb
- University of Georgia; Department of Biochemistry and Molecular Biology; Life Sciences Bldg., University of Georgia, Athens GA 30602-7229, USA
| | - Michael W.W. Adams
- University of Georgia; Department of Biochemistry and Molecular Biology; Life Sciences Bldg., University of Georgia, Athens GA 30602-7229, USA
| | - Robert M. Kelly
- North Carolina State University; Department of Chemical and Biomolecular Engineering; EB-1, 911 Partners Way Raleigh NC 27695-7905 USA
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Srirangan K, Liu X, Tran TT, Charles TC, Moo-Young M, Chou CP. Engineering of Escherichia coli for direct and modulated biosynthesis of poly(3-hydroxybutyrate-co-3-hydroxyvalerate) copolymer using unrelated carbon sources. Sci Rep 2016; 6:36470. [PMID: 27819347 PMCID: PMC5098226 DOI: 10.1038/srep36470] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2016] [Accepted: 10/14/2016] [Indexed: 12/13/2022] Open
Abstract
While poly(3-hydroxybutyrate-co-3-hydroxyvalerate) [P(3HB-co-3HV)] is a biodegradable commodity plastic with broad applications, its microbial synthesis is hindered by high production costs primarily associated with the supplementation of related carbon substrates (e.g. propionate or valerate). Here we report construction of engineered Escherichia coli strains for direct synthesis of P(3HB-co-3HV) from an unrelated carbon source (e.g. glucose or glycerol). First, an E. coli strain with an activated sleeping beauty mutase (Sbm) operon was used to generate propionyl-CoA as a precursor. Next, two acetyl-CoA moieties or acetyl-CoA and propionyl-CoA were condensed to form acetoacetyl-CoA and 3-ketovaleryl-CoA, respectively, by functional expression of β-ketothiolases from Cupriavidus necator (i.e. PhaA and BktB). The resulting thioester intermediates were channeled into the polyhydroxyalkanoate (PHA) biosynthetic pathway through functional expression of acetoacetyl-CoA reductase (PhaB) for thioester reduction and PHA synthase (PhaC) for subsequent polymerization. Metabolic engineering of E. coli host strains was further conducted to enhance total PHA content and the 3-hydroxyvaleryl (3HV) monomer fraction in the copolymer. Using a selection of engineered E. coli strains for batch cultivation with an unrelated carbon source, we achieved high-level P(3HB-co-3HV) production with the 3HV monomer fraction ranging from 3 to 19 mol%, demonstrating the potential industrial applicability of these whole-cell biocatalysts.
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Affiliation(s)
- Kajan Srirangan
- Department of Chemical Engineering , University of Waterloo, 200 University Avenue West Waterloo, Ontario N2L 3G1 Canada
| | - Xuejia Liu
- Department of Chemical Engineering , University of Waterloo, 200 University Avenue West Waterloo, Ontario N2L 3G1 Canada
| | - Tam T Tran
- Department of Biology, University of Waterloo, Waterloo, Ontario, Canada
| | - Trevor C Charles
- Department of Biology, University of Waterloo, Waterloo, Ontario, Canada
| | - Murray Moo-Young
- Department of Chemical Engineering , University of Waterloo, 200 University Avenue West Waterloo, Ontario N2L 3G1 Canada
| | - C Perry Chou
- Department of Chemical Engineering , University of Waterloo, 200 University Avenue West Waterloo, Ontario N2L 3G1 Canada
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Reaction kinetic analysis of the 3-hydroxypropionate/4-hydroxybutyrate CO 2 fixation cycle in extremely thermoacidophilic archaea. Metab Eng 2016; 38:446-463. [PMID: 27771364 DOI: 10.1016/j.ymben.2016.10.009] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2016] [Revised: 09/07/2016] [Accepted: 10/17/2016] [Indexed: 12/21/2022]
Abstract
The 3-hydroxypropionate/4-hydroxybutyrate (3HP/4HB) cycle fixes CO2 in extremely thermoacidophilic archaea and holds promise for metabolic engineering because of its thermostability and potentially rapid pathway kinetics. A reaction kinetics model was developed to examine the biological and biotechnological attributes of the 3HP/4HB cycle as it operates in Metallosphaera sedula, based on previous information as well as on kinetic parameters determined here for recombinant versions of five of the cycle enzymes (malonyl-CoA/succinyl-CoA reductase, 3-hydroxypropionyl-CoA synthetase, 3-hydroxypropionyl-CoA dehydratase, acryloyl-CoA reductase, and succinic semialdehyde reductase). The model correctly predicted previously observed features of the cycle: the 35-65% split of carbon flux through the acetyl-CoA and succinate branches, the high abundance and relative ratio of acetyl-CoA/propionyl-CoA carboxylase (ACC) and MCR, and the significance of ACC and hydroxybutyryl-CoA synthetase (HBCS) as regulated control points for the cycle. The model was then used to assess metabolic engineering strategies for incorporating CO2 into chemical intermediates and products of biotechnological importance: acetyl-CoA, succinate, and 3-hydroxypropionate.
