Vlaardingerbroek I, Beerens B, Rose L, Fokkens L, Cornelissen BJC, Rep M. Exchange of core chromosomes and horizontal transfer of lineage-specific chromosomes in Fusarium oxysporum: chromosome transfer and exchange in F. oxysporum. Environ Microbiol. 2016. doi:10.1111/1462-2920.13281.
Google Scholar
Gordon JL, Byrne KP, Wolfe KH. Mechanisms of chromosome number evolution in yeast. PLoS Genet. 2011;7:e1002190 (Fay JC, editor).
Article
CAS
Google Scholar
Ketel C, Wang HSW, McClellan M, Bouchonville K, Selmecki A, Lahav T, et al. Neocentromeres form efficiently at multiple possible loci in Candida albicans. PLoS Genet. 2009;5:e1000400 (Copenhaver GP, editor).
Article
CAS
Google Scholar
Hane JK, Rouxel T, Howlett BJ, Kema GH, Goodwin SB, Oliver RP. A novel mode of chromosomal evolution peculiar to filamentous Ascomycete fungi. Genome Biol. 2011;12:R45.
Article
Google Scholar
Naumova E, Naumov G, Fournier P, Nguyen HV, Gaillardin C. Chromosomal polymorphism of the yeast Yarrowia lipolytica and related species: electrophoretic karyotyping and hybridization with cloned genes. Curr Genet. 1993;23:450–4.
Article
CAS
Google Scholar
Beopoulos A, Desfougeres T, Sabirova J, Zinjarde S, Neuvéglise C, Nicaud J-M. The hydrocarbon-degrading oleaginous yeast Yarrowia lipolytica. In: Timmis KN, editor. Handb. Hydrocarb. Lipid Microbiol. [Internet]. Berlin, Heidelberg: Springer Berlin Heidelberg; 2010. p. 2111–2121. http://link.springer.com/10.1007/978-3-540-77587-4_152. Accessed 10 Jun 2016.
Madzak C, Tréton B, Blanchin-Roland S. Strong hybrid promoters and integrative expression/secretion vectors for quasi-constitutive expression of heterologous proteins in the yeast Yarrowia lipolytica. J Mol Microbiol Biotechnol. 2000;2:207–16.
CAS
Google Scholar
Wickerham LJ, Kurtzman CP, Herman AI. Sexual reproduction in Candida lipolytica. Science. 1970;167:1141.
Article
CAS
Google Scholar
Pomraning KR, Baker SE. Draft genome sequence of the dimorphic yeast Yarrowia lipolytica strain W29. Genome Announc. 2015;3:e01211–5.
Article
Google Scholar
Liu L, Alper HS. Draft genome sequence of the oleaginous yeast Yarrowia lipolytica PO1f, a commonly used metabolic engineering host. Genome Announc. 2014;2:e00652-14.
Article
Google Scholar
Kretzschmar A, Otto C, Holz M, Werner S, Hübner L, Barth G. Increased homologous integration frequency in Yarrowia lipolytica strains defective in non-homologous end-joining. Curr Genet. 2013;59:63–72.
Article
CAS
Google Scholar
Verbeke J, Beopoulos A, Nicaud J-M. Efficient homologous recombination with short length flanking fragments in Ku70 deficient Yarrowia lipolytica strains. Biotechnol Lett. 2013;35:571–6.
Article
CAS
Google Scholar
Titorenko VI, Chan H, Rachubinski RA. Fusion of small peroxisomal vesicles in vitro reconstructs an early step in the in vivo multistep peroxisome assembly pathway of Yarrowia lipolytica. J Cell Biol. 2000;148:29–44.
Article
CAS
Google Scholar
Fickers P, Marty A, Nicaud JM. The lipases from Yarrowia lipolytica: genetics, production, regulation, biochemical characterization and biotechnological applications. Biotechnol Adv. 2011;29:632–44.
Article
CAS
Google Scholar
Kerkhoven EJ, Pomraning KR, Baker SE, Nielsen J. Regulation of amino-acid metabolism controls flux to lipid accumulation in Yarrowia lipolytica. Npj Syst Biol Appl. 2016;2:16005.
Article
Google Scholar
Kavšček M, Bhutada G, Madl T, Natter K. Optimization of lipid production with a genome-scale model of Yarrowia lipolytica. BMC Syst Biol [Internet]. 2015; 9. http://www.biomedcentral.com/1752-0509/9/72. Accessed 15 Jan 2016.
