Advertisement

Current Microbiology

, Volume 75, Issue 1, pp 57–70 | Cite as

Genome Characterization of Oleaginous Aspergillus oryzae BCC7051: A Potential Fungal-Based Platform for Lipid Production

  • Chinae Thammarongtham
  • Intawat Nookaew
  • Tayvich Vorapreeda
  • Tanawut Srisuk
  • Miriam L. Land
  • Sukanya Jeennor
  • Kobkul Laoteng
Article

Abstract

The selected robust fungus, Aspergillus oryzae strain BCC7051 is of interest for biotechnological production of lipid-derived products due to its capability to accumulate high amount of intracellular lipids using various sugars and agro-industrial substrates. Here, we report the genome sequence of the oleaginous A. oryzae BCC7051. The obtained reads were de novo assembled into 25 scaffolds spanning of 38,550,958 bps with predicted 11,456 protein-coding genes. By synteny mapping, a large rearrangement was found in two scaffolds of A. oryzae BCC7051 as compared to the reference RIB40 strain. The genetic relationship between BCC7051 and other strains of A. oryzae in terms of aflatoxin production was investigated, indicating that the A. oryzae BCC7051 was categorized into group 2 nonaflatoxin-producing strain. Moreover, a comparative analysis of the structural genes focusing on the involvement in lipid metabolism among oleaginous yeast and fungi revealed the presence of multiple isoforms of metabolic enzymes responsible for fatty acid synthesis in BCC7051. The alternative routes of acetyl-CoA generation as oleaginous features and malate/citrate/pyruvate shuttle were also identified in this A. oryzae strain. The genome sequence generated in this work is a dedicated resource for expanding genome-wide study of microbial lipids at systems level, and developing the fungal-based platform for production of diversified lipids with commercial relevance.

Notes

Acknowledgements

We gratefully thank Uppsala Genome Center for Pacific BioScience platform sequencing service. We also thank Comparative Genomics Group, Division of BioScience, Oak Ridge National Laboratory for computational resources for gene prediction.

Funding

This work was financially supported by National Center for Genetic Engineering and Biotechnology (Project No. P-14-50613). The Swedish Research Council (VR-2013-4504) is acknowledged for financial support of Intawat Nookaew and sequencing.

Compliance with Ethical Standards

Conflict of interest

Authors declare that they have no conflict of interest regarding this study.

Ethical Approval

This article does not contain any studies with human participants or animals performed by any of the authors.

