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Sun Y, Ruiz Orduna A, Zhang Z, Feakins SJ, Jetter R. Biosynthesis of barley wax β-diketones: a type-III polyketide synthase condensing two fatty acyl units. Nat Commun 2023; 14:7284. [PMID: 37949901 PMCID: PMC10638390 DOI: 10.1038/s41467-023-42917-9] [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: 10/20/2022] [Accepted: 10/25/2023] [Indexed: 11/12/2023] Open
Abstract
The surface coatings of cereal plants are dominated by waxy β-diketones crucial for drought resistance and, therefore, grain yield. Here, barley (Hordeum vulgare) wax analyses reveal β-diketone and associated 2-alkanol ester profiles suggesting a common C16 3-ketoacid precursor. Isotope analysis further shows that the major (C31) diketone is synthesized from two plastidial C16 acyl units. Previous studies identified a gene cluster encoding enzymes responsible for β-diketone formation in barley, but left their biochemical functions unknown. Various assays now characterize one of these enzymes as a thioesterase producing long-chain (mainly C16) 3-ketoacids, and another one as a polyketide synthase (PKS) condensing the 3-ketoacids with long-chain (mainly C16) acyl-CoAs into β-diketones. The two enzymes are localized to the plastids and Endoplasmic Reticulum (ER), respectively, implying substrate transfer between these two sub-cellular compartments. Overall, our findings define a two-step pathway involving an unprecedented PKS reaction leading directly to the β-diketone products.
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Affiliation(s)
- Yulin Sun
- Department of Botany, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Alberto Ruiz Orduna
- Department of Chemistry, University of British Columbia, Vancouver, BC, V6T 1Z1, Canada
| | - Zhonghang Zhang
- Department of Botany, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Sarah J Feakins
- Department of Earth Sciences, University of Southern California, 3651 Trousdale Pkwy, Los Angeles, CA, 90089, USA
| | - Reinhard Jetter
- Department of Botany, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada.
- Department of Chemistry, University of British Columbia, Vancouver, BC, V6T 1Z1, Canada.
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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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Fan L, Zhu X, Sun S, Yu C, Huang X, Ness R, Dugan LL, Shu L, Seidner DL, Murff HJ, Fodor AA, Azcarate-Peril MA, Shrubsole MJ, Dai Q. Ca:Mg ratio, medium-chain fatty acids, and the gut microbiome. Clin Nutr 2022; 41:2490-2499. [PMID: 36223712 PMCID: PMC9588659 DOI: 10.1016/j.clnu.2022.08.031] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 08/04/2022] [Accepted: 08/31/2022] [Indexed: 12/26/2022]
Abstract
BACKGROUND & AIMS Ketogenic medium-chain fatty acids (MCFAs) with profound health benefits are commonly found in dairy products, palm kernel oil and coconut oil. We hypothesize that magnesium (Mg) supplementation leads to enhanced gut microbial production of MCFAs and, in turn, increased circulating MCFAs levels. METHODS We tested this hypothesis in the Personalized Prevention of Colorectal Cancer Trial (PPCCT) (NCT01105169), a double-blind 2 × 2 factorial randomized controlled trial enrolling 240 participants. Six 24-h dietary recalls were performed for all participants at the baseline and during the intervention period. Based on the baseline 24-h dietary recalls, the Mg treatment used a personalized dose of Mg supplementation that would reduce the calcium (Ca): Mg intake ratio to around 2.3. We measured plasma MCFAs, sugars, ketone bodies and tricarboxylic acid cycle (TCA cycle) metabolites using the Metabolon's global Precision Metabolomics™ LC-MS platform. Whole-genome shotgun metagenomics (WGS) sequencing was performed to assess microbiota in stool samples, rectal swabs, and rectal biopsies. RESULTS Personalized Mg treatment (mean dose 205.58 mg/day with a range from 77.25 to 389.55 mg/day) significantly increased the plasma levels of C7:0, C8:0, and combined C7:0 and C8:0 by 18.45%, 25.28%, and 24.20%, respectively, compared to 14.15%, 10.12%, and 12.62% decreases in the placebo arm. The effects remain significant after adjusting for age, sex, race and baseline level (P = 0.0126, P = 0.0162, and P = 0.0031, respectively) and FDR correction at 0.05 (q = 0.0324 for both C7:0 and C8:0). Mg treatment significantly reduced the plasma level of sucrose compared to the placebo arm (P = 0.0036 for multivariable-adjusted and P = 0.0216 for additional FDR correction model) whereas alterations in daily intakes of sucrose, fructose, glucose, maltose and C8:0 from baseline to the end of trial did not differ between two arms. Mediation analysis showed that combined C7:0 and C8:0 partially mediated the effects of Mg treatment on total and individual ketone bodies (P for indirect effect = 0.0045, 0.0043, and 0.03, respectively). The changes in plasma levels of C7:0 and C8:0 were significantly and positively correlated with the alterations in stool microbiome α diversity (r = 0.51, p = 0.0023 and r = 0.34, p = 0.0497, respectively) as well as in stool abundance for the signatures of MCFAs-related microbiota with acyl-ACP thioesterase gene producing C7:0 (r = 0.46, p = 0.0067) and C8:0 (r = 0.49, p = 0.003), respectively, following Mg treatment. CONCLUSIONS Optimizing Ca:Mg intake ratios to around 2.3 through 12-week personalized Mg supplementation leads to increased circulating levels of MCFAs (i.e. C7:0 and C8:0), which is attributed to enhanced production from gut microbial fermentation and, maybe, sucrose consumption.