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Srirangan K, Bruder M, Akawi L, Miscevic D, Kilpatrick S, Moo-Young M, Chou CP. Recent advances in engineering propionyl-CoA metabolism for microbial production of value-added chemicals and biofuels. Crit Rev Biotechnol 2016; 37:701-722. [PMID: 27557613 DOI: 10.1080/07388551.2016.1216391] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Diminishing fossil fuel reserves and mounting environmental concerns associated with petrochemical manufacturing practices have generated significant interests in developing whole-cell biocatalytic systems for the production of value-added chemicals and biofuels. Although acetyl-CoA is a common natural biogenic precursor for the biosynthesis of numerous metabolites, propionyl-CoA is unpopular and non-native to most organisms. Nevertheless, with its C3-acyl moiety as a discrete building block, propionyl-CoA can serve as another key biogenic precursor to several biological products of industrial importance. As a result, engineering propionyl-CoA metabolism, particularly in genetically tractable hosts with the use of inexpensive feedstocks, has paved an avenue for novel biomanufacturing. Herein, we present a systematic review on manipulation of propionyl-CoA metabolism as well as relevant genetic and metabolic engineering strategies for microbial production of value-added chemicals and biofuels, including odd-chain alcohols and organic acids, bio(co)polymers and polyketides. [Formula: see text].
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Affiliation(s)
| | - Mark Bruder
- a Department of Chemical Engineering , University of Waterloo , Waterloo , ON , Canada
| | - Lamees Akawi
- a Department of Chemical Engineering , University of Waterloo , Waterloo , ON , Canada
| | - Dragan Miscevic
- a Department of Chemical Engineering , University of Waterloo , Waterloo , ON , Canada
| | - Shane Kilpatrick
- a Department of Chemical Engineering , University of Waterloo , Waterloo , ON , Canada
| | - Murray Moo-Young
- a Department of Chemical Engineering , University of Waterloo , Waterloo , ON , Canada
| | - C Perry Chou
- a Department of Chemical Engineering , University of Waterloo , Waterloo , ON , Canada
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40
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Mirza N, Crocoll C, Erik Olsen C, Ann Halkier B. Engineering of methionine chain elongation part of glucoraphanin pathway in E. coli. Metab Eng 2016; 35:31-37. [DOI: 10.1016/j.ymben.2015.09.012] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2014] [Revised: 07/24/2015] [Accepted: 09/02/2015] [Indexed: 12/12/2022]
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41
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Engineering Escherichia coli for Microbial Production of Butanone. Appl Environ Microbiol 2016; 82:2574-2584. [PMID: 26896132 DOI: 10.1128/aem.03964-15] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2015] [Accepted: 02/12/2016] [Indexed: 11/20/2022] Open
Abstract
To expand the chemical and molecular diversity of biotransformation using whole-cell biocatalysts, we genetically engineered a pathway in Escherichia coli for heterologous production of butanone, an important commodity ketone. First, a 1-propanol-producing E. coli host strain with its sleeping beauty mutase (Sbm) operon being activated was used to increase the pool of propionyl-coenzyme A (propionyl-CoA). Subsequently, molecular heterofusion of propionyl-CoA and acetyl-CoA was conducted to yield 3-ketovaleryl-CoA via a CoA-dependent elongation pathway. Lastly, 3-ketovaleryl-CoA was channeled into the clostridial acetone formation pathway for thioester hydrolysis and subsequent decarboxylation to form butanone. Biochemical, genetic, and metabolic factors affecting relative levels of ketogenesis, acidogenesis, and alcohol genesis under selected fermentative culture conditions were investigated. Using the engineered E. coli strain for batch cultivation with 30 g liter(-1)glycerol as the carbon source, we achieved coproduction of 1.3 g liter(-1)butanone and 2.9 g liter(-1)acetone. The results suggest that approximately 42% of spent glycerol was utilized for ketone biosynthesis, and thus they demonstrate potential industrial applicability of this microbial platform.
