Abstract
The basidiomycetous fungus Pseudozyma aphidis is able to convert vegetable oils to abundant amounts of the biosurfactant mannosylerythritol lipid (MEL) with a unique product pattern of MEL-A, MEL-B, MEL-C, and MEL-D. To investigate the metabolism of MEL production, we analyzed the transcriptome of P. aphidis DSM 70725 under MEL-inducing and non-inducing conditions using deep sequencing. Following manual curation of the previously described in silico gene models based on RNA-Seq data, we were able to generate an experimentally verified gene annotation containing 6347 genes. Using this database, our expression analysis revealed that only four of the five cluster genes required for MEL synthesis were clearly induced by the presence of soybean oil. The acetyltransferase encoding gene PaGMAT1 was expressed on a much lower level, which may explain the secretion of MEL with different degrees of acetylation in P. aphidis. In parallel to MEL synthesis, microscopic observations showed morphological changes accompanied by expression of genes responsible for cell development, indicative of a coregulation between MEL synthesis and cell morphology. In addition a set of transcription factors was identified which may be responsible for regulation of MEL synthesis and cell development. The upregulation of genes required for nitrogen metabolism and other assimilation processes indicate additional metabolic pathways required under the MEL-inducing conditions used. We also searched for a conserved gene cluster for cellobiose lipids (CL) but only found seven genes with limited homology distributed over the genome. However, we detected characteristic TLC spots in fermentations using P. aphidis DSM 70725, indicative of CL secretion.
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References
Anderson MD, Che P, Song J, Nikolau BJ, Wurtele ES (1998) 3-Methylcrotonyl-coenzyme A carboxylase is a component of the mitochondrial leucine catabolic pathway in plants. Plant Physiol 118:1127–1138. doi:10.1104/pp. 118.4.1127
Arutchelvi JI, Bhaduri S, Uppara PV, Doble M (2008) Mannosylerythritol lipids: a review. J Ind Microbiol Biotechnol 35:1559–1570. doi:10.1007/s10295-008-0460-4
Bölker M, Basse CW, Schirawski J (2008) Ustilago maydis secondary metabolism—from genomics to biochemistry. Fungal Genet Biol 45(Suppl 1):88–93. doi:10.1016/j.fgb.2008.05.007
Boothroyd B, Thorn JA, Haskins RH (1955) Biochemistry of the Ustilaginales X. The biosynthesis of ustilagic acid. Can J Biochem Physiol 33:289–296. doi:10.1139/o55-039
Conesa A, Götz S, García-Gómez JM, Terol J, Talón M, Robles M (2005) Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research. Bioinformatics 21:3674–3676. doi:10.1093/bioinformatics/bti610
Cosgrove DJ (1996) Plant cell enlargement and the action of expansins. Bioessays 18:533–540. doi:10.1002/bies.950180704
Elìas-Villalobos A, Fernández-Álvarez A, Ibeas JI (2011) The general transcriptional repressor Tup1 is required for dimorphism and virulence in a fungal plant pathogen. PLOS Pathog. doi:10.1371/journal.ppat.1002235
Freitag J, Ast J, Linne U, Stehlik T, Martorana D, Bölker M, Sandrock B (2014) Peroxisomes contribute to biosynthesis of extracellular glycolipids in fungi. Mol Microbiol 93:24–36. doi:10.1111/mmi.12642
Grumaz C, Lorenz S, Stevens P, Lindemann E, Schock U, Retey J, Rupp S, Sohn K (2013) Species and condition specific adaptation of the transcriptional landscapes in Candida albicans and Candida dubliniensis. BMC Genomics 14:212. doi:10.1186/1471-2164-14-212