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Affiliation(s)
- Lei Fan
- Department of Medicine, Division of Epidemiology, Vanderbilt Epidemiology Center, Vanderbilt University School of Medicine, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Xiangzhu Zhu
- Department of Medicine, Division of Epidemiology, Vanderbilt Epidemiology Center, Vanderbilt University School of Medicine, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Shan Sun
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, NC, USA
| | - Chang Yu
- Department of Biostatistics, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Xiang Huang
- Department of Medicine, Division of Epidemiology, Vanderbilt Epidemiology Center, Vanderbilt University School of Medicine, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Reid Ness
- Department of Medicine, Division of Gastroenterology, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Laura L Dugan
- Veterans Health Administration-Tennessee Valley Healthcare System Geriatric Research Education Clinical Center (GRECC), HSR&D Center, Vanderbilt University Medical Center, Nashville, TN, USA; Vanderbilt Brain Institute, Vanderbilt University, Nashville, TN, USA; Division of Geriatric Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Lihua Shu
- Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Douglas L Seidner
- Center for Human Nutrition, Department of Gastroenterology, Hepatology and Nutrition, Digestive Disease and Surgical Institute, Cleveland Clinic, OH, USA
| | - Harvey J Murff
- Veterans Health Administration-Tennessee Valley Healthcare System Geriatric Research Education Clinical Center (GRECC), HSR&D Center, Vanderbilt University Medical Center, Nashville, TN, USA; Division of Geriatric Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Anthony A Fodor
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, NC, USA
| | - M Andrea Azcarate-Peril
- Department of Medicine, Division of Gastroenterology and Hepatology, and UNC Microbiome Core, Center for Gastrointestinal Biology and Disease, School of Medicine, University of North Carolina, Chapel Hill, NC, USA
| | - Martha J Shrubsole
- Department of Medicine, Division of Epidemiology, Vanderbilt Epidemiology Center, Vanderbilt University School of Medicine, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Qi Dai
- Department of Medicine, Division of Epidemiology, Vanderbilt Epidemiology Center, Vanderbilt University School of Medicine, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN, USA.
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Choi BY, Shim D, Kong F, Auroy P, Lee Y, Li-Beisson Y, Lee Y, Yamaoka Y. The Chlamydomonas transcription factor MYB1 mediates lipid accumulation under nitrogen depletion. THE NEW PHYTOLOGIST 2022; 235:595-610. [PMID: 35383411 DOI: 10.1111/nph.18141] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Accepted: 03/29/2022] [Indexed: 06/14/2023]
Abstract
Microalgae accumulate high levels of oil under stress, but the underlying biosynthetic pathways are not fully understood. We sought to identify key regulators of lipid metabolism under stress conditions. We found that the Chlamydomonas reinhardtii gene encoding the MYB-type transcription factor MYB1 is highly induced under stress conditions. Two myb1 mutants accumulated less total fatty acids and storage lipids than their parental strain upon nitrogen (N) depletion. Transcriptome analysis revealed that genes involved in lipid metabolism are highly enriched in the wild-type but not in the myb1-1 mutant after 4 h of N depletion. Among these genes were several involved in the transport of fatty acids from the chloroplast to the endoplasmic reticulum (ER): acyl-ACP thioesterase (FAT1), Fatty Acid EXporters (FAX1, FAX2), and long-chain acyl-CoA synthetase1 (LACS1). Furthermore, overexpression of FAT1 in the chloroplast increased lipid production. These results suggest that, upon N depletion, MYB1 promotes lipid accumulation by facilitating fatty acid transport from the chloroplast to the ER. This study identifies MYB1 as an important positive regulator of lipid accumulation in C. reinhardtii upon N depletion, adding another player to the established regulators of this process, including NITROGEN RESPONSE REGULATOR 1 (NRR1) and TRIACYLGLYCEROL ACCUMULATION REGULATOR 1 (TAR1).
