201
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Kot AM, Błażejak S, Kurcz A, Gientka I, Kieliszek M. Rhodotorula glutinis-potential source of lipids, carotenoids, and enzymes for use in industries. Appl Microbiol Biotechnol 2016; 100:6103-6117. [PMID: 27209039 PMCID: PMC4916194 DOI: 10.1007/s00253-016-7611-8] [Citation(s) in RCA: 93] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2016] [Revised: 04/29/2016] [Accepted: 05/02/2016] [Indexed: 11/23/2022]
Abstract
Rhodotorula glutinis is capable of synthesizing numerous valuable compounds with a wide industrial usage. Biomass of this yeast constitutes sources of microbiological oils, and the whole pool of fatty acids is dominated by oleic, linoleic, and palmitic acid. Due to its composition, the lipids may be useful as a source for the production of the so-called third-generation biodiesel. These yeasts are also capable of synthesizing carotenoids such as β-carotene, torulene, and torularhodin. Due to their health-promoting characteristics, carotenoids are commonly used in the cosmetic, pharmaceutical, and food industries. They are also used as additives in fodders for livestock, fish, and crustaceans. A significant characteristic of R. glutinis is its capability to produce numerous enzymes, in particular, phenylalanine ammonia lyase (PAL). This enzyme is used in the food industry in the production of l-phenylalanine that constitutes the substrate for the synthesis of aspartame—a sweetener commonly used in the food industry.
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Affiliation(s)
- Anna M Kot
- Department of Biotechnology, Microbiology and Food Evaluation, Faculty of Food Sciences, Warsaw University of Life Sciences, Nowoursynowska 159C, 02-776, Warsaw, Poland.
| | - Stanisław Błażejak
- Department of Biotechnology, Microbiology and Food Evaluation, Faculty of Food Sciences, Warsaw University of Life Sciences, Nowoursynowska 159C, 02-776, Warsaw, Poland
| | - Agnieszka Kurcz
- Department of Biotechnology, Microbiology and Food Evaluation, Faculty of Food Sciences, Warsaw University of Life Sciences, Nowoursynowska 159C, 02-776, Warsaw, Poland
| | - Iwona Gientka
- Department of Biotechnology, Microbiology and Food Evaluation, Faculty of Food Sciences, Warsaw University of Life Sciences, Nowoursynowska 159C, 02-776, Warsaw, Poland
| | - Marek Kieliszek
- Department of Biotechnology, Microbiology and Food Evaluation, Faculty of Food Sciences, Warsaw University of Life Sciences, Nowoursynowska 159C, 02-776, Warsaw, Poland
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202
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Yang X, Chen G, Du H, Miao M, Feng B. Behavior of Yarrowia lipolytica Lipase Lip2 under high hydrostatic pressure: Conformational changes and isokineticity diagram. ACTA ACUST UNITED AC 2016. [DOI: 10.1016/j.molcatb.2016.02.011] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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203
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Iwama R, Kobayashi S, Ishimaru C, Ohta A, Horiuchi H, Fukuda R. Functional roles and substrate specificities of twelve cytochromes P450 belonging to CYP52 family in n-alkane assimilating yeast Yarrowia lipolytica. Fungal Genet Biol 2016; 91:43-54. [PMID: 27039152 DOI: 10.1016/j.fgb.2016.03.007] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2015] [Revised: 03/16/2016] [Accepted: 03/29/2016] [Indexed: 11/26/2022]
Abstract
Yarrowia lipolytica possesses twelve ALK genes, which encode cytochromes P450 in the CYP52 family. In this study, using a Y. lipolytica strain from which all twelve ALK genes had been deleted, strains individually expressing each of the ALK genes were constructed and their roles and substrate specificities were determined by observing their growth on n-alkanes and analyzing fatty acid metabolism. The results suggested that the twelve Alk proteins can be categorized into four groups based on their substrate specificity: Alk1p, Alk2p, Alk9p, and Alk10p, which have significant activities to hydroxylate n-alkanes; Alk4p, Alk5p, and Alk7p, which have significant activities to hydroxylate the ω-terminal end of dodecanoic acid; Alk3p and Alk6p, which have significant activities to hydroxylate both n-alkanes and dodecanoic acid; and Alk8p, Alk11p, and Alk12p, which showed faint or no activities to oxidize these substrates. The involvement of Alk proteins in the oxidation of fatty alcohols and fatty aldehydes was also analyzed by measuring viability of the mutant deleted for twelve ALK genes in medium containing dodecanol and by observing growth on dodecanal of a mutant strain, in which twelve ALK genes were deleted along with four fatty aldehyde dehydrogenase genes. It was suggested that ALK gene(s) is/are involved in the detoxification of dodecanol and the assimilation of dodecanal. These results imply that genes encoding CYP52-family P450s have undergone multiplication and diversification in Y. lipolytica for assimilation of various hydrophobic compounds.
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Affiliation(s)
- Ryo Iwama
- Department of Biotechnology, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Satoshi Kobayashi
- Department of Biotechnology, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Chiaki Ishimaru
- Department of Biotechnology, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Akinori Ohta
- Department of Biological Chemistry, College of Bioscience and Biotechnology, Chubu University, 1200 Matsumoto-cho, Kasugai, Aichi 487-8501, Japan
| | - Hiroyuki Horiuchi
- Department of Biotechnology, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Ryouichi Fukuda
- Department of Biotechnology, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo 113-8657, Japan.
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204
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Shabbir Hussain M, Gambill L, Smith S, Blenner MA. Engineering Promoter Architecture in Oleaginous Yeast Yarrowia lipolytica. ACS Synth Biol 2016; 5:213-23. [PMID: 26635071 DOI: 10.1021/acssynbio.5b00100] [Citation(s) in RCA: 67] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Eukaryotic promoters have a complex architecture to control both the strength and timing of gene transcription spanning up to thousands of bases from the initiation site. This complexity makes rational fine-tuning of promoters in fungi difficult to predict; however, this very same complexity enables multiple possible strategies for engineering promoter strength. Here, we studied promoter architecture in the oleaginous yeast, Yarrowia lipolytica. While recent studies have focused on upstream activating sequences, we systematically examined various components common in fungal promoters. Here, we examine several promoter components including upstream activating sequences, proximal promoter sequences, core promoters, and the TATA box in autonomously replicating expression plasmids and integrated into the genome. Our findings show that promoter strength can be fine-tuned through the engineering of the TATA box sequence, core promoter, and upstream activating sequences. Additionally, we identified a previously unreported oleic acid responsive transcription enhancement in the XPR2 upstream activating sequences, which illustrates the complexity of fungal promoters. The promoters engineered here provide new genetic tools for metabolic engineering in Y. lipolytica and provide promoter engineering strategies that may be useful in engineering other non-model fungal systems.
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Affiliation(s)
- Murtaza Shabbir Hussain
- Department of Chemical and Biomolecular Engineering and ‡Department of Genetics and Biochemistry, Clemson University, Clemson, South Carolina 29634, United States
| | - Lauren Gambill
- Department of Chemical and Biomolecular Engineering and ‡Department of Genetics and Biochemistry, Clemson University, Clemson, South Carolina 29634, United States
| | - Spencer Smith
- Department of Chemical and Biomolecular Engineering and ‡Department of Genetics and Biochemistry, Clemson University, Clemson, South Carolina 29634, United States
| | - Mark A. Blenner
- Department of Chemical and Biomolecular Engineering and ‡Department of Genetics and Biochemistry, Clemson University, Clemson, South Carolina 29634, United States
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205
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Silverman AM, Qiao K, Xu P, Stephanopoulos G. Functional overexpression and characterization of lipogenesis-related genes in the oleaginous yeast Yarrowia lipolytica. Appl Microbiol Biotechnol 2016; 100:3781-98. [DOI: 10.1007/s00253-016-7376-0] [Citation(s) in RCA: 74] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2015] [Revised: 01/14/2016] [Accepted: 02/02/2016] [Indexed: 11/24/2022]
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206
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Vorapreeda T, Thammarongtham C, Cheevadhanarak S, Laoteng K. Genome mining of fungal lipid-degrading enzymes for industrial applications. MICROBIOLOGY-SGM 2016; 161:1613-1626. [PMID: 26271808 DOI: 10.1099/mic.0.000127] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Lipases are interesting enzymes, which contribute important roles in maintaining lipid homeostasis and cellular metabolisms. Using available genome data, seven lipase families of oleaginous and non-oleaginous yeast and fungi were categorized based on the similarity of their amino acid sequences and conserved structural domains. Of them, triacylglycerol lipase (patatin-domain-containing protein) and steryl ester hydrolase (abhydro_lipase-domain-containing protein) families were ubiquitous enzymes found in all species studied. The two essential lipases rendered signature characteristics of integral membrane proteins that might be targeted to lipid monolayer particles. At least one of the extracellular lipase families existed in each species of yeast and fungi. We found that the diversity of lipase families and the number of genes in individual families of oleaginous strains were greater than those identified in non-oleaginous species, which might play a role in nutrient acquisition from surrounding hydrophobic substrates and attribute to their obese phenotype. The gene/enzyme catalogue and relevant informative data of the lipases provided by this study are not only valuable toolboxes for investigation of the biological role of these lipases, but also convey potential in various industrial applications.