Blazeck J, Hill A, Liu L, Knight R, Miller J, Pan A, et al. Harnessing Yarrowia lipolytica lipogenesis to create a platform for lipid and biofuel production. Nat Commun [Internet]. 2014; 5. http://www.nature.com/doifinder/10.1038/ncomms4131. Accessed 15 Jan 2016.
Matthaus F, Ketelhot M, Gatter M, Barth G. Production of lycopene in the non-carotenoid-producing yeast Yarrowia lipolytica. Appl Environ Microbiol. 2014;80:1660–9.
Article
CAS
Google Scholar
Xue Z, Sharpe PL, Hong S-P, Yadav NS, Xie D, Short DR, et al. Production of omega-3 eicosapentaenoic acid by metabolic engineering of Yarrowia lipolytica. Nat Biotechnol. 2013;31:734–40.
Article
CAS
Google Scholar
Wolinski H, Kohlwein SD. Single yeast cell imaging. Methods Mol Biol Clifton NJ. 2014;1205:91–109.
Article
CAS
Google Scholar
Dimmer KS. Fluorescence Staining of Mitochondria for morphology analysis in Saccharomyces cerevisiae. In: Xiao W, editor. Yeast Protoc [Internet]. New York: Springer New York; 2014. p. 131–52. http://link.springer.com/10.1007/978-1-4939-0799-1_9. Accessed 28 Mar 2016.
Wolinski H, Kohlwein SD. Microscopic and spectroscopic techniques to investigate lipid droplet formation and turnover in yeast. Methods Mol Biol Clifton NJ. 2015;1270:289–305.
Article
CAS
Google Scholar
Chaffin WL, López-Ribot JL, Casanova M, Gozalbo D, Martínez JP. Cell wall and secreted proteins of Candida albicans: identification, function, and expression. Microbiol Mol Biol Rev. 1998;62:130–80.
CAS
Google Scholar
Ram AFJ, Klis FM. Identification of fungal cell wall mutants using susceptibility assays based on Calcofluor white and Congo red. Nat Protoc. 2006;1:2253–6.
Article
CAS
Google Scholar
Gulshan K, Moye-Rowley WS. Multidrug resistance in fungi. Eukaryot Cell. 2007;6:1933–42.
Article
CAS
Google Scholar
Fotopoulos V. Never say dye: new roles for an old fluorochrome. Plant Signal Behav. 2012;7:342–4.
Article
CAS
Google Scholar
Aguedo M, Waché Y, Belin J-M. Intracellular pH-dependent efflux of the fluorescent probe pyranine in the yeast Yarrowia lipolytica. FEMS Microbiol Lett. 2001;200:185–9.
Article
CAS
Google Scholar
Pomraning KR, Wei S, Karagiosis SA, Kim Y-M, Dohnalkova AC, Arey BW, et al. Comprehensive metabolomic, lipidomic and microscopic profiling of Yarrowia lipolytica during lipid accumulation identifies targets for increased lipogenesis. PLOS ONE. 2015;10:e0123188 (Nowrousian M, editor).
Article
CAS
Google Scholar
Chalfie M, Tu Y, Euskirchen G, Ward W, Prasher D. Green fluorescent protein as a marker for gene expression. Science. 1994;263:802–5.
Article
CAS
Google Scholar
Nicaud J-M, Madzak C, van den Broek P, Gysler C, Duboc P, Niederberger P, et al. Protein expression and secretion in the yeast Yarrowia lipolytica. FEMS Yeast Res. 2002;2:371–9.
CAS
Google Scholar
Barth G, Gaillardin C. Yarrowia lipolytica. Nonconv Yeasts Biotechnol [Internet]. Berlin, Heidelberg: Springer Berlin Heidelberg; 1996. p. 313–88. http://www.springerlink.com/index/10.1007/978-3-642-79856-6_10. Accessed 4 May 2016.
Wang Z-P, Xu H-M, Wang G-Y, Chi Z, Chi Z-M. Disruption of the MIG1 gene enhances lipid biosynthesis in the oleaginous yeast Yarrowia lipolytica ACA-DC 50109. Biochim Biophys Acta BBA-Mol Cell Biol Lipids. 2013;1831:675–82.
Article
CAS
Google Scholar
Dulermo R, Gamboa-Meléndez H, Dulermo T, Thevenieau F, Nicaud J-M. The fatty acid transport protein Fat1p is involved in the export of fatty acids from lipid bodies in Yarrowia lipolytica. FEMS Yeast Res. 2014;14:883–96.