References

  1. 1.
    Ageitos JM, Vallejo JA, Veiga-Crespo P, Villa TG (2011) Oily yeasts as oleaginous cell factories. Appl Microbiol Biotechnol 90:1219–1227CrossRefPubMedGoogle Scholar
  2. 2.
    Bhatnagar D, Ehrlich KC, Cleveland TE (2003) Molecular genetic analysis and regulation of aflatoxin biosynthesis. Appl Microbiol Biotechnol 61:83–93CrossRefPubMedGoogle Scholar
  3. 3.
    Brown DW, Adams TH, Keller P (1996) Aspergillus has distinct fatty acid synthases for primary and secondary metabolism. Proc Natl Acad Sci USA 93:14873–14877CrossRefPubMedPubMedCentralGoogle Scholar
  4. 4.
    Cary JW, Wright M, Bhatnagar D, Lee R, Chu FS (1996) Molecular characterization of an Aspergillus parasiticus dehydrogenase gene, norA, located on the aflatoxin biosynthesis gene cluster. Appl Environ Microbiol 62:360–366PubMedPubMedCentralGoogle Scholar
  5. 5.
    Chang PK, Horn BW, Dorner JW (2005) Sequence breakpoints in the aflatoxin biosynthesis gene cluster and flanking regions in nonaflatoxigenic Aspergillus flavus isolates. Fungal Genet Biol 42:914–923CrossRefPubMedGoogle Scholar
  6. 6.
    Coghlan A, Eichler EE, Oliver SG, Paterson AH, Stein L (2005) Chromosome evolution in eukaryotes: a multi-kingdom perspective. Trends Genet 21:673–682CrossRefPubMedGoogle Scholar
  7. 7.
    Colson I, Delneri D, Oliver SG (2004) Effect of reciprocal chromosomal translocations on the fitness of Saccharomyces cerevisiae. EMBO Rep 5:392–398CrossRefPubMedPubMedCentralGoogle Scholar
  8. 8.
    Edgar RC (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 32:1792–1797CrossRefPubMedPubMedCentralGoogle Scholar
  9. 9.
    Fedorova ND, Khaldi N, Joardar VS, Maiti R, Amedeo P, Anderson MJ, Crabtree J, Silva JC, Badger JH, Albarraq A, Angiuoli S, Bussey H, Bowyer P, Cotty PJ, Dyer PS, Egan A, Galens K, Fraser-Liggett CM, Haas BJ, Inman JM, Kent R, Lemieux S, Malavazi I, Orvis J, Roemer T, Ronning CM, Sundaram JP, Sutton G, Turnrt G, Venter JC, White OR, Whitty BR, Youngman P, Wolfe KH, Goldman GH, Wortman JR, Jiang B, Denning DW, Nierman WC (2008) Genomic islands in the pathogenic filamentous fungus Aspergillus fumigatus. PLoS Genet 4:e1000046CrossRefPubMedPubMedCentralGoogle Scholar
  10. 10.
    Felsenstein J (1985) Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39:783–791CrossRefPubMedGoogle Scholar
  11. 11.
    Finn RD, Coggill P, Eberhardt RY, Eddy SR, Mistry J, Mitchell AL, Potter SC, Qureshi M, Sangrador-Vegas A, Salazar GA, Tate J, Bateman A (2016) The Pfam protein families database: towards a more sustainable future. Nucleic Acid Res 44:D279–D285CrossRefPubMedGoogle Scholar
  12. 12.
    Fischer G, Neuvéglise C, Durrens P, Gaillardin C, Dujon B (2001) Evolution of gene order in the genomes of two related yeast species. Genome Res 11:2009–2019CrossRefPubMedGoogle Scholar
  13. 13.
    Fraser JA, Huang JC, Pukkila-Worley R, Alspaugh A, Mitchell TG, Heitman J (2005) Chromosomal translocation and segmental duplication in Cryptococcus neoformans. Eukaryot Cell 4:401–406CrossRefPubMedPubMedCentralGoogle Scholar
  14. 14.
    Galperin MY, Makarova KS, Wolf YI, Koonin EV (2015) Expanded microbial genome coverage and improved protein family annotation in the COG database. Nucleic Acid Res 43:D261–D269CrossRefPubMedGoogle Scholar
  15. 15.
    Haft DH, Selengut JD, Ritchter RA, Harkins D, Basu MK, Beck E (2013) TIGRFAMs and genome properties in 2013. Nucleic Acid Res 41:D387–D395CrossRefPubMedGoogle Scholar
  16. 16.
    Kiyota T, Hamada R, Sakamoto K, Iwashita K, Yamada O, Mikami S (2011) Aflatoxin non-productivity of Aspergillus oryzae caused by loss of function in the aflJ gene product. J Biosci Bioeng 111:512–517CrossRefPubMedGoogle Scholar
  17. 17.
    Kobayashi T, Abe K, Asai K, Gomi K, Juvvadi PR, Kato M, Kitamoto K, Takeuchi M, Machida M (2007) Genomics of Aspergillus oryzae. Biosci Biotechnol Biochem 71:646–670CrossRefPubMedGoogle Scholar
  18. 18.