Guida A, Lindstadt C, Maguire SL, Ding C, Higgins DG, Corton NJ, Berriman M, Butler G (2011) Using RNA-seq to determine the transcriptional landscape and the hypoxic response of the pathogenic yeast Candida parapsilosis. BMC Genomics 12:628. doi:10.1186/1471-2164-12-628
Hewald S, Linne U, Scherer M, Marahiel MA, Kämper J, Bölker M (2006) Identification of a gene cluster for biosynthesis of mannosylerythritol lipids in the basidiomycetous fungus Ustilago maydis. Appl Environ Microbiol 72:5469–5477. doi:10.1128/AEM. 00506-06
Horst RJ, Zeh C, Saur A, Sonnewald S, Sonnewald U, Voll LM (2012) The Ustilago maydis Nit2 homolog regulates nitrogen utilization and is required for efficient induction of filamentous growth. Eukaryot Cell 11:368–380. doi:10.1128/EC.05191-11
Im JH, Yanagishita H, Ikegami T, Takeyama Y, Idemoto Y, Koura N, Kitamoto D (2003) Mannosylerythritol lipids, yeast glycolipid biosurfactants, are potential affinity ligand materials for human immunoglobulin G. J Biomed Mater Res A 65:379–385. doi:10.1002/jbm.a.10491
Imura T, Ohta N, Inoue K, Yagi N, Negishi H, Yanagishita H, Kitamoto D (2006) Naturally engineered glycolipid biosurfactants leading to distinctive self-assembled structures. Chemistry 12:2434–2440. doi:10.1002/chem.200501199
Imura T, Masuda Y, Ito S, Worakitkanchanakul W, Morita T, Fukuoka T, Sakai H, Abe M, Kitamoto D (2008) Packing density of glycolipid biosurfactant monolayers give a significant effect on their binding affinity toward immunoglobulin G. J Oleo Sci 57:415–422. doi:10.5650/jos.57.415
Inoh Y, Furuno T, Hirashima N, Kitamoto D, Nakanishi M (2010) The ratio of unsaturated fatty acids in biosurfactants affects the efficiency of gene transfection. Int J Pharm 398:225–230. doi:10.1016/j.ijpharm.2010.07.042
Inoh Y, Furuno T, Hirashima N, Kitamoto D, Nakanishi M (2011) Rapid delivery of small interfering RNA by biosurfactant MEL-A-containing liposomes. Biochem Biophys Res Commun 414:635–640. doi:10.1016/j.bbrc.2011.09.147
Kämper J, Kahmann R, Bölker M, Ma LJ, Brefort T, Saville BJ, Banuett F, Kronstad JW, Gold SE, Müller O, Perlin MH, Wösten HA, de Vries R, Ruiz-Herrera J, Reynaga-Pena CG, Snetselaar K, McCann M, Perez-Martín J, Feldbrügge M, Basse CW, Steinberg G, Ibeas JI, Holloman W, Guzman P, Farman M, Stajich JE, Sentandreu R, González-Prieto JM, Kennell JC, Molina L, Schirawski J, Mendoza-Mendoza A, Greilinger D, Münch K, Rössel N, Scherer M, Vranes M, Ladendorf O, Vincon V, Fuchs U, Sandrock B, Meng S, Ho EC, Cahill MJ, Boyce KJ, Klose J, Klosterman SJ, Deelstra HJ, Ortiz-Castellanos L, Li W, Sanchez-Alonso P, Schreier PH, Häuser-Hahn I, Vaupel M, Koopmann E, Friedrich G, Voss H, Schlüter T, Margolis J, Platt D, Swimmer C, Gnirke A, Chen F, Vysotskaia V, Mannhaupt G, Güldener U, Münsterkötter M, Haase D, Oesterheld M, Mewes HW, Mauceli EW, DeCaprio D, Wade CM, Butler J, Young S, Jaffe DB, Calvo S, Nusbaum C, Galagan J, Birren BW (2006) Insights from the genome of the biotrophic fungal plant pathogen Ustilago maydis. Nature 444:97–101. doi:10.1038/nature05248
Kitamoto D, Nemoto T, Yanagishita H, Nakane T, Kitamoto H, Nakahara T (1993) Fatty-acid metabolism of mannosylerythritol lipids as biosurfactants produced by Candida antarctica. J Jpn Oil Chem Soc 42:346–358
Kitamoto D, Ikegami T, Suzuki GT, Sasaki A, Takeyama Y, Idemoto Y, Koura N, Yanagishita H (2001) Microbial conversion of n-alkanes into glycolipid biosurfactants, mannosylerythritol lipids, by Pseudozyma (Candida antarctica). Biotechnol Lett 23:1709–1714. doi:10.1023/A:1012464717259