Article
CAS
Google Scholar
Tenagy, Park JS, Iwama R, Kobayashi S, Ohta A, Horiuchi H, et al. Involvement of acyl-CoA synthetase genes in n-alkane assimilation and fatty acid utilization in yeast Yarrowia lipolytica. FEMS Yeast Res. 2015;15:fov031 (Nielsen J, editor).
Article
CAS
Google Scholar
Blazeck J, Liu L, Redden H, Alper H. Tuning gene expression in Yarrowia lipolytica by a hybrid promoter approach. Appl Environ Microbiol. 2011;77:7905–14.
Article
CAS
Google Scholar
Martinez-Vazquez A, Gonzalez-Hernandez A, Domínguez Á, Rachubinski R, Riquelme M, Cuellar-Mata P, et al. Identification of the transcription factor Znc1p, which regulates the yeast-to-hypha transition in the dimorphic yeast Yarrowia lipolytica. PLoS ONE. 2013;8:e66790 (Bassilana M, editor).
Article
CAS
Google Scholar
Pédelacq J-D, Cabantous S, Tran T, Terwilliger TC, Waldo GS. Engineering and characterization of a superfolder green fluorescent protein. Nat Biotechnol. 2006;24:79–88.
Article
CAS
Google Scholar
Fickers P, Le Dall M, Gaillardin C, Thonart P, Nicaud J. New disruption cassettes for rapid gene disruption and marker rescue in the yeast Yarrowia lipolytica. J Microbiol Methods. 2003;55:727–37.
Article
CAS
Google Scholar
Yang J, Nie L, Chen B, Liu Y, Kong Y, Wang H, et al. Hygromycin-resistance vectors for gene expression in Pichia pastoris. Yeast Chichester Engl. 2014;31:115–25.
Article
CAS
Google Scholar
Fennessy D, Grallert A, Krapp A, Cokoja A, Bridge AJ, Petersen J, et al. Extending the Schizosaccharomyces pombe molecular genetic toolbox. PLoS ONE. 2014;9:e97683.
Article
CAS
Google Scholar
Carroll Anne M, Sweigard James A. Barbara valent. Improved vectors for selecting resistance to hygromycin. Fungal Genet Newsl. 1994;41:22.
Google Scholar
Punt PJ, Oliver RP, Dingemanse MA, Pouwels PH, van den Hondel CA. Transformation of Aspergillus based on the hygromycin B resistance marker from Escherichia coli. Gene. 1987;56:117–24.
Article
CAS
Google Scholar
Le Dall MT, Nicaud JM, Gaillardin C. Multiple-copy integration in the yeast Yarrowia lipolytica. Curr Genet. 1994;26:38–44.
Article
Google Scholar
Dujon B, Sherman D, Fischer G, Durrens P, Casaregola S, Lafontaine I, et al. Genome evolution in yeasts. Nature. 2004;430:35–44.
Article
Google Scholar
Gibson DG, Young L, Chuang R-Y, Venter JC, Hutchison CA, Smith HO. Enzymatic assembly of DNA molecules up to several hundred kilobases. Nat Methods. 2009;6:343–5.
Article
CAS
Google Scholar
Fournier P, Abbas A, Chasles M, Kudla B, Ogrydziak DM, Yaver D, et al. Colocalization of centromeric and replicative functions on autonomously replicating sequences isolated from the yeast Yarrowia lipolytica. Proc Natl Acad Sci USA. 1993;90:4912–6.
Article
CAS
Google Scholar
Pan P, Hua Q. Reconstruction and in silico analysis of metabolic network for an oleaginous yeast, Yarrowia lipolytica. PLoS ONE. 2012;7:e51535.
Article
CAS
Google Scholar
Ratledge C, Wynn JP. The biochemistry and molecular biology of lipid accumulation in oleaginous microorganisms. Adv Appl Microbiol. 2002;51:1–51.
Article
CAS
Google Scholar
Dulermo T, Lazar Z, Dulermo R, Rakicka M, Haddouche R, Nicaud J-M. Analysis of ATP-citrate lyase and malic enzyme mutants of Yarrowia lipolytica points out the importance of mannitol metabolism in fatty acid synthesis. Biochim Biophys Acta. 2015;1851:1107–17.
Article
CAS
Google Scholar
Qiao K, Imam Abidi SH, Liu H, Zhang H, Chakraborty S, Watson N, et al. Engineering lipid overproduction in the oleaginous yeast Yarrowia lipolytica. Metab Eng. 2015;29:56–65.
Article
CAS
Google Scholar
Tai M, Stephanopoulos G. Engineering the push and pull of lipid biosynthesis in oleaginous yeast Yarrowia lipolytica for biofuel production. Metab Eng. 2013;15:1–9.