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42
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Kumar G, Johnson JL, Frantom PA. Improving Functional Annotation in the DRE-TIM Metallolyase Superfamily through Identification of Active Site Fingerprints. Biochemistry 2016; 55:1863-72. [PMID: 26935545 DOI: 10.1021/acs.biochem.5b01193] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Within the DRE-TIM metallolyase superfamily, members of the Claisen-like condensation (CC-like) subgroup catalyze C-C bond-forming reactions between various α-ketoacids and acetyl-coenzyme A. These reactions are important in the metabolic pathways of many bacterial pathogens and serve as engineering scaffolds for the production of long-chain alcohol biofuels. To improve functional annotation and identify sequences that might use novel substrates in the CC-like subgroup, a combination of structural modeling and multiple-sequence alignments identified active site residues on the third, fourth, and fifth β-strands of the TIM-barrel catalytic domain that are differentially conserved within the substrate-diverse enzyme families. Using α-isopropylmalate synthase and citramalate synthase from Methanococcus jannaschii (MjIPMS and MjCMS), site-directed mutagenesis was used to test the role of each identified position in substrate selectivity. Kinetic data suggest that residues at the β3-5 and β4-7 positions play a significant role in the selection of α-ketoisovalerate over pyruvate in MjIPMS. However, complementary substitutions in MjCMS fail to alter substrate specificity, suggesting residues in these positions do not contribute to substrate selectivity in this enzyme. Analysis of the kinetic data with respect to a protein similarity network for the CC-like subgroup suggests that evolutionarily distinct forms of IPMS utilize residues at the β3-5 and β4-7 positions to affect substrate selectivity while the different versions of CMS use unique architectures. Importantly, mapping the identities of residues at the β3-5 and β4-7 positions onto the protein similarity network allows for rapid annotation of probable IPMS enzymes as well as several outlier sequences that may represent novel functions in the subgroup.
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Affiliation(s)
- Garima Kumar
- Department of Chemistry, The University of Alabama , 250 Hackberry Lane, Tuscaloosa, Alabama 35487, United States
| | - Jordyn L Johnson
- Department of Chemistry, The University of Alabama , 250 Hackberry Lane, Tuscaloosa, Alabama 35487, United States
| | - Patrick A Frantom
- Department of Chemistry, The University of Alabama , 250 Hackberry Lane, Tuscaloosa, Alabama 35487, United States
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43
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Sun X, Shen X, Jain R, Lin Y, Wang J, Sun J, Wang J, Yan Y, Yuan Q. Synthesis of chemicals by metabolic engineering of microbes. Chem Soc Rev 2016; 44:3760-85. [PMID: 25940754 DOI: 10.1039/c5cs00159e] [Citation(s) in RCA: 77] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Metabolic engineering is a powerful tool for the sustainable production of chemicals. Over the years, the exploration of microbial, animal and plant metabolism has generated a wealth of valuable genetic information. The prudent application of this knowledge on cellular metabolism and biochemistry has enabled the construction of novel metabolic pathways that do not exist in nature or enhance existing ones. The hand in hand development of computational technology, protein science and genetic manipulation tools has formed the basis of powerful emerging technologies that make the production of green chemicals and fuels a reality. Microbial production of chemicals is more feasible compared to plant and animal systems, due to simpler genetic make-up and amenable growth rates. Here, we summarize the recent progress in the synthesis of biofuels, value added chemicals, pharmaceuticals and nutraceuticals via metabolic engineering of microbes.