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Affiliation(s)
- Bae Young Choi
- Department of Life Science, Pohang University of Science and Technology (POSTECH), Pohang, 37673, Korea
| | - Donghwan Shim
- Department of Biological Sciences, Chungnam National University, Daejeon, 34134, Korea
| | - Fantao Kong
- Department of Life Science, Pohang University of Science and Technology (POSTECH), Pohang, 37673, Korea
- School of Bioengineering, Dalian University of Technology, Dalian, 116024, China
| | - Pascaline Auroy
- CEA, CNRS, BIAM, Institut de Biosciences et Biotechnologies Aix-Marseille, Aix Marseille Université, CEA Cadarache, Saint Paul-Lez-Durance, 13108, France
| | - Yuree Lee
- School of Biological Sciences, Seoul National University, Seoul, 08826, Korea
- Research Center for Plant Plasticity, Seoul National University, Seoul, 08826, Korea
- Plant Genomics and Breeding Institute, Seoul National University, Seoul, 08826, Korea
| | - Yonghua Li-Beisson
- CEA, CNRS, BIAM, Institut de Biosciences et Biotechnologies Aix-Marseille, Aix Marseille Université, CEA Cadarache, Saint Paul-Lez-Durance, 13108, France
| | - Youngsook Lee
- Department of Life Science, Pohang University of Science and Technology (POSTECH), Pohang, 37673, Korea
| | - Yasuyo Yamaoka
- Division of Biotechnology, The Catholic University of Korea, Bucheon, 420-743, Korea
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Li B, Chen C, Jia J, He L. Research progress on antineoplastic, antibacterial, and anti-inflammatory activities of seven-membered heterocyclic derivatives. Curr Med Chem 2022; 29:5076-5096. [PMID: 35345989 DOI: 10.2174/0929867329666220328123953] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 12/20/2021] [Accepted: 12/30/2021] [Indexed: 11/22/2022]
Abstract
Abstract:
Seven-membered heterocyclic compounds are important drug scaffolds, because of their unique chemical structures. They widely exist in natural products and show a variety of biological activities. They have commonly been used in central nervous system drugs in the past 30 years. In the past decade, there are many studies on the activities of antitumor, antibacterial, etc. Herein, we summarize the research advances in different kinds of seven-membered heterocyclic compounds containing nitrogen, oxygen, and sulfur heteroatoms with antitumor, antisepsis, and anti-inflammation activities in the past ten years, which is expected to be beneficial to the development and design of novel drugs for the corresponding indications.
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Affiliation(s)
- Bin Li
- Department of Medicinal Chemistry, West China School of Pharmacy, Sichuan University, Chengdu 610041, China
| | - Chen Chen
- Department of Medicinal Chemistry, West China School of Pharmacy, Sichuan University, Chengdu 610041, China
| | - Jingjing Jia
- Department of Medicinal Chemistry, West China School of Pharmacy, Sichuan University, Chengdu 610041, China
| | - Ling He
- Department of Medicinal Chemistry, West China School of Pharmacy, Sichuan University, Chengdu 610041, China
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6
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GUPTA S, UNDALE VR, LAKHADIVE K. Novel Targets for Antimicrobials. Turk J Pharm Sci 2020; 17:565-575. [PMID: 33177939 PMCID: PMC7650728 DOI: 10.4274/tjps.galenos.2020.90197] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Accepted: 04/21/2020] [Indexed: 12/01/2022]
Abstract
Antimicrobial resistance (AMR) is the phenomenon developed by microorganism on exposure to antimicrobial agents, making them unresponsive. Development of microbial confrontation is a severe rising risk to global community well-being as treatment in addition, management of such resistant microbial infections is difficult and challenging. The situation requires action across all government sectors and society. The change in the molecular target on which antimicrobial drugs act is one of the key mechanisms behind AMR. One of the approaches to battle with AMR can be exploring newer molecular targets in microbes and discovering new molecules accordingly. There are various examples of novel targets such as biomolecules involving in biosynthesis of cell wall, biosynthesis of aromatic amino acid, cell disunion, biosynthesis of fatty acid, and isoprenoid biosynthesis and tRNA synthetases. Fatty acid biosynthesis (FAB) and their enzymes among all the above is the more appealing target for the advancement of new antimicrobial agents. Number of promising inhibitors have been developed for bacterial fatty acid synthesis (FAS) and also few of them are clinically used. Some of these potential inhibitors are found to be used in development of new antibacterial as a lead compound and have been discovered from high throughput screening processes like Platencimycin and their analogue, Platencin. The review majorly encompasses bacterial FAB in type II FAS system and potential inhibitors with respective targets of novel antibacterial.