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Affiliation(s)
- Tayvich Vorapreeda
- Biochemical Engineering and Pilot Plant Research and Development Laboratory, National Center for Genetic Engineering and Biotechnology (BIOTEC) at King Mongkut's University of Technology Thonburi, Bangkhuntien, Bangkok 10150, Thailand
| | - Chinae Thammarongtham
- Biochemical Engineering and Pilot Plant Research and Development Laboratory, National Center for Genetic Engineering and Biotechnology (BIOTEC) at King Mongkut's University of Technology Thonburi, Bangkhuntien, Bangkok 10150, Thailand
| | - Supapon Cheevadhanarak
- School of Bioresources and Technology, King Mongkut's University of Technology Thonburi, Bangkhuntien, Bangkok 10150, Thailand.,Pilot Plant Development and Training Institute, King Mongkut's University of Technology Thonburi, Bangkhuntien, Bangkok 10150, Thailand
| | - Kobkul Laoteng
- Bioprocess Technology Laboratory, Bioresources Technology Unit, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Thailand Science Park, Pathum Thani 12120, Thailand
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207
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Asfaram A, Ghaedi M, Ghezelbash GR, Dil EA, Tyagi I, Agarwal S, Gupta VK. Biosorption of malachite green by novel biosorbent Yarrowia lipolytica isf7: Application of response surface methodology. J Mol Liq 2016. [DOI: 10.1016/j.molliq.2015.12.075] [Citation(s) in RCA: 70] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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208
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Kang WR, Seo MJ, An JU, Shin KC, Oh DK. Production of δ-decalactone from linoleic acid via 13-hydroxy-9(Z)-octadecenoic acid intermediate by one-pot reaction using linoleate 13-hydratase and whole Yarrowia lipolytica cells. Biotechnol Lett 2016; 38:817-23. [PMID: 26758723 DOI: 10.1007/s10529-016-2041-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2015] [Accepted: 01/06/2016] [Indexed: 11/28/2022]
Abstract
OBJECTIVE To produce δ-decalactone from linoleic acid by one-pot reaction using linoleate 13-hydratase with supplementation with whole Yarrowia lipolytica cells. RESULTS Whole Y. lipolytica cells at 25 g l(-1) produced1.9 g l(-1) δ-decalactone from 7.5 g 13-hydroxy-9(Z)-octadecenoic acid l(-1) at pH 7.5 and 30 °C for 21 h. Linoleate 13-hydratase from Lactobacillus acidophilus at 3.5 g l(-1) with supplementation with 25 g Y. lipolytica cells l(-1) in one pot at 3 h produced 1.9 g l(-1) δ-decalactone from 10 g linoleic acid l(-1) via 13-hydroxy-9(Z)-octadecenoic acid intermediate at pH 7.5 and 30°C after 18 h, with a molar conversion yield of 31 % and productivity of 106 mg l(-1) h(-1). CONCLUSION To the best of our knowledge, this is the first production of δ-decalactone using unsaturated fatty acid.
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Affiliation(s)
- Woo-Ri Kang
- Department of Bioscience and Biotechnology, Konkuk University, 1 Hwayang-dong, Gwangjin-gu, Seoul, 143-701, Republic of Korea
| | - Min-Ju Seo
- Department of Bioscience and Biotechnology, Konkuk University, 1 Hwayang-dong, Gwangjin-gu, Seoul, 143-701, Republic of Korea
| | - Jung-Ung An
- Department of Bioscience and Biotechnology, Konkuk University, 1 Hwayang-dong, Gwangjin-gu, Seoul, 143-701, Republic of Korea
| | - Kyung-Chul Shin
- Department of Bioscience and Biotechnology, Konkuk University, 1 Hwayang-dong, Gwangjin-gu, Seoul, 143-701, Republic of Korea
| | - Deok-Kun Oh
- Department of Bioscience and Biotechnology, Konkuk University, 1 Hwayang-dong, Gwangjin-gu, Seoul, 143-701, Republic of Korea.
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209
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Engineering Yarrowia lipolytica for Campesterol Overproduction. PLoS One 2016; 11:e0146773. [PMID: 26751680 PMCID: PMC4709189 DOI: 10.1371/journal.pone.0146773] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2015] [Accepted: 12/22/2015] [Indexed: 11/22/2022] Open
Abstract
Campesterol is an important precursor for many sterol drugs, e.g. progesterone and hydrocortisone. In order to produce campesterol in Yarrowia lipolytica, C-22 desaturase encoding gene ERG5 was disrupted and the heterologous 7-dehydrocholesterol reductase (DHCR7) encoding gene was constitutively expressed. The codon-optimized DHCR7 from Rallus norvegicus, Oryza saliva and Xenapus laevis were explored and the strain with the gene DHCR7 from X. laevis achieved the highest titer of campesterol due to D409 in substrate binding sites. In presence of glucose as the carbon source, higher biomass conversion yield and product yield were achieved in shake flask compared to that using glycerol and sunflower seed oil. Nevertheless, better cell growth rate was observed in medium with sunflower seed oil as the sole carbon source. Through high cell density fed-batch fermentation under carbon source restriction strategy, a titer of 453±24.7 mg/L campesterol was achieved with sunflower seed oil as the carbon source, which is the highest reported microbial titer known. Our study has greatly enhanced campesterol accumulation in Y. lipolytica, providing new insight into producing complex and desired molecules in microbes.
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210
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Liu HH, Ji XJ, Huang H. Biotechnological applications of Yarrowia lipolytica: Past, present and future. Biotechnol Adv 2015; 33:1522-46. [DOI: 10.1016/j.biotechadv.2015.07.010] [Citation(s) in RCA: 128] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2014] [Revised: 07/13/2015] [Accepted: 07/29/2015] [Indexed: 01/01/2023]
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211
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Lee JJ, Chen L, Cao B, Chen WN. Engineering Rhodosporidium toruloides with a membrane transporter facilitates production and separation of carotenoids and lipids in a bi-phasic culture. Appl Microbiol Biotechnol 2015; 100:869-77. [DOI: 10.1007/s00253-015-7102-3] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2015] [Revised: 09/18/2015] [Accepted: 10/15/2015] [Indexed: 01/29/2023]
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212
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Efficient synthesis of (R)-2-chloro-1-phenylethol using a yeast carbonyl reductase with broad substrate spectrum and 2-propanol as cosubstrate. Biochem Eng J 2015. [DOI: 10.1016/j.bej.2015.08.009] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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213
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Li W, Shen H, Ma M, Liu L, Cui C, Chen B, Fan D, Tan T. Synthesis of ethyl oleate by esterification in a solvent-free system using lipase immobilized on PDMS-modified nonwoven viscose fabrics. Process Biochem 2015. [DOI: 10.1016/j.procbio.2015.07.012] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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214
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Optimization of lipid production with a genome-scale model of Yarrowia lipolytica. BMC SYSTEMS BIOLOGY 2015; 9:72. [PMID: 26503450 PMCID: PMC4623914 DOI: 10.1186/s12918-015-0217-4] [Citation(s) in RCA: 77] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/15/2015] [Accepted: 10/07/2015] [Indexed: 12/19/2022]
Abstract
Background Yarrowia lipolytica is a non-conventional yeast that is extensively investigated for its ability to excrete citrate or to accumulate large amounts of storage lipids, which is of great significance for single cell oil production. Both traits are thus of interest for basic research as well as for biotechnological applications but they typically occur simultaneously thus lowering the respective yields. Therefore, engineering of strains with high lipid content relies on novel concepts such as computational simulation to better understand the two competing processes and to eliminate citrate excretion. Results Using a genome-scale model (GSM) of baker's yeast as a scaffold, we reconstructed the metabolic network of Y. lipolytica and optimized it for use in flux balance analysis (FBA), with the aim to simulate growth and lipid production phases of this yeast. We validated our model and found the predictions of the growth behavior of Y. lipolytica in excellent agreement with experimental data. Based on these data, we successfully designed a fed-batch strategy to avoid citrate excretion during the lipid production phase. Further analysis of the network suggested that the oxygen demand of Y. lipolytica is reduced upon induction of lipid synthesis. According to this finding we hypothesized that a reduced aeration rate might induce lipid accumulation. This prediction was indeed confirmed experimentally. In a fermentation combining these two strategies lipid content of the biomass was increased by 80 %, and lipid yield was improved more than four-fold, compared to standard conditions. Conclusions Genome scale network reconstructions provide a powerful tool to predict the effects of genetic modifications and the metabolic response to environmental conditions. The high accuracy and the predictive value of a newly reconstructed GSM of Y. lipolytica to optimize growth conditions for lipid accumulation are demonstrated. Based on these findings, further strategies for engineering Y. lipolytica towards higher efficiency in single cell oil production are discussed. Electronic supplementary material The online version of this article (doi:10.1186/s12918-015-0217-4) contains supplementary material, which is available to authorized users.