    Kurtz S, Phillippy A, Delcher AL, Smoot M, Shumway M, Antonescu C, Salzberg SL (2004) Versatile and open software for comparing large genomes. Genome Biol 5:R12CrossRefPubMedPubMedCentralGoogle Scholar
  19. 19.
    Kusumoto K, Yabe K, Nogata Y, Ohta H (1998) Transcript of a homolog of aflR, a regulatory gene for aflatoxin synthesis in Aspergillus parasiticus, was not detected in Aspergillus oryzae strains. FEMS Microbiol Lett 169:303–307CrossRefPubMedGoogle Scholar
  20. 20.
    Kusumoto K, Nogata Y, Ohta H (2000) Directed deletions in the aflatoxin biosynthesis gene homolog cluster of Aspergillus oryzae. Curr Genet 37:104–111CrossRefPubMedGoogle Scholar
  21. 21.
    Lee YH, Tominaga M, Hayashi R, Sakamoto K, Yamada O, Akita O (2006) Aspergillus oryzae strains with a large deletion of the aflatoxin biosynthetic homologous gene cluster differentiated by chromosomal breakage. Appl Microbiol Biotechnol 72:339–345CrossRefPubMedGoogle Scholar
  22. 22.
    Letunic I, Doerks T, Bork P (2015) SMART: recent updates, new developments and status in 2015. Nucleic Acid Res 43:D257–D260CrossRefPubMedGoogle Scholar
  23. 23.
    Machida M, Asai K, Sano M, Tanaka T, Kumagai T, Terai G, Kusumoto K, Arima T, Akita O, Kashiwagi Y, Abe K, Gomi K, Horiuchi H, Kitamoto K, Kobayashi T, Takeuchi M, Denning DW, Galagan JE, Nierman WC, Yu J, Archer DB, Bennett JW, Bhatnagar D, Cleveland TE, Fedorova ND, Gotoh O, Horikawa H, Hosoyama A, Ichinomiya M, Igarashi R, Iwashita K, Juvvadi PR, Kato M, Kato Y, Kin T, Kokubun A, Maeda H, Maeyama N, Maruyama J, Nagasaki H, Nakajima T, Oda K, Okada K, Paulsen I, Sakamoto K, Sawano T, Takahashi M, Takase K, Terabayashi Y, Wortman JR, Yamada O, Yamagata Y, Anazawa H, Hata Y, Koide Y, Komori T, Koyama Y, Minetoki T, Suharnan S, Tanaka A, Isono K, Kuhara S, Ogasawara N, Kikuchi H (2005) Genome sequencing and analysis of Aspergillus oryzae. Nature 438:1157–1161CrossRefPubMedGoogle Scholar
  24. 24.
    Marchler-Bauer A, Anderson JB, DeWeese-Scott C, Fedorova ND, Geer LY, He S, Hurwitz DI, Jackson JD, Jacobs AR, Lanczycki CJ, Liebert CA, Liu C, Madej T, Marchler GH, Mazumder R, Nikolskaya AN, Panchenko AR, Rao BS, Shoemaker BA, Simonyan V, Song JS, Thiessen PA, Vasudevan S, Wang Y, Yamashita RA, Yin JJ, Bryant SH (2003) CDD: a curated Entrez database of conserved domain alignments. Nucleic Acid Res 31:383–387CrossRefPubMedPubMedCentralGoogle Scholar
  25. 25.
    Marchler-Bauer A, Derbyshire MK, Gonzales NR, Lu S, Chitsaz F, Geer LY, Geer RC, He J, Gwadz M, Hurwitz DI, Lanczycki CJ, Lu F, Marchler GH, Song JS, Thanki N, Wang Z, Yamashita RA, Zhang D, Zheng C, Bryant SH (2015) CDD: NCBI’s conserved domain database. Nucleic Acid Res 43:D222–D226CrossRefPubMedGoogle Scholar
  26. 26.
    Mario S, Mark D, Robert B, David H (2008) Using native and syntenically mapped cDNA alignments to improve de novo gene finding. Bioinformatics 24:637–644CrossRefGoogle Scholar
  27. 27.
    Meng X, Yang J, Xu X, Zhang L, Nie Q, Xian M (2009) Biodiesel production from oleaginous microorganisms. Renew Energy 34:1–5CrossRefGoogle Scholar
  28. 28.
    Morita T, Koike H, Hagiwara H, Ito E, Machida M, Sato S, Have H, Kitamoto D (2014) Genome and transcriptome analysis of the Basidiomycetous yeast Pseudozyma antarctica producing extracellular glycolipids, mannosylerythritol lipids. PLoS ONE 9(2):e86490CrossRefPubMedPubMedCentralGoogle Scholar
  29. 29.
    Pérez-Ortín JE, Querol A, Puig S, Barrio E (2002) Molecular characterization of chromosomal rearrangement involved in the adaptive evolution of yeast strains. Genome Res 12:1533–1539CrossRefPubMedPubMedCentralGoogle Scholar
  30. 30.
    Pietrocola F, Galluzzi L, Bravo-San Pedro JM, Madeo F, Kroemer G (2015) Acetyl-coenzyme A: a central metabolite and second messenger. Cell Metab 21:805–821CrossRefPubMedGoogle Scholar
  31. 31.
    Ratledge C (1991) Microorganisms for lipids. Acta Biotechnol 11:429–438CrossRefGoogle Scholar
  32. 32.
    Ratledge C (2002) Regulation of lipid accumulation in oleaginous micro-organisms. Biochem Soc Trans 30:1047–1050CrossRefPubMedGoogle Scholar
