1
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Gough AM, Parker AC, O'Bryan PJ, Whitehead TR, Roy S, Garcia BL, Hoffman PS, Jeffrey Smith C, Rocha ER. New functions of pirin proteins and a 2-ketoglutarate: Ferredoxin oxidoreductase ortholog in Bacteroides fragilis metabolism and their impact on antimicrobial susceptibility to metronidazole and amixicile. Microbiologyopen 2024; 13:e1429. [PMID: 39109824 PMCID: PMC11304471 DOI: 10.1002/mbo3.1429] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2024] [Revised: 07/05/2024] [Accepted: 07/12/2024] [Indexed: 08/10/2024] Open
Abstract
The understanding of how central metabolism and fermentation pathways regulate antimicrobial susceptibility in the anaerobic pathogen Bacteroides fragilis is still incomplete. Our study reveals that B. fragilis encodes two iron-dependent, redox-sensitive regulatory pirin protein genes, pir1 and pir2. The mRNA expression of these genes increases when exposed to oxygen and during growth in iron-limiting conditions. These proteins, Pir1 and Pir2, influence the production of short-chain fatty acids and modify the susceptibility to metronidazole and amixicile, a new inhibitor of pyruvate: ferredoxin oxidoreductase in anaerobes. We have demonstrated that Pir1 and Pir2 interact directly with this oxidoreductase, as confirmed by two-hybrid system assays. Furthermore, structural analysis using AlphaFold2 predicts that Pir1 and Pir2 interact stably with several central metabolism enzymes, including the 2-ketoglutarate:ferredoxin oxidoreductases Kor1AB and Kor2CDAEBG. We used a series of metabolic mutants and electron transport chain inhibitors to demonstrate the extensive impact of bacterial metabolism on metronidazole and amixicile susceptibility. We also show that amixicile is an effective antimicrobial against B. fragilis in an experimental model of intra-abdominal infection. Our investigation led to the discovery that the kor2AEBG genes are essential for growth and have dual functions, including the formation of 2-ketoglutarate via the reverse TCA cycle. However, the metabolic activity that bypasses the function of Kor2AEBG following the addition of phospholipids or fatty acids remains undefined. Overall, our study provides new insights into the central metabolism of B. fragilis and its regulation by pirin proteins, which could be exploited for the development of new narrow-spectrum antimicrobials in the future.
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Affiliation(s)
- Andrea M. Gough
- Department of Microbiology and ImmunologyBrody School of Medicine at East Carolina UniversityGreenvilleNorth CarolinaUSA
| | - Anita C. Parker
- Department of Microbiology and ImmunologyBrody School of Medicine at East Carolina UniversityGreenvilleNorth CarolinaUSA
| | | | | | - Sourav Roy
- Department of Microbiology and ImmunologyBrody School of Medicine at East Carolina UniversityGreenvilleNorth CarolinaUSA
| | - Brandon L. Garcia
- Department of Microbiology and ImmunologyBrody School of Medicine at East Carolina UniversityGreenvilleNorth CarolinaUSA
| | - Paul S. Hoffman
- Department of Medicine, Division of Infectious Diseases and International HealthUniversity of VirginiaCharlottesvilleVirginiaUSA
| | - C. Jeffrey Smith
- Department of Microbiology and ImmunologyBrody School of Medicine at East Carolina UniversityGreenvilleNorth CarolinaUSA
| | - Edson R. Rocha
- Department of Microbiology and ImmunologyBrody School of Medicine at East Carolina UniversityGreenvilleNorth CarolinaUSA
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2
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Yang X, Cui L, Li S, Ma C, Kosma DK, Zhao H, Lü S. Fatty alcohol oxidase 3 (FAO3) and FAO4b connect the alcohol- and alkane-forming pathways in Arabidopsis stem wax biosynthesis. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:3018-3029. [PMID: 35560209 DOI: 10.1093/jxb/erab532] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Accepted: 12/03/2021] [Indexed: 06/15/2023]
Abstract
The alcohol- and alkane-forming pathways in cuticular wax biosynthesis are well characterized in Arabidopsis. However, potential interactions between the two pathways remain unclear. Here, we reveal that mutation of CER4, the key gene in the alcohol-forming pathway, also led to a deficiency in the alkane-forming pathway in distal stems. To trace the connection between the two pathways, we characterized two homologs of fatty alcohol oxidase (FAO), FAO3 and FAO4b, which were highly expressed in distal stems and localized to the endoplasmic reticulum. The amounts of waxes from the alkane-forming pathway were significantly decreased in stems of fao4b and much lower in fao3 fao4b plants, indicative of an overlapping function for the two proteins in wax synthesis. Additionally, overexpression of FAO3 and FAO4b in Arabidopsis resulted in a dramatic reduction of primary alcohols and significant increases of aldehydes and related waxes. Moreover, expressing FAO3 or FAO4b led to significantly decreased amounts of C18-C26 alcohols in yeast co-expressing CER4 and FAR1. Collectively, these findings demonstrate that FAO3 and FAO4b are functionally redundant in suppressing accumulation of primary alcohols and contributing to aldehyde production, which provides a missing and long-sought-after link between these two pathways in wax biosynthesis.
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Affiliation(s)
- Xianpeng Yang
- College of Life Sciences, Shandong Normal University, Jinan, 250014, China
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, 430062, China
| | - Lili Cui
- Institute of Environment and Ecology, Shandong Normal University, Jinan, 250014, China
| | - Shipeng Li
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, 430062, China
| | - Changle Ma
- College of Life Sciences, Shandong Normal University, Jinan, 250014, China
| | - Dylan K Kosma
- Department of Biochemistry and Molecular Biology, University of Nevada, Reno, NV 89557, USA
| | - Huayan Zhao
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, 430062, China
| | - Shiyou Lü
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, 430062, China
- Hubei Hongshan Laboratory, Wuhan, 430070, China
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3
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Sirota FL, Maurer-Stroh S, Li Z, Eisenhaber F, Eisenhaber B. Functional Classification of Super-Large Families of Enzymes Based on Substrate Binding Pocket Residues for Biocatalysis and Enzyme Engineering Applications. Front Bioeng Biotechnol 2021; 9:701120. [PMID: 34409021 PMCID: PMC8366029 DOI: 10.3389/fbioe.2021.701120] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Accepted: 07/12/2021] [Indexed: 11/13/2022] Open
Abstract
Large enzyme families such as the groups of zinc-dependent alcohol dehydrogenases (ADHs), long chain alcohol oxidases (AOxs) or amine dehydrogenases (AmDHs) with, sometimes, more than one million sequences in the non-redundant protein database and hundreds of experimentally characterized enzymes are excellent cases for protein engineering efforts aimed at refining and modifying substrate specificity. Yet, the backside of this wealth of information is that it becomes technically difficult to rationally select optimal sequence targets as well as sequence positions for mutagenesis studies. In all three cases, we approach the problem by starting with a group of experimentally well studied family members (including those with available 3D structures) and creating a structure-guided multiple sequence alignment and a modified phylogenetic tree (aka binding site tree) based just on a selection of potential substrate binding residue positions derived from experimental information (not from the full-length sequence alignment). Hereupon, the remaining, mostly uncharacterized enzyme sequences can be mapped; as a trend, sequence grouping in the tree branches follows substrate specificity. We show that this information can be used in the target selection for protein engineering work to narrow down to single suitable sequences and just a few relevant candidate positions for directed evolution towards activity for desired organic compound substrates. We also demonstrate how to find the closest thermophile example in the dataset if the engineering is aimed at achieving most robust enzymes.