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Affiliation(s)
- Suchita GUPTA
- Dr. D.Y. Patil Institute of Pharmaceutical Sciences and Research, Pimpri, Pune, Maharashtra
| | | | - Kedar LAKHADIVE
- Dr. D.Y. Patil Institute of Pharmaceutical Sciences and Research, Pimpri, Pune, Maharashtra
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7
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Abstract
Biocatalytic systems (e.g., multienzyme pathways or complexes) enable the conversion of simple sugars into complex products under ambient conditions and, thus, represent promising platforms for the synthesis of renewable fuels and chemicals. Unfortunately, to date, many of these systems have proven difficult to engineer without a detailed understanding of the kinetic relationships that regulate the concerted action of their constituent enzymes. This study develops a mechanistic kinetic model of the fatty acid synthase (FAS) of Escherichia coli and uses that model to determine how different FAS components work together to control the production of free fatty acids-precursors to a wide range of oleochemicals. Perturbational analyses indicate that the modification or overexpression of a single FAS component can depress fatty acid production (a commonly observed phenomenon) by sequestering the proteins with which it interacts and/or by depleting common substrate pools. Compositional studies, in turn, suggest that simple changes in the ratios of FAS components can alter the average length of fatty acids but show that specialized enzymes (i.e., highly specific ketoacyl synthases or thioesterases) are required for narrow product profiles. Intriguingly, a sensitivity analysis indicates that two components primarily influence-and, thus, enable fine control over-total production, but suggests that the enzymes that regulate product profile are more broadly influential. Findings thus reveal the general importance of kinetic considerations in efforts to engineer fatty acid biosynthesis and provide strategies-and a kinetic model-for incorporating those considerations into FAS designs.
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Affiliation(s)
- Sophia Ruppe
- Department of Chemical and Biological Engineering, University of Colorado, Boulder, 3415 Colorado Avenue, Boulder, Colorado 80303, United States
| | - Jerome M. Fox
- Department of Chemical and Biological Engineering, University of Colorado, Boulder, 3415 Colorado Avenue, Boulder, Colorado 80303, United States
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8
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Tuning of acyl-ACP thioesterase activity directed for tailored fatty acid synthesis. Appl Microbiol Biotechnol 2018; 102:3173-3182. [DOI: 10.1007/s00253-018-8770-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2017] [Revised: 01/03/2018] [Accepted: 01/05/2018] [Indexed: 12/16/2022]
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9
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Feng Y, Wang Y, Liu J, Liu Y, Cao X, Xue S. Structural Insight into Acyl-ACP Thioesterase toward Substrate Specificity Design. ACS Chem Biol 2017; 12:2830-2836. [PMID: 28991437 DOI: 10.1021/acschembio.7b00641] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Acyl-ACP thioesterase (TE) catalyzes the hydrolysis of thioester bonds during type II fatty acid synthesis and directly determines fatty acid chain length. Most TEs are responsible for recognition of 16:0 and 18:1 substrates, while specific TEs interrupt acyl-ACP elongation at C8-C14. However, the acyl selection mechanism of TE has not been thoroughly elucidated to date. In this study, the crystal structure of the C12-specific thioesterase FatB from Umbellularia californica, which consists of two independent hotdog domains, was determined. An uncanonical Asp-His-Glu catalytic network was identified on the C-terminal hotdog domain, whereas the substrate binding pocket was determined to be on the N-terminal hotdog domain. Moreover, we elucidated UcFatB's substrate selection mechanism, which is accommodated by several unconservative amino acids on the β5, β2, and β4 sheets and enclosed by T137 on the α1 helix. On this basis, the C12-specific TE was rationally redesigned toward C14 selectivity by tuning the substrate binding pocket capacity. The T137G mutant demonstrated comparative relative activity on C14 substrates compared to C12 substrates in vitro. Furthermore, the reconstructed UcFatB_T137G achieved C14 fatty acid content up to 40% in contrast to 10% C14 from the wild type in engineered E. coli cells. The unraveled substrate selection mechanism of TE provides a new strategy for tailoring fatty acid synthesis.
