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Groves JT, Feng L, Austin RN. Structure and Function of Alkane Monooxygenase (AlkB). Acc Chem Res 2023; 56:3665-3675. [PMID: 38032826 PMCID: PMC11623191 DOI: 10.1021/acs.accounts.3c00590] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2023]
Abstract
Every year, perhaps as much as 800 million tons of hydrocarbons enters the environment; alkanes make up a large percentage of it. Most are transformed by organisms that utilize these molecules as sources of energy and carbon. Both aerobic and anaerobic alkane transformation chemistries exist, capitalizing on the presence of alkanes in both oxic and anoxic environments. Over the past 40 years, tremendous progress has been made in understanding the structure and mechanism of enzymes that catalyze the transformation of methane. By contrast, progress involving enzymes that transform liquid alkanes has been slower with the first structures of AlkB, the predominant aerobic alkane hydroxylase in the environment, appearing in 2023. Because of the fundamental importance of C-H bond activation chemistries, interest in understanding how biology activates and transforms alkanes is high.In this Account, we focus on steps we have taken to understand the mechanism and structure of alkane monooxygenase (AlkB), the metalloenzyme that dominates the transformation of liquid alkanes in the environment (not to be confused with another AlkB that is an α-ketogluturate-dependent enzyme involved in DNA repair). First, we briefly describe what is known about the prevalence of AlkB in the environment and its role in the carbon cycle. Then we review the key findings from our recent high-resolution cryoEM structure of AlkB and highlight important similarities and differences in the structures of members of class III diiron enzymes. Functional studies, which we summarize, from a number of single residue variants enable us to say a great deal about how the structure of AlkB facilitates its function. Next, we overview work from our laboratories using mechanistically diagnostic radical clock substrates to characterize the mechanism of AlkB and contextualize the results we have obtained on AlkB with results we have obtained on other alkane-oxidizing enzymes and explain these results in light of the enzyme's structure. Finally, we integrate recent work in our laboratories with information from prior studies of AlkB, and relevant model systems, to create a holistic picture of the enzyme. We end by pointing to critical questions that still need to be answered, questions about the electronic structure of the active site of the enzyme throughout the reaction cycle and about whether and to what extent the enzyme plays functional roles in biology beyond simply initiating the degradation of alkanes.
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Affiliation(s)
- John T Groves
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
| | - Liang Feng
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, California 94305, United States
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Lou H, Song L, Li X, Zi H, Chen W, Gao Y, Zheng S, Fei Z, Sun X, Wu J. The Torreya grandis genome illuminates the origin and evolution of gymnosperm-specific sciadonic acid biosynthesis. Nat Commun 2023; 14:1315. [PMID: 36898990 PMCID: PMC10006428 DOI: 10.1038/s41467-023-37038-2] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Accepted: 02/28/2023] [Indexed: 03/12/2023] Open
Abstract
Torreya plants produce dry fruits with assorted functions. Here, we report the 19-Gb chromosome-level genome assembly of T. grandis. The genome is shaped by ancient whole-genome duplications and recurrent LTR retrotransposon bursts. Comparative genomic analyses reveal key genes involved in reproductive organ development, cell wall biosynthesis and seed storage. Two genes encoding a C18 Δ9-elongase and a C20 Δ5-desaturase are identified to be responsible for sciadonic acid biosynthesis and both are present in diverse plant lineages except angiosperms. We demonstrate that the histidine-rich boxes of the Δ5-desaturase are crucial for its catalytic activity. Methylome analysis reveals that methylation valleys of the T. grandis seed genome harbor genes associated with important seed activities, including cell wall and lipid biosynthesis. Moreover, seed development is accompanied by DNA methylation changes that possibly fuel energy production. This study provides important genomic resources and elucidates the evolutionary mechanism of sciadonic acid biosynthesis in land plants.
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Affiliation(s)
- Heqiang Lou
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, 311300, Zhejiang, China
| | - Lili Song
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, 311300, Zhejiang, China
| | - Xiaolong Li
- Collaborative Innovation Center for Efficient and Green Production of Agriculture in Mountainous Areas of Zhejiang Province, Zhejiang A&F University, Hangzhou, 311300, Zhejiang, China.,Key Laboratory of Quality and Safety Control for Subtropical Fruit and Vegetable, Ministry of Agriculture and Rural Affairs, Hangzhou, 311300, Zhejiang, China
| | - Hailing Zi
- Novogene Bioinformatics Institute, 100083, Beijing, China
| | - Weijie Chen
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, 311300, Zhejiang, China
| | - Yadi Gao
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, 311300, Zhejiang, China
| | - Shan Zheng
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, 311300, Zhejiang, China
| | - Zhangjun Fei
- Boyce Thompson Institute, Cornell University, Ithaca, NY, 14853, USA. .,U.S. Department of Agriculture-Agricultural Research Service, Robert W. Holley Center for Agriculture and Health, Ithaca, NY, 14853, USA.