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215
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Chen CY, Huang YC, Yang TY, Jian JY, Chen WL, Yang CH. Degradation of konjac glucomannan by Thermobifida fusca thermostable β-mannanase from yeast transformant. Int J Biol Macromol 2015; 82:1-6. [PMID: 26476245 DOI: 10.1016/j.ijbiomac.2015.10.008] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2015] [Revised: 10/01/2015] [Accepted: 10/03/2015] [Indexed: 11/19/2022]
Abstract
Native konjac glucomannan was used as the substrate for thermophilic actinomycetes, Thermobifida fusca BCRC19214, to produce β-mannanase. The β-mannanase was purified and five internal amino acid sequences were determined by LC-MS/MS. These sequences had high homology with the β-mannanase from T. fusca YX. The tfm gene which encoded the β-mannanase was cloned, sequenced and heterologous expressed in Yarrowia lipolytica P01 g expression system. Recombinant heterologous expression resulted in extracellular β-mannanase production at levels as high as 3.16 U/ml in the culture broth within 48 h cultivation. The recombinant β-mannanase from Y. lipolytica transformant had superior thermal property. The optimal temperature of the recombinant β-mannanase from Y. lipolytica transformant (pYLSC1-tfm) was 80°C. When native konjac glucomannan was incubated with the recombinant β-mannanase from Y. lipolytica transformant (pYLSC1-tfm) at 50°C, there was a fast decrease of viscosity happen during the initial phase of reaction. This viscosity reduction was accompanied by an increase of reducing sugars. The surface of konjac glucomannan film became smooth. After 24h of treatment, the DPw of native konjac glucomannan decreased from 6,435,139 to 3089.
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Affiliation(s)
- Cheng-Yu Chen
- Department of Cosmetic Science, Providence University, Taichung 43301, Taiwan; Graduate Institute of Biotechnology, National Chung Hsing University, Taichung 40227, Taiwan
| | - Yu-Chun Huang
- Department of Cosmetic Science, Providence University, Taichung 43301, Taiwan
| | - Ting-Ya Yang
- Department of Cosmetic Science, Providence University, Taichung 43301, Taiwan
| | - Jhen-Yi Jian
- Department of Cosmetic Science, Providence University, Taichung 43301, Taiwan
| | - Wei-Lin Chen
- Department of Cosmetic Science, Providence University, Taichung 43301, Taiwan; Department of Applied Chemistry, Providence University, Taichung 43301, Taiwan
| | - Chao-Hsun Yang
- Department of Cosmetic Science, Providence University, Taichung 43301, Taiwan; Department of Applied Chemistry, Providence University, Taichung 43301, Taiwan.
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216
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Kobayashi S, Tezaki S, Horiuchi H, Fukuda R, Ohta A. Acidic phospholipid-independent interaction of Yas3p, an Opi1-family transcriptional repressor ofYarrowia lipolytica, with the endoplasmic reticulum. Yeast 2015; 32:691-701. [DOI: 10.1002/yea.3096] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2015] [Revised: 07/31/2015] [Accepted: 08/05/2015] [Indexed: 11/08/2022] Open
Affiliation(s)
| | - Satoshi Tezaki
- Department of Biotechnology; The University of Tokyo; Japan
| | | | | | - Akinori Ohta
- Department of Biotechnology; The University of Tokyo; Japan
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217
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Gopalakrishnan S, Maranas CD. Achieving Metabolic Flux Analysis for S. cerevisiae at a Genome-Scale: Challenges, Requirements, and Considerations. Metabolites 2015; 5:521-35. [PMID: 26393660 PMCID: PMC4588810 DOI: 10.3390/metabo5030521] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2015] [Accepted: 09/04/2015] [Indexed: 12/11/2022] Open
Abstract
Recent advances in 13C-Metabolic flux analysis (13C-MFA) have increased its capability to accurately resolve fluxes using a genome-scale model with narrow confidence intervals without pre-judging the activity or inactivity of alternate metabolic pathways. However, the necessary precautions, computational challenges, and minimum data requirements for successful analysis remain poorly established. This review aims to establish the necessary guidelines for performing 13C-MFA at the genome-scale for a compartmentalized eukaryotic system such as yeast in terms of model and data requirements, while addressing key issues such as statistical analysis and network complexity. We describe the various approaches used to simplify the genome-scale model in the absence of sufficient experimental flux measurements, the availability and generation of reaction atom mapping information, and the experimental flux and metabolite labeling distribution measurements to ensure statistical validity of the obtained flux distribution. Organism-specific challenges such as the impact of compartmentalization of metabolism, variability of biomass composition, and the cell-cycle dependence of metabolism are discussed. Identification of errors arising from incorrect gene annotation and suggested alternate routes using MFA are also highlighted.
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Affiliation(s)
- Saratram Gopalakrishnan
- Department of Chemical Engineering, The Pennsylvania State University, University Park, PA, USA.
| | - Costas D Maranas
- Department of Chemical Engineering, The Pennsylvania State University, University Park, PA, USA.