Article
CAS
Google Scholar
Ivessa AS, Schneiter R, Kohlwein SD. Yeast acetyl-CoA carboxylase is associated with the cytoplasmic surface of the endoplasmic reticulum. Eur J Cell Biol. 1997;74:399–406.
CAS
Google Scholar
Hoja U, Marthol S, Hofmann J, Stegner S, Schulz R, Meier S, et al. HFA1 encoding an organelle-specific acetyl-CoA carboxylase controls mitochondrial fatty acid synthesis in Saccharomyces cerevisiae. J Biol Chem. 2004;279:21779–86.
Article
CAS
Google Scholar
Kolodziej SJ, Penczek PA, Schroeter JP, Stoops JK. Structure-function relationships of the Saccharomyces cerevisiae fatty acid synthase. Three-dimensional structure. J Biol Chem. 1996;271:28422–9.
Article
CAS
Google Scholar
Tehlivets O, Scheuringer K, Kohlwein SD. Fatty acid synthesis and elongation in yeast. Biochim Biophys Acta. 2007;1771:255–70.
Article
CAS
Google Scholar
Athenstaedt K, Jolivet P, Boulard C, Zivy M, Negroni L, Nicaud J-M, et al. Lipid particle composition of the yeast Yarrowia lipolytica depends on the carbon source. Proteomics. 2006;6:1450–9.
Article
CAS
Google Scholar
Athenstaedt K, Daum G. Biosynthesis of phosphatidic acid in lipid particles and endoplasmic reticulum of Saccharomyces cerevisiae. J Bacteriol. 1997;179:7611–6.
Article
CAS
Google Scholar
Benghezal M, Roubaty C, Veepuri V, Knudsen J, Conzelmann A. SLC1 and SLC4 encode partially redundant acyl-coenzyme A 1-acylglycerol-3-phosphate O-acyltransferases of budding yeast. J Biol Chem. 2007;282:30845–55.
Article
CAS
Google Scholar
Jain S, Stanford N, Bhagwat N, Seiler B, Costanzo M, Boone C, et al. Identification of a novel lysophospholipid acyltransferase in Saccharomyces cerevisiae. J Biol Chem. 2007;282:30562–9.
Article
CAS
Google Scholar
Ayciriex S, Le Guédard M, Camougrand N, Velours G, Schoene M, Leone S, et al. YPR139c/LOA1 encodes a novel lysophosphatidic acid acyltransferase associated with lipid droplets and involved in TAG homeostasis. Mol Biol Cell. 2012;23:233–46.
Article
CAS
Google Scholar
Henry SA, Kohlwein SD, Carman GM. Metabolism and regulation of glycerolipids in the yeast Saccharomyces cerevisiae. Genetics. 2012;190:317–49.
Article
CAS
Google Scholar
Kohlwein SD, Veenhuis M, van der Klei IJ. Lipid droplets and peroxisomes: key players in cellular lipid homeostasis or a matter of fat–store ‘em up or burn’em down. Genetics. 2013;193:1–50.
Article
CAS
Google Scholar
Carman GM, Han G-S. Regulation of phospholipid synthesis in the yeast Saccharomyces cerevisiae. Annu Rev Biochem. 2011;80:859–83.
Article
CAS
Google Scholar
Pascual F, Carman GM. Phosphatidate phosphatase, a key regulator of lipid homeostasis. Biochim Biophys Acta. 2013;1831:514–22.
Article
CAS
Google Scholar
Raetz CR. Enzymology, genetics, and regulation of membrane phospholipid synthesis in Escherichia coli. Microbiol Rev. 1978;42:614–59.
CAS
Google Scholar
Carman GM, Han G-S. Phosphatidic acid phosphatase, a key enzyme in the regulation of lipid synthesis. J Biol Chem. 2009;284:2593–7.
Article
CAS
Google Scholar
Su W-M, Han G-S, Casciano J, Carman GM. Protein kinase A-mediated phosphorylation of Pah1p phosphatidate phosphatase functions in conjunction with the Pho85p-Pho80p and Cdc28p-cyclin B kinases to regulate lipid synthesis in yeast. J Biol Chem. 2012;287:33364–76.
Article
CAS
Google Scholar
Su W-M, Han G-S, Carman GM. Cross-talk phosphorylations by protein kinase C and Pho85p-Pho80p protein kinase regulate Pah1p phosphatidate phosphatase abundance in Saccharomyces cerevisiae. J Biol Chem. 2014;289:18818–30.
