Genome and transcriptome analysis of the basidiomycetous yeast Pseudozyma antarctica producing extracellular glycolipids, mannosylerythritol lipids

PLoS ONE

Volumn 9, Issue 2, 2014, Pages

  Morita, Tomotake ^a   Koike, Hideaki ^a   Hagiwara, Hiroko ^a   Ito, Emi ^a   Machida, Masayuki ^a   Sato, Shun ^a   Habe, Hiroshi ^a   Kitamoto, Dai ^a  

^a NATIONAL INSTITUTE OF ADVANCED INDUSTRIAL SCIENCE AND TECHNOLOGY AIST   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

ACETYL COENZYME A; ADENOSINE TRIPHOSPHATE; CARBON; CITRATE LYASE; FATTY ACID; GLUCOSE; GLYCOLIPID; LYASE; MANNOSYLERYTHRITOL; SOYBEAN OIL; TRANSCRIPTOME; UNCLASSIFIED DRUG; MANNOSYLERYTHRITOL LIPID;

ACL GENE; ARTICLE; BASIDIOMYCETES; CARBON SOURCE; CLASSIFICATION; CONTROLLED STUDY; DNA MICROARRAY; ENZYME SYNTHESIS; FATTY ACID METABOLISM; FUNGAL GENE; FUNGAL GENOME; FUNGAL STRAIN; FUNGUS CULTURE; GENE EXPRESSION PROFILING; GENE NUMBER; GENETIC CONSERVATION; GENOME ANALYSIS; LIPID METABOLISM; LIPID TRANSPORT; LIPOGENESIS; NONHUMAN; NUCLEOTIDE SEQUENCE; PSEUDOZYMA ANTARCTICA; RNA ANALYSIS; SACCHAROMYCES CEREVISIAE; SYNTENY; UPREGULATION; USTILAGO MAYDIS; GENETICS; METABOLISM; PHYLOGENY; PROCEDURES;

BASIDIOMYCOTA; GENE EXPRESSION PROFILING; GENOME, FUNGAL; GLUCOSE; GLYCOLIPIDS; PHYLOGENY; SACCHAROMYCES CEREVISIAE; SOYBEAN OIL; TRANSCRIPTOME;

EID: 84896135582     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0086490     Document Type: Article

References (59)