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218
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Fan Y, Ortiz-Urquiza A, Garrett T, Pei Y, Keyhani NO. Involvement of a caleosin in lipid storage, spore dispersal, and virulence in the entomopathogenic filamentous fungus,Beauveria bassiana. Environ Microbiol 2015; 17:4600-14. [DOI: 10.1111/1462-2920.12990] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2015] [Accepted: 07/14/2015] [Indexed: 12/18/2022]
Affiliation(s)
- Yanhua Fan
- Biotechnology Research Center; Southwest University; Chongqing Beibei China
- Department of Microbiology and Cell Science; Institute of Food and Agricultural Sciences; University of Florida; Gainesville FL 32611 USA
| | - Almudena Ortiz-Urquiza
- Department of Microbiology and Cell Science; Institute of Food and Agricultural Sciences; University of Florida; Gainesville FL 32611 USA
| | - Timothy Garrett
- Department of Pathology, Immunology, and Laboratory Medicine; College of Medicine; University of Florida; Gainesville FL 32610 USA
| | - Yan Pei
- Biotechnology Research Center; Southwest University; Chongqing Beibei China
| | - Nemat O. Keyhani
- Department of Microbiology and Cell Science; Institute of Food and Agricultural Sciences; University of Florida; Gainesville FL 32611 USA
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219
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Zhao C, Gu D, Nambou K, Wei L, Chen J, Imanaka T, Hua Q. Metabolome analysis and pathway abundance profiling of Yarrowia lipolytica cultivated on different carbon sources. J Biotechnol 2015; 206:42-51. [DOI: 10.1016/j.jbiotec.2015.04.005] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2014] [Revised: 04/02/2015] [Accepted: 04/08/2015] [Indexed: 10/23/2022]
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220
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Tenagy, Park JS, Iwama R, Kobayashi S, Ohta A, Horiuchi H, Fukuda R. Involvement of acyl-CoA synthetase genes in n-alkane assimilation and fatty acid utilization in yeast Yarrowia lipolytica. FEMS Yeast Res 2015; 15:fov031. [PMID: 26019148 DOI: 10.1093/femsyr/fov031] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/21/2015] [Indexed: 01/19/2023] Open
Abstract
Here, we investigated the roles of YAL1 (FAA1) and FAT1 encoding acyl-CoA synthetases (ACSs) and three additional orthologs of ACS genes FAT2-FAT4 of the yeast Yarrowia lipolytica in the assimilation or utilization of n-alkanes and fatty acids. ACS deletion mutants were generated to characterize their function. The FAT1 deletion mutant exhibited decreased growth on n-alkanes of 10-18 carbons, whereas the FAA1 mutant showed growth reduction on n-alkane of 16 carbons. However, FAT2-FAT4 deletion mutants did not show any growth defects, suggesting that FAT1 and FAA1 are involved in the activation of fatty acids produced during the metabolism of n-alkanes. In contrast, deletions of FAA1 and FAT1-FAT4 conferred no defect in growth on fatty acids. The wild-type strain grew in the presence of cerulenin, an inhibitor of fatty acid synthesis, by utilizing exogenously added fatty acid or fatty acid derived from n-alkane when oleic acid or n-alkane of 18 carbons was supplemented. However, the FAA1 deletion mutant did not grow, indicating a critical role for FAA1 in the utilization of fatty acids. Fluorescent microscopic observation and biochemical analyses suggested that Fat1p is present in the peroxisome and Faa1p is localized in the cytosol and to membranes.
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Affiliation(s)
- Tenagy
- Department of Biotechnology, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Jun Seok Park
- Department of Biotechnology, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Ryo Iwama
- Department of Biotechnology, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Satoshi Kobayashi
- Department of Biotechnology, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Akinori Ohta
- Department of Biological Chemistry, College of Bioscience and Biotechnology, Chubu University, 1200 Matsumoto-cho, Kasugai, Aichi 487-8501, Japan
| | - Hiroyuki Horiuchi
- Department of Biotechnology, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Ryouichi Fukuda
- Department of Biotechnology, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo 113-8657, Japan
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Sekova VY, Isakova EP, Deryabina YI. Biotechnological applications of the extremophilic yeast Yarrowia lipolytica (review). APPL BIOCHEM MICRO+ 2015. [DOI: 10.1134/s0003683815030151] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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222
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New biofuel alternatives: integrating waste management and single cell oil production. Int J Mol Sci 2015; 16:9385-405. [PMID: 25918941 PMCID: PMC4463594 DOI: 10.3390/ijms16059385] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2015] [Revised: 02/26/2015] [Accepted: 04/14/2015] [Indexed: 11/29/2022] Open
Abstract
Concerns about greenhouse gas emissions have increased research efforts into alternatives in bio-based processes. With regard to transport fuel, bioethanol and biodiesel are still the main biofuels used. It is expected that future production of these biofuels will be based on processes using either non-food competing biomasses, or characterised by low CO2 emissions. Many microorganisms, such as microalgae, yeast, bacteria and fungi, have the ability to accumulate oils under special culture conditions. Microbial oils might become one of the potential feed-stocks for biodiesel production in the near future. The use of these oils is currently under extensive research in order to reduce production costs associated with the fermentation process, which is a crucial factor to increase economic feasibility. An important way to reduce processing costs is the use of wastes as carbon sources. The aim of the present review is to describe the main aspects related to the use of different oleaginous microorganisms for lipid production and their performance when using bio-wastes. The possibilities for combining hydrogen (H2) and lipid production are also explored in an attempt for improving the economic feasibility of the process.
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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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224
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Guo H, Liu P, Madzak C, Du G, Zhou J, Chen J. Identification and application of keto acids transporters in Yarrowia lipolytica. Sci Rep 2015; 5:8138. [PMID: 25633653 PMCID: PMC4311248 DOI: 10.1038/srep08138] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2014] [Accepted: 01/08/2015] [Indexed: 01/18/2023] Open
Abstract
Production of organic acids by microorganisms is of great importance for obtaining building-block chemicals from sustainable biomass. Extracellular accumulation of organic acids involved a series of transporters, which play important roles in the accumulation of specific organic acid while lack of systematic demonstration in eukaryotic microorganisms. To circumvent accumulation of by-product, efforts have being orchestrated to carboxylate transport mechanism for potential clue in Yarrowia lipolytica WSH-Z06. Six endogenous putative transporter genes, YALI0B19470g, YALI0C15488g, YALI0C21406g, YALI0D24607g, YALI0D20108g and YALI0E32901g, were identified. Transport characteristics and substrate specificities were further investigated using a carboxylate-transport-deficient Saccharomyces cerevisiae strain. These transporters were expressed in Y. lipolytica WSH-Z06 to assess their roles in regulating extracellular keto acids accumulation. In a Y. lipolytica T1 line over expressing YALI0B19470g, α-ketoglutarate accumulated to 46.7 g·L−1, whereas the concentration of pyruvate decreased to 12.3 g·L−1. Systematic identification of these keto acids transporters would provide clues to further improve the accumulation of specific organic acids with higher efficiency in eukaryotic microorganisms.
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Affiliation(s)
- Hongwei Guo
- 1] School of Biotechnology and Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China [2] Synergetic Innovation Center of Food Safety and Nutrition, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Peiran Liu
- School of Biotechnology and Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Catherine Madzak
- UMR1238 Microbiologie et Génétique Moléculaire, INRA/CNRS/AgroPan's Tech, CBAI, BP 01, 78850 Thiverval-Grignon, France
| | - Guocheng Du
- 1] School of Biotechnology and Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China [2] Synergetic Innovation Center of Food Safety and Nutrition, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Jingwen Zhou
- 1] School of Biotechnology and Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China [2] Synergetic Innovation Center of Food Safety and Nutrition, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Jian Chen
- 1] School of Biotechnology and Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China [2] Synergetic Innovation Center of Food Safety and Nutrition, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
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225
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Lane S, Zhang S, Wei N, Rao C, Jin YS. Development and physiological characterization of cellobiose-consuming Yarrowia lipolytica. Biotechnol Bioeng 2015; 112:1012-22. [PMID: 25421388 DOI: 10.1002/bit.25499] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2014] [Revised: 10/20/2014] [Accepted: 11/17/2014] [Indexed: 12/19/2022]
Abstract
Yarrowia lipolytica is a promising production host for a wide range of molecules, but limited sugar consumption abilities prevent utilization of an abundant source of renewable feedstocks. In this study we created a Y. lipolytica strain capable of utilizing cellobiose as a sole carbon source by using endogenous promoters to express the cellodextrin transporter cdt-1 and intracellular β-glucosidase gh1-1 from Neurospora crassa. The engineered strain was also capable of simultaneous co-consumption of glucose and cellobiose. Although cellobiose was consumed slower than glucose when engineered strains were cultured with excess nitrogen, culturing with limited nitrogen led to cellobiose consumption rates comparable to those of glucose. Under limited nitrogen conditions, the engineered strain produced citric acid as a major product and we observed greater citric acid yields from cellobiose (0.37 g/g) than glucose (0.28 g/g). Culturing with a sole carbon source of either glucose or cellobiose induced additional differences on cell physiology and metabolism and a link is suggested to evasion of glucose-sensing mechanisms through intracellular creation and consumption of glucose. We ultimately applied this cellobiose-utilization system to produce citric acid from bioconversion of crystalline cellulose through simultaneous saccharification and fermentation (SSF).