Article
CAS
Google Scholar
Choi H-S, Su W-M, Han G-S, Plote D, Xu Z, Carman GM. Pho85p-Pho80p phosphorylation of yeast Pah1p phosphatidate phosphatase regulates its activity, location, abundance, and function in lipid metabolism. J Biol Chem. 2012;287:11290–301.
Article
CAS
Google Scholar
Athenstaedt K. YALI0E32769 g (DGA1) and YALI0E16797 g (LRO1) encode major triacylglycerol synthases of the oleaginous yeast Yarrowia lipolytica. Biochim Biophys Acta. 2011;1811:587–96.
Article
CAS
Google Scholar
Beopoulos A, Haddouche R, Kabran P, Dulermo T, Chardot T, Nicaud J-M. Identification and characterization of DGA2, an acyltransferase of the DGAT1 acyl-CoA:diacylglycerol acyltransferase family in the oleaginous yeast Yarrowia lipolytica. New insights into the storage lipid metabolism of oleaginous yeasts. Appl Microbiol Biotechnol. 2012;93:1523–37.
Article
CAS
Google Scholar
Oelkers P, Tinkelenberg A, Erdeniz N, Cromley D, Billheimer JT, Sturley SL. A lecithin cholesterol acyltransferase-like gene mediates diacylglycerol esterification in yeast. J Biol Chem. 2000;275:15609–12.
Article
CAS
Google Scholar
Zweytick D, Leitner E, Kohlwein SD, Yu C, Rothblatt J, Daum G. Contribution of Are1p and Are2p to steryl ester synthesis in the yeast Saccharomyces cerevisiae. Eur J Biochem FEBS. 2000;267:1075–82.
Article
CAS
Google Scholar
Dulermo T, Tréton B, Beopoulos A, Kabran Gnankon AP, Haddouche R, Nicaud J-M. Characterization of the two intracellular lipases of Y. lipolytica encoded by TGL3 and TGL4 genes: new insights into the role of intracellular lipases and lipid body organisation. Biochim Biophys Acta. 2013;1831:1486–95.
Article
CAS
Google Scholar
Ham HJ, Rho HJ, Shin SK, Yoon H-J. The TGL2 gene of Saccharomyces cerevisiae encodes an active acylglycerol lipase located in the mitochondria. J Biol Chem. 2010;285:3005–13.
Article
CAS
Google Scholar
Ansari AM, Ahmed AK, Matsangos AE, Lay F, Born LJ, Marti G, et al. Cellular GFP toxicity and immunogenicity: potential confounders in in vivo cell tracking experiments. Stem Cell Rev Rep. 2016;12:553–9.
Article
CAS
Google Scholar
Breker M, Gymrek M, Moldavski O, Schuldiner M. LoQAtE–localization and quantitation ATlas of the yeast proteomE. A new tool for multiparametric dissection of single-protein behavior in response to biological perturbations in yeast. Nucleic Acids Res. 2014;42:D726–30.
Article
CAS
Google Scholar
Huh W-K, Falvo JV, Gerke LC, Carroll AS, Howson RW, Weissman JS, et al. Global analysis of protein localization in budding yeast. Nature. 2003;425:686–91.
Article
CAS
Google Scholar
Jonikas MC, Collins SR, Denic V, Oh E, Quan EM, Schmid V, et al. Comprehensive characterization of genes required for protein folding in the endoplasmic reticulum. Science. 2009;323:1693–7.
Article
CAS
Google Scholar
Dean N, Zhang YB, Poster JB. The VRG4 gene is required for GDP-mannose transport into the lumen of the Golgi in the yeast, Saccharomyces cerevisiae. J Biol Chem. 1997;272:31908–14.
Article
CAS
Google Scholar
Hung N-J, Johnson AW. Nuclear recycling of the Pre-60S ribosomal subunit-associated factor Arx1 depends on Rei1 in Saccharomyces cerevisiae. Mol Cell Biol. 2006;26:3718–27.
Article
CAS
Google Scholar
Hung N-J, Lo K-Y, Patel SS, Helmke K, Johnson AW. Arx1 is a nuclear export receptor for the 60S ribosomal subunit in yeast. Mol Biol Cell. 2008;19:735–44.
Article
CAS
Google Scholar
Foster MW, Forrester MT, Stamler JS. A protein microarray-based analysis of S-nitrosylation. Proc Natl Acad Sci USA. 2009;106:18948–53.
