Genome sequencing and analysis of Aspergillus oryzae

Nature

Volumn 438, Issue 7071, 2005, Pages 1157-1161

  Machida, Masayuki ^a   Asai, Kiyoshi ^a   Sano, Motoaki ^a   Tanaka, Toshihiro ^b   Kumagai, Toshitaka ^a   Terai, Goro ^a,s   Kusumoto, Ken Ichi ^c   Arima, Toshihide ^d   Akita, Osamu ^d   Kashiwagi, Yutaka ^c   Abe, Keietsu ^e   Gomi, Katsuya ^e   Horiuchi, Hiroyuki ^f   Kitamoto, Katsuhiko ^f   Kobayashi, Tetsuo ^g   Takeuchi, Michio ^h   Denning, David W ⁱ   Galagan, James E ^j   Nierman, William C ^k,l   Yu, Jiujiang ^m   Archer, David B ⁿ   Bennett, Joan W ^o   Bhatnagar, Deepak ^m   Cleveland, Thomas E ^m   Fedorova, Natalie D ^k   Gotoh, Osamu ^a   Horikawa, Hiroshi ^b   Hosoyama, Akira ^b   Ichinomiya, Masayuki ^f   Igarashi, Rie ^b   Iwashita, Kazuhiro ^d   Juvvadi, Praveen Rao ^f   Kato, Masashi ^g   Kato, Yumiko ^b   Kin, Taishin ^a   Kokubun, Akira ^b   Maeda, Hiroshi ^e   Maeyama, Noriko ^b   Maruyama, Jun Ichi ^f   Nagasaki, Hideki ^a   Nakajima, Tasuku ^e   Oda, Ken ^d   Okada, Kinya ^a   Paulsen, Ian ^k   Sakamoto, Kazutoshi ^d   Sawano, Toshihiko ^b   Takahashi, Mikio ^b   Takase, Kumiko ^a   Terabayashi, Yasunobu ^a   Wortman, Jennifer R ^k   Yamada, Osamu ^d   Yamagata, Youhei ^e   Anazawa, Hideharu ^p   Hata, Yoji ^q   Koide, Yoshinao ^r   Komori, Takashi ^s   Koyama, Yasuji ^t   Minetoki, Toshitaka ^u   Suharnan, Sivasundaram ^v   Tanaka, Akimitsu ^w   Isono, Katsumi ^b   Kuhara, Satoru ^x   Ogasawara, Naotake ^y   Kikuchi, Hisashi ^b   more..

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

^b NATIONAL INSTITUTE OF TECHNOLOGY AND EVALUATION   (Japan)

^c NATIONAL FOOD RESEARCH INSTITUTE   (Japan)

^d NATIONAL RESEARCH INSTITUTE OF BREWING   (Japan)

^e TOHOKU UNIVERSITY   (Japan)

^f UNIVERSITY OF TOKYO   (Japan)

^g NAGOYA UNIVERSITY   (Japan)

^h TOKYO UNIVERSITY OF AGRICULTURE AND TECHNOLOGY   (Japan)

ⁱ UNIVERSITY OF MANCHESTER   (United Kingdom)

^j BROAD INSTITUTE OF MIT AND HARVARD   (United States)

^k J CRAIG VENTER INSTITUTE   (United States)

^l GEORGE WASHINGTON UNIVERSITY   (United States)

^m SOUTHERN REGIONAL RESEARCH CENTER   (United States)

ⁿ UNIVERSITY OF NOTTINGHAM   (United Kingdom)

^o TULANE UNIVERSITY   (United States)

^p KYOWA HAKKO KOGYO CO LTD   (Japan)

^q Gekkeikan Sake Company Ltd   (Japan)

^r Amano Enzyme Inc   (Japan)

^s INTEC Web and Genome Informatics Corp   (Japan)

^t KIKKOMAN CORPORATION   (Japan)

^u Ozeki Corporation   (Japan)

^v AxioHelix Co Ltd   (Japan)

^w Higeta Shoyu Co Ltd   (Japan)

^x KYUSHU UNIVERSITY   (Japan)

^y NARA INSTITUTE OF SCIENCE AND TECHNOLOGY   (Japan)

more..

Author keywords

[No Author keywords available]

Indexed keywords

ENZYMES; GENES; GENETIC ENGINEERING; HYDROLYSIS; PROTEINS;

AFLATOXIN; ASPERGILLUS ORYZAE; GENOME SEQUENCING;

FUNGI;

AMINO ACID; HYDROLASE;

FUNGUS;

AMINO ACID METABOLISM; AMINO ACID TRANSPORT; ARTICLE; ASPERGILLUS ORYZAE; COMPARATIVE STUDY; CONTROLLED STUDY; FERMENTATION; FUNGAL METABOLISM; GENE EXPRESSION; GENE SEQUENCE; GENOME; GENOME ANALYSIS; NONHUMAN; PRIORITY JOURNAL;

ASPERGILLUS; ASPERGILLUS FLAVUS; ASPERGILLUS FUMIGATUS; ASPERGILLUS ORYZAE; FUNGI;

EID: 29244442741     PISSN: 00280836     EISSN: 14764687     Source Type: Journal    
DOI: 10.1038/nature04300     Document Type: Article

References (30)

