Survey of the transcriptome of Aspergillus oryzae via massively parallel mRNA sequencing

Nucleic Acids Research

Volumn 38, Issue 15, 2010, Pages 5075-5087

  Wang, Bin ^a   Guo, Guangwu ^b,c,d   Wang, Chao ^a   Lin, Ying ^a   Wang, Xiaoning ^a   Zhao, Mouming ^a   Guo, Yong ^a   He, Minghui ^a,d   Zhang, Yong ^d   Pan, Li ^a  

^a SOUTH CHINA UNIVERSITY OF TECHNOLOGY   (China)

^b Chinese Academy of Sciences   (China)

^c UNIVERSITY OF CHINESE ACADEMY OF SCIENCES   (China)

^d BGI SHENZHEN   (China)

Author keywords

[No Author keywords available]

Indexed keywords

MESSENGER RNA; TRANSCRIPTOME; UNTRANSLATED REGION;

ALTERNATIVE RNA SPLICING; ARTICLE; ASPERGILLUS ORYZAE; CONTROLLED STUDY; EXON; FUNGAL GENE; FUNGUS CULTURE; GENE EXPRESSION; INTERMETHOD COMPARISON; LIQUID CULTURE; NONHUMAN; OPEN READING FRAME; PRIORITY JOURNAL; RNA SEQUENCE; START CODON; TRANSCRIPTOMICS; UNTRANSLATED REGION; CHEMISTRY; FUNGAL GENOME; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENETIC TRANSCRIPTION; GENETICS; METABOLISM; SEQUENCE ANALYSIS;

ASPERGILLUS ORYZAE; FUNGI;

ALTERNATIVE SPLICING; ASPERGILLUS ORYZAE; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, FUNGAL; GENOME, FUNGAL; RNA, MESSENGER; SEQUENCE ANALYSIS, RNA; TRANSCRIPTION, GENETIC; UNTRANSLATED REGIONS;

EID: 77956107299     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkq256     Document Type: Article

References (46)