1. Boekhout T (1995) Pseudozyma Bandoni emend. Boekhout, a genus for yeast-like anamorphs of Ustilaginales. J Gen Appl Microbiol 41: 359-366.
2. Boekhout T, Fell JW (1998) Pseudozyma Bandoni emend. Boekhout and a comparison with the yeast state of Ustilago maydis (de Candolle) Corda. In: Kurtzman CP, Fell JWThe yeasts: a taxonomic study 4th ed. Amsterdam: Elsevier Science Publishers; 790-797.
3. Wang QM, Jia JH, Bai FY (2006) Pseudozyma hubeiensis sp. nov. and Pseudozyma shanxiensis sp. nov., novel ustilaginomycetous anamorphic yeast species from plant leaves. Int. J Syst Evol Microbiol 56: 289-293.
4. Golubev W, Sugita T, Golubev N (2007) An ustilaginomycetous yeast, Pseudozyma graminicola sp. nov., isolated from the leaves of pasture plants. Mycoscience 48: 29-33. (Pubitemid 46198759)
5. Seo HS, Um HJ, Min J, Rhee SK, Cho TJ, et al. (2007) Pseudozyma jejuensis sp. nov., a novel cutinolytic ustilaginomycetous yeast species that is able to degrade plastic waste. FEMS Yeast Res 7: 1035-1045. (Pubitemid 47256361)
6. Morita T, Ogura Y, Takashima M, Hirose N, Fukuoka T, et al. (2011) Isolation of Pseudozyma churashimaensis sp. nov., a novel ustilaginomycetous yeast species as a producer of glycolipid biosurfactants, mannosylerythritol lipids. J Biosci Bioeng 112: 137-144.
7. Köse Ö, Tüter M, Ayşe Aksoy H (2002) Immobilized Candida antarctica lipase-catalyzed alcoholysis of cotton seed oil in a solvent-free medium. Bioresour Technol 83: 125-129.
8. Schmid RD, Verger R (1998) Lipases: interfacial enzymes with attractive applications. Angew Chem Int Ed 37: 1608-1633.
9. Blank K, Morfill J, Gumpp H, Gaub HE (2006) Functional expression of Candida antarctica lipase B in Eschericha coli. J Biotechnol 125: 474-483. (Pubitemid 44333128)
10. Kitamoto HK, Shinozaki Y, Cao XH, Morita T, Konishi M, et al. (2011) Phyllosphere yeasts rapidly break down biodegradable plastics. AMB Express 1: 44.
11. Kitamoto D, Haneishi K, Nakahara T, Tabuchi T (1990) Production of mannosylerythritol lipids by Candida antarctica from vegetable oils. Agric Biol Chem 54: 37-40.
12. Kitamoto D, Isoda H, Nakahara T (2002) Functional and potential applications of glycolipid biosurfactants. J Biosci Bioeng 94: 187-201.
13. Kitamoto D, Morita T, Fukuoka T, Konishi M, Imura T (2009) Self-assembling properties of glycolipid biosurfactants and their potential applications. Curr Opin Colloid Interface Sci 14: 315-328.
14. Morita T, Fukuoka T, Imura T, Kitamoto D (2013) Production of mannosylerythritol lipids and their application in cosmetics. Appl Microbiol Biotechnol 97: 4691-4700.
15. Imura T, Hikosaka Y, Worakitkanchanakul W, Sakai H, Abe M, et al. (2007) Aqueous-phase behavior of natural glycolipid biosurfactant mannosylerythritol lipid A: sponge, cubic, and lamellar phases. Langmuir 23: 1659-1663. (Pubitemid 46406110)
16. Ito S, Imura T, Fukuoka T, Morita T, Sakai H, et al. (2007) Kinetic studies on the interactions between glycolipid biosurfactant assembled monolayers and various classes of immunoglobulins using surface plasmon resonance. Colloids Surf B Biointerfaces 58: 165-171. (Pubitemid 46921453)
17. Morita T, Fukuoka T, Imura T, Kitamoto D (2009) Production of glycolipid biosurfactants by basidiomycetous yeasts. Biotechnol Appl Biochem 53: 39-49.
18. Hewald S, Josephs K, Bölker M (2005) Genetic analysis of biosurfactant production in Ustilago maydis. Appl Environ Microbiol 71: 3033-3040. (Pubitemid 40807208)
19. Hewald S, Linne U, Scherer M, Marahiel MA, Kämper J, et al. (2006) Identification of a gene cluster for biosynthesis of mannosylerythritol lipids in the basidiomycetous fungus Ustilago maydis. Appl Environ Microbiol 72: 5469-5477.
20. Spoeckner S, Wray V, Nimtz M, Lang S (1999) Glycolipids of the smut fungus Ustilago maydis from cultivation on renewable resources. Appl Microbiol Biotechnol 51: 33-39. (Pubitemid 29066643)