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Affiliation(s)
- Yanbin Feng
- Marine
Bioengineering Group, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Yayue Wang
- Marine
Bioengineering Group, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jiao Liu
- Marine
Bioengineering Group, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yinghui Liu
- Marine
Bioengineering Group, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Xupeng Cao
- Marine
Bioengineering Group, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Song Xue
- Marine
Bioengineering Group, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
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10
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Finzel K, Beld J, Burkart MD, Charkoudian LK. Utilizing Mechanistic Cross-Linking Technology to Study Protein-Protein Interactions: An Experiment Designed for an Undergraduate Biochemistry Lab. JOURNAL OF CHEMICAL EDUCATION 2017; 94:375-379. [PMID: 29255327 PMCID: PMC5731787 DOI: 10.1021/acs.jchemed.6b00453] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Over the past decade, mechanistic crosslinking probes have been used to study protein-protein interactions in natural product biosynthetic pathways. This approach is highly interdisciplinary, combining elements of protein biochemistry, organic chemistry, and computational docking. The development of an experiment to engage undergraduate students in multidisciplinary research is described that leverages mechanistic crosslinking probes to study protein conformations and protein-protein interactions. This experiment provides students with a platform to learn chemoenzymatic synthesis, polyacrylamide gel electrophoresis, biochemical assays, and computational docking all while exploring a contemporary biochemical topic.
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Affiliation(s)
- Kara Finzel
- Department of Chemistry and Biochemistry, University of California-San Diego, La Jolla, CA 92093, United States
| | - Joris Beld
- Department of Chemistry and Biochemistry, University of California-San Diego, La Jolla, CA 92093, United States
| | - Michael D. Burkart
- Department of Chemistry and Biochemistry, University of California-San Diego, La Jolla, CA 92093, United States
| | - Louise K. Charkoudian
- Department of Chemistry, Haverford College, Haverford, Pennsylvania, 19041, United States
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11
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Tan KWM, Lee YK. Expression of the heterologous Dunaliella tertiolecta fatty acyl-ACP thioesterase leads to increased lipid production in Chlamydomonas reinhardtii. J Biotechnol 2017; 247:60-67. [PMID: 28279815 DOI: 10.1016/j.jbiotec.2017.03.004] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2016] [Revised: 03/03/2017] [Accepted: 03/04/2017] [Indexed: 12/22/2022]
Abstract
Biofuel production from genetically-engineered microalgae is currently among the most widely studied strategies in generating renewable energy. However, microalgae currently suffer from low oil yields which limit the commercial feasibility of industrial-scale production. A major bottleneck in cost-efficient biofuel production from microalgae is the dilemma between biomass productivity and lipid accumulation. When grown under stressful culture conditions such as nitrogen depletion, microalgae accumulate large amounts of neutral lipids, but it comes at the expense of growth which negatively impacts overall lipid productivity. Overexpression of acyl-ACP thioesterases (TE) had been successful in increasing the production of fatty acids (FA) in prokaryotes such as E. coli and cyanobacteria, but has not been effectively tested in microalgae. In this study, we introduced a TE from D. tertiolecta (DtTE) into C. reinhardtii to investigate its effects on FA production without compromising growth. The results indicate that C. reinhardtii transformants were able to produce 63 and 94% more neutral lipids than the wild-type, which translates to an approximately 56% improvement in total lipids, without compromising growth. These findings demonstrate the cross-species functionality of TE, and provide a platform for further studies into using TE as a strategy to increase biofuel production from microalgae.
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Affiliation(s)
- Kenneth Wei Min Tan
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117545
| | - Yuan Kun Lee
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117545.