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Affiliation(s)
- Stephan Lane
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, 61801; Energy Biosciences Institute, University of Illinois at Urbana-Champaign, Urbana, Illinios, 61801; Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, Illinois, 61801
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Li M, Yu X, Wang F, Zhai C, Shen W, Yu X, Wang X, Ma L. Secretory expression of organophosphorus hydrolase OPHC2 in Yarrowia lipolytica Polg. JOURNAL OF ENVIRONMENTAL SCIENCE AND HEALTH. PART. B, PESTICIDES, FOOD CONTAMINANTS, AND AGRICULTURAL WASTES 2015; 50:691-697. [PMID: 26273753 DOI: 10.1080/03601234.2015.1048101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
In the present study, recombinant organophosphorus hydrolase OPHC2 was successfully produced by Yarrowia lipolytica and purified. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) and western blot analyses showed a major polypeptide band of 36 kDa. The purified enzyme was optimally active at 65°C and pH 8.5 and also displayed good thermal and pH stability using methyl parathion (O,O-dimethyl-O-4-p-nitrophenyl phosphorothioate) as a substrate. Moreover, as Y. lipolytica is a non-pathogenic, generally regarded as safe (GRAS) yeast, the cell culture supernatant can be used directly on vegetables and fruits that are contaminated by organophosphorus pesticides.
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Affiliation(s)
- Meng Li
- a Hubei Collaborative Innovation Center for Green Transformation of Bio-resources, Hubei Key Laboratory of Industrial Biotechnology, College of Life Sciences, Hubei University , Wuhan , Hubei Province , P. R. China
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227
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Miranda AF, Taha M, Wrede D, Morrison P, Ball AS, Stevenson T, Mouradov A. Lipid production in association of filamentous fungi with genetically modified cyanobacterial cells. BIOTECHNOLOGY FOR BIOFUELS 2015; 8:179. [PMID: 26550031 PMCID: PMC4635583 DOI: 10.1186/s13068-015-0364-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2015] [Accepted: 10/22/2015] [Indexed: 05/22/2023]
Abstract
BACKGROUND Numerous strategies have evolved recently for the generation of genetically modified or synthetic microalgae and cyanobacteria designed for production of ethanol, biodiesel and other fuels. In spite of their obvious attractiveness there are still a number of challenges that can affect their economic viability: the high costs associated with (1) harvesting, which can account for up to 50 % of the total biofuel's cost, (2) nutrients supply and (3) oil extraction. Fungal-assisted bio-flocculation of microalgae is gaining increasing attention due to its high efficiency, no need for added chemicals and low energy inputs. The implementation of renewable alternative carbon, nitrogen and phosphorus sources from agricultural wastes and wastewaters for growing algae and fungi makes this strategy economically attractive. RESULTS This work demonstrates that the filamentous fungi, Aspergillus fumigatus can efficiently flocculate the unicellular cyanobacteria Synechocystis PCC 6803 and its genetically modified derivatives that have been altered to enable secretion of free fatty acids into growth media. Secreted free fatty acids are potentially used by fungal cells as a carbon source for growth and ex-novo production of lipids. For most of genetically modified strains the total lipid yields extracted from the fungal-cyanobacterial pellets were found to be higher than additive yields of lipids and total free fatty acids produced by fungal and Synechocystis components when grown in mono-cultures. The synergistic effect observed in fungal-Synechocystis associations was also found in bioremediation rates when animal husbandry wastewater was used an alternative source of nitrogen and phosphorus. CONCLUSION Fungal assisted flocculation can complement and assist in large scale biofuel production from wild-type and genetically modified Synechocystis PCC 6803 strains by (1) efficient harvesting of cyanobacterial cells and (2) producing of high yields of lipids accumulated in fungal-cyanobacterial pellets.
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Affiliation(s)
- Ana F. Miranda
- School of Applied Sciences, Royal Melbourne Institute of Technology University, Bundoora, VIC 3083 Australia
| | - Mohamed Taha
- School of Applied Sciences, Royal Melbourne Institute of Technology University, Bundoora, VIC 3083 Australia
| | - Digby Wrede
- School of Applied Sciences, Royal Melbourne Institute of Technology University, Bundoora, VIC 3083 Australia
| | - Paul Morrison
- School of Applied Sciences, Royal Melbourne Institute of Technology University, Bundoora, VIC 3083 Australia
| | - Andrew S. Ball
- School of Applied Sciences, Royal Melbourne Institute of Technology University, Bundoora, VIC 3083 Australia
| | - Trevor Stevenson
- School of Applied Sciences, Royal Melbourne Institute of Technology University, Bundoora, VIC 3083 Australia
| | - Aidyn Mouradov
- School of Applied Sciences, Royal Melbourne Institute of Technology University, Bundoora, VIC 3083 Australia
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228
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Guo Z, Duquesne S, Bozonnet S, Cioci G, Nicaud JM, Marty A, O’Donohue MJ. Development of cellobiose-degrading ability in Yarrowia lipolytica strain by overexpression of endogenous genes. BIOTECHNOLOGY FOR BIOFUELS 2015; 8:109. [PMID: 26244054 PMCID: PMC4524412 DOI: 10.1186/s13068-015-0289-9] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2015] [Accepted: 07/22/2015] [Indexed: 05/03/2023]
Abstract
BACKGROUND Yarrowia lipolytica, one of the most widely studied "nonconventional" oleaginous yeast species, is unable to grow on cellobiose. Engineering cellobiose-degrading ability into this yeast is a vital step towards the development of cellulolytic biocatalysts suitable for consolidated bioprocessing. RESULTS In the present work, we identified six genes encoding putative β-glucosidases in the Y. lipolytica genome. To study these, homologous expression was attempted in Y. lipolytica JMY1212 Zeta. Two strains overexpressing BGL1 (YALI0F16027g) and BGL2 (YALI0B14289g) produced β-glucosidase activity and were able to degrade cellobiose, while the other four did not display any detectable activity. The two active β-glucosidases, one of which was mainly cell-associated while the other was present in the extracellular medium, were purified and characterized. The two Bgls were most active at 40-45°C and pH 4.0-4.5, and exhibited hydrolytic activity on various β-glycoside substrates. Specifically, Bgl1 displayed 12.5-fold higher catalytic efficiency on cellobiose than Bgl2. Significantly, in experiments where cellobiose or cellulose (performed in the presence of a β-glucosidase-deficient commercial cellulase cocktail produced by Trichoderma reseei) was used as carbon source for aerobic cultivation, Y. lipolytica ∆pox co-expressing BGL1 and BGL2 grew better than the Y. lipolytica strains expressing single BGLs. The specific growth rate and biomass yield of Y. lipolytica JMY1212 co-expressing BGL1 and BGL2 were 0.15 h(-1) and 0.50 g-DCW/g-cellobiose, respectively, similar to that of the control grown on glucose. CONCLUSIONS We conclude that the bi-functional Y. lipolytica developed in the current study represents a vital step towards the creation of a cellulolytic yeast strain that can be used for lipid production from lignocellulosic biomass. When used in combination with commercial cellulolytic cocktails, this strain will no doubt reduce enzyme requirements and thus costs.