1. Nevalainen, K.M., Te'o, V.S. and Bergquist, P.L. (2005) Heterologous protein expression in filamentous fungi. Trends Biotechnol., 23, 468-474.
2. Machida, M., Asai, K., Sano, M., Tanaka, T., Kumagai, T., Terai, G., Kusumoto, K., Arima, T., Akita, O., Kashiwagi, Y. et al. (2005) Genome sequencing and analysis of Aspergillus oryzae. Nature, 438, 1157-1161.
3. Akao, T., Sano, M., Yamada, O., Akeno, T., Fujii, K., Goto, K., Ohashi-Kunihiro, S., Takase, K., Yasukawa-Watanabe, M., Yamaguchi, K. et al. (2007) Analysis of expressed sequence tags from the fungus Aspergillus oryzae cultured under different conditions. DNA Res., 14, 47-57.
4. Vongsangnak, W., Olsen, P., Hansen, K., Krogsgaard, S. and Nielsen, J. (2008) Improved annotation through genome-scale metabolic modeling of Aspergillus oryzae. BMC Genomics, 9, 245.
5. Andersen, M.R., Vongsangnak, W., Panagiotou, G., Salazar, M.P., Lehmann, L. and Nielsen, J. (2008) A trispecies Aspergillus microarray: comparative transcriptomics of three Aspergillus species. Proc. Natl Acad. Sci. USA, 105, 4387-4392.
6. Tamano, K., Sano, M., Yamane, N., Terabayashi, Y., Toda, T., Sunagawa, M., Koike, H., Hatamoto, O., Umitsuki, G., Takahashi, 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.
7. Nagalakshmi, U., Wang, Z., Waern, K., Shou, C., Raha, D., Gerstein, M. and Snyder, M. (2008) The transcriptional landscape of the yeast genome defined by RNA sequencing. Science, 320, 1344-1349.
8. Wilhelm, B.T., Marguerat, S., Watt, S., Schubert, F., Wood, V., Goodhead, I., Penkett, C.J., Rogers, J. and Bahler, J. (2008) Dynamic repertoire of a eukaryotic transcriptome surveyed at single-nucleotide resolution. Nature, 453, 1239-1243.
9. Hillier, L.W., Reinke, V., Green, P., Hirst, M., Marra, M.A. and Waterston, R.H. (2009) Massively parallel sequencing of the polyadenylated transcriptome of C. elegans. Genome Res., 19, 657-666.
10. Cloonan, N., Forrest, A.R.R., Kolle, G., Gardiner, B.B.A., Faulkner, G.J., Brown, M.K., Taylor, D.F., Steptoe, A.L., Wani, S., Bethel, G. et al. (2008) Stem cell transcriptome profiling via massive-scale mRNA sequencing. Nat. Methods, 5, 613-619.
11. Mortazavi, A., Williams, B.A., McCue, K., Schaeffer, L. and Wold, B. (2008) Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat. Methods, 5, 621-628.
12. Pan, Q., Shai, O., Lee, L.J., Frey, J. and Blencowe, B.J. (2008) Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing. Nat. Genet., 40, 1413-1415.
13. Sultan, M., Schulz, M.H., Richard, H., Magen, A., Klingenhoff, A., Scherf, M., Seifert, M., Borodina, T., Soldatov, A., Parkhomchuk, D. et al. (2008) A global view of gene activity and alternative splicing by deep sequencing of the human transcriptome. Science, 321, 956-960.
14. Wang, E.T., Sandberg, R., Luo, S., Khrebtukova, I., Zhang, L., Mayr, C., Kingsmore, S.F., Schroth, G.P. and Burge, C.B. (2008) Alternative isoform regulation in human tissue transcriptomes. Nature, 456, 470-476.
15. Maher, C.A., Kumar-Sinha, C., Cao, X.H., Kalyana-Sundaram, S., Han, B., Jing, X.J., Sam, L., Barrette, T., Palanisamy, N. and Chinnaiyan, A.M. (2009) Transcriptome sequencing to detect gene fusions in cancer. Nature, 458, 97-101.
16. Ishida, H., Matsumura, K., Hata, Y., Kawato, A., Suginami, K., Abe, Y., Imayasu, S. and Ichishima, E. (2001) Establishment of a hyper-protein production system in submerged Aspergillus oryzae culture under tyrosinase-encoding gene (melO) promoter control. Appl. Microbiol. Biotechnol., 57, 131-137.
17. Li, R., Li, Y., Kristiansen, K. and Wang, J. (2008) SOAP: short oligonucleotide alignment program. Bioinformatics, 24, 713-714.
18. Stanke, M., Diekhans, M., Baertsch, R. and Haussler, D. (2008) Using native and syntenically mapped cDNA alignments to improve de novo gene finding. Bioinformatics, 24, 637-644.
19. Conesa, A., Gotz, S., Garcia-Gomez, J.M., Terol, J., Talon, M. and Robles, M. (2005) Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research. Bioinformatics, 21, 3674-3676.
20. Wang, L., Feng, Z., Wang, X., Wang, X. and Zhang, X. (2010) DEGseq: an R package for identifying differentially expressed genes from RNA-seq data. Bioinformatics, 26, 136-138.