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Affiliation(s)
- Xinxiao Sun
- State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, 15#, Beisanhuan East Road, Chaoyang District, Beijing 100029, China.
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44
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Carlin DA, Caster RW, Wang X, Betzenderfer SA, Chen CX, Duong VM, Ryklansky CV, Alpekin A, Beaumont N, Kapoor H, Kim N, Mohabbot H, Pang B, Teel R, Whithaus L, Tagkopoulos I, Siegel JB. Kinetic Characterization of 100 Glycoside Hydrolase Mutants Enables the Discovery of Structural Features Correlated with Kinetic Constants. PLoS One 2016; 11:e0147596. [PMID: 26815142 PMCID: PMC4729467 DOI: 10.1371/journal.pone.0147596] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2015] [Accepted: 01/06/2016] [Indexed: 11/18/2022] Open
Abstract
The use of computational modeling algorithms to guide the design of novel enzyme catalysts is a rapidly growing field. Force-field based methods have now been used to engineer both enzyme specificity and activity. However, the proportion of designed mutants with the intended function is often less than ten percent. One potential reason for this is that current force-field based approaches are trained on indirect measures of function rather than direct correlation to experimentally-determined functional effects of mutations. We hypothesize that this is partially due to the lack of data sets for which a large panel of enzyme variants has been produced, purified, and kinetically characterized. Here we report the kcat and KM values of 100 purified mutants of a glycoside hydrolase enzyme. We demonstrate the utility of this data set by using machine learning to train a new algorithm that enables prediction of each kinetic parameter based on readily-modeled structural features. The generated dataset and analyses carried out in this study not only provide insight into how this enzyme functions, they also provide a clear path forward for the improvement of computational enzyme redesign algorithms.
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Affiliation(s)
- Dylan Alexander Carlin
- Biophysics Graduate Group, University of California Davis, California, United States of America
| | - Ryan W. Caster
- Genome Center, University of California Davis, Davis, California, United States of America
| | - Xiaokang Wang
- Department of Biomedical Engineering, University of California Davis, Davis, California, United States of America
| | | | - Claire X. Chen
- Genome Center, University of California Davis, Davis, California, United States of America
| | - Veasna M. Duong
- Genome Center, University of California Davis, Davis, California, United States of America
| | - Carolina V. Ryklansky
- Genome Center, University of California Davis, Davis, California, United States of America
| | - Alp Alpekin
- Genome Center, University of California Davis, Davis, California, United States of America
| | - Nathan Beaumont
- Genome Center, University of California Davis, Davis, California, United States of America
| | - Harshul Kapoor
- Genome Center, University of California Davis, Davis, California, United States of America
| | - Nicole Kim
- Genome Center, University of California Davis, Davis, California, United States of America
| | - Hosna Mohabbot
- Genome Center, University of California Davis, Davis, California, United States of America
| | - Boyu Pang
- Genome Center, University of California Davis, Davis, California, United States of America
| | - Rachel Teel
- Genome Center, University of California Davis, Davis, California, United States of America
| | - Lillian Whithaus
- Genome Center, University of California Davis, Davis, California, United States of America
| | - Ilias Tagkopoulos
- Genome Center, University of California Davis, Davis, California, United States of America
- Department of Computer Science, University of California Davis, Davis, California, United States of America
| | - Justin B. Siegel
- Genome Center, University of California Davis, Davis, California, United States of America
- Department of Chemistry, University of California Davis, Davis, California, United States of America
- Department of Biochemistry & Molecular Medicine, University of California Davis, Davis, California, United States of America
- * E-mail:
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45
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Otte KB, Hauer B. Enzyme engineering in the context of novel pathways and products. Curr Opin Biotechnol 2015; 35:16-22. [DOI: 10.1016/j.copbio.2014.12.011] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2014] [Revised: 12/11/2014] [Accepted: 12/14/2014] [Indexed: 01/04/2023]
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46
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Boock JT, Gupta A, Prather KLJ. Screening and modular design for metabolic pathway optimization. Curr Opin Biotechnol 2015; 36:189-98. [DOI: 10.1016/j.copbio.2015.08.013] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Revised: 08/07/2015] [Accepted: 08/10/2015] [Indexed: 11/26/2022]
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47