| | - Xuepeng Sun
- Collaborative Innovation Center for Efficient and Green Production of Agriculture in Mountainous Areas of Zhejiang Province, Zhejiang A&F University, Hangzhou, 311300, Zhejiang, China. .,Key Laboratory of Quality and Safety Control for Subtropical Fruit and Vegetable, Ministry of Agriculture and Rural Affairs, Hangzhou, 311300, Zhejiang, China.
| | - Jiasheng Wu
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, 311300, Zhejiang, China.
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Hambalko J, Gajdoš P, Nicaud JM, Ledesma-Amaro R, Tupec M, Pichová I, Čertík M. Biosynthesis of Fatty Acid Derivatives by Recombinant Yarrowia lipolytica Containing MsexD2 and MsexD3 Desaturase Genes from Manduca sexta. J Fungi (Basel) 2023; 9:jof9010114. [PMID: 36675935 PMCID: PMC9862095 DOI: 10.3390/jof9010114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 01/09/2023] [Accepted: 01/11/2023] [Indexed: 01/19/2023] Open
Abstract
One of the most interesting groups of fatty acid derivates is the group of conjugated fatty acids from which the most researched include: conjugated linoleic acid (CLA) and conjugated linolenic acid (CLNA), which are associated with countless health benefits. Sex pheromone mixtures of some insect species, including tobacco horn-worm (Manduca sexta), are typical for the production of uncommon C16 long conjugated fatty acids with two and three conjugated double bonds, as opposed to C18 long CLA and CLNA. In this study, M. sexta desaturases MsexD2 and MsexD3 were expressed in multiple strains of Y. lipolytica with different genotypes. Experiments with the supplementation of fatty acid methyl esters into the medium resulted in the production of novel fatty acids. Using GCxGC-MS, 20 new fatty acids with two or three double bonds were identified. Fatty acids with conjugated or isolated double bonds, or a combination of both, were produced in trace amounts. The results of this study prove that Y. lipolytica is capable of synthesizing C16-conjugated fatty acids. Further genetic optimization of the Y. lipolytica genome and optimization of the fermentation process could lead to increased production of novel fatty acid derivatives with biotechnologically interesting properties.
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Affiliation(s)
- Jaroslav Hambalko
- Institute of Biotechnology, Faculty of Chemical and Food Technology, Slovak University of Technology, Radlinského 9, 812 37 Bratislava, Slovakia
| | - Peter Gajdoš
- Institute of Biotechnology, Faculty of Chemical and Food Technology, Slovak University of Technology, Radlinského 9, 812 37 Bratislava, Slovakia
| | - Jean-Marc Nicaud
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Domaine de Vilvert, 78352 Jouy-en-Josas, France
| | - Rodrigo Ledesma-Amaro
- Department of Bioengineering and Imperial College Centre for Synthetic Biology, Faculty of Engineering, Imperial College, London SW7 2AZ, UK
| | - Michal Tupec
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo náměstí 542/2, 160 00 Prague 6, Czech Republic
| | - Iva Pichová
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo náměstí 542/2, 160 00 Prague 6, Czech Republic
| | - Milan Čertík
- Institute of Biotechnology, Faculty of Chemical and Food Technology, Slovak University of Technology, Radlinského 9, 812 37 Bratislava, Slovakia
- Correspondence:
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Gu J, Wang D, Wang Q, Liu W, Chen X, Li X, Yang F. Novel β-Glucosidase Mibgl3 from Microbacterium sp. XT11 with Oligoxanthan-Hydrolyzing Activity. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:8713-8724. [PMID: 35793414 DOI: 10.1021/acs.jafc.2c03386] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
The enzymatic pathway of xanthan depolymerization has been predicted previously; however, the β-glucosidase and unsaturated glucuronyl hydrolase in this system have not been cloned and characterized. This lack of knowledge hinders rational modification of xanthan and exploration of new applications. In this work, we report on the properties of Mibgl3, a xanthan-degrading enzyme isolated from Microbacterium sp. XT11. Mibgl3 exhibits typical structural features of the GH3 family but shares low sequence identity with reported GH3 enzymes. The activity of Mibgl3 can be inhibited by Cu2+, Fe2+, Zn2+, and glucose. Unlike most β-glucosidases, Mibgl3 can tolerate a wide pH range and is activated by high concentrations of NaCl. This improves the commercial value of Mibgl3. In particular, Mibgl3 exhibits higher substrate specificity toward oligoxanthan than other β-glucosidases. Ion chromatography, ultrahigh-performance liquid chromatography-mass spectrometry (UPLC-MS), and GC-MS results showed that Mibgl3 could effectively hydrolyze oligoxanthan to release glucose and glucuronate. Therefore, Mibgl3 might play an important role in xanthan depolymerization by functioning as hydrolase of both the xanthan backbone and sidechains. This knowledge of the enzymatic properties and hydrolysis mechanism of a β-glucosidase will be beneficial for future applications.