Article
CAS
Google Scholar
Orozco H, Matallana E, Aranda A. Oxidative stress tolerance, adenylate cyclase, and autophagy are key players in the chronological life span of Saccharomyces cerevisiae during Winemaking. Appl Environ Microbiol. 2012;78:2748–57.
Article
CAS
Google Scholar
Reinders J, Zahedi RP, Pfanner N, Meisinger C, Sickmann A. Toward the complete yeast mitochondrial proteome: multidimensional separation techniques for mitochondrial proteomics. J Proteome Res. 2006;5:1543–54.
Article
CAS
Google Scholar
Hess DC, Myers CL, Huttenhower C, Hibbs MA, Hayes AP, Paw J, et al. Computationally driven, quantitative experiments discover genes required for mitochondrial biogenesis. PLoS Genet. 2009;5:e1000407 (Kim SK, editor).
Article
CAS
Google Scholar
Delmer DP. Dimethylsulfoxide as a potential tool for analysis of compartmentation in living plant cells. Plant Physiol. 1979;64:623–9.
Article
CAS
Google Scholar
Evans Christopher T, Ratledge Colin. Effect of nitrogen source on lipid accumulation in Oleaginous yeasts. J Gen Microbiol. 1984;130:1693–704.
CAS
Google Scholar
Park WS, Murphy PA, Glatz BA. Lipid metabolism and cell composition of the oleaginous yeast Apiotrichum curvatum grown at different carbon to nitrogen ratios. Can J Microbiol. 1990;36:318–26.
Article
CAS
Google Scholar
Cescut J, Fillaudeau L, Molina-Jouve C, Uribelarrea J-L. Carbon accumulation in Rhodotorula glutinis induced by nitrogen limitation. Biotechnol Biofuels. 2014;7:164.
Article
CAS
Google Scholar
Calvey CH, Su Y-K, Willis LB, McGee M, Jeffries TW. Nitrogen limitation, oxygen limitation, and lipid accumulation in Lipomyces starkeyi. Bioresour Technol. 2016;200:780–8.
Article
CAS
Google Scholar
Liu T, Li Y, Liu F, Wang C. The enhanced lipid accumulation in oleaginous microalga by the potential continuous nitrogen-limitation (CNL) strategy. Bioresour Technol. 2016;203:150–9.
Article
CAS
Google Scholar
Ushinsky SC, Bussey H, Ahmed AA, Wang Y, Friesen J, Williams BA, et al. Histone H1 in Saccharomyces cerevisiae. Yeast Chichester Engl. 1997;13:151–61.
Article
CAS
Google Scholar
Sorger D, Athenstaedt K, Hrastnik C, Daum G. A yeast strain lacking lipid particles bears a defect in ergosterol formation. J Biol Chem. 2004;279:31190–6.
Article
CAS
Google Scholar
Chung S-K, Lee K-W, Kang HI, Yamashita C, Kudo M, Yoshida Y. Design and synthesis of potential inhibitors of the ergosterol biosynthesis as antifungal agents. Bioorg Med Chem. 2000;8:2475–86.
Article
CAS
Google Scholar
Van Den Hazel HB, Kielland-Brandt MC, Winther JR. Review: biosynthesis and function of yeast vacuolar proteases. Yeast Chichester Engl. 1996;12:1–16.
Article
Google Scholar
Spencer J, Phister TG, Smart KA, Greetham D. Tolerance of pentose utilising yeast to hydrogen peroxide-induced oxidative stress. BMC Res. Notes. 2014;7:151.
Article
CAS
Google Scholar
Lopes M, Mota M, Belo I. Comparison of Yarrowia lipolytica and Pichia pastoris cellular response to different agents of oxidative stress. Appl Biochem Biotechnol. 2013;170:448–58.
Article
CAS
Google Scholar
Biryukova EN, Medentsev AG, Arinbasarova AY, Akimenko VK. Tolerance of the yeast Yarrowia lipolytica to oxidative stress. Microbiology. 2006;75:243–7.
Article
CAS
Google Scholar
Kawasse FM, Amaral PF, Rocha-Leão MHM, Amaral AL, Ferreira EC, Coelho MAZ. Morphological analysis of Yarrowia lipolytica under stress conditions through image processing. Bioprocess Biosyst Eng. 2003;25:371–5.
Article
CAS
Google Scholar
Eitzen GA, Szilard RK, Rachubinski RA. Enlarged peroxisomes are present in oleic acid-grown Yarrowia lipolytica overexpressing the PEX16 gene encoding an intraperoxisomal peripheral membrane peroxin. J Cell Biol. 1997;137:1265–78.