Klose J, de Sa MM, Kronstad JW (2004) Lipid-induced filamentous growth in Ustilago maydis. Mol Microbiol 52:823–835. doi:10.1111/j.1365-2958.2004.04019.x
Konishi M, Hatada Y, Horiuchi J (2013) Draft genome sequence of the basidiomycetous yeast-like fungus Pseudozyma hubeiensis SY62, which produces an abundant amount of the biosurfactant mannosylerythritol lipids. Genome Announc 1:e00409–00413. doi:10.1128/genomeA. 00409-13
Lorenz S, Günther M, Grumaz C, Rupp S, Zibek S, Sohn K (2014) Genome sequence of the basidiomycetous fungus Pseudozyma aphidis DSM 70725, an efficient producer of biosurfactant mannosylerythritol lipids. Genome Announc 2:e00053–00014. doi:10.1128/genomeA. 00053-14
Morita T, Konishi M, Fukuoka T, Imura T, Kitamoto D (2007a) Physiological differences in the formation of the glycolipid biosurfactants, mannosylerythritol lipids, between Pseudozyma antarctica and Pseudozyma aphidis. Appl Microbiol Biotechnol 74:307–315. doi:10.1007/s00253-006-0672-3
Morita T, Konishi M, Fukuoka T, Imura T, Kitamoto HK, Kitamoto D (2007b) Characterization of the genus Pseudozyma by the formation of glycolipid biosurfactants, mannosylerythritol lipids. FEMS Yeast Res 7:286–292. doi:10.1111/j.1567-1364.2006.00154.x
Morita T, Kitagawa M, Suzuki M, Yamamoto S, Sogabe A, Yanagidani S, Imura T, Fukuoka T, Kitamoto D (2009) A yeast glycolipid biosurfactant, mannosylerythritol lipid, shows potential moisturizing activity toward cultured human skin cells: the recovery effect of MEL-A on the SDS-damaged human skin cells. J Oleo Sci 58:639–642. doi:10.5650/jos.58.639
Morita T, Ito E, Kitamoto HK, Takegawa K, Fukuoka T, Imura T, Kitamoto D (2010) Identification of the gene PaEMT1 for biosynthesis of mannosylerythritol lipids in the basidiomycetous yeast Pseudozyma antarctica. Yeast 27:905–917. doi:10.1002/yea.1794
Morita T, Ishibashi Y, Hirose N, Wada K, Takahashi M, Fukuoka T, Imura T, Sakai H, Abe M, Kitamoto D (2011) Production and characterization of a glycolipid biosurfactant, mannosylerythritol lipid B, from sugarcane juice by Ustilago scitaminea NBRC 32730. Biosci Biotechnol Biochem 75:1371–1376. doi:10.1271/bbb.110221
Morita T, Fukuoka T, Imura T, Kitamoto D (2013a) Accumulation of cellobiose lipids under nitrogen-limiting conditions by two ustilaginomycetous yeasts, Pseudozyma aphidis and Pseudozyma hubeiensis. FEMS Yeast Res 13:44–49. doi:10.1111/1567-1364.12005
Morita T, Koike H, Koyama Y, Hagiwara H, Ito E, Fukuoka T, Imura T, Machida M, Kitamoto D (2013b) Genome sequence of the basidiomycetous yeast Pseudozyma antarctica T-34, a producer of the glycolipid biosurfactants mannosylerythritol lipids. Genome Announc 1:e0006413. doi:10.1128/genomeA. 00064-13
Morita T, Fukuoka T, Imura T, Kitamoto D (2013c) Production of mannosylerythritol lipids and their application in cosmetics. Appl Microbiol Biotechnol 97:4691–4700. doi:10.1007/s00253-013-4858-1
Morita T, Koike H, Hagiwara H, Ito E, Machida M, Sato S, Habe H, Kitamoto D (2014) Genome and transcriptome analysis of the basidiomycetous yeast Pseudozyma antarctica producing extracellular glycolipids, mannosylerythritol lipids. PLoS ONE 9:e86490. doi:10.1371/journal.pone.0086490
Mortazavi A, Williams BA, McCue K, Schaeffer L, Wold B (2008) Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat Methods 5:621–628. doi:10.1038/nmeth.1226
Ness SA (1999) Myb binding proteins: regulators and cohorts in transformation. Oncogene 18:3039–3046. doi:10.1038/sj.onc.1202726