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Affiliation(s)
- Fernanda L Sirota
- Bioinformatics Institute (BII), Agency for Science Technology and Research (ASTAR), Singapore, Singapore
| | - Sebastian Maurer-Stroh
- Bioinformatics Institute (BII), Agency for Science Technology and Research (ASTAR), Singapore, Singapore.,Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Zhi Li
- Department of Chemical and Biomolecular Engineering, National University of Singapore, Singapore, Singapore
| | - Frank Eisenhaber
- Bioinformatics Institute (BII), Agency for Science Technology and Research (ASTAR), Singapore, Singapore.,Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (ASTAR), Singapore, Singapore.,School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Birgit Eisenhaber
- Bioinformatics Institute (BII), Agency for Science Technology and Research (ASTAR), Singapore, Singapore.,Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (ASTAR), Singapore, Singapore
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4
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Chernova AI, Gubaev RF, Singh A, Sherbina K, Goryunova SV, Martynova EU, Goryunov DV, Boldyrev SV, Vanyushkina AA, Anikanov NA, Stekolshchikova EA, Yushina EA, Demurin YN, Mukhina ZM, Gavrilova VA, Anisimova IN, Karabitsina YI, Alpatieva NV, Chang PL, Khaitovich P, Mazin PV, Nuzhdin SV. Genotyping and lipid profiling of 601 cultivated sunflower lines reveals novel genetic determinants of oil fatty acid content. BMC Genomics 2021; 22:505. [PMID: 34225652 PMCID: PMC8256595 DOI: 10.1186/s12864-021-07768-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Accepted: 06/03/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Sunflower is an important oilseed crop domesticated in North America approximately 4000 years ago. During the last century, oil content in sunflower was under strong selection. Further improvement of oil properties achieved by modulating its fatty acid composition is one of the main directions in modern oilseed crop breeding. RESULTS We searched for the genetic basis of fatty acid content variation by genotyping 601 inbred sunflower lines and assessing their lipid and fatty acid composition. Our genome-wide association analysis based on the genotypes for 15,483 SNPs and the concentrations of 23 fatty acids, including minor fatty acids, revealed significant genetic associations for eleven of them. Identified genomic regions included the loci involved in rare fatty acids variation on chromosomes 3 and 14, explaining up to 34.5% of the total variation of docosanoic acid (22:0) in sunflower oil. CONCLUSIONS This is the first large scale implementation of high-throughput lipidomic profiling to sunflower germplasm characterization. This study contributes to the genetic characterization of Russian sunflower collections, which made a substantial contribution to the development of sunflower as the oilseed crop worldwide, and provides new insights into the genetic control of oil composition that can be implemented in future studies.
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Affiliation(s)
- Alina I Chernova
- Skolkovo Institute of Science and Technology (Skoltech), Bolshoy Boulevard 30, bld. 1, Moscow, 121205, Russia. .,LLC "OIL GENE", Skolkovo Innovation Center, Moscow, Russia.
| | - Rim F Gubaev
- Skolkovo Institute of Science and Technology (Skoltech), Bolshoy Boulevard 30, bld. 1, Moscow, 121205, Russia.,LLC "OIL GENE", Skolkovo Innovation Center, Moscow, Russia
| | - Anupam Singh
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, 90089, USA
| | - Katrina Sherbina
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, 90089, USA
| | - Svetlana V Goryunova
- Skolkovo Institute of Science and Technology (Skoltech), Bolshoy Boulevard 30, bld. 1, Moscow, 121205, Russia.,Vavilov Institute of General Genetics, Russian Academy of Sciences, Gubkin st. 3, Moscow, 119991, Russia.,FSBSI Lorch Potato Research Institute, Lorkha Str. 23, Kraskovo, 140051, Russia
| | - Elena U Martynova
- Skolkovo Institute of Science and Technology (Skoltech), Bolshoy Boulevard 30, bld. 1, Moscow, 121205, Russia
| | - Denis V Goryunov
- Skolkovo Institute of Science and Technology (Skoltech), Bolshoy Boulevard 30, bld. 1, Moscow, 121205, Russia.,MSU A.N. Belozersky Institute of Physico-Chemical Biology, Leninsky Gori 1, Building 40, Moscow, 119992, Russia
| | - Stepan V Boldyrev
- Skolkovo Institute of Science and Technology (Skoltech), Bolshoy Boulevard 30, bld. 1, Moscow, 121205, Russia.,LLC "OIL GENE", Skolkovo Innovation Center, Moscow, Russia
| | - Anna A Vanyushkina
- Skolkovo Institute of Science and Technology (Skoltech), Bolshoy Boulevard 30, bld. 1, Moscow, 121205, Russia
| | - Nikolay A Anikanov
- Skolkovo Institute of Science and Technology (Skoltech), Bolshoy Boulevard 30, bld. 1, Moscow, 121205, Russia
| | - Elena A Stekolshchikova
- Skolkovo Institute of Science and Technology (Skoltech), Bolshoy Boulevard 30, bld. 1, Moscow, 121205, Russia
| | - Ekaterina A Yushina
- Skolkovo Institute of Science and Technology (Skoltech), Bolshoy Boulevard 30, bld. 1, Moscow, 121205, Russia.,FSBSI N P Bochkov Research Center of Medical Genetics, Moskvorechye St.1, Moscow, 115522, Russia
| | - Yakov N Demurin
- Pustovoit All-Russia Research Institute of Oilseed Crops, Filatova St. 17, Krasnodar, 350038, Russia
| | | | - Vera A Gavrilova
- N. I. Vavilov Research Institute of Plant Genetic Resources (VIR), 42 B. Morskaja, St. Petersburg, 190000, Russia
| | - Irina N Anisimova
- N. I. Vavilov Research Institute of Plant Genetic Resources (VIR), 42 B. Morskaja, St. Petersburg, 190000, Russia
| | - Yulia I Karabitsina
- N. I. Vavilov Research Institute of Plant Genetic Resources (VIR), 42 B. Morskaja, St. Petersburg, 190000, Russia
| | - Natalia V Alpatieva
- N. I. Vavilov Research Institute of Plant Genetic Resources (VIR), 42 B. Morskaja, St. Petersburg, 190000, Russia
| | - Peter L Chang
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, 90089, USA
| | - Philipp Khaitovich
- Skolkovo Institute of Science and Technology (Skoltech), Bolshoy Boulevard 30, bld. 1, Moscow, 121205, Russia
| | - Pavel V Mazin
- Skolkovo Institute of Science and Technology (Skoltech), Bolshoy Boulevard 30, bld. 1, Moscow, 121205, Russia
| | - Sergey V Nuzhdin
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, 90089, USA
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5
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Ribeaucourt D, Bissaro B, Lambert F, Lafond M, Berrin JG. Biocatalytic oxidation of fatty alcohols into aldehydes for the flavors and fragrances industry. Biotechnol Adv 2021; 56:107787. [PMID: 34147589 DOI: 10.1016/j.biotechadv.2021.107787] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Revised: 06/13/2021] [Accepted: 06/15/2021] [Indexed: 01/11/2023]
Abstract
From Egyptian mummies to the Chanel n°5 perfume, fatty aldehydes have long been used and keep impacting our senses in a wide range of foods, beverages and perfumes. Natural sources of fatty aldehydes are threatened by qualitative and quantitative variability while traditional chemical routes are insufficient to answer the society shift toward more sustainable and natural products. The production of fatty aldehydes using biotechnologies is therefore the most promising alternative for the flavors and fragrances industry. In this review, after drawing the portrait of the origin and characteristics of fragrant fatty aldehydes, we present the three main classes of enzymes that catalyze the reaction of fatty alcohols oxidation into aldehydes, namely alcohol dehydrogenases, flavin-dependent alcohol oxidases and copper radical alcohol oxidases. The constraints, challenges and opportunities to implement these oxidative enzymes in the flavors and fragrances industry are then discussed. By setting the scene on the biocatalytic production of fatty aldehydes, and providing a critical assessment of its potential, we expect this review to contribute to the development of biotechnology-based solutions in the flavors and fragrances industry.