Article
CAS
Google Scholar
Szilard RK, Titorenko VI, Veenhuis M, Rachubinski RA. Pay32p of the yeast Yarrowia lipolytica is an intraperoxisomal component of the matrix protein translocation machinery. J Cell Biol. 1995;131:1453–69.
Article
CAS
Google Scholar
Titorenko VI, Smith JJ, Szilard RK, Rachubinski RA. Pex20p of the Yeast Yarrowia lipolytica is required for the oligomerization of thiolase in the cytosol and for its targeting to the peroxisome. J Cell Biol. 1998;142:403–20.
Article
CAS
Google Scholar
Wriessnegger T, Gübitz G, Leitner E, Ingolic E, Cregg J, de la Cruz BJ, et al. Lipid composition of peroxisomes from the yeast Pichia pastoris grown on different carbon sources. Biochim Biophys Acta. 2007;1771:455–61.
Article
CAS
Google Scholar
Nazarko T, Nicaud J, Sibirny A. Observation of the peroxisome-vacuole dynamics by fluorescence microscopy with a single filter set. Cell Biol Int. 2005;29:65–70.
Article
CAS
Google Scholar
Chang J, Mast FD, Fagarasanu A, Rachubinski DA, Eitzen GA, Dacks JB, et al. Pex3 peroxisome biogenesis proteins function in peroxisome inheritance as class V myosin receptors. J Cell Biol. 2009;187:233–46.
Article
CAS
Google Scholar
Kabran P, Rossignol T, Gaillardin C, Nicaud J-M, Neuveglise C. Alternative splicing regulates targeting of malate dehydrogenase in Yarrowia lipolytica. DNA Res. 2012;19:231–44.
Article
CAS
Google Scholar
Dulermo T, Nicaud J-M. Involvement of the G3P shuttle and β-oxidation pathway in the control of TAG synthesis and lipid accumulation in Yarrowia lipolytica. Metab Eng. 2011;13:482–91.
Article
CAS
Google Scholar
Gould SJ, Kalish JE, Morrell JC, Bjorkman J, Urquhart AJ, Crane DI. Pex13p is an SH3 protein of the peroxisome membrane and a docking factor for the predominantly cytoplasmic PTs1 receptor. J Cell Biol. 1996;135:85–95.
Article
CAS
Google Scholar
Elgersma Y, Kwast L, Klein A, Voorn-Brouwer T, van den Berg M, Metzig B, et al. The SH3 domain of the Saccharomyces cerevisiae peroxisomal membrane protein Pex13p functions as a docking site for Pex5p, a mobile receptor for the import PTS1-containing proteins. J Cell Biol. 1996;135:97–109.
Article
CAS
Google Scholar
Smith JJ, Aitchison JD. Peroxisomes take shape. Nat Rev Mol Cell Biol. 2013;14:803–17.
Article
CAS
Google Scholar
Manjithaya R, Nazarko TY, Farré J-C, Subramani S. Molecular mechanism and physiological role of pexophagy. FEBS Lett. 2010;584:1367–73.
Article
CAS
Google Scholar
Hutchins MU, Veenhuis M, Klionsky DJ. Peroxisome degradation in Saccharomyces cerevisiae is dependent on machinery of macroautophagy and the Cvt pathway. J Cell Sci. 1999;112(Pt 22):4079–87.
CAS
Google Scholar
Cordero Otero R, Gaillardin C. Efficient selection of hygromycin-B-resistant Yarrowia lipolytica transformants. Appl Microbiol Biotechnol. 1996;46:143–8.
Article
CAS
Google Scholar
Ruiz-Pavón L, Domínguez A. Characterization of the Yarrowia lipolytica YlSRP72 gene, a component of the yeast signal recognition particle. Int Microbiol Off J Span Soc Microbiol. 2007;10:283–9.
Google Scholar
Handee W, Li X, Hall KW, Deng X, Li P, Benning C, et al. An energy-independent pro-longevity function of triacylglycerol in yeast. PLOS Genet. 2016;12:e1005878 (Longo VD, editor).
Article
CAS
Google Scholar
Pomraning KR, Kim Y-M, Nicora CD, Chu RK, Bredeweg EL, Purvine SO, et al. Multi-omics analysis reveals regulators of the response to nitrogen limitation in Yarrowia lipolytica. BMC Genomics [Internet]. 2016; 17. http://www.biomedcentral.com/1471-2164/17/138. Accessed 30 Mar 2016.