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Affiliation(s)
- Jinyun Gu
- School of Biological Engineering, Dalian Polytechnic University, Ganjingzi-qu, Dalian 116034, P. R. China
| | - Dandan Wang
- School of Biological Engineering, Dalian Polytechnic University, Ganjingzi-qu, Dalian 116034, P. R. China
| | - Qian Wang
- School of Biological Engineering, Dalian Polytechnic University, Ganjingzi-qu, Dalian 116034, P. R. China
| | - Weiming Liu
- School of Biological Engineering, Dalian Polytechnic University, Ganjingzi-qu, Dalian 116034, P. R. China
| | - Xiaoyi Chen
- School of Biological Engineering, Dalian Polytechnic University, Ganjingzi-qu, Dalian 116034, P. R. China
| | - Xianzhen Li
- School of Biological Engineering, Dalian Polytechnic University, Ganjingzi-qu, Dalian 116034, P. R. China
| | - Fan Yang
- School of Biological Engineering, Dalian Polytechnic University, Ganjingzi-qu, Dalian 116034, P. R. China
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Wang J, Song Y, Hwarari DT, Liang XH, Ding JH, Yan MW, Wu FA, Wang J, Sheng S. Fatty acid synthases and desaturases are essential for the biosynthesis of α-linolenic acid and metamorphosis in a major mulberry pest, Glyphodes pyloalis walker (Lepidoptera: Pyralidae). PEST MANAGEMENT SCIENCE 2022; 78:2629-2642. [PMID: 35362207 DOI: 10.1002/ps.6895] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2022] [Revised: 03/15/2022] [Accepted: 04/01/2022] [Indexed: 05/28/2023]
Abstract
BACKGROUND α-linolenic acid is an essential unsaturated fatty acid in organisms. However, there is a large gap between α-linolenic acid accumulation and its synthesis mechanism in insects. Fatty acid synthases (FASs) and desaturases (Desats) are vital enzymes required for the synthesis of unsaturated fatty acids. RESULTS The pupae of Glyphodes pyloalis (Lepidoptera: Pyralidae), which is a destructive pest of mulberry trees, contain the highest level of α-linolenic acid compared to other life-history stages. To further explore the synthesis mechanism of α-linolenic acid in G. pyloalis pupae, we constructed a pupal transcriptome dataset and identified 106 genes related to fatty acid metabolism from it. Among these, two fatty acid synthases (GpylFAS) and five desaturases (GpylDesat) were identified. A qRT-PCR validation revealed that GpylFAS1 and GpylDesat1, 2, 3, 5 were expressed highest at pupal stages. Furthermore, the content of α-linolenic acid decreased significantly after silencing GpylFAS1 and GpylDesat5, respectively. Besides, knocking down GpylFAS1 or GpylDesat5 resulted in more malformed pupae and adults, as well as lower emergence rates. Meanwhile, silencing GpylFAS1 or GpylDesat5 affected the expressions of the other GpylFASs and GpylDesats. CONCLUSION The present results illustrate the pivotal function of FASs and Desats in α-linolenic acid biosynthesis and metamorphosis in insects. Our research also broadens the sources of unsaturated fatty acids, especially for α-linolenic acid from insects, and provides novel insights for the management of mulberry insect pests from the perspective of utilization rather than control. © 2022 Society of Chemical Industry.