  33. 33.
    Ruenwai R, Cheevadhanarak S, Rachdawong S, Tanticharoen M, Laoteng K (2010) Oxygen-induced expression of Δ6-, Δ9- and Δ12-desaturase genes modulate fatty acid composition in Mucor rouxii. Appl Microbiol Biotechnol 86:327–334CrossRefPubMedGoogle Scholar
  34. 34.
    Shin GH, Veen M, Stahl U, Lang C (2012) Overexpression of genes of the fatty acid biosynthesis pathway leads to accumulation of sterols in Saccharomyces cerevisiae. Yeast 29:371–383CrossRefPubMedGoogle Scholar
  35. 35.
    Soderlund C, Bomhoff M, Nelson WM (2011) Symap v3.4: 2 turnkey synteny system with application to plant genomes. Nucleic Acid Res 39:e68CrossRefPubMedPubMedCentralGoogle Scholar
  36. 36.
    Stanke M, Diekhans M, Baertsch R, Haussler D (2008) Using native and syntenically mapped cDNA alignments to improve de novo gene finding. Bioinformatics 24:637–644CrossRefPubMedGoogle Scholar
  37. 37.
    Takeda I, Tamano K, Yamane N, Ishii T, Miura A, Umemura M, Terai G, Baker SE, Koike H, Machida M (2014) Genome sequence of the Mucoromycotina fungus Umbelopsis isabellina, an effective producer of lipids. Genome Announc. doi: 10.1128/genomeA.00071-14 Google Scholar
  38. 38.
    Tamano K, Bruno KS, Karagiosis SA, Culley DE, Deng S, Collett JR, Umemura M, Koike H, Baker SE, Machida M (2013) Increased production of fatty acids and triacylglycerides in Aspergillus oryzae by enhancing expressions of fatty acid synthesis-related genes. Appl Genet Mol Biotechnol 97:269–281Google Scholar
  39. 39.
    Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S (2011) MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 28:2731–2739CrossRefPubMedPubMedCentralGoogle Scholar
  40. 40.
    Tatusov RL, Fedorova ND, Jackson JD, Jacobs AR, Kiryutin B, Koonin EV, Krylov DM, Mazumder R, Mekhedov SL, Nikolskaya AN, Rao BS, Smirnov S, Sverdlov AV, Vasudevan S, Wolf YI, Yin JJ, Natale DA (2003) The COG database: an updated version includes eukaryotes. BMC Bioinform 4:41CrossRefGoogle Scholar
  41. 41.
    Tominaga M, Lee YH, Hayashi R, Suzuki Y, Yamada O, Sakamoto K, Gotoh K, Akita O (2006) Molecular analysis of an inactive aflatoxin biosynthesis gene cluster in Aspergillus oryzae RIB strains. Appl Microbiol Biotechnol 72:484–490Google Scholar
  42. 42.
    Vongsangnak W, Olsen P, Hansen K, Krogsgaard S, Nielsen J (2008) Improved annotation through genome-scale metabolic modeling of Aspergillus oryzae. BMC Genomics 9:245CrossRefPubMedPubMedCentralGoogle Scholar
  43. 43.
    Vongsangnak W, Ruenwai R, Tang X, Hu X, Zhang H, Shen B, Song Y, Laoteng K (2013) Genome-scale analysis of the metabolic networks of oleaginous Zygomycete fungi. Gene 521:180–190CrossRefPubMedGoogle Scholar
  44. 44.
    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 158:217–228CrossRefPubMedGoogle Scholar
  45. 45.
    Wynn JP, Hamid AA, Li Y, Ratledge C (2001) Biochemical events leading to the diversion of carbon into storage lipids in the oleaginous fungi Mucor circinelloides and Mortierella alpina. Microbiology 147:2857–2864CrossRefPubMedGoogle Scholar
  46. 46.
    Yu J (2012) Current understanding on aflatoxin biosynthesis and future perspective in reducing aflatoxin contamination. Toxins 4:1024–1057CrossRefPubMedPubMedCentralGoogle Scholar
  47. 47.
    Zhang Y, Min Q, Xu J, Zhang K, Chen S, Wang H, Li D (2016) Effect of malate on docosahexaenoic acid production from Schizochytrium sp. B4D1. Electronic J Biotechnol 19:56–60CrossRefGoogle Scholar
  48. 48.
    Zhao L, Cánovas-Márquez JT, Tang X, Chen H, Chen YQ, Chen W, Garre V, Song V, Ratledge C (2016) Role of malate transporter in lipid accumulation of oleaginous fungus Mucor circinelloides. Appl Microbiol Biotechnol 100:1297–1305CrossRefPubMedGoogle Scholar
  49. 49.
    Zhu Z, Zhang S, Liu H, Shen H, Lin X, Yang F, Zhou YJ, Jin G, Ye M, Zou H, Zhao ZK (2012) A multi-omic map of the lipid-producing yeast Rhodosporidium toruloides. Nat Commun 3:1112CrossRefPubMedPubMedCentralGoogle Scholar