Mekouar M, Blanc-Lenfle I, Ozanne C, Da Silva C, Cruaud C, Wincker P, et al. Detection and analysis of alternative splicing in Yarrowia lipolytica reveal structural constraints facilitating nonsense-mediated decay of intron-retaining transcripts. Genome Biol. 2010;11:R65.
Article
CAS
Google Scholar
Morin N, Cescut J, Beopoulos A, Lelandais G, Le Berre V, Uribelarrea J-L, et al. Transcriptomic analyses during the transition from biomass production to lipid accumulation in the oleaginous yeast Yarrowia lipolytica. PLoS ONE. 2011;6:e27966.
Article
CAS
Google Scholar
Colot HV, Park G, Turner GE, Ringelberg C, Crew CM, Litvinkova L, et al. A high-throughput gene knockout procedure for Neurospora reveals functions for multiple transcription factors. Proc Natl Acad Sci. 2006;103:10352–7.
Article
CAS
Google Scholar
Jefferson RA, Kavanagh TA, Bevan MW. GUS fusions: beta-glucuronidase as a sensitive and versatile gene fusion marker in higher plants. EMBO J. 1987;6:3901–7.
CAS
Google Scholar
Holsters M, de Waele D, Depicker A, Messens E, van Montagu M, Schell J. Transfection and transformation of Agrobacterium tumefaciens. Mol Gen Genet MGG. 1978;163:181–7.
Article
CAS
Google Scholar
de Groot MJA, Bundock P, Hooykaas PJ, Beijersbergen AGM. Agrobacterium tumefaciens-mediated transformation of filamentous fungi. Nat Biotechnol. 1998;16:839–42.
Article
Google Scholar
Murray MG, Thompson WF. Rapid isolation of high molecular weight plant DNA. Nucleic Acids Res. 1980;8:4321–6.
Article
CAS
Google Scholar
Zerbino DR. Using the Velvet de novo assembler for short-read sequencing technologies. Curr Protoc Bioinforma. Ed. Board Andreas Baxevanis Al. 2010; Chapter 11: Unit 11.5.
Trapnell C, Pachter L, Salzberg SL. TopHat: discovering splice junctions with RNA-Seq. Bioinforma Oxf Engl. 2009;25:1105–11.
Article
CAS
Google Scholar
Götz S, García-Gómez JM, Terol J, Williams TD, Nagaraj SH, Nueda MJ, et al. High-throughput functional annotation and data mining with the Blast2GO suite. Nucleic Acids Res. 2008;36:3420–35.
Article
CAS
Google Scholar
Kent WJ. BLAT–the BLAST-like alignment tool. Genome Res. 2002;12:656–64.
Article
CAS
Google Scholar
Langmead B, Trapnell C, Pop M, Salzberg SL. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol. 2009;10:R25.
Article
CAS
Google Scholar
Gritz L, Davies J. Plasmid-encoded hygromycin B resistance: the sequence of hygromycin B phosphotransferase gene and its expression in Escherichia coli and Saccharomyces cerevisiae. Gene. 1983;25:179–88.
Article
CAS
Google Scholar
Gietz RD, Woods RA. Transformation of yeast by lithium acetate/single-stranded carrier DNA/polyethylene glycol method. Methods Enzymol. 2002;350:87–96.
Article
CAS
Google Scholar
Ghaemmaghami S, Huh W-K, Bower K, Howson RW, Belle A, Dephoure N, et al. Global analysis of protein expression in yeast. Nature. 2003;425:737–41.
Article
CAS
Google Scholar
Gietz RD. Yeast transformation by the LiAc/SS carrier DNA/PEG method. Methods Mol Biol Clifton NJ. 2014;1163:33–44.
Article
CAS
Google Scholar
Schneider CA, Rasband WS, Eliceiri KW. NIH Image to ImageJ: 25 years of image analysis. Nat Methods. 2012;9:671–5.
Article
CAS
Google Scholar
Carpenter AE, Jones TR, Lamprecht MR, Clarke C, Kang IH, Friman O, et al. Cell profiler: image analysis software for identifying and quantifying cell phenotypes. Genome Biol. 2006;7:R100.
Article
CAS
Google Scholar
Schindelin J, Arganda-Carreras I, Frise E, Kaynig V, Longair M, Pietzsch T, et al. Fiji: an open-source platform for biological-image analysis. Nat Methods. 2012;9:676–82.
Article
CAS
Google Scholar
Gaillardin CM, Charoy V, Heslot H. A study of copulation, sporulation and meiotic segregation in Candida lipolytica. Arch Mikrobiol. 1973;92(1):69–83.
Article
CAS
Google Scholar