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Affiliation(s)
- Zhongpeng Guo
- />LISBP-Biocatalysis Group, INSA/INRA UMR 792, Université de Toulouse, 135 Avenue de Rangueil, 31077 Toulouse, France
- />INRA, UMR792 Ingénierie des Systèmes Biologiques et des Procédés, 31400 Toulouse, France
- />CNRS, UMR5504, 31400 Toulouse, France
| | - Sophie Duquesne
- />LISBP-Biocatalysis Group, INSA/INRA UMR 792, Université de Toulouse, 135 Avenue de Rangueil, 31077 Toulouse, France
- />INRA, UMR792 Ingénierie des Systèmes Biologiques et des Procédés, 31400 Toulouse, France
- />CNRS, UMR5504, 31400 Toulouse, France
| | - Sophie Bozonnet
- />LISBP-Biocatalysis Group, INSA/INRA UMR 792, Université de Toulouse, 135 Avenue de Rangueil, 31077 Toulouse, France
- />INRA, UMR792 Ingénierie des Systèmes Biologiques et des Procédés, 31400 Toulouse, France
- />CNRS, UMR5504, 31400 Toulouse, France
| | - Gianluca Cioci
- />LISBP-Biocatalysis Group, INSA/INRA UMR 792, Université de Toulouse, 135 Avenue de Rangueil, 31077 Toulouse, France
- />INRA, UMR792 Ingénierie des Systèmes Biologiques et des Procédés, 31400 Toulouse, France
- />CNRS, UMR5504, 31400 Toulouse, France
| | - Jean-Marc Nicaud
- />INRA, UMR1319 Micalis, 78352 Jouy-en-Josas, France
- />AgroParisTech, UMR Micalis, 78352 Jouy-en-Josas, France
| | - Alain Marty
- />LISBP-Biocatalysis Group, INSA/INRA UMR 792, Université de Toulouse, 135 Avenue de Rangueil, 31077 Toulouse, France
- />INRA, UMR792 Ingénierie des Systèmes Biologiques et des Procédés, 31400 Toulouse, France
- />CNRS, UMR5504, 31400 Toulouse, France
| | - Michael Joseph O’Donohue
- />LISBP-Biocatalysis Group, INSA/INRA UMR 792, Université de Toulouse, 135 Avenue de Rangueil, 31077 Toulouse, France
- />INRA, UMR792 Ingénierie des Systèmes Biologiques et des Procédés, 31400 Toulouse, France
- />CNRS, UMR5504, 31400 Toulouse, France
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229
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Yu AQ, Pratomo Juwono NK, Leong SSJ, Chang MW. Production of Fatty Acid-derived valuable chemicals in synthetic microbes. Front Bioeng Biotechnol 2014; 2:78. [PMID: 25566540 PMCID: PMC4275033 DOI: 10.3389/fbioe.2014.00078] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2014] [Accepted: 12/10/2014] [Indexed: 12/18/2022] Open
Abstract
Fatty acid derivatives, such as hydroxy fatty acids, fatty alcohols, fatty acid methyl/ethyl esters, and fatty alka(e)nes, have a wide range of industrial applications including plastics, lubricants, and fuels. Currently, these chemicals are obtained mainly through chemical synthesis, which is complex and costly, and their availability from natural biological sources is extremely limited. Metabolic engineering of microorganisms has provided a platform for effective production of these valuable biochemicals. Notably, synthetic biology-based metabolic engineering strategies have been extensively applied to refactor microorganisms for improved biochemical production. Here, we reviewed: (i) the current status of metabolic engineering of microbes that produce fatty acid-derived valuable chemicals, and (ii) the recent progress of synthetic biology approaches that assist metabolic engineering, such as mRNA secondary structure engineering, sensor-regulator system, regulatable expression system, ultrasensitive input/output control system, and computer science-based design of complex gene circuits. Furthermore, key challenges and strategies were discussed. Finally, we concluded that synthetic biology provides useful metabolic engineering strategies for economically viable production of fatty acid-derived valuable chemicals in engineered microbes.
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Affiliation(s)
- Ai-Qun Yu
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore , Singapore , Singapore ; Synthetic Biology Research Program, National University of Singapore , Singapore , Singapore
| | - Nina Kurniasih Pratomo Juwono
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore , Singapore , Singapore ; Synthetic Biology Research Program, National University of Singapore , Singapore , Singapore
| | - Susanna Su Jan Leong
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore , Singapore , Singapore ; Synthetic Biology Research Program, National University of Singapore , Singapore , Singapore ; Singapore Institute of Technology , Singapore , Singapore
| | - Matthew Wook Chang
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore , Singapore , Singapore ; Synthetic Biology Research Program, National University of Singapore , Singapore , Singapore
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230
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The influence of oxygen limitation for the production of succinic acid with recombinant strains of Yarrowia lipolytica. Appl Microbiol Biotechnol 2014; 99:1675-86. [DOI: 10.1007/s00253-014-6252-z] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2014] [Revised: 11/17/2014] [Accepted: 11/18/2014] [Indexed: 01/13/2023]
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231
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Sibirny A, Madzak C, Fickers P. Genetic engineering of nonconventional yeasts for the production of valuable compounds. Microb Biotechnol 2014. [DOI: 10.1201/b17587-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
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232
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Yuzbasheva EY, Yuzbashev TV, Mostova EB, Perkovskaya NI, Sineokii SP. Microbial synthesis of biodiesel and its prospects. APPL BIOCHEM MICRO+ 2014. [DOI: 10.1134/s0003683814090075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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233
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Hexokinase—A limiting factor in lipid production from fructose in Yarrowia lipolytica. Metab Eng 2014; 26:89-99. [DOI: 10.1016/j.ymben.2014.09.008] [Citation(s) in RCA: 94] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2014] [Revised: 08/27/2014] [Accepted: 09/12/2014] [Indexed: 01/21/2023]
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234
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Pénicaud C, Landaud S, Jamme F, Talbot P, Bouix M, Ghorbal S, Fonseca F. Physiological and biochemical responses of Yarrowia lipolytica to dehydration induced by air-drying and freezing. PLoS One 2014; 9:e111138. [PMID: 25350121 PMCID: PMC4211883 DOI: 10.1371/journal.pone.0111138] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2014] [Accepted: 09/29/2014] [Indexed: 11/23/2022] Open
Abstract
Organisms that can withstand anhydrobiosis possess the unique ability to temporarily and reversibly suspend their metabolism for the periods when they live in a dehydrated state. However, the mechanisms underlying the cell's ability to tolerate dehydration are far from being fully understood. The objective of this study was to highlight, for the first time, the cellular damage to Yarrowia lipolytica as a result of dehydration induced by drying/rehydration and freezing/thawing. Cellular response was evaluated through cell cultivability determined by plate counts, esterase activity and membrane integrity assessed by flow cytometry, and the biochemical composition of cells as determined by FT-IR spectroscopy. The effects of the harvesting time (in the log or stationary phase) and of the addition of a protective molecule, trehalose, were investigated. All freshly harvested cells exhibited esterase activity and no alteration of membrane integrity. Cells freshly harvested in the stationary phase presented spectral contributions suggesting lower nucleic acid content and thicker cell walls, as well as longer lipid chains than cells harvested in the log phase. Moreover, it was found that drying/rehydration induced cell plasma membrane permeabilization, loss of esterase activity with concomitant protein denaturation, wall damage and oxidation of nucleic acids. Plasma membrane permeabilization and loss of esterase activity could be reduced by harvesting in the stationary phase and/or with trehalose addition. Protein denaturation and wall damage could be reduced by harvesting in the stationary phase. In addition, it was shown that measurements of loss of membrane integrity and preservation of esterase activity were suitable indicators of loss and preservation of cultivability, respectively. Conversely, no clear effect of freezing/thawing could be observed, probably because of the favorable operating conditions applied. These results give insights into Y. lipolytica mechanisms of cellular response to dehydration and provide a basis to better understand its ability to tolerate anhydrobiosis.