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Affiliation(s)
- David Ribeaucourt
- INRAE, Aix Marseille Univ, UMR1163 Biodiversité et Biotechnologie Fongiques, 13009 Marseille, France; V. Mane Fils, 620 route de Grasse, 06620 Le Bar sur Loup, France; Aix Marseille Univ, CNRS, Centrale Marseille, iSm2, Marseille, France.
| | - Bastien Bissaro
- INRAE, Aix Marseille Univ, UMR1163 Biodiversité et Biotechnologie Fongiques, 13009 Marseille, France
| | - Fanny Lambert
- V. Mane Fils, 620 route de Grasse, 06620 Le Bar sur Loup, France
| | - Mickael Lafond
- Aix Marseille Univ, CNRS, Centrale Marseille, iSm2, Marseille, France
| | - Jean-Guy Berrin
- INRAE, Aix Marseille Univ, UMR1163 Biodiversité et Biotechnologie Fongiques, 13009 Marseille, France.
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6
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Zhang L, Xiu X, Wang Z, Jiang Y, Fan H, Su J, Sui S, Wang S, Wang R, Li J, Wang J, Li N, Wang J. Increasing Long-Chain Dicarboxylic Acid Production in Candida tropicalis by Engineering Fatty Transporters. Mol Biotechnol 2021; 63:544-555. [PMID: 33786739 DOI: 10.1007/s12033-021-00319-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Accepted: 03/20/2021] [Indexed: 01/03/2023]
Abstract
Candida tropicalis can metabolize alkanes or fatty acids to produce long-chain dicarboxylic acids (DCAs). Fatty acid transporters located on the cell or peroxisome membrane may play an important role in this process. Using amino acid sequence homologous alignment, two putative proteins, CtFat1p and CtPxa1p, located on the cell and peroxisome membrane were found, respectively. Moreover, single- and double-knockout homologous recombination technology was used to study ctfat1p and ctpxa1p gene effects on DCA synthesis. In comparison to the wild-type strain, long-chain DCA yield decreased by 65.14%, 88.38% and 56.19% after single and double-copy knockout of ctfat1p genes and double-copy knockout of ctpxa1p genes, respectively, indicating that the knockout of ctfat1p and ctpxa1p genes had a significant effect on the conversion of oils and fats into long-chain DCAs by C. tropicalis. However, the yield of long-chain DCAs increased by 21.90% after single-knockout of the ctpxa1p gene, indicating that the single-knockout of the ctpxa1p gene may reduce fatty acid transport to peroxisome for further oxidation. Moreover, to improve the intracellular transport rate of fatty acids, ctfat1p copy number increased, increasing DCA yield by 30.10%. These results may provide useful information for enhancing the production of long-chain DCAs by C. tropicalis.
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Affiliation(s)
- Lihua Zhang
- State Key Laboratory of Biobased Material and Green Papermaking (LBMP), Qilu University of Technology, Jinan, 250353, Shandong, People's Republic of China
| | - Xiang Xiu
- School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, People's Republic of China
| | - Zirui Wang
- State Key Laboratory of Biobased Material and Green Papermaking (LBMP), Qilu University of Technology, Jinan, 250353, Shandong, People's Republic of China
| | - Yanjun Jiang
- State Key Laboratory of Biobased Material and Green Papermaking (LBMP), Qilu University of Technology, Jinan, 250353, Shandong, People's Republic of China
| | - Han Fan
- State Key Laboratory of Biobased Material and Green Papermaking (LBMP), Qilu University of Technology, Jinan, 250353, Shandong, People's Republic of China
| | - Jing Su
- State Key Laboratory of Biobased Material and Green Papermaking (LBMP), Qilu University of Technology, Jinan, 250353, Shandong, People's Republic of China
| | - Songsen Sui
- Zhucheng Dongxiao Biotechnology Co., Ltd, Xinxing Town, Zhucheng, Shandong, 262200, People's Republic of China
| | - Songjiang Wang
- Zhucheng Dongxiao Biotechnology Co., Ltd, Xinxing Town, Zhucheng, Shandong, 262200, People's Republic of China
| | - Ruiming Wang
- State Key Laboratory of Biobased Material and Green Papermaking (LBMP), Qilu University of Technology, Jinan, 250353, Shandong, People's Republic of China
| | - Junlin Li
- Zhucheng Dongxiao Biotechnology Co., Ltd, Xinxing Town, Zhucheng, Shandong, 262200, People's Republic of China
| | - Junqing Wang
- State Key Laboratory of Biobased Material and Green Papermaking (LBMP), Qilu University of Technology, Jinan, 250353, Shandong, People's Republic of China.
| | - Nan Li
- Collage of Biotechnology, Tianjin University of Science and Technology, Tianjin, 300457, People's Republic of China.
| | - Jianbin Wang
- Zhucheng Dongxiao Biotechnology Co., Ltd, Xinxing Town, Zhucheng, Shandong, 262200, People's Republic of China
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7
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Palys S, Pham TTM, Tsang A. Biosynthesis of Alkylcitric Acids in Aspergillus niger Involves Both Co-localized and Unlinked Genes. Front Microbiol 2020; 11:1378. [PMID: 32695080 PMCID: PMC7338620 DOI: 10.3389/fmicb.2020.01378] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Accepted: 05/28/2020] [Indexed: 01/08/2023] Open
Abstract
Filamentous fungi are an abundant source of bioactive secondary metabolites (SMs). In many cases, the biosynthetic processes of SMs are not well understood. This work focuses on a group of SMs, the alkylcitric acids, each of which contains a saturated alkyl "tail," and a citrate-derived "head." We initially identified their biosynthetic gene cluster and the transcriptional regulator (akcR) involved in the biosynthesis of alkylcitrates in the filamentous fungus Aspergillus niger by examining the functional annotation of SM gene clusters predicted from genomic data. We overexpressed the transcription regulator gene akcR and obtained from one liter of culture filtrate 8.5 grams of extract, which are represented by seven alkylcitric acids as determined by NMR. Hexylaconitic acid A comprised 94.1% of the total production, and four of the seven identified alkylcitrates have not been reported previously. Analysis of orthologous alkylcitrate gene clusters in the Aspergilli revealed that in A. oryzae and A. flavus an in-cluster gene displays sequence similarity to cis-aconitate decarboxylase, the orthologue of which in A. niger, NRRL3_00504, is located on a different chromosome. Overexpression of the A. niger NRRL3_00504 and akcR genes together shifted the profile of alkylcitrates production from primarily hexylaconitic acids to mainly hexylitaconic acids, suggesting that NRRL3_00504 encodes an enzyme with hexyl aconitate decarboxylase activity. We also detected two additional, previously unreported, alkylcitric acids in the double overexpression strain. This study shows that phylogenomic analysis together with experimental manipulations can be used to reconstruct a more complete biosynthetic pathway in generating a broader spectrum of alkylcitric compounds. The approach adopted here has the potential of elucidating the complexity of other SM biosynthetic pathways in fungi.
