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Su Y, Mangus AM, Cordell WT, Pfleger BF. Overcoming barriers to medium-chain fatty alcohol production. Curr Opin Biotechnol 2024; 85:103063. [PMID: 38219523 PMCID: PMC10922944 DOI: 10.1016/j.copbio.2023.103063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 12/19/2023] [Accepted: 12/20/2023] [Indexed: 01/16/2024]
Abstract
Medium-chain fatty alcohols (mcFaOHs) are aliphatic primary alcohols containing six to twelve carbons that are widely used in materials, pharmaceuticals, and cosmetics. Microbial biosynthesis has been touted as a route to less-abundant chain-length molecules and as a sustainable alternative to current petrochemical processes. Several metabolic engineering strategies for producing mcFaOHs have been demonstrated in the literature, yet processes continue to suffer from poor selectivity and mcFaOH toxicity, leading to reduced titers, rates, and yields of the desired compounds. This opinion examines the current state of microbial mcFaOH biosynthesis, summarizing engineering efforts to tailor selectivity and improve product tolerance by implementing engineering strategies that circumvent or overcome mcFaOH toxicity.
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Affiliation(s)
- Yun Su
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Anna M Mangus
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - William T Cordell
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Brian F Pfleger
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, WI 53706, USA.
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2
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Xu Y, Singer SD, Chen G. Protein interactomes for plant lipid biosynthesis and their biotechnological applications. PLANT BIOTECHNOLOGY JOURNAL 2023; 21:1734-1744. [PMID: 36762506 PMCID: PMC10440990 DOI: 10.1111/pbi.14027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 01/18/2023] [Accepted: 02/06/2023] [Indexed: 06/18/2023]
Abstract
Plant lipids have essential biological roles in plant development and stress responses through their functions in cell membrane formation, energy storage and signalling. Vegetable oil, which is composed mainly of the storage lipid triacylglycerol, also has important applications in food, biofuel and oleochemical industries. Lipid biosynthesis occurs in multiple subcellular compartments and involves the coordinated action of various pathways. Although biochemical and molecular biology research over the last few decades has identified many proteins associated with lipid metabolism, our current understanding of the dynamic protein interactomes involved in lipid biosynthesis, modification and channelling is limited. This review examines advances in the identification and characterization of protein interactomes involved in plant lipid biosynthesis, with a focus on protein complexes consisting of different subunits for sequential reactions such as those in fatty acid biosynthesis and modification, as well as transient or dynamic interactomes formed from enzymes in cooperative pathways such as assemblies of membrane-bound enzymes for triacylglycerol biosynthesis. We also showcase a selection of representative protein interactome structures predicted using AlphaFold2, and discuss current and prospective strategies involving the use of interactome knowledge in plant lipid biotechnology. Finally, unresolved questions in this research area and possible approaches to address them are also discussed.
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Affiliation(s)
- Yang Xu
- Department of Molecular and Cellular BiologyUniversity of GuelphGuelphOntarioCanada
| | - Stacy D. Singer
- Agriculture and Agri‐Food Canada, Lethbridge Research and Development CentreLethbridgeAlbertaCanada
| | - Guanqun Chen
- Department of Agricultural, Food and Nutritional ScienceUniversity of AlbertaEdmontonAlbertaCanada
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3
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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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Mains K, Fox JM. Ketosynthase mutants enable short-chain fatty acid biosynthesis in E. coli. Metab Eng 2023; 77:118-127. [PMID: 36963462 DOI: 10.1016/j.ymben.2023.03.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Revised: 03/16/2023] [Accepted: 03/20/2023] [Indexed: 03/26/2023]
Abstract
Cells build fatty acids in tightly regulated assembly lines, or fatty acid synthases (FASs), in which β-ketoacyl-acyl carrier protein (ACP) synthases (KSs) catalyze sequential carbon-carbon bond forming reactions that generate acyl-ACPs of varying lengths-precursors for a diverse set of lipids and oleochemicals. To date, most efforts to control fatty acid synthesis in engineered microbes have focused on modifying termination enzymes such as acyl-ACP thioesterases, which release free fatty acids from acyl-ACPs. Changes to the substrate specificity of KSs provide an alternative-and, perhaps, more generalizable-approach that focuses on controlling the acyl-ACPs available for downstream products. This study combines mutants of FabF and FabB, the two elongating KSs of the E. coli FAS, with in vitro and in vivo analyses to explore the use of KS mutants to control fatty acid synthesis. In vitro, single amino acid substitutions in the gating loop and acyl binding pocket of FabF shifted the product profiles of reconstituted FASs toward short chains and showed that KS mutants, alone, can cause large shifts in average length (i.e., 6.5-13.5). FabB, which is essential for unsaturated fatty acid synthesis, blunted this effect in vivo, but exogenously added cis-vaccenic acid (C18:1) enabled sufficient transcriptional repression of FabB to restore it. Strikingly, a single mutant of FabB afforded titers of octanoic acid as high as those generated by an engineered thioesterase. Findings indicate that fatty acid synthesis must be decoupled from microbial growth to resolve the influence of KS mutants on fatty acid profiles but show that these mutants offer a versatile approach for tuning FAS outputs.