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12
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Jung W, Kim EJ, Han SJ, Choi HG, Kim S. Characterization of Stearoyl-CoA Desaturases from a Psychrophilic Antarctic Copepod, Tigriopus kingsejongensis. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2016; 18:564-574. [PMID: 27627903 DOI: 10.1007/s10126-016-9714-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2015] [Accepted: 07/25/2016] [Indexed: 06/06/2023]
Abstract
Stearoyl-CoA desaturase is a key regulator in fatty acid metabolism that catalyzes the desaturation of stearic acid to oleic acid and controls the intracellular levels of monounsaturated fatty acids (MUFAs). Two stearoyl-CoA desaturases (SCD, Δ9 desaturases) genes were identified in an Antarctic copepod, Tigriopus kingsejongensis, that was collected in a tidal pool near the King Sejong Station, King George Island, Antarctica. Full-length complementary DNA (cDNA) sequences of two T. kingsejongensis SCDs (TkSCDs) were obtained from next-generation sequencing and isolated by reverse transcription PCR. DNA sequence lengths of the open reading frames of TkSCD-1 and TkSCD-2 were determined to be 1110 and 681 bp, respectively. The molecular weights deduced from the corresponding genes were estimated to be 43.1 kDa (TkSCD-1) and 26.1 kDa (TkSCD-2). The amino acid sequences were compared with those of fatty acid desaturases and sterol desaturases from various organisms and used to analyze the relationships among TkSCDs. As assessed by heterologous expression of recombinant proteins in Escherichia coli, the enzymatic functions of both stearoyl-CoA desaturases revealed that the amount of C16:1 and C18:1 fatty acids increased by greater than 3-fold after induction with isopropyl β-D-thiogalactopyranoside. In particular, C18:1 fatty acid production increased greater than 10-fold in E. coli expressing TkSCD-1 and TkSCD-2. The results of this study suggest that both SCD genes from an Antarctic marine copepod encode a functional desaturase that is capable of increasing the amounts of palmitoleic acid and oleic acid in a prokaryotic expression system.
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Affiliation(s)
- Woongsic Jung
- Division of Polar Life Sciences, Korea Polar Research Institute, KIOST, Incheon, 21990, Republic of Korea
| | - Eun Jae Kim
- Division of Polar Life Sciences, Korea Polar Research Institute, KIOST, Incheon, 21990, Republic of Korea
- Department of Polar Life Sciences, University of Science and Technology, Incheon, 21990, Republic of Korea
| | - Se Jong Han
- Division of Polar Life Sciences, Korea Polar Research Institute, KIOST, Incheon, 21990, Republic of Korea
- Department of Polar Life Sciences, University of Science and Technology, Incheon, 21990, Republic of Korea
| | - Han-Gu Choi
- Division of Polar Life Sciences, Korea Polar Research Institute, KIOST, Incheon, 21990, Republic of Korea
| | - Sanghee Kim
- Division of Polar Life Sciences, Korea Polar Research Institute, KIOST, Incheon, 21990, Republic of Korea.
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13
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Beld J, Abbriano R, Finzel K, Hildebrand M, Burkart MD. Probing fatty acid metabolism in bacteria, cyanobacteria, green microalgae and diatoms with natural and unnatural fatty acids. MOLECULAR BIOSYSTEMS 2016; 12:1299-312. [PMID: 26886879 DOI: 10.1039/c5mb00804b] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
In both eukaryotes and prokaryotes, fatty acid synthases are responsible for the biosynthesis of fatty acids in an iterative process, extending the fatty acid by two carbon units every cycle. Thus, odd numbered fatty acids are rarely found in nature. We tested whether representatives of diverse microbial phyla have the ability to incorporate odd-chain fatty acids as substrates for their fatty acid synthases and their downstream enzymes. We fed various odd and short chain fatty acids to the bacterium Escherichia coli, cyanobacterium Synechocystis sp. PCC 6803, green microalga Chlamydomonas reinhardtii and diatom Thalassiosira pseudonana. Major differences were observed, specifically in the ability among species to incorporate and elongate short chain fatty acids. We demonstrate that E. coli, C. reinhardtii, and T. pseudonana can produce longer fatty acid products from short chain precursors (C3 and C5), while Synechocystis sp. PCC 6803 lacks this ability. However, Synechocystis can incorporate and elongate longer chain fatty acids due to acyl-acyl carrier protein synthetase (AasS) activity, and knockout of this protein eliminates the ability to incorporate these fatty acids. In addition, expression of a characterized AasS from Vibrio harveyii confers a similar capability to E. coli. The ability to desaturate exogenously added fatty acids was only observed in Synechocystis and C. reinhardtii. We further probed fatty acid metabolism of these organisms by feeding desaturase inhibitors to test the specificity of long-chain fatty acid desaturases. In particular, supplementation with thia fatty acids can alter fatty acid profiles based on the location of the sulfur in the chain. We show that coupling sensitive gas chromatography mass spectrometry to supplementation of unnatural fatty acids can reveal major differences between fatty acid metabolism in various organisms. Often unnatural fatty acids have antibacterial or even therapeutic properties. Feeding of short precursors now gives us easy access to these extended molecules.