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Affiliation(s)
| | | | - Adrian Tsang
- Centre for Structural and Functional Genomics, Concordia University, Montreal, QC, Canada
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8
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Werner N, Zibek S. Biotechnological production of bio-based long-chain dicarboxylic acids with oleogenious yeasts. World J Microbiol Biotechnol 2017; 33:194. [PMID: 28983758 DOI: 10.1007/s11274-017-2360-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Accepted: 09/26/2017] [Indexed: 01/15/2023]
Abstract
Long-chain α,ω-dicarboxylic acids (DCAs) are versatile chemical intermediates of industrial importance used as building blocks for the production of polymers, lubricants, or adhesives. The majority of industrial long-chain DCAs is produced from petro-chemical resources. An alternative is their biotechnological production from renewable materials like plant oil fatty acids by microbial fermentation using oleogenious yeasts. Oleogenious yeasts are natural long-chain DCA producers, which have to be genetically engineered for high-yield DCA production. Although, some commercialized fermentation processes using engineered yeasts are reported, bio-based long-chain DCAs are still far from being a mass product. Further progress in bioprocess engineering and rational strain design is necessary to advance their further commercialization. The present article reviews the basic strategies, as well as novel approaches in the strain design of oleogenious yeasts, such as the combination of traditional metabolic engineering with system biology strategies for high-yield long-chain DCA production. Therefore a detailed overview of the involved metabolic processes for the biochemical long-chain DCA synthesis is given.
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Affiliation(s)
- Nicole Werner
- Fraunhofer Institute for Interfacial Engineering and Biotechnology IGB, Stuttgart, Germany
| | - Susanne Zibek
- Fraunhofer Institute for Interfacial Engineering and Biotechnology IGB, Stuttgart, Germany.
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9
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Combinatorial Engineering of Yarrowia lipolytica as a Promising Cell Biorefinery Platform for the de novo Production of Multi-Purpose Long Chain Dicarboxylic Acids. FERMENTATION-BASEL 2017. [DOI: 10.3390/fermentation3030040] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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10
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Enabling tools for high-throughput detection of metabolites: Metabolic engineering and directed evolution applications. Biotechnol Adv 2017; 35:950-970. [PMID: 28723577 DOI: 10.1016/j.biotechadv.2017.07.005] [Citation(s) in RCA: 79] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Revised: 06/07/2017] [Accepted: 07/11/2017] [Indexed: 12/21/2022]
Abstract
Within the Design-Build-Test Cycle for strain engineering, rapid product detection and selection strategies remain challenging and limit overall throughput. Here we summarize a wide variety of modalities that transduce chemical concentrations into easily measured absorbance, luminescence, and fluorescence signals. Specifically, we cover protein-based biosensors (including transcription factors), nucleic acid-based biosensors, coupled enzyme reactions, bioorthogonal chemistry, and fluorescent and chromogenic dyes and substrates as modalities for detection. We focus on the use of these methods for strain engineering and enzyme discovery and conclude with remarks on the current and future state of biosensor development for application in the metabolic engineering field.
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11
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Kim S, Cheong S, Chou A, Gonzalez R. Engineered fatty acid catabolism for fuel and chemical production. Curr Opin Biotechnol 2016; 42:206-215. [DOI: 10.1016/j.copbio.2016.07.004] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2016] [Revised: 07/07/2016] [Accepted: 07/14/2016] [Indexed: 10/21/2022]
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12
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Takahashi F, Igarashi K, Hagihara H. Identification of the fatty alcohol oxidase FAO1 from Starmerella bombicola and improved novel glycolipids production in an FAO1 knockout mutant. Appl Microbiol Biotechnol 2016; 100:9519-9528. [DOI: 10.1007/s00253-016-7702-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2016] [Revised: 06/20/2016] [Accepted: 06/23/2016] [Indexed: 11/30/2022]
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13
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Mishra P, Park GY, Lakshmanan M, Lee HS, Lee H, Chang MW, Ching CB, Ahn J, Lee DY. Genome-scale metabolic modeling and in silico analysis of lipid accumulating yeast Candida tropicalis for dicarboxylic acid production. Biotechnol Bioeng 2016; 113:1993-2004. [PMID: 26915092 DOI: 10.1002/bit.25955] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2015] [Revised: 11/25/2015] [Accepted: 02/14/2016] [Indexed: 02/02/2023]
Abstract
Recently, the bio-production of α,ω-dicarboxylic acids (DCAs) has gained significant attention, which potentially leads to the replacement of the conventional petroleum-based products. In this regard, the lipid accumulating yeast Candida tropicalis, has been recognized as a promising microbial host for DCA biosynthesis: it possess the unique ω-oxidation pathway where the terminal carbon of α-fatty acids is oxidized to form DCAs with varying chain lengths. However, despite such industrial importance, its cellular physiology and lipid accumulation capability remain largely uncharacterized. Thus, it is imperative to better understand the metabolic behavior of this lipogenic yeast, which could be achieved by a systems biological approach. To this end, herein, we reconstructed the genome-scale metabolic model of C. tropicalis, iCT646, accounting for 646 unique genes, 945 metabolic reactions, and 712 metabolites. Initially, the comparative network analysis of iCT646 with other yeasts revealed several distinctive metabolic reactions, mainly within the amino acid and lipid metabolism including the ω-oxidation pathway. Constraints-based flux analysis was, then, employed to predict the in silico growth rates of C. tropicalis which are highly consistent with the cellular phenotype observed in glucose and xylose minimal media chemostat cultures. Subsequently, the lipid accumulation capability of C. tropicalis was explored in comparison with Saccharomyces cerevisiae, indicating that the formation of "citrate pyruvate cycle" is essential to the lipid accumulation in oleaginous yeasts. The in silico flux analysis also highlighted the enhanced ability of pentose phosphate pathway as NADPH source rather than malic enzyme during lipogenesis. Finally, iCT646 was successfully utilized to highlight the key directions of C. tropicalis strain design for the whole cell biotransformation application to produce long-chain DCAs from alkanes. Biotechnol. Bioeng. 2016;113: 1993-2004. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Pranjul Mishra
- Department of Chemical and Biomolecular Engineering, National University of Singapore, 4 Engineering Drive 4, 117585, Singapore
| | - Gyu-Yeon Park
- Biotechnology Process Engineering Center, KRIBB, 30 Yeongudanji-ro, Ochang-eup, Cheongwon-gu, Cheongju, 363-883, Korea.,Bioprocess Department, University of Science and Technology, 217 Gajeong-ro, Yuseong-gu, Daejeon, 305-350, Korea
| | - Meiyappan Lakshmanan
- Bioprocessing Technology Institute, Agency for Science, Technology and Research (A*STAR), 20 Biopolis Way, #06-01, Centros, 138668, Singapore
| | - Hee-Seok Lee
- Biotechnology Process Engineering Center, KRIBB, 30 Yeongudanji-ro, Ochang-eup, Cheongwon-gu, Cheongju, 363-883, Korea.,Bioprocess Department, University of Science and Technology, 217 Gajeong-ro, Yuseong-gu, Daejeon, 305-350, Korea
| | - Hongweon Lee
- Biotechnology Process Engineering Center, KRIBB, 30 Yeongudanji-ro, Ochang-eup, Cheongwon-gu, Cheongju, 363-883, Korea.,Bioprocess Department, University of Science and Technology, 217 Gajeong-ro, Yuseong-gu, Daejeon, 305-350, Korea
| | - Matthew Wook Chang
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore.,NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), Life Sciences Institute, National University of Singapore, 28 Medical Drive, 117456, Singapore
| | - Chi Bun Ching
- Department of Chemical and Biomolecular Engineering, National University of Singapore, 4 Engineering Drive 4, 117585, Singapore
| | - Jungoh Ahn
- Biotechnology Process Engineering Center, KRIBB, 30 Yeongudanji-ro, Ochang-eup, Cheongwon-gu, Cheongju, 363-883, Korea. .,Bioprocess Department, University of Science and Technology, 217 Gajeong-ro, Yuseong-gu, Daejeon, 305-350, Korea.
| | - Dong-Yup Lee
- Department of Chemical and Biomolecular Engineering, National University of Singapore, 4 Engineering Drive 4, 117585, Singapore. .,Bioprocessing Technology Institute, Agency for Science, Technology and Research (A*STAR), 20 Biopolis Way, #06-01, Centros, 138668, Singapore. .,NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), Life Sciences Institute, National University of Singapore, 28 Medical Drive, 117456, Singapore.