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Affiliation(s)
- Caroline Pénicaud
- INRA, UMR782 Génie et Microbiologie des Procédés Alimentaires, Thiverval-Grignon, France
- AgroParisTech, UMR782 Génie et Microbiologie des Procédés Alimentaires, Thiverval-Grignon, France
| | - Sophie Landaud
- INRA, UMR782 Génie et Microbiologie des Procédés Alimentaires, Thiverval-Grignon, France
- AgroParisTech, UMR782 Génie et Microbiologie des Procédés Alimentaires, Thiverval-Grignon, France
| | | | - Pauline Talbot
- INRA, UMR782 Génie et Microbiologie des Procédés Alimentaires, Thiverval-Grignon, France
- AgroParisTech, UMR782 Génie et Microbiologie des Procédés Alimentaires, Thiverval-Grignon, France
| | - Marielle Bouix
- INRA, UMR782 Génie et Microbiologie des Procédés Alimentaires, Thiverval-Grignon, France
- AgroParisTech, UMR782 Génie et Microbiologie des Procédés Alimentaires, Thiverval-Grignon, France
| | - Sarrah Ghorbal
- INRA, UMR782 Génie et Microbiologie des Procédés Alimentaires, Thiverval-Grignon, France
- AgroParisTech, UMR782 Génie et Microbiologie des Procédés Alimentaires, Thiverval-Grignon, France
| | - Fernanda Fonseca
- INRA, UMR782 Génie et Microbiologie des Procédés Alimentaires, Thiverval-Grignon, France
- AgroParisTech, UMR782 Génie et Microbiologie des Procédés Alimentaires, Thiverval-Grignon, France
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Iwama R, Kobayashi S, Ohta A, Horiuchi H, Fukuda R. Fatty aldehyde dehydrogenase multigene family involved in the assimilation of n-alkanes in Yarrowia lipolytica. J Biol Chem 2014; 289:33275-86. [PMID: 25315778 DOI: 10.1074/jbc.m114.596890] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
In the n-alkane assimilating yeast Yarrowia lipolytica, n-alkanes are oxidized to fatty acids via fatty alcohols and fatty aldehydes, after which they are utilized as carbon sources. Here, we show that four genes (HFD1-HFD4) encoding fatty aldehyde dehydrogenases (FALDHs) are involved in the metabolism of n-alkanes in Y. lipolytica. A mutant, in which all of four HFD genes are deleted (Δhfd1-4 strain), could not grow on n-alkanes of 12-18 carbons; however, the expression of one of those HFD genes restored its growth on n-alkanes. Production of Hfd2Ap or Hfd2Bp, translation products of transcript variants generated from HFD2 by the absence or presence of splicing, also supported the growth of the Δhfd1-4 strain on n-alkanes. The FALDH activity in the extract of the wild-type strain was increased when cells were incubated in the presence of n-decane, whereas this elevation in FALDH activity by n-decane was not observed in Δhfd1-4 strain extract. Substantial FALDH activities were detected in the extracts of Escherichia coli cells expressing the HFD genes. Fluorescent microscopic observation suggests that Hfd3p and Hfd2Bp are localized predominantly in the peroxisome, whereas Hfd1p and Hfd2Ap are localized in both the endoplasmic reticulum and the peroxisome. These results suggest that the HFD multigene family is responsible for the oxidation of fatty aldehydes to fatty acids in the metabolism of n-alkanes, and raise the possibility that Hfd proteins have diversified by gene multiplication and RNA splicing to efficiently assimilate or detoxify fatty aldehydes in Y. lipolytica.
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Affiliation(s)
- Ryo Iwama
- From the Department of Biotechnology, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo 113-8657 and
| | - Satoshi Kobayashi
- From the Department of Biotechnology, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo 113-8657 and
| | - Akinori Ohta
- the Department of Biological Chemistry, College of Bioscience and Biotechnology, Chubu University, 1200 Matsumoto-cho, Kasugai, Aichi 487-8501, Japan
| | - Hiroyuki Horiuchi
- From the Department of Biotechnology, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo 113-8657 and
| | - Ryouichi Fukuda
- From the Department of Biotechnology, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo 113-8657 and
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236
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Assortment of carbon sources in medium for Yarrowia lipolytica lipase production: A statistical approach. ANN MICROBIOL 2014; 65:1495-1503. [PMID: 26273239 PMCID: PMC4529471 DOI: 10.1007/s13213-014-0988-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2014] [Accepted: 09/16/2014] [Indexed: 10/25/2022] Open
Abstract
Glycerol is considered an important renewable feedstock as well as an undesirable side-product of biodiesel production. The aim of this study was to determine whether supplementing a culture medium with a combination of three different carbon sources (olive oil, glucose and glycerol) would optimize lipase production by the yeast Yarrowia lipolytica. The optimization experiments were conducted with a statistical approach using the mixture design. Analysis of the response surface revealed that it would be possible to compose a medium in which both an an extracellular lipase activity of 0.1 U/mL and up to 37.5 g/L of pure glycerol could be obtained. An YPO-Gl30 medium consisting of 30 g/L glycerol and 19.2 mL/L olive oil was selected for further investigation. Although a high biomass yield was found in all cultures, the glycerol content of the YPO-Gl30 medium slightly influenced yeast growth, but it did not prolong the duration of the lag phase. The hydrolytic activity of the extracellular lipases produced in YPO-Gl30 medium was satisfactory.
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237
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Cavka A, Jo¨nsson LJ. Comparison of the growth of filamentous fungi and yeasts in lignocellulose-derived media. BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY 2014. [DOI: 10.1016/j.bcab.2014.04.003] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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238
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Steensels J, Snoek T, Meersman E, Nicolino MP, Voordeckers K, Verstrepen KJ. Improving industrial yeast strains: exploiting natural and artificial diversity. FEMS Microbiol Rev 2014; 38:947-95. [PMID: 24724938 PMCID: PMC4293462 DOI: 10.1111/1574-6976.12073] [Citation(s) in RCA: 257] [Impact Index Per Article: 25.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2013] [Revised: 01/31/2014] [Accepted: 04/02/2014] [Indexed: 12/23/2022] Open
Abstract
Yeasts have been used for thousands of years to make fermented foods and beverages, such as beer, wine, sake, and bread. However, the choice for a particular yeast strain or species for a specific industrial application is often based on historical, rather than scientific grounds. Moreover, new biotechnological yeast applications, such as the production of second-generation biofuels, confront yeast with environments and challenges that differ from those encountered in traditional food fermentations. Together, this implies that there are interesting opportunities to isolate or generate yeast variants that perform better than the currently used strains. Here, we discuss the different strategies of strain selection and improvement available for both conventional and nonconventional yeasts. Exploiting the existing natural diversity and using techniques such as mutagenesis, protoplast fusion, breeding, genome shuffling and directed evolution to generate artificial diversity, or the use of genetic modification strategies to alter traits in a more targeted way, have led to the selection of superior industrial yeasts. Furthermore, recent technological advances allowed the development of high-throughput techniques, such as 'global transcription machinery engineering' (gTME), to induce genetic variation, providing a new source of yeast genetic diversity.
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Affiliation(s)
- Jan Steensels
- Laboratory for Genetics and Genomics, Centre of Microbial and Plant Genetics (CMPG), KU LeuvenLeuven, Belgium
- Laboratory for Systems Biology, VIBLeuven, Belgium
| | - Tim Snoek
- Laboratory for Genetics and Genomics, Centre of Microbial and Plant Genetics (CMPG), KU LeuvenLeuven, Belgium
- Laboratory for Systems Biology, VIBLeuven, Belgium
| | - Esther Meersman
- Laboratory for Genetics and Genomics, Centre of Microbial and Plant Genetics (CMPG), KU LeuvenLeuven, Belgium
- Laboratory for Systems Biology, VIBLeuven, Belgium
| | - Martina Picca Nicolino
- Laboratory for Genetics and Genomics, Centre of Microbial and Plant Genetics (CMPG), KU LeuvenLeuven, Belgium
- Laboratory for Systems Biology, VIBLeuven, Belgium
| | - Karin Voordeckers
- Laboratory for Genetics and Genomics, Centre of Microbial and Plant Genetics (CMPG), KU LeuvenLeuven, Belgium
- Laboratory for Systems Biology, VIBLeuven, Belgium
| | - Kevin J Verstrepen
- Laboratory for Genetics and Genomics, Centre of Microbial and Plant Genetics (CMPG), KU LeuvenLeuven, Belgium
- Laboratory for Systems Biology, VIBLeuven, Belgium
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239
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240
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Emmerstorfer A, Wriessnegger T, Hirz M, Pichler H. Overexpression of membrane proteins from higher eukaryotes in yeasts. Appl Microbiol Biotechnol 2014; 98:7671-98. [PMID: 25070595 DOI: 10.1007/s00253-014-5948-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2014] [Revised: 07/08/2014] [Accepted: 07/09/2014] [Indexed: 02/08/2023]
Abstract
Heterologous expression and characterisation of the membrane proteins of higher eukaryotes is of paramount interest in fundamental and applied research. Due to the rather simple and well-established methods for their genetic modification and cultivation, yeast cells are attractive host systems for recombinant protein production. This review provides an overview on the remarkable progress, and discusses pitfalls, in applying various yeast host strains for high-level expression of eukaryotic membrane proteins. In contrast to the cell lines of higher eukaryotes, yeasts permit efficient library screening methods. Modified yeasts are used as high-throughput screening tools for heterologous membrane protein functions or as benchmark for analysing drug-target relationships, e.g., by using yeasts as sensors. Furthermore, yeasts are powerful hosts for revealing interactions stabilising and/or activating membrane proteins. We also discuss the stress responses of yeasts upon heterologous expression of membrane proteins. Through co-expression of chaperones and/or optimising yeast cultivation and expression strategies, yield-optimised hosts have been created for membrane protein crystallography or efficient whole-cell production of fine chemicals.