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Affiliation(s)
- Joris Beld
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0358, USA.
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14
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Zhou Y, Luo Y, Yang YS, Lu L, Zhu HL. Study of acylhydrazone derivatives with deoxygenated seven-membered rings as potential β-ketoacyl-acyl carrier protein synthase III (FabH) inhibitors. MEDCHEMCOMM 2016. [DOI: 10.1039/c6md00263c] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Fatty acid biosynthesis is essential for bacterial survival.
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Affiliation(s)
- Yang Zhou
- State Key Laboratory of Pharmaceutical Biotechnology
- Nanjing University
- Nanjing 210023
- People's Republic of China
| | - Yin Luo
- State Key Laboratory of Pharmaceutical Biotechnology
- Nanjing University
- Nanjing 210023
- People's Republic of China
| | - Yu-Shun Yang
- State Key Laboratory of Pharmaceutical Biotechnology
- Nanjing University
- Nanjing 210023
- People's Republic of China
| | - Liang Lu
- State Key Laboratory of Pharmaceutical Biotechnology
- Nanjing University
- Nanjing 210023
- People's Republic of China
| | - Hai-Liang Zhu
- State Key Laboratory of Pharmaceutical Biotechnology
- Nanjing University
- Nanjing 210023
- People's Republic of China
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15
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Gu H, Jinkerson RE, Davies FK, Sisson LA, Schneider PE, Posewitz MC. Modulation of Medium-Chain Fatty Acid Synthesis in Synechococcus sp. PCC 7002 by Replacing FabH with a Chaetoceros Ketoacyl-ACP Synthase. FRONTIERS IN PLANT SCIENCE 2016; 7:690. [PMID: 27303412 PMCID: PMC4880568 DOI: 10.3389/fpls.2016.00690] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2016] [Accepted: 05/05/2016] [Indexed: 05/12/2023]
Abstract
The isolation or engineering of algal cells synthesizing high levels of medium-chain fatty acids (MCFAs) is attractive to mitigate the high clouding point of longer chain fatty acids in algal based biodiesel. To develop a more informed understanding of MCFA synthesis in photosynthetic microorganisms, we isolated several algae from Great Salt Lake and screened this collection for MCFA accumulation to identify strains naturally accumulating high levels of MCFA. A diatom, Chaetoceros sp. GSL56, accumulated particularly high levels of C14 (up to 40%), with the majority of C14 fatty acids allocated in triacylglycerols. Using whole cell transcriptome sequencing and de novo assembly, putative genes encoding fatty acid synthesis enzymes were identified. Enzymes from this Chaetoceros sp. were expressed in the cyanobacterium Synechococcus sp. PCC 7002 to validate gene function and to determine whether eukaryotic enzymes putatively lacking bacterial evolutionary control mechanisms could be used to improve MCFA production in this promising production strain. Replacement of the Synechococcus 7002 native FabH with a Chaetoceros ketoacyl-ACP synthase III increased MCFA synthesis up to fivefold. The level of increase is dependent on promoter strength and culturing conditions.