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Mak WS, Tran S, Marcheschi R, Bertolani S, Thompson J, Baker D, Liao JC, Siegel JB. Integrative genomic mining for enzyme function to enable engineering of a non-natural biosynthetic pathway. Nat Commun 2015; 6:10005. [PMID: 26598135 PMCID: PMC4673503 DOI: 10.1038/ncomms10005] [Citation(s) in RCA: 65] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2015] [Accepted: 10/23/2015] [Indexed: 01/20/2023] Open
Abstract
The ability to biosynthetically produce chemicals beyond what is commonly found in Nature requires the discovery of novel enzyme function. Here we utilize two approaches to discover enzymes that enable specific production of longer-chain (C5–C8) alcohols from sugar. The first approach combines bioinformatics and molecular modelling to mine sequence databases, resulting in a diverse panel of enzymes capable of catalysing the targeted reaction. The median catalytic efficiency of the computationally selected enzymes is 75-fold greater than a panel of naively selected homologues. This integrative genomic mining approach establishes a unique avenue for enzyme function discovery in the rapidly expanding sequence databases. The second approach uses computational enzyme design to reprogramme specificity. Both approaches result in enzymes with >100-fold increase in specificity for the targeted reaction. When enzymes from either approach are integrated in vivo, longer-chain alcohol production increases over 10-fold and represents >95% of the total alcohol products. The modification of enzymes to generate desired compounds by non-natural pathways is a useful route for the production of commodity chemicals. Here, the authors show two approaches—genome mining and computational enzyme design—to generate higher alcohols from sugar.
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Affiliation(s)
- Wai Shun Mak
- Department of Chemistry, University of California Davis, One Shields Avenue, Davis, California 95616, USA
| | - Stephen Tran
- Department of Bioinformatics, University of California, Los Angeles, 172 Boyer Hall Box 951570, 611 Charles E. Young Drive East, Los Angeles, California 90095-1570, USA
| | - Ryan Marcheschi
- Department of Chemical and Biomolecular Engineering, University of California Los Angeles, 5531 Boelter Hall, Los Angeles, California 90095-1592, USA
| | - Steve Bertolani
- Department of Chemistry, University of California Davis, One Shields Avenue, Davis, California 95616, USA
| | - James Thompson
- Department of Biochemistry, University of Washington, 1705 NE Pacific St Seattle, Washington 98195-7350, USA
| | - David Baker
- Department of Biochemistry, University of Washington, 1705 NE Pacific St Seattle, Washington 98195-7350, USA
| | - James C Liao
- Department of Chemical and Biomolecular Engineering, University of California Los Angeles, 5531 Boelter Hall, Los Angeles, California 90095-1592, USA.,Institute for Genomics and Proteomics, University of California Los Angeles, 611 Young Drive East, Los Angeles, California 90095, USA
| | - Justin B Siegel
- Department of Chemistry, University of California Davis, One Shields Avenue, Davis, California 95616, USA.,Department of Biochemistry and Molecular Medicine, University of California Davis, 2700 Stockton Boulevard, Suite 2102, Sacramento, California 95817, USA.,Genome Center, University of California Davis, 451 Health Sciences Drive, Davis, California 95616, USA
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48
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Kang A, Lee TS. Converting Sugars to Biofuels: Ethanol and Beyond. Bioengineering (Basel) 2015; 2:184-203. [PMID: 28952477 PMCID: PMC5597089 DOI: 10.3390/bioengineering2040184] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2015] [Revised: 10/15/2015] [Accepted: 10/20/2015] [Indexed: 11/16/2022] Open
Abstract
To date, the most significant sources of biofuels are starch- or sugarcane-based ethanol, which have been industrially produced in large quantities in the USA and Brazil, respectively. However, the ultimate goal of biofuel production is to produce fuels from lignocellulosic biomass-derived sugars with optimal fuel properties and compatibility with the existing fuel distribution infrastructure. To achieve this goal, metabolic pathways have been constructed to produce various fuel molecules that are categorized into fermentative alcohols (butanol and isobutanol), non-fermentative alcohols from 2-keto acid pathways, fatty acids-derived fuels and isoprenoid-derived fuels. This review will focus on current metabolic engineering efforts to improve the productivity and the yield of several key biofuel molecules. Strategies used in these metabolic engineering efforts can be summarized as follows: (1) identification of better enzymes; (2) flux control of intermediates and precursors; (3) elimination of competing pathways; (4) redox balance and cofactor regeneration; and (5) bypassing regulatory mechanisms. In addition to metabolic engineering approaches, host strains are optimized by improving sugar uptake and utilization, and increasing tolerance to toxic hydrolysates, metabolic intermediates and/or biofuel products.