1. Gomi, K., Iimura, Y. & Hara, S. Integrative transformation of Aspergillus oryzae with a plasmid containing the Aspergillus nidulans argB gene. Agric. Biol. Chem. 51, 2549-2555 (1987).
2. Christensen, T. et al. High level expression of recombinant genes in Aspergillus oryzae. Bio/Technology 6, 1419-1422 (1988).
3. Ward, P. P. et al. Production of biologically active recombinant human lactoferrin in Aspergillus oryzae. Bio/Technology 10, 784-789 (1992).
4. Tsuchiya, K. et al. High level expression of the synthetic human lysozyme gene in Aspergillus oryzae. Appl. Microbiol. Biotechnol. 38, 109-114 (1992).
5. Galagan, J. E. et al. Sequencing of Aspergillus nidulans and comparative analysis with A. fumigatus and A. oryzae. Nature doi:10.1038/nature04341 (this issue).
6. Nierman, W. et al. Genomic sequence of the pathogenic and allergenic filamentous fungus Aspergillus fumigatus. Nature doi:10.1038/nature04332 (this issue).
7. Kitamoto, K., Kimura, K., Gomi, K. & Kumagai, C. Electrophoretic karyotype and gene assignment to chromosomes of Aspergillus oryzae. Biosci. Biotechnol. Biochem. 58, 1467-1470 (1994).
8. Archer, D. B. & Dyer, P. S. From genomics to post-genomics in Aspergillus. Curr. Opin. Microbiol. 7, 499-504 (2004).
9. Tatusov, R. L. et al. The COG database: an updated version includes eukaryotes. BMC Bioinformatics 4, 41 (2003).
10. van den Brink, H. M., van Gorcom, R. F., van den Hondel, C. A. & Punt, P. J. Cytochrome P450 enzyme systems in fungi. Fungal Genet. Biol. 23, 1-17 (1998).
11. Yu, J., Whitelaw, C. A., Nierman, W. C., Bhatnagar, D. & Cleveland, T. E. Aspergillus flavus expressed sequence tags for identification of genes with putative roles in aflatoxin contamination of crops. FEMS Microbiol. Lett. 237, 333-340 (2004).
12. Ferea, T. L., Botstein, D., Brown, P. O. & Rosenzweig, R. F. Systematic changes in gene expression patterns following adaptive evolution in yeast. Proc. Natl Acad. Sci. USA 96, 9721-9726 (1999).
13. Sakaguchi, K., Takagi, M., Horiuchi, H. & Gomi, K. in Applied Molecular Genetics in Filamentous Fungi (eds Kinghorn, J. R. & Turner, G.) 54-99 (Blackie Academic & Professional, Glasgow, 1992).
14. Hata, Y. et al. Nucleotide sequence and expression of the glucoamylase-encoding gene (glaA) from Aspergillus oryzae. Gene 108, 145-150 (1991).
15. Hori, H. & Osawa, S. Origin and evolution of organisms as deduced from 5S ribosomal RNA sequences. Mol. Biol. Evol. 4, 445-472 (1987).
16. Langkjaer, R. B., Cliften, P. F., Johnston, M. & Piskur, J. Yeast genome duplication was followed by asynchronous differentiation of duplicated genes. Nature 421, 848-852 (2003).
17. Prade, R. A., Griffith, J., Kochut, K., Arnold, J. & Timberlake, W. E. In vitro reconstruction of the Aspergillus (=Emericella) nidulans genome. Proc. Natl Acad. Sci. USA 94, 14564-14569 (1997).
18. Lawrence, J. G. & Hartl, D. L. Inference of horizontal genetic transfer from molecular data: an approach using the bootstrap. Genetics 131, 753-760 (1992).
19. Masel, A. M., He, C., Poplawski, A. M., Irwin, J. A. G. & Manners, J. M. Molecular evidence for chromosome transfer between biotypes of Colletotrichum gloeosporioides. Mol. Plant-Microbe Interact. 9, 339-348 (1996).
20. Dunham, M. J. et al. Characteristic genome rearrangements in experimental evolution of Saccharomyces cerevisiae. Proc. Natl Acad. Sci. USA 99, 16144-16149 (2002).
21. Maeda, H. et al. Transcriptional analysis of genes for energy catabolism and hydrolytic enzymes in the filamentous fungus Aspergillus oryzae using cDNA microarrays and expressed sequence tags. Appl. Microbiol. Biotechnol. 65, 74-83 (2004).
22. Geiser, D. M., Pitt, J. I. & Taylor, J. W. Cryptic speciation and recombination in the aflatoxin-producing fungus Aspergillus flavus. Proc. Natl Acad. Sci. USA 95, 388-393 (1998).
23. Iimura, Y., Gomi, K., Uzu, H. & Hara, S. Transformation of Aspergillus oryzae through plasmid-mediated complementation of the methionine-auxotrohpic mutation. Agric. Biol. Chem. 51, 323-328 (1987).
24. Watson, J. & Thompson, W. F. Purification and restriction endonuclease analysis of plant nuclear DNA. Methods Enzymol. 118, 57-75 (1986).
25. Lowe, T. M. & Eddy, S. R. tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res. 25, 955-964 (1997).
26. Gotoh, O. Homology-based gene structure prediction: simplified matching algorithm using a translated codon (tron) and improved accuracy by allowing for long gaps. Bioinformatics 16, 190-202 (2000).
27. Asai, K., Itou, K., Ueno, Y. & Yada, T. Recognition of human genes by stochastic parsing. Pac. Symp. Biocomput. 3, 228-239 (1998).
28. Majoros, W. H., Pertea, M., Antonescu, C. & Salzberg, S. L. GlimmerM, Exonomy and Unveil: three ab initio eukaryotic genefinders. Nucleic Acids Res. 31, 3601-3604 (2003).
29. Florea, L., Hartzell, G., Zhang, Z., Rubin, G. M. & Miller, W. A computer program for aligning a cDNA sequence with a genomic DNA sequence. Genome Res. 8, 967-974 (1998).
30. Thompson, J. D., Gibson, T. J., Plewniak, F., Jeanmougin, F. & Higgins, D. G. The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res. 25, 4876-4882 (1997).