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14
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Iwama R, Kobayashi S, Ohta A, Horiuchi H, Fukuda R. Alcohol dehydrogenases and an alcohol oxidase involved in the assimilation of exogenous fatty alcohols in Yarrowia lipolytica. FEMS Yeast Res 2015; 15:fov014. [DOI: 10.1093/femsyr/fov014] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/17/2015] [Indexed: 01/21/2023] Open
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15
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Martins I, Hartmann DO, Alves PC, Martins C, Garcia H, Leclercq CC, Ferreira R, He J, Renaut J, Becker JD, Silva Pereira C. Elucidating how the saprophytic fungus Aspergillus nidulans uses the plant polyester suberin as carbon source. BMC Genomics 2014; 15:613. [PMID: 25043916 PMCID: PMC4117967 DOI: 10.1186/1471-2164-15-613] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2014] [Accepted: 07/16/2014] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND Lipid polymers in plant cell walls, such as cutin and suberin, build recalcitrant hydrophobic protective barriers. Their degradation is of foremost importance for both plant pathogenic and saprophytic fungi. Regardless of numerous reports on fungal degradation of emulsified fatty acids or cutin, and on fungi-plant interactions, the pathways involved in the degradation and utilisation of suberin remain largely overlooked. As a structural component of the plant cell wall, suberin isolation, in general, uses harsh depolymerisation methods that destroy its macromolecular structure. We recently overcame this limitation isolating suberin macromolecules in a near-native state. RESULTS Suberin macromolecules were used here to analyse the pathways involved in suberin degradation and utilisation by Aspergillus nidulans. Whole-genome profiling data revealed the complex degrading enzymatic machinery used by this saprophytic fungus. Initial suberin modification involved ester hydrolysis and ω-hydroxy fatty acid oxidation that released long chain fatty acids. These fatty acids were processed through peroxisomal β-oxidation, leading to up-regulation of genes encoding the major enzymes of these pathways (e.g. faaB and aoxA). The obtained transcriptome data was further complemented by secretome, microscopic and spectroscopic analyses. CONCLUSIONS Data support that during fungal growth on suberin, cutinase 1 and some lipases (e.g. AN8046) acted as the major suberin degrading enzymes (regulated by FarA and possibly by some unknown regulatory elements). Suberin also induced the onset of sexual development and the boost of secondary metabolism.
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Affiliation(s)
- Isabel Martins
- />Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
| | - Diego O Hartmann
- />Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
| | - Paula C Alves
- />Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
| | - Celso Martins
- />Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
- />Instituto de Biologia Experimental e Tecnológica (iBET), Av. da República, 2781-901 Oeiras, Portugal
| | - Helga Garcia
- />Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
| | - Céline C Leclercq
- />Proteomics Platform, Centre de Recherche Public - Gabriel Lippmann, Belvaux, Luxembourg
| | - Rui Ferreira
- />Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
| | - Ji He
- />Cancer Genomics Research Laboratory, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, DHHS, (previously, the Scientific Computing department, Samuel Roberts Noble Foundation, USA, 8717 Grovemont Circle, 20877 Gaithersburg, MD USA
| | - Jenny Renaut
- />Proteomics Platform, Centre de Recherche Public - Gabriel Lippmann, Belvaux, Luxembourg
| | - Jörg D Becker
- />Instituto Gulbenkian de Ciência, Rua da Quinta Grande 6, 2780-156 Oeiras, Portugal
| | - Cristina Silva Pereira
- />Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
- />Instituto de Biologia Experimental e Tecnológica (iBET), Av. da República, 2781-901 Oeiras, Portugal
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16
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Gatter M, Förster A, Bär K, Winter M, Otto C, Petzsch P, Ježková M, Bahr K, Pfeiffer M, Matthäus F, Barth G. A newly identified fatty alcohol oxidase gene is mainly responsible for the oxidation of long-chain ω-hydroxy fatty acids in Yarrowia lipolytica. FEMS Yeast Res 2014; 14:858-72. [PMID: 24931727 DOI: 10.1111/1567-1364.12176] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2013] [Revised: 06/06/2014] [Accepted: 06/07/2014] [Indexed: 11/30/2022] Open
Abstract
Nine potential (fatty) alcohol dehydrogenase genes and one alcohol oxidase gene were identified in Yarrowia lipolytica by comparative sequence analysis. All relevant genes were deleted in Y. lipolytica H222ΔP which is lacking β-oxidation. Resulting transformants were tested for their ability to accumulate ω-hydroxy fatty acids and dicarboxylic acids in the culture medium. The deletion of eight alcohol dehydrogenase genes (FADH, ADH1-7), which may be involved in ω-oxidation, led only to a slightly increased accumulation of ω-hydroxy fatty acids, whereas the deletion of the fatty alcohol oxidase gene (FAO1), which has not been described yet in Y. lipolytica, exhibited a considerably higher effect. The combined deletion of the eight (fatty) alcohol dehydrogenase genes and the alcohol oxidase gene further reduced the formation of dicarboxylic acids. These results indicate that both (fatty) alcohol dehydrogenases and an alcohol oxidase are involved in ω-oxidation of long-chain fatty acids whereby latter plays the major role. This insight marks the first step toward the biotechnological production of long-chain ω-hydroxy fatty acids with the help of the nonconventional yeast Y. lipolytica. The overexpression of FAO1 can be further used to improve existing strains for the production of dicarboxylic acids.
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Affiliation(s)
- Michael Gatter
- Institute of Microbiology, Dresden University of Technology, Dresden, Germany
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17
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Chakraborty M, Goel M, Chinnadayyala SR, Dahiya UR, Ghosh SS, Goswami P. Molecular characterization and expression of a novel alcohol oxidase from Aspergillus terreus MTCC6324. PLoS One 2014; 9:e95368. [PMID: 24752075 PMCID: PMC3994049 DOI: 10.1371/journal.pone.0095368] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2013] [Accepted: 03/26/2014] [Indexed: 11/28/2022] Open
Abstract
The alcohol oxidase (AOx) cDNA from Aspergillus terreus MTCC6324 with an open reading frame (ORF) of 2001 bp was constructed from n-hexadecane induced cells and expressed in Escherichia coli with a yield of ∼4.2 mg protein g−1 wet cell. The deduced amino acid sequences of recombinant rAOx showed maximum structural homology with the chain B of aryl AOx from Pleurotus eryngii. A functionally active AOx was achieved by incubating the apo-AOx with flavin adenine dinucleotide (FAD) for ∼80 h at 16°C and pH 9.0. The isoelectric point and mass of the apo-AOx were found to be 6.5±0.1 and ∼74 kDa, respectively. Circular dichroism data of the rAOx confirmed its ordered structure. Docking studies with an ab-initio protein model demonstrated the presence of a conserved FAD binding domain with an active substrate binding site. The rAOx was specific for aryl alcohols and the order of its substrate preference was 4-methoxybenzyl alcohol >3-methoxybenzyl alcohol>3, 4-dimethoxybenzyl alcohol > benzyl alcohol. A significantly high aggregation to ∼1000 nm (diameter) and catalytic efficiency (kcat/Km) of 7829.5 min−1 mM−1 for 4-methoxybenzyl alcohol was also demonstrated for rAOx. The results infer the novelty of the AOx and its potential biocatalytic application.