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Affiliation(s)
- Huiya Gu
- Department of Chemistry and Geochemistry, Colorado School of Mines, GoldenCO, USA
| | - Robert E. Jinkerson
- Department of Plant Biology, Carnegie Institution for Science, StanfordCA, USA
| | - Fiona K. Davies
- Department of Chemistry and Geochemistry, Colorado School of Mines, GoldenCO, USA
| | - Lyle A. Sisson
- Department of Chemistry and Geochemistry, Colorado School of Mines, GoldenCO, USA
| | - Philip E. Schneider
- Department of Chemistry and Geochemistry, Colorado School of Mines, GoldenCO, USA
| | - Matthew C. Posewitz
- Department of Chemistry and Geochemistry, Colorado School of Mines, GoldenCO, USA
- *Correspondence: Matthew C. Posewitz,
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Finzel K, Lee DJ, Burkart MD. Using modern tools to probe the structure-function relationship of fatty acid synthases. Chembiochem 2015; 16:528-547. [PMID: 25676190 PMCID: PMC4545599 DOI: 10.1002/cbic.201402578] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2014] [Indexed: 12/25/2022]
Abstract
Fatty acid biosynthesis is essential to life and represents one of the most conserved pathways in nature, preserving the same handful of chemical reactions across all species. Recent interest in the molecular details of the de novo fatty acid synthase (FAS) has been heightened by demand for renewable fuels and the emergence of multidrug-resistant bacterial strains. Central to FAS is the acyl carrier protein (ACP), a protein chaperone that shuttles the growing acyl chain between catalytic enzymes within the FAS. Human efforts to alter fatty acid biosynthesis for oil production, chemical feedstock, or antimicrobial purposes has been met with limited success, due in part to a lack of detailed molecular information behind the ACP-partner protein interactions inherent to the pathway. This review will focus on recently developed tools for the modification of ACP and analysis of protein-protein interactions, such as mechanism-based crosslinking, and the studies exploiting them. Discussion specific to each enzymatic domain will focus first on mechanism and known inhibitors, followed by available structures and known interactions with ACP. Although significant unknowns remain, new understandings of the intricacies of FAS point to future advances in manipulating this complex molecular factory.
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Affiliation(s)
- Kara Finzel
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093-0358 (USA)
| | - D. John Lee
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093-0358 (USA)
| | - Michael D. Burkart
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093-0358 (USA)
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Beld J, Lee DJ, Burkart MD. Fatty acid biosynthesis revisited: structure elucidation and metabolic engineering. MOLECULAR BIOSYSTEMS 2015; 11:38-59. [PMID: 25360565 PMCID: PMC4276719 DOI: 10.1039/c4mb00443d] [Citation(s) in RCA: 121] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Fatty acids are primary metabolites synthesized by complex, elegant, and essential biosynthetic machinery. Fatty acid synthases resemble an iterative assembly line, with an acyl carrier protein conveying the growing fatty acid to necessary enzymatic domains for modification. Each catalytic domain is a unique enzyme spanning a wide range of folds and structures. Although they harbor the same enzymatic activities, two different types of fatty acid synthase architectures are observed in nature. During recent years, strained petroleum supplies have driven interest in engineering organisms to either produce more fatty acids or specific high value products. Such efforts require a fundamental understanding of the enzymatic activities and regulation of fatty acid synthases. Despite more than one hundred years of research, we continue to learn new lessons about fatty acid synthases' many intricate structural and regulatory elements. In this review, we summarize each enzymatic domain and discuss efforts to engineer fatty acid synthases, providing some clues to important challenges and opportunities in the field.
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Affiliation(s)
- Joris Beld
- Department of Chemistry and Biochemistry, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0358, USA.
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18
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Beld J, Cang H, Burkart MD. Visualizing the chain-flipping mechanism in fatty-acid biosynthesis. Angew Chem Int Ed Engl 2014; 53:14456-61. [PMID: 25354391 PMCID: PMC4425425 DOI: 10.1002/anie.201408576] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2014] [Indexed: 11/08/2022]
Abstract
The acyl carrier protein (ACP) from fatty acid synthases sequesters elongating products within its hydrophobic core, but this dynamic mechanism remains poorly understood. We exploited solvatochromic pantetheine probes attached to ACP that fluoresce when sequestered. The addition of a catalytic partner lures the cargo out of the ACP and into the active site of the enzyme, thus enhancing fluorescence to reveal the elusive chain-flipping mechanism. This activity was confirmed by the use of a dual solvatochromic cross-linking probe and solution-phase NMR spectroscopy. The chain-flipping mechanism was visualized by single-molecule fluorescence techniques, thus demonstrating specificity between the Escherichia coli ACP and its ketoacyl synthase catalytic partner KASII.
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Affiliation(s)
- Joris Beld
- Department of Chemistry and Biochemistry, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0358, USA
| | - Hu Cang
- Waitt Advanced Biophotonics Center, The Salk Institute for Biological Studies, La Jolla, California, USA
| | - Michael D. Burkart
- Department of Chemistry and Biochemistry, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0358, USA
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Beld J, Cang H, Burkart MD. Visualizing the Chain-Flipping Mechanism in Fatty-Acid Biosynthesis. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201408576] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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