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Affiliation(s)
- Aram Kang
- Joint BioEnergy Institute, Emeryville, CA 94608, USA.
- Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
| | - Taek Soon Lee
- Joint BioEnergy Institute, Emeryville, CA 94608, USA.
- Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
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49
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Kremer F, Blank LM, Jones PR, Akhtar MK. A Comparison of the Microbial Production and Combustion Characteristics of Three Alcohol Biofuels: Ethanol, 1-Butanol, and 1-Octanol. Front Bioeng Biotechnol 2015; 3:112. [PMID: 26301219 PMCID: PMC4526805 DOI: 10.3389/fbioe.2015.00112] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2015] [Accepted: 07/21/2015] [Indexed: 11/13/2022] Open
Abstract
Over the last decade, microbes have been engineered for the manufacture of a variety of biofuels. Saturated linear-chain alcohols have great potential as transport biofuels. Their hydrocarbon backbones, as well as oxygenated content, confer combustive properties that make it suitable for use in internal combustion engines. Herein, we compared the microbial production and combustion characteristics of ethanol, 1-butanol, and 1-octanol. In terms of productivity and efficiency, current microbial platforms favor the production of ethanol. From a combustion standpoint, the most suitable fuel for spark-ignition engines would be ethanol, while for compression-ignition engines it would be 1-octanol. However, any general conclusions drawn at this stage regarding the most superior biofuel would be premature, as there are still many areas that need to be addressed, such as large-scale purification and pipeline compatibility. So far, the difficulties in developing and optimizing microbial platforms for fuel production, particularly for newer fuel candidates, stem from our poor understanding of the myriad biological factors underpinning them. A great deal of attention therefore needs to be given to the fundamental mechanisms that govern biological processes. Additionally, research needs to be undertaken across a wide range of disciplines to overcome issues of sustainability and commercial viability.
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Affiliation(s)
- Florian Kremer
- Institute for Combustion Engines (VKA), RWTH Aachen University , Aachen , Germany
| | - Lars M Blank
- Aachen Biology and Biotechnology (ABBt), Institute of Applied Microbiology (iAMB), RWTH Aachen University , Aachen , Germany
| | - Patrik R Jones
- Department of Life Sciences, Imperial College London , London , UK
| | - M Kalim Akhtar
- Institute of Molecular Plant Sciences, School of Biological Sciences, University of Edinburgh , Edinburgh , UK
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50
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Spakowicz DJ, Strobel SA. Biosynthesis of hydrocarbons and volatile organic compounds by fungi: bioengineering potential. Appl Microbiol Biotechnol 2015; 99:4943-51. [PMID: 25957494 DOI: 10.1007/s00253-015-6641-y] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2015] [Revised: 04/22/2015] [Accepted: 04/29/2015] [Indexed: 01/05/2023]
Abstract
Recent advances in the biological production of fuels have relied on the optimization of pathways involving genes from diverse organisms. Several recent articles have highlighted the potential to expand the pool of useful genes by looking to filamentous fungi. This review highlights the enzymes and organisms used for the production of a variety of fuel types and commodity chemicals with a focus on the usefulness and promise of those from filamentous fungi.
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Affiliation(s)
- Daniel J Spakowicz
- Department of Molecular Biophysics and Biochemistry, Yale University, 260/266 Whitney Avenue, PO Box 208114, New Haven, CT, 06520-8114, USA
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