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Affiliation(s)
- Mitun Chakraborty
- Department of Biotechnology, Indian Institute of Technology Guwahati, Assam, India
| | - Manish Goel
- Department of Biotechnology, Indian Institute of Technology Guwahati, Assam, India
| | | | - Ujjwal Ranjan Dahiya
- Department of Biotechnology, Indian Institute of Technology Guwahati, Assam, India
| | - Siddhartha Sankar Ghosh
- Department of Biotechnology, Indian Institute of Technology Guwahati, Assam, India
- * E-mail: (SSG); (PG)
| | - Pranab Goswami
- Department of Biotechnology, Indian Institute of Technology Guwahati, Assam, India
- * E-mail: (SSG); (PG)
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18
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Cintolesi A, Rodríguez-Moyá M, Gonzalez R. Fatty acid oxidation: systems analysis and applications. WILEY INTERDISCIPLINARY REVIEWS-SYSTEMS BIOLOGY AND MEDICINE 2013; 5:575-85. [DOI: 10.1002/wsbm.1226] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2013] [Revised: 03/26/2013] [Accepted: 03/29/2013] [Indexed: 12/30/2022]
Affiliation(s)
- Angela Cintolesi
- Department of Chemical and Biomolecular Engineering; Rice University; Houston TX USA
| | - María Rodríguez-Moyá
- Department of Chemical and Biomolecular Engineering; Rice University; Houston TX USA
| | - Ramon Gonzalez
- Department of Chemical and Biomolecular Engineering; Rice University; Houston TX USA
- Department of Bioengineering; Rice University; Houston TX USA
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19
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An overview on alcohol oxidases and their potential applications. Appl Microbiol Biotechnol 2013; 97:4259-75. [DOI: 10.1007/s00253-013-4842-9] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2012] [Revised: 03/06/2013] [Accepted: 03/07/2013] [Indexed: 10/27/2022]
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20
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Rajangam AS, Gidda SK, Craddock C, Mullen RT, Dyer JM, Eastmond PJ. Molecular characterization of the fatty alcohol oxidation pathway for wax-ester mobilization in germinated jojoba seeds. PLANT PHYSIOLOGY 2013; 161:72-80. [PMID: 23166353 PMCID: PMC3532287 DOI: 10.1104/pp.112.208264] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2012] [Accepted: 11/16/2012] [Indexed: 05/02/2023]
Abstract
Jojoba (Simmondsia chinensis) is the only plant species known to use liquid wax esters (WEs) as a primary seed storage reserve. Upon germination, WE hydrolysis releases very-long-chain fatty alcohols, which must be oxidized to fatty acids by the sequential action of a fatty alcohol oxidase (FAO) and a fatty aldehyde dehydrogenase (FADH) before they can be β-oxidized. Here, we describe the cloning and characterization of genes for each of these two activities. Jojoba FAO and FADH are 52% and 68% identical to Arabidopsis (Arabidopsis thaliana) FAO3 and ALDH3H1, respectively. The genes are expressed most strongly in the cotyledons of jojoba seedlings following germination, but transcripts can also be detected in vegetative tissues. Proteomic analysis indicated that the FAO and FADH proteins can be detected on wax bodies, but they localized to the endoplasmic reticulum when they were expressed as amino-terminal green fluorescent protein fusions in tobacco (Nicotiana tabacum) leaves. Recombinant jojoba FAO and FADH proteins are active on very-long-chain fatty alcohol and fatty aldehyde substrates, respectively, and have biochemical properties consistent with those previously reported in jojoba cotyledons. Coexpression of jojoba FAO and FADH in Arabidopsis enhanced the in vivo rate of fatty alcohol oxidation more than 4-fold. Taken together, our data suggest that jojoba FAO and FADH constitute the very-long-chain fatty alcohol oxidation pathway that is likely to be necessary for efficient WE mobilization following seed germination.
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Affiliation(s)
| | - Satinder K. Gidda
- School of Life Sciences, University of Warwick, Coventry, Warwickshire CV4 7AL, United Kingdom (A.S.R., C.C.)
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada N1G 2W1 (S.K.G., R.T.M.)
- United States Department of Agriculture-Agricultural Research Service, United States Arid-Land Agricultural Research Center, Maricopa, Arizona 85238 (J.M.D.)
- Department of Crop Biology and Plant Science, Rothamsted Research, Harpenden, Hertfordshire AL5 2JQ, United Kingdom (P.J.E.)
| | | | - Robert T. Mullen
- School of Life Sciences, University of Warwick, Coventry, Warwickshire CV4 7AL, United Kingdom (A.S.R., C.C.)
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada N1G 2W1 (S.K.G., R.T.M.)
- United States Department of Agriculture-Agricultural Research Service, United States Arid-Land Agricultural Research Center, Maricopa, Arizona 85238 (J.M.D.)
- Department of Crop Biology and Plant Science, Rothamsted Research, Harpenden, Hertfordshire AL5 2JQ, United Kingdom (P.J.E.)
| | - John M. Dyer
- School of Life Sciences, University of Warwick, Coventry, Warwickshire CV4 7AL, United Kingdom (A.S.R., C.C.)
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada N1G 2W1 (S.K.G., R.T.M.)
- United States Department of Agriculture-Agricultural Research Service, United States Arid-Land Agricultural Research Center, Maricopa, Arizona 85238 (J.M.D.)
- Department of Crop Biology and Plant Science, Rothamsted Research, Harpenden, Hertfordshire AL5 2JQ, United Kingdom (P.J.E.)
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Tuckwell D, Denning DW, Bowyer P. A public resource for metabolic pathway mapping ofAspergillus fumigatusAf293. Med Mycol 2011; 49 Suppl 1:S114-9. [DOI: 10.3109/13693786.2010.490243] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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22
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Johanson T, Parachin NS, Adamis P, Gorwa-Grauslund MF. Identification of a Candida sp. reductase behind bicyclic exo-alcohol production. ACTA ACUST UNITED AC 2009. [DOI: 10.1016/j.molcatb.2008.11.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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23
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Silva-Jiménez H, Zazueta-Novoa V, Durón-Castellanos A, Rodríguez-Robelo C, Leal-Morales CA, Zazueta-Sandoval R. Intracellular distribution of fatty alcohol oxidase activity in Mucor circinelloides YR-1 isolated from petroleum contaminated soils. Antonie van Leeuwenhoek 2009; 96:527-35. [DOI: 10.1007/s10482-009-9368-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2009] [Accepted: 07/15/2009] [Indexed: 10/20/2022]
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24
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Kurdyukov S, Faust A, Trenkamp S, Bär S, Franke R, Efremova N, Tietjen K, Schreiber L, Saedler H, Yephremov A. Genetic and biochemical evidence for involvement of HOTHEAD in the biosynthesis of long-chain alpha-,omega-dicarboxylic fatty acids and formation of extracellular matrix. PLANTA 2006; 224:315-29. [PMID: 16404574 DOI: 10.1007/s00425-005-0215-7] [Citation(s) in RCA: 122] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2005] [Accepted: 12/09/2005] [Indexed: 05/06/2023]
Abstract
In plants, extracellular matrix polymers built from polysaccharides and cuticular lipids have structural and protective functions. The cuticle is found to be ten times thinner in Arabidopsis thaliana (L.) Heynh than in many other plants, and there is evidence that it is unusual in having a high content of alpha-,omega-dicarboxylic fatty acids (FAs) in its polyesters. We designated the new organ fusion mutant hth-12 after it appeared to be allelic to adhesion of calyx edges (ace) and hothead (hth), upon molecular cloning of the gene by transposon tagging. This mutant is deficient in its ability to oxidize long-chain omega-hydroxy FAs to omega-oxo FAs, which results in leaf polyesters in decreased alpha-,omega-dicarboxylic FAs and increased omega-hydroxy FAs. These chemical phenotypes lead to disorder of the cuticle membrane structure in hth-12. ACE/HTH is a single-domain protein showing sequence similarity to long-chain FA omega-alcohol dehydrogenases from Candida species, and we hypothesize that it may catalyze the next step after cytochrome P450 FA omega-hydroxylases in the omega-oxidation pathway. We show that ACE/HTH is specifically expressed in epidermal cells. It appears very likely therefore that the changes in the amount of alpha-,omega-dicarboxylic FAs in hth-12 reflect the different composition of cuticular polyesters. The ACE/HTH gene is also expressed in root epidermal cells which do not form a polyester membrane on the exterior surface, thereby making it possible that the end products of the pathway, alpha-,omega-dicarboxylic FAs, are generally required for the cross-linking that ensures the integrity of the outer epidermal cell wall.