21. Boothroyd B, Thorn JA, Haskins RH (1956) Biochemistry of the ustilaginales. XII. Characterization of extracellular glycolipids produced by Ustilago sp. Can J Biochem Physiol 34: 10-14.
22. Fluharty AL, O'Brien JS (1969) A mannose- and erythritol-containing glycolipid from Ustilago maydis. Biochemistry 8: 2627-2632.
23. Kitamoto D, Ikegami T, Suzuki T, Sasaki A, Takeyama Y, et al. (2001) Microbial conversion of n-alkanes into glycolipid biosurfactants, mannosylerythritol lipids, by Pseudozyma (Candida antarctica) . Biotechnol Lett 23: 1709-1714. (Pubitemid 33019901)
24. Morita T, Konishi M, Fukuoka T, Imura T, Kitamoto D (2006) Discovery of Pseudozyma rugulosa NBRC 10877 as a novel producer of the glycolipid biosurfactants, mannosylerythritol lipids, based on rDNA sequence. Appl Microbiol Biotechnol 73: 305-313. (Pubitemid 350262607)
25. Rau U, Nguyen LA, Roeper H, Koch H, Lang S (2005) Fed-batch bioreactor production of mannosylerythritol lipids secreted by Pseudozyma aphidis. Appl Microbiol Biotechnol 68: 607-613. (Pubitemid 41549975)
26. Konishi M, Nagahama T, Fukuoka T, Morita T, Imura T, et al. (2011) Yeast extract stimulates production of glycolipid biosurfactants, mannosylerythritol lipids, by Pseudozyma hubeiensis SY62. J Biosci Bioeng 111: 702-705.
27. Kitamoto D, Yanagishita H, Haraya K, Kitamoto H (1998) Contribution of a chain-shortening pathway to the biosynthesis of the fatty acids of mannosylerythritol lipid (biosurfactant) in the yeast Candida antarctica: Effect of β-oxidation inhibitors on biosurfactant synthesis. Biotechnol Lett 20: 813-818. (Pubitemid 28458762)
28. Morita T, Konishi M, Fukuoka T, Imura T, Kitamoto HK, et al. (2007) Characterization of the genus Pseudozyma by the formation of glycolipid biosurfactants, mannosylerythritol lipids. FEMS Yeast Res 7: 286-292.
29. Fukuoka T, Morita T, Konishi M, Imura T, Sakai H, et al. (2007) Structural characterization and surface-active properties of a new glycolipid biosurfactant, mono-acylated mannosylerythritol lipid, produced from glucose by Pseudozyma antarctica. Appl Microbiol Biotechnol 76: 801-810. (Pubitemid 47340931)
30. Fukuoka T, Morita T, Konishi M, Imura T, Kitamoto D (2007) Characterization of new glycolipid biosurfactants, tri-acylated mannosylerythritol lipids, produced by Pseudozyma yeasts. Biotechnol Lett 29: 1111-1118. (Pubitemid 46800641)
31. Morita T, Koike H, Koyama Y, Hagiwara H, Ito E, et al. (2013) 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.
32. Kanehisa M, Goto S, Hattori M, Aoki-Kinoshita KF, Itoh M, et al. (2006) From genomics to chemical genomics: new developments in KEGG. Nucleic Acids Res 34(Database issue): D354-357.
33. Koonin EV, Fedorova ND, Jackson JD, Jacobs AR, Krylov DM, et al. (2004) A comprehensive evolutionary classification of proteins encoded in complete eukaryotic genomes. Genome Biol 5: R7.
34. Camacho C, Coulouris G, Avagyan V, Ma N, Papadopoulos J, et al. (2009) BLAST+: architecture and applications. BMC Bioinformatics 10: 421. doi: 10.1186/1471-2105-10-421.
35. Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, et al. (2000) Gene ontology: tool for the unification of biology. Nat Genet 25: 25-29. (Pubitemid 30257031)
36. Kurtz S, Phillippy A, Delcher AL, Smoot M, Shumway M, et al, (2004) Versatile and open software for comparing large genomes. Genome Biology 5: R12.
37. Vorapreeda T, Thammarongtham C, Cheevadhanarak S, Laoteng K (2012) Alternative routes of acetyl-CoA synthesis identified by comparative genomic analysis: involvement in the lipid production of oleaginous yeast and fungi. Microbiology 158: 217-228.
38. Tamano K, Bruno KS, Karagiosis SA, Culley DE, Deng S, et al.(2013) Increased production of fatty acids and triglycerides in Aspergillus oryzae by enhancing expressions of fatty acid synthesis-related genes. Appl Microbiol Biotechnol. 97: 269-281.