Copyright information

© Springer Science+Business Media, LLC 2017

Authors and Affiliations

  • Chinae Thammarongtham
    • 1
  • Intawat Nookaew
    • 2
    • 3
    • 4
  • Tayvich Vorapreeda
    • 1
  • Tanawut Srisuk
    • 5
  • Miriam L. Land
    • 4
  • Sukanya Jeennor
    • 6
  • Kobkul Laoteng
    • 6
  1. 1.Biochemical Engineering and Pilot Plant Research and Development Laboratory, National Center for Genetic Engineering and Biotechnology (BIOTEC)King Mongkut’s University of Technology ThonburiBangkokThailand
  2. 2.Department of Biomedical Informatics, College of MedicineUniversity of Arkansas for Medical SciencesLittle RockUSA
  3. 3.Department of Biology and Biological EngineeringChalmers University of TechnologyGothenburgSweden
  4. 4.Comparative Genomics Group, Biosciences DivisionOak Ridge National LaboratoryOak RidgeUSA
  5. 5.Systems Biology and Bioinformatics Research Group, Pilot Plant Development and Training InstituteKing Mongkut’s University of Technology ThonburiBangkokThailand
  6. 6.Bioprocess Technology Laboratory, Food Biotechnology Research Unit, National Center for Genetic Engineering and Biotechnology (BIOTEC)National Science and Technology Development Agency (NSTDA)Pathum ThaniThailand

Personalised recommendations