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Affiliation(s)
- Sergey Kurdyukov
- Max-Planck-Institut für Züchtungsforschung, Carl von Linné Weg 10, 50829 Cologne, Germany
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25
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Mandaokar A, Thines B, Shin B, Lange BM, Choi G, Koo YJ, Yoo YJ, Choi YD, Choi G, Browse J. Transcriptional regulators of stamen development in Arabidopsis identified by transcriptional profiling. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2006; 46:984-1008. [PMID: 16805732 DOI: 10.1111/j.1365-313x.2006.02756.x] [Citation(s) in RCA: 231] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
In Arabidopsis, jasmonate is required for stamen and pollen maturation. Mutants deficient in jasmonate synthesis, such as opr3, are male-sterile but become fertile when jasmonate is applied to developing flower buds. We have used ATH1 oligonucleotide arrays to follow gene expression in opr3 stamens for 22 h following jasmonate treatment. In these experiments, a total of 821 genes were specifically induced by jasmonate and 480 genes were repressed. Comparisons with data from previous studies indicate that these genes constitute a stamen-specific jasmonate transcriptome, with a large proportion (70%) of the genes expressed in the sporophytic tissue but not in the pollen. Bioinformatics tools allowed us to associate many of the induced genes with metabolic pathways that are probably upregulated during jasmonate-induced maturation. Our pathway analysis led to the identification of specific genes within larger families of homologues that apparently encode stamen-specific isozymes. Extensive additional analysis of our dataset identified 13 transcription factors that may be key regulators of the stamen maturation processes triggered by jasmonate. Two of these transcription factors, MYB21 and MYB24, are the only members of subgroup 19 of the R2R3 family of MYB proteins. A myb21 mutant obtained by reverse genetics exhibited shorter anther filaments, delayed anther dehiscence and greatly reduced male fertility. A myb24 mutant was phenotypically wild-type, but production of a myb21myb24 double mutant indicated that introduction of the myb24 mutation exacerbated all three aspects of the myb21 phenotype. Exogenous jasmonate could not restore fertility to myb21 or myb21myb24 mutant plants. Together with the data from transcriptional profiling, these results indicate that MYB21 and MYB24 are induced by jasmonate and mediate important aspects of the jasmonate response during stamen development.
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Affiliation(s)
- Ajin Mandaokar
- Institute of Biological Chemistry, Washington State University, Pullman, Washington 99164-6340, USA
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26
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Kumar AK, Goswami P. Functional characterization of alcohol oxidases from Aspergillus terreus MTCC 6324. Appl Microbiol Biotechnol 2006; 72:906-11. [PMID: 16547701 DOI: 10.1007/s00253-006-0381-y] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2006] [Revised: 02/15/2006] [Accepted: 02/15/2006] [Indexed: 11/25/2022]
Abstract
Short chain alcohol oxidase (SCAO), long chain alcohol oxidase (LCAO), secondary alcohol oxidase (SAO), and aryl alcohol oxidase (AAO) activities were localized in the microsome of Aspergillus terreus during growth of the fungi on n-hexadecane. Zymogram analysis of the microsomes of n-hexadecane-grown cells in polyacrylamide gel electrophoresis showed distinct bands, H4, H3, H2, and H1, in a sequence of their molecular weight (Mr) from high to low. The Mr of the isozymes corresponding to the bands H4, H3, and H2 were close to each other and were higher than 272 kDa. While, the Mr of the isozyme H1 was found to be approximately 48 kDa. H1 gave activity only as SCAO. Although the substrates for other bands were varied, strong (S), medium (M), and weak (W) activity for the bands were as follows: H2: SAO (S), AAO (S), LCAO (M), SCAO (S); H3: LCAO (S), SCAO (S); H4: SCAO (S), LCAO (W), SAO (W). The pH and temperature optima of these isozymes were found to be 8.5+/-0.5 and 30+/-1 degrees C, respectively. The stability of the isozymes was drastically decreased beyond 30 degrees C. The SAO showed 33% enantiomeric excess for the R(-)2-octanol over S(+)2-octanol, which may be correlated with the lower Michaelis-Menten constant (K (M)) values of the enzyme for the R(-)2-octanol than the S(+)2-octanol. The fluorescence emission spectra of the chromatographically purified SCAO at 443 nm excitation were similar to that obtained with authentic flavin adenine dinucleotide.
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Affiliation(s)
- A Kiran Kumar
- Department of Biotechnology, Indian Institute of Technology Guwahati, North Guwahati, Assam 781039, India
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27
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Cheng Q, Sanglard D, Vanhanen S, Liu HT, Bombelli P, Smith A, Slabas AR. Candida yeast long chain fatty alcohol oxidase is a c-type haemoprotein and plays an important role in long chain fatty acid metabolism. Biochim Biophys Acta Mol Cell Biol Lipids 2005; 1735:192-203. [PMID: 16046182 DOI: 10.1016/j.bbalip.2005.06.006] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2005] [Revised: 06/17/2005] [Accepted: 06/20/2005] [Indexed: 11/18/2022]
Abstract
The industrial yeasts Candida tropicalis or Candida cloacae are able to grow on a variety of long chain alkanes and fatty acids as the sole carbon source. The complete oxidation of these substrates involves two sequential oxidative pathways: omega-oxidation, comprising the P450 alkane oxidase, a flavin-dependent membrane-bound long chain fatty alcohol oxidase [FAO] and a possible separate aldehyde oxidase [F.M. Dickinson, C. Wadforth, Purification and some properties of alcohol oxidase from alkane-grown Candida tropicalis, Biochem. J. 282 (1992) 325-331], and the beta-oxidation pathway, which utilises acylCoA substrates. We recently purified the membrane-bound long chain fatty alcohol oxidase FAO1 and confirmed it is also a c-type haemoprotein. Multiple isoforms may exist for many of these long chain fatty alcohol oxidases and the in vivo requirements for individual genes with respect to specific substrates are still being elucidated. In vitro reconstitution experiments have demonstrated that in Candida maltosa, the cytochrome P450 52A3 gene product can completely oxidise alkanes to dicarboxylic acids [U. Scheller, T. Zimmer, D. Becher, F. Schauer, W. Schunck, Oxygenation Cascade in Conversion of n-Alkanes to, -Dioic Acids Catalyzed by Cytochrome P450 52A3, J. Biol. Chem. 273 (1998) 32528-32534], potentially obviating requirements for a long chain alcohol oxidase. Here, we directly determine in vivo the role of the long chain alcohol oxidase (FAOT) in C. tropicalis, grown on a variety of substrates, followed by gene deletion. The faot double knockout has no detectable faot activity and is incapable of growth on octadecane, but it grows well on oleic acid, palmitic acid and shorter chain alkanes/fatty acids. A spontaneous mutation[s] may have occurred in the faot double gene knockout of C. tropicalis resulting in its inability to grow on oleic acid and hexadecane. The mutations demonstrate that different pathways of octadecane, hexadecane, oleic acid and palmitic acid utilisation exist in C. tropicalis.