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Affiliation(s)
- Anita Emmerstorfer
- ACIB-Austrian Centre of Industrial Biotechnology, Petersgasse 14, 8010, Graz, Austria
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241
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Saygün A, Şahin-Yeşilçubuk N, Aran N. Effects of Different Oil Sources and Residues on Biomass and Metabolite Production by Yarrowia lipolytica YB 423-12. J AM OIL CHEM SOC 2014. [DOI: 10.1007/s11746-014-2506-2] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
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242
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Fabiszewska AU, Stolarzewicz IA, Zamojska WM, Białecka-Florjańczyk E. Carbon source impact on Yarrowia lipolytica KKP 379 lipase production. APPL BIOCHEM MICRO+ 2014. [DOI: 10.1134/s000368381404005x] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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243
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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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244
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Jiang Y, Li L, Zhang H, Feng W, Tan T. Lid Closure Mechanism of Yarrowia lipolytica Lipase in Methanol Investigated by Molecular Dynamics Simulation. J Chem Inf Model 2014; 54:2033-41. [DOI: 10.1021/ci500163y] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Yang Jiang
- Beijing
Key Lab of Bioprocess,
College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
| | - Lingli Li
- Beijing
Key Lab of Bioprocess,
College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
| | - Haiyang Zhang
- Beijing
Key Lab of Bioprocess,
College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
| | - Wei Feng
- Beijing
Key Lab of Bioprocess,
College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
| | - Tianwei Tan
- Beijing
Key Lab of Bioprocess,
College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
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245
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Metabolism of Hydrophobic Carbon Sources and Regulation of It inn-Alkane-Assimilating YeastYarrowia lipolytica. Biosci Biotechnol Biochem 2014; 77:1149-54. [DOI: 10.1271/bbb.130164] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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246
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Functional Differentiation of Chitin Synthases inYarrowia lipolytica. Biosci Biotechnol Biochem 2014; 77:1275-81. [DOI: 10.1271/bbb.130111] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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247
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Dimorphism and hydrocarbon metabolism in Yarrowia lipolytica var. indica. Arch Microbiol 2014; 196:545-56. [DOI: 10.1007/s00203-014-0990-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2013] [Revised: 04/03/2014] [Accepted: 05/03/2014] [Indexed: 10/25/2022]
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248
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Zinjarde S, Apte M, Mohite P, Kumar AR. Yarrowia lipolytica and pollutants: Interactions and applications. Biotechnol Adv 2014; 32:920-33. [PMID: 24780156 DOI: 10.1016/j.biotechadv.2014.04.008] [Citation(s) in RCA: 81] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2013] [Revised: 02/21/2014] [Accepted: 04/18/2014] [Indexed: 11/25/2022]
Abstract
Yarrowia lipolytica is a dimorphic, non-pathogenic, ascomycetous yeast species with distinctive physiological features and biochemical characteristics that are significant in environment-related matters. Strains naturally present in soils, sea water, sediments and waste waters have inherent abilities to degrade hydrocarbons such as alkanes (short and medium chain) and aromatic compounds (biphenyl and dibenzofuran). With the application of slow release fertilizers, design of immobilization techniques and development of microbial consortia, scale-up studies and in situ applications have been possible. In general, hydrocarbon uptake in this yeast is mediated by attachment to large droplets (via hydrophobic cell surfaces) or is aided by surfactants and emulsifiers. Subsequently, the internalized hydrocarbons are degraded by relevant enzymes innately present in the yeast. Some wild-type or recombinant strains also detoxify nitroaromatic (2,4,6-trinitrotoluene), halogenated (chlorinated and brominated hydrocarbons) and organophosphate (methyl parathion) compounds. The yeast can tolerate some metals and detoxify them via different biomolecules. The biomass (unmodified, in combination with sludge, magnetically-modified and in the biofilm form) has been employed in the biosorption of hexavalent chromium ions from aqueous solutions. Yeast cells have also been applied in protocols related to nanoparticle synthesis. The treatment of oily and solid wastes with this yeast reduces chemical oxygen demand or value-added products (single cell oil, single cell protein, surfactants, organic acids and polyalcohols) are obtained. On account of all these features, the microorganism has established a place for itself and is of considerable value in environment-related applications.
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Affiliation(s)
- Smita Zinjarde
- Institute of Bioinformatics and Biotechnology, University of Pune, Pune 411 007, India.
| | - Mugdha Apte
- Institute of Bioinformatics and Biotechnology, University of Pune, Pune 411 007, India
| | - Pallavi Mohite
- Institute of Bioinformatics and Biotechnology, University of Pune, Pune 411 007, India
| | - Ameeta Ravi Kumar
- Institute of Bioinformatics and Biotechnology, University of Pune, Pune 411 007, India
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249
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Guo H, Madzak C, Du G, Zhou J, Chen J. Effects of pyruvate dehydrogenase subunits overexpression on the α-ketoglutarate production in Yarrowia lipolytica WSH-Z06. Appl Microbiol Biotechnol 2014; 98:7003-12. [PMID: 24760229 DOI: 10.1007/s00253-014-5745-0] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2013] [Revised: 03/18/2014] [Accepted: 03/31/2014] [Indexed: 10/25/2022]
Abstract
Yarrowia lipolytica WSH-Z06 harbours a promising capability to oversynthesize α-ketoglutarate (α-KG). Its wide utilization is hampered by the formation of high concentrations of pyruvate. In this study, a metabolic strategy for the overexpression of the α and β subunits of pyruvate dehydrogenase E1, E2 and E3 components was designed to reduce the accumulation of pyruvate. Elevated expression level of α subunit of E1 component improved the α-KG production and reduced the pyruvate accumulation. Due to a reduction in the acetyl-CoA supply, neither the growth of cells nor the synthesis of α-KG was restrained by the overexpression of β subunit of E1, E2 and E3 components. Furthermore, via the overexpression of these thiamine pyrophosphate (TPP)-binding subunits, the dependency of pyruvate dehydrogenase on thiamine was diminished in strains T1 and T2, in which α and β subunits of E1 component were separately overexpressed. In these two recombinant strains, the accumulation of pyruvate was insensitive to variations in exogenous thiamine. The results suggest that α-KG production can be enhanced by altering the dependence on TPP of pyruvate dehydrogenase and that the competition for the cofactor can be switched to ketoglutarate dehydrogenase via separate overexpression of the TPP-binding subunits of pyruvate dehydrogenase. The results presented here provided new clue to improve α-KG production.
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Affiliation(s)
- Hongwei Guo
- School of Biotechnology and Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, China
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250
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Koch B, Schmidt C, Daum G. Storage lipids of yeasts: a survey of nonpolar lipid metabolism in Saccharomyces cerevisiae, Pichia pastoris, and Yarrowia lipolytica. FEMS Microbiol Rev 2014; 38:892-915. [PMID: 24597968 DOI: 10.1111/1574-6976.12069] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2013] [Revised: 02/21/2014] [Accepted: 02/21/2014] [Indexed: 11/29/2022] Open
Abstract
Biosynthesis and storage of nonpolar lipids, such as triacylglycerols (TG) and steryl esters (SE), have gained much interest during the last decades because defects in these processes are related to severe human diseases. The baker's yeast Saccharomyces cerevisiae has become a valuable tool to study eukaryotic lipid metabolism because this single-cell microorganism harbors many enzymes and pathways with counterparts in mammalian cells. In this article, we will review aspects of TG and SE metabolism and turnover in the yeast that have been known for a long time and combine them with new perceptions of nonpolar lipid research. We will provide a detailed insight into the mechanisms of nonpolar lipid synthesis, storage, mobilization, and degradation in the yeast S. cerevisiae. The central role of lipid droplets (LD) in these processes will be addressed with emphasis on the prevailing view that this compartment is more than only a depot for TG and SE. Dynamic and interactive aspects of LD with other organelles will be discussed. Results obtained with S. cerevisiae will be complemented by recent investigations of nonpolar lipid research with Yarrowia lipolytica and Pichia pastoris. Altogether, this review article provides a comprehensive view of nonpolar lipid research in yeast.
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Affiliation(s)
- Barbara Koch
- Institute of Biochemistry, Graz University of Technology, Graz, Austria
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