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Affiliation(s)
- Jiao Wang
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, China
| | - Yan Song
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, China
| | - Delight T Hwarari
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, China
| | - Xin-Hao Liang
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, China
| | - Jian-Hao Ding
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, China
| | - Meng-Wen Yan
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, China
| | - Fu-An Wu
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, China
- The Key Laboratory of Silkworm and Mulberry Genetic Improvement, Ministry of Agriculture, Sericultural Research Institute, Chinese Academy of Agricultural Science, Zhenjiang, China
| | - Jun Wang
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, China
- The Key Laboratory of Silkworm and Mulberry Genetic Improvement, Ministry of Agriculture, Sericultural Research Institute, Chinese Academy of Agricultural Science, Zhenjiang, China
| | - Sheng Sheng
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, China
- The Key Laboratory of Silkworm and Mulberry Genetic Improvement, Ministry of Agriculture, Sericultural Research Institute, Chinese Academy of Agricultural Science, Zhenjiang, China
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Petkevicius K, Koutsoumpeli E, Betsi PC, Ding BJ, Kildegaard KR, Jensen H, Mezo N, Mazziotta A, Gabrielsson A, Sinkwitz C, Lorantfy B, Holkenbrink C, Löfstedt C, Raptopoulos D, Konstantopoulou M, Borodina I. Biotechnological production of the European corn borer sex pheromone in the yeast Yarrowia lipolytica. Biotechnol J 2021; 16:e2100004. [PMID: 33656777 DOI: 10.1002/biot.202100004] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Revised: 02/15/2021] [Accepted: 02/19/2021] [Indexed: 12/27/2022]
Abstract
The European corn borer (ECB) Ostrinia nubilalis is a widespread pest of cereals, particularly maize. Mating disruption with the sex pheromone is a potentially attractive method for managing this pest; however, chemical synthesis of pheromones requires expensive starting materials and catalysts and generates hazardous waste. The goal of this study was to develop a biotechnological method for the production of ECB sex pheromone. Our approach was to engineer the oleaginous yeast Yarrowia lipolytica to produce (Z)-11-tetradecenol (Z11-14:OH), which can then be chemically acetylated to (Z)-11-tetradecenyl acetate (Z11-14:OAc), the main pheromone component of the Z-race of O. nubilalis. First, a C14 platform strain with increased biosynthesis of myristoyl-CoA was obtained by introducing a point mutation into the α-subunit of fatty acid synthase, replacing isoleucine 1220 with phenylalanine (Fas2pI1220F ). The intracellular accumulation of myristic acid increased 8.4-fold. Next, fatty acyl-CoA desaturases (FAD) and fatty acyl-CoA reductases (FAR) from nine different species of Lepidoptera were screened in the C14 platform strain, individually and in combinations. A titer of 29.2 ± 1.6 mg L-1 Z11-14:OH was reached in small-scale cultivation with an optimal combination of a FAD (Lbo_PPTQ) from Lobesia botrana and FAR (HarFAR) from Helicoverpa armigera. When the second copies of FAD and FAR genes were introduced, the titer improved 2.1-fold. The native FAS1 gene's overexpression led to a further 1.5-fold titer increase, reaching 93.9 ± 11.7 mg L-1 in small-scale cultivation. When the same engineered strain was cultivated in controlled 1 L bioreactors in fed-batch mode, 188.1 ± 13.4 mg L-1 of Z11-14:OH was obtained. Fatty alcohols were extracted from the biomass and chemically acetylated to obtain Z11-14:OAc. Electroantennogram experiments showed that males of the Z-race of O. nubilalis were responsive to biologically-derived pheromone blend. Behavioral bioassays in a wind tunnel revealed attraction of male O. nubilalis, although full precopulatory behavior was observed less often than for the chemically synthesized pheromone blend. The study paves the way for the production of ECB pheromone by fermentation.
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Affiliation(s)
- Karolis Petkevicius
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark.,BioPhero ApS, Copenhagen Ø, Denmark
| | - Eleni Koutsoumpeli
- Chemical Ecology and Natural Products Laboratory, Institute of Biosciences and Applications, National Centre of Scientific Research, Athens, Greece
| | - Petri Christina Betsi
- Chemical Ecology and Natural Products Laboratory, Institute of Biosciences and Applications, National Centre of Scientific Research, Athens, Greece
| | - Bao-Jian Ding
- Department of Biology, Lund University, Lund, Sweden
| | | | | | | | | | | | | | | | | | | | | | - Maria Konstantopoulou
- Chemical Ecology and Natural Products Laboratory, Institute of Biosciences and Applications, National Centre of Scientific Research, Athens, Greece
| | - Irina Borodina
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark.,BioPhero ApS, Copenhagen Ø, Denmark
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