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Affiliation(s)
- Kathryn Mains
- Department of Chemical and Biological Engineering, University of Colorado, Boulder, 3415 Colorado Avenue, Boulder, CO, 80303, USA
| | - Jerome M Fox
- Department of Chemical and Biological Engineering, University of Colorado, Boulder, 3415 Colorado Avenue, Boulder, CO, 80303, USA.
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Yang T, Yang Y, Yang M, Ren J, Xue C, Feng Y, Xue S. Conformational Changes of Acyl Carrier Protein Switch the Chain Length Preference of Acyl-ACP Thioesterase ChFatB2. Int J Mol Sci 2023; 24:ijms24076864. [PMID: 37047837 PMCID: PMC10095102 DOI: 10.3390/ijms24076864] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 04/04/2023] [Accepted: 04/04/2023] [Indexed: 04/09/2023] Open
Abstract
Microbial fatty acids are synthesized by Type II fatty acid synthase and could be tailored by acyl-ACP thioesterase. With the prospects of medium-chain fatty-acid-derivative biofuels, the selectivity of thioesterase has been studied to control the fatty acid product chain length. Here, we report an alternative approach by manipulating the acyl carrier protein portion of acyl-ACP to switch the chain length propensity of the thioesterase. It was demonstrated that ChFatB2 from Cuphea hookeriana preferred C10-ACP to C8-ACP with ACP from E. coli, while converting preference to C8-ACP with ACP from Cuphea lanceolate. Circular dichroism (CD) results indicated that the C8-EcACP encountered a 34.4% α-helix increment compared to C10-EcACP, which resulted in an approximate binding affinity decrease in ChFatB2 compared to C10-EcACP. Similarly, the C10-ClACP2 suffered a 45% decrease in helix content compared to C8–ClACP2, and the conformational changes resulted in an 18% binding affinity decline with ChFatB2 compared with C10-ClACP2. In brief, the study demonstrates that the ACP portion of acyl-ACP contributes to the selectivity of acyl-ACP thioesterase, and the conformational changes of EcACP and ClACP2 switch the chain length preference of ChFatB2 between C8 and C10. The result provides fundamentals for the directed synthesis of medium-chain fatty acids based on regulating the conformational changes of ACPs.
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Affiliation(s)
- Tianxiang Yang
- School of Bioengineering, Dalian University of Technology, Dalian 116023, China
| | - Yunlong Yang
- School of Bioengineering, Dalian University of Technology, Dalian 116023, China
| | - Ming Yang
- School of Bioengineering, Dalian University of Technology, Dalian 116023, China
| | - Jiangang Ren
- School of Bioengineering, Dalian University of Technology, Dalian 116023, China
| | - Changying Xue
- School of Bioengineering, Dalian University of Technology, Dalian 116023, China
| | - Yanbin Feng
- School of Bioengineering, Dalian University of Technology, Dalian 116023, China
| | - Song Xue
- School of Bioengineering, Dalian University of Technology, Dalian 116023, China
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Peoples J, Ruppe S, Mains K, Cipriano EC, Fox JM. A Kinetic Framework for Modeling Oleochemical Biosynthesis in E. coli. Biotechnol Bioeng 2022; 119:3149-3161. [PMID: 35959746 DOI: 10.1002/bit.28209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Revised: 08/01/2022] [Accepted: 08/07/2022] [Indexed: 11/06/2022]
Abstract
Microorganisms build fatty acids with biocatalytic assembly lines, or fatty acid synthases (FASs), that can be repurposed to produce a broad set of fuels and chemicals. Despite their versatility, the product profiles of FAS-based pathways are challenging to adjust without experimental iteration, and off-target products are common. This study uses a detailed kinetic model of the E. coli FAS as a foundation to model nine oleochemical pathways. These models provide good fits to experimental data and help explain unexpected results from in vivo studies. An analysis of pathways for alkanes and fatty acid ethyl esters, for example, suggests that reductions in titer caused by enzyme overexpression-an experimentally consistent phenomenon-can result from shifts in metabolite pools that are incompatible with the substrate specificities of downstream enzymes, and a focused examination of multiple alcohol pathways indicates that coordinated shifts in enzyme concentrations provide a general means of tuning the product profiles of pathways with promiscuous components. The study concludes by integrating all models into a graphical user interface. The models supplied by this work provide a versatile kinetic framework for studying oleochemical pathways in different biochemical contexts. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Jackson Peoples
- Department of Chemical and Biological Engineering, University of Colorado, Boulder, 3415 Colorado Avenue, Boulder, CO, 80303
| | - Sophia Ruppe
- Department of Chemical and Biological Engineering, University of Colorado, Boulder, 3415 Colorado Avenue, Boulder, CO, 80303
| | - Kathryn Mains
- Department of Chemical and Biological Engineering, University of Colorado, Boulder, 3415 Colorado Avenue, Boulder, CO, 80303
| | - Elia C Cipriano
- Department of Chemical and Biological Engineering, University of Colorado, Boulder, 3415 Colorado Avenue, Boulder, CO, 80303
| | - Jerome M Fox
- Department of Chemical and Biological Engineering, University of Colorado, Boulder, 3415 Colorado Avenue, Boulder, CO, 80303
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