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Affiliation(s)
- Qi Cheng
- Department of Biological and Biomedical Sciences, University of Durham, South Road, Durham DH1 3LE, UK
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Fickers P, Benetti PH, Waché Y, Marty A, Mauersberger S, Smit MS, Nicaud JM. Hydrophobic substrate utilisation by the yeast , and its potential applications. FEMS Yeast Res 2005; 5:527-43. [PMID: 15780653 DOI: 10.1016/j.femsyr.2004.09.004] [Citation(s) in RCA: 395] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2004] [Revised: 09/27/2004] [Accepted: 09/30/2004] [Indexed: 10/26/2022] Open
Abstract
The alkane-assimilating yeast Yarrowia lipolytica degrades very efficiently hydrophobic substrates such as n-alkanes, fatty acids, fats and oils for which it has specific metabolic pathways. An overview of the oxidative degradation pathways for alkanes and triglycerides in Y. lipolytica is given, with new insights arising from the recent genome sequencing of this yeast. This includes the interaction of hydrophobic substrates with yeast cells, their uptake and transport, the primary alkane oxidation to the corresponding fatty alcohols and then by different enzymes to fatty acids, and the subsequent degradation in peroxisomal beta-oxidation or storage into lipid bodies. Several enzymes involved in hydrophobic substrate utilisation belong to multigene families, such as lipases/esterases (LIP genes), cytochromes P450 (ALK genes) and peroxisomal acyl-CoA oxidases (POX genes). Examples are presented demonstrating that wild-type and genetically engineered strains of Y. lipolytica can be used for alkane and fatty-acid bioconversion, such as aroma production, for production of SCP and SCO, for citric acid production, in bioremediation, in fine chemistry, for steroid biotransformation, and in food industry. These examples demonstrate distinct advantages of Y. lipolytica for their use in bioconversion reactions of biotechnologically interesting hydrophobic substrates.
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Affiliation(s)
- P Fickers
- Centre Wallon de Biologie Industrielle, Service de Technologie Microbienne, Université de Liège, Boulevard du Rectorat, Bâtiment 40, B-4000 Liège, Belgium
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Eirich LD, Craft DL, Steinberg L, Asif A, Eschenfeldt WH, Stols L, Donnelly MI, Wilson CR. Cloning and characterization of three fatty alcohol oxidase genes from Candida tropicalis strain ATCC 20336. Appl Environ Microbiol 2004; 70:4872-9. [PMID: 15294826 PMCID: PMC492379 DOI: 10.1128/aem.70.8.4872-4879.2004] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Candida tropicalis (ATCC 20336) converts fatty acids to long-chain dicarboxylic acids via a pathway that includes among other reactions the oxidation of omega-hydroxy fatty acids to omega-aldehydes by a fatty alcohol oxidase (FAO). Three FAO genes (one gene designated FAO1 and two putative allelic genes designated FAO2a and FAO2b), have been cloned and sequenced from this strain. A comparison of the DNA sequence homology and derived amino acid sequence homology between these three genes and previously published Candida FAO genes indicates that FAO1 and FAO2 are distinct genes. Both genes were individually cloned and expressed in Escherichia coli. The substrate specificity and K(m) values for the recombinant FAO1 and FAO2 were significantly different. Particularly striking is the fact that FAO1 oxidizes omega-hydroxy fatty acids but not 2-alkanols, whereas FAO2 oxidizes 2-alkanols but not omega-hydroxy fatty acids. Analysis of extracts of strain H5343 during growth on fatty acids indicated that only FAO1 was highly induced under these conditions. FAO2 contains one CTG codon, which codes for serine (amino acid 177) in C. tropicalis but codes for leucine in E. coli. An FAO2a construct, with a TCG codon (codes for serine in E. coli) substituted for the CTG codon, was prepared and expressed in E. coli. Neither the substrate specificity nor the K(m) values for the FAO2a variant with a serine at position 177 were radically different from those of the variant with a leucine at that position.
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Affiliation(s)
- L Dudley Eirich
- Cognis Corporation, Research and Technology, Building 53, 4900 Este Ave., Cincinnati, OH 45232, USA.
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Cheng Q, Liu HT, Bombelli P, Smith A, Slabas AR. Functional identification of AtFao3, a membrane bound long chain alcohol oxidase inArabidopsis thaliana. FEBS Lett 2004; 574:62-8. [PMID: 15358540 DOI: 10.1016/j.febslet.2004.07.086] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2004] [Accepted: 07/23/2004] [Indexed: 12/01/2022]
Abstract
The Arabidopsis thalina genome database was searched for homologues of the Candida cloacae fao1 gene which encodes a membrane bound, flavin-containing, hydrogen peroxide generating, long chain alcohol oxidase. This gene has not been isolated from plants or animals. Four putative candidates were found in the database but their function has not been proven. The cDNAs for two of them were cloned by RT-PCR from Arabidopis suspension culture and one of them [AtFAO3] was overexpressed in Escherichia coli and shown to functionally express long chain alcohol oxidase activity. The protein has been solubilised and retains biological activity thereby preparing the way for crystallographic studies. This is the first functional proof identifying a long chain alcohol oxidase in higher plants.
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Affiliation(s)
- Qi Cheng
- Department of Biological Sciences, University of Durham, South Road, Durham DH1 3LE, UK
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Graham IA, Eastmond PJ. Pathways of straight and branched chain fatty acid catabolism in higher plants. Prog Lipid Res 2002; 41:156-81. [PMID: 11755682 DOI: 10.1016/s0163-7827(01)00022-4] [Citation(s) in RCA: 191] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Significant advances in our knowledge of fatty acid breakdown in plants have been made since the subject was last comprehensively reviewed in the early 1990s. Many of the genes encoding the enzymes of peroxisomal beta-oxidation of straight chain fatty acids have now been identified. Biochemical genetic approaches in the model plant, Arabidopsis thaliana, have been particularly useful not only in the identification and functional characterisation of genes involved in fatty acid beta-oxidation but also in establishing the role of beta-oxidation at different stages in plant development. Advances in our understanding of branched chain amino acid catabolism have provided convincing evidence that mitochondria play an important role in this process. This work is discussed in the context of the long running debate on the sub-cellular localisation of fatty acid beta-oxidation in plants. A significant aspect of this review is that it provides the opportunity to present a comprehensive analysis of the complete Arabidopsis genome sequence for each of the different gene families that are known to be involved in beta-, alpha-, and omega-oxidation of fatty acids in plants. Inevitably, this increase in information, as well as providing many answers also raises many new intriguing questions, particularly as regards the regulation and physiological role of fatty acid catabolism throughout the higher plant life cycle.
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Affiliation(s)
- Ian A Graham
- Centre for Novel Agricultural Products, Department of Biology, University of York, Heslington, YO10 5DD, York, UK.
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Current awareness on comparative and functional genomics. Yeast 2000; 17:255-62. [PMID: 11025539 PMCID: PMC2448367 DOI: 10.1002/1097-0061(20000930)17:3<255::aid-yea9>3.0.co;2-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
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