39. Grigoriev IV, Nordberg H, Shabalov I, Aerts A, Cantor M, et al. (2011) The Genome Portal of the Department of Energy Joint Genome Institute. Nucl Acids Res 40: D26-D32. doi: 10.1093/nar/gkr947.
40. Katoh K, Asimenos G, Toh H (2009) Multiple Alignment of DNA Sequences with MAFFT. Methods Mol Biol 537: 39-64. doi: 10.1007/978-1-59745-251-9-3.
41. Punta M, Coggill PC, Eberhardt RY, Mistry J, Tate J, et al. (2012) The Pfam protein families database. Nucleic Acids Res 40 (Database issue): D290-301. doi: 10.1093/nar/gkr1065.
42. Stamatakis A, Hoover P, Rougemont J (2008) A rapid bootstrap algorithm for the RAxML Web servers. Syst Biol 57: 758-771.
43. Tamano K, Sano M, Yamane N, Terabayashi Y, Toda T, et al. (2008) Transcriptional regulation of genes on the non-syntenic blocks of Aspergillus oryzae and its functional relationship to solid-state cultivation. Fungal Genet Biol 45: 139-151.
44. R Development Core Team (2009) R: A Language and Environment for Statistical. Computing, R Foundation for Statistical Computing, Vienna, Austria.
45. Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, et al. (2004) Bioconductor: open software development for computational biology and bioinformatics. Genome Biol 5: R80.
46. Yang YH, Paquet AC (2005) Preprocessing two-color spotted arrays. In: Gentleman RC, Carey VJ, Huber W, Irizarry RA, Dudoit S (Eds.). 2005. Bioinformatics and Computational Biology Solutions using R and Bioconductor. Springer Science+Business Media Inc., New York, 49-90.
47. Subramanian A, Tamayo P, Mootha VK, Mukherjee S, Ebert BL, et al. (2005) Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles. Proc Natl Acad Sci USA 102: 15545-15550. (Pubitemid 41528093)
48. Hynes MJ, Murray SL (2010) ATP-citrate lyase is required for production of cytosolic acetyl coenzyme A and development in Aspergillus nidulans. Eukaryot Cell 9: 1039-1048.
49. Fatland BL, Ke J, Anderson MD, Mentzen WI, Cui LW, et al. (2002) Molecular characterization of a heteromeric ATP-citrate lyase that generates cytosolic acetyl-coenzyme A in Arabidopsis. Plant Physiol. 130: 740-756. (Pubitemid 35235286)
50. Kämper J, Kahmann R, Bölker M, Ma LJ, Brefort T, et al. (2006) Insights from the genome of the biotrophic fungal plant pathogen Ustilago maydis. Nature 444: 97-101. (Pubitemid 44684763)
51. Dean RA, Talbot NJ, Ebbole DJ, Farman ML, Mitchell TK, et al. (2005) The genome sequence of the rice blast fungus Magnaporthe grisea. Nature 434: 980-986. (Pubitemid 40586040)
52. Mendgen K, Hahn M (2002) Plant infection and the establishment of fungal biotrophy. Trends Plant Sci 7: 352-356. (Pubitemid 36726502)
53. Dean RA (2007) Fungal gene clusters. Nat Biotechnol 25: 67.
54. Morita T, Konishi M, Fukuoka T, Imura T, Kitamoto D (2006) Analysis of expressed sequence tags from the anamorphic basidiomycetous yeast, Pseudozyma antarctica, which produces glycolipid biosurfactants, mannosylerythritol lipids. Yeast 23: 661-671. (Pubitemid 44210054)
55. 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. (Pubitemid 47482392)
56. Schirawski J, Mannhaupt G, Münch K, Brefort T, Schipper K, et al. (2010) Pathogenicity determinants in smut fungi revealed by genome comparison. Science 330: 1546-1548.
57. Konishi M, Morita T, Fukuoka T, Imura T, Kakugawa K, et al. (2007) Production of different types of mannosylerythritol lipids as biosurfactants by the newly isolated yeast strains belonging to the genus Pseudozyma. Appl Microbiol Biotechnol 75: 521-531. (Pubitemid 46776542)
58. KoitabashiM, Noguchi MT, Sameshima-Yamashita Y, Hiradate S, Suzuki K, et al. (2012) Degradation of biodegradable plastic mulch films in soil environment by phylloplane fungi isolated from gramineous plants. AMB Express 2: 40. doi: 10.1186/2191-0855-2-40.
59. Morita T, Ito E, Kitamoto HK, Takegawa K, Fukuoka T, et al. (2010) Identification of the gene PaEMT1 for biosynthesis of mannosylerythritol lipids in the basidiomycetous yeast Pseudozyma antarctica. Yeast 27: 905-917.