Nikolaidis N, Doran N, Cosgrove DJ (2014) Plant expansins in bacteria and fungi: evolution by horizontal gene transfer and independent domain fusion. Mol Biol Evol 31:376–386. doi:10.1093/molbev/mst206
Rau U, Nguyen LA, Roeper H, Koch H, Lang S (2005a) Fed-batch bioreactor production of mannosylerythritol lipids secreted by Pseudozyma aphidis. Appl Microbiol Biotechnol 68:607–613. doi:10.1007/s00253-005-1906-5
Rau U, Nguyen LA, Roeper H, Koch H, Lang S (2005b) Downstream processing of mannosylerythritol lipids produced by Pseudozyma aphidis. Eur J Lipid Sci Technol 107:373–380. doi:10.1002/ejlt.200401122
Smyth GK (2005) Limma: linear models for microarray data. In: Gentleman R, Carey VJ, Huber W, Irizarry RA, Dudoit S (eds) Bioinformatics and computational biology solutions using R and Bioconductor. Springer, New York, NY, pp 397–420
Storey JD, Tibshirani R (2003) Statistical significance for genomewide studies. Proc Natl Acad Sci U S A 100:9440–9445. doi:10.1073/pnas.1530509100
Teichmann B, Linne U, Hewald S, Marahiel MA, Bölker M (2007) A biosynthetic gene cluster for a secreted cellobiose lipid with antifungal activity from Ustilago maydis. Mol Microbiol 66:525–533. doi:10.1111/j.1365-2958.2007.05941.x
Teichmann B, Liu L, Schink KO, Bölker M (2010) Activation of the ustilagic acid biosynthesis gene cluster in Ustilago maydis by the C2H2 zinc finger transcription factor Rua1. Appl Environ Microbiol 76:2633–2640. doi:10.1128/AEM. 02211-09
Trapnell C, Pachter L, Salzberg SL (2009) TopHat: discovering splice junctions with RNA-Seq. Bioinformatics 25:1105–1111. doi:10.1093/bioinformatics/btp120
Trapnell C, Roberts A, Goff L, Pertea G, Kim D, Kelley DR, Pimentel H, Salzberg SL, Rinn JL, Pachter L (2012) Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks. Nat Protoc 7:562–578. doi:10.1038/nprot.2012.016
Wang L, Feng Z, Wang X, Wang X, Zhang X (2010) DEGseq: an R package for identifying differentially expressed genes from RNA-seq data. Bioinformatics 26:136–138. doi:10.1093/bioinformatics/btp612
Yamamoto S, Morita T, Fukuoka T, Imura T, Yanagidani S, Sogabe A, Kitamoto D, Kitagawa M (2012) The moisturizing effects of glycolipid biosurfactants, mannosylerythritol lipids, on human skin. J Oleo Sci 61:407–412. doi:10.5650/jos.61.407
Yamamoto S, Fukuoka T, Imura T, Morita T, Yanagidani S, Kitamoto D, Kitagawa M (2013) Production of a novel mannosylerythritol lipid containing a hydroxy fatty acid from castor oil by Pseudozyma tsukubaensis. J Oleo Sci 62:381–389. doi:10.5650/jos.62.381
Yoshida S, Morita T, Shinozaki Y, Watanabe T, Sameshima-Yamashita Y, Koitabashi M, Kitamoto D, Kitamoto H (2014) Mannosylerythritol lipids secreted by phyllosphere yeast Pseudozyma antarctica is associated with its filamentous growth and propagation on plant surfaces. Appl Microbiol Biotechnol 98:6419–6429. doi:10.1007/s00253-014-5675-x
Acknowledgments
This work was funded by an ERA-NET grant (no. 0315928A, ERA-IB10.039, “BioSurf—Novel Production Strategies for Biosurfactants”). It was further supported by a PhD scholarship of the “Deutsche Bundestiftung Umwelt” (DBU).
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Günther, M., Grumaz, C., Lorenz, S. et al. The transcriptomic profile of Pseudozyma aphidis during production of mannosylerythritol lipids. Appl Microbiol Biotechnol 99, 1375–1388 (2015). https://doi.org/10.1007/s00253-014-6359-2
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DOI: https://doi.org/10.1007/s00253-014-6359-2