21. Bindea, G., Mlecnik, B., Hackl, H., Charoentong, P., Tosolini, M., Kirilovsky, A., Fridman, W.H., Pages, F., Trajanoski, Z. and Galon, J. (2009) ClueGO: a Cytoscape plug-in to decipher functionally grouped gene ontology and pathway annotation networks. Bioinformatics, 25, 1091-1093.
22. Ruiz-Echevarria, M.J. and Peltz, S.W. (2000) The RNA binding protein Pub1 modulates the stability of transcripts containing upstream open reading frames. Cell, 101, 741-751.
23. Vilela, C. and McCarthy, J.E. (2003) Regulation of fungal gene expression via short open reading frames in the mRNA 50untranslated region. Mol. Microbiol., 49, 859-867.
24. Hinnebusch, A.G. (2005) Translational regulation of GCN4 and the general amino acid control of yeast. Annu. Rev. Microbiol., 59, 407-450.
25. Modrek, B. and Lee, C. (2002) A genomic view of alternative splicing. Nat. Genet., 30, 13-19.
26. Loftus, B.J., Fung, E., Roncaglia, P., Rowley, D., Amedeo, P., Bruno, D., Vamathevan, J., Miranda, M., Anderson, I.J., Fraser, J.A. et al. (2005) The genome of the basidiomycetous yeast and human pathogen Cryptococcus neoformans. Science, 307, 1321-1324.
27. Ho, E.C., Cahill, M.J. and Saville, B.J. (2007) Gene discovery and transcript analyses in the corn smut pathogen Ustilago maydis: expressed sequence tag and genome sequence comparison. BMC Genomics, 8, 334.
28. McGuire, A.M., Pearson, M.D., Neafsey, D.E. and Galagan, J.E. (2008) Cross-kingdom patterns of alternative splicing and splice recognition. Genome Biol., 9, R50.
29. Ebbole, D.J., Jin, Y., Thon, M., Pan, H., Bhattarai, E., Thomas, T. and Dean, R. (2004) Gene discovery and gene expression in the rice blast fungus, Magnaporthe grisea: analysis of expressed sequence tags. Mol. Plant Microbe Interact., 17, 1337-1347.
30. Berget, S.M. (1995) Exon recognition in vertebrate splicing. J. Biol. Chem., 270, 2411-2414.
31. Romfo, C.M., Alvarez, C.J., van Heeckeren, W.J., Webb, C.J. and Wise, J.A. (2000) Evidence for splice site pairing via intron definition in Schizosaccharomyces pombe. Mol. Cell. Biol., 20, 7955-7970.
32. Ast, G. (2004) How did alternative splicing evolve? Nat. Rev. Genet., 5, 773-782.
33. Hata, Y., Ishida, H., Ichikawa, E., Kawato, A., Suginami, K. and Imayasu, S. (1998) Nucleotide sequence of an alternative glucoamylase-encoding gene (glaB) expressed in solid-state culture of Aspergillus oryzae. Gene, 207, 127-134.
34. Maeda, H., Sano, M., Maruyama, Y., Tanno, T., Akao, T., Totsuka, Y., Endo, M., Sakurada, R., Yamagata, Y., Machida, M. et al. (2004) 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.
35. Oda, K., Kakizono, D., Yamada, O., Iefuji, H., Akita, O. and Iwashita, K. (2006) Proteomic analysis of extracellular proteins from Aspergillus oryzae grown under submerged and solid-state culture conditions. Appl. Environ. Microbiol., 72, 3448-3457.
36. Akao, T., Gomi, K., Goto, K., Okazaki, N. and Akita, O. (2002) Subtractive cloning of cDNA from Aspergillus oryzae differentially regulated between solid-state culture and liquid (submerged) culture. Curr. Genet., 41, 275-281.
37. Ye, L. and Pan, L. (2008) A comparison of the unfolded protein response in solid-state with submerged cultures of Aspergillus oryzae. Biosci. Biotechnol. Biochem., 72, 2998-3001.
38. Ma, Y.J. and Hendershot, L.M. (2001) The unfolding tale of the unfolded protein response. Cell, 107, 827-830.
39. Kasuya, T., Nakajima, H. and Kitamoto, K. (1999) Cloning and characterization of the bipA gene encoding ER chaperone BiP from Aspergillus oryzae. J. Biosci. Bioeng., 88, 472-478.
40. Maruyama, J.I., Ohnuma, H., Yoshikawa, A., Kadokura, H., Nakajima, H. and Kitamoto, K. (2000) Production and product quality assessment of human hepatitis B virus pre-S2 antigen in submerged and solid-state cultures of Aspergillus oryzae. J. Biosci. Bioeng., 90, 118-120.
41. Leber, J.H., Bernales, S. and Walter, P. (2004) IRE1-independent gain control of the unfolded protein response. PLoS Biol., 2, 1197-1207.
42. Patil, C.K., Li, H. and Walter, P. (2004) Gcn4p and novel upstream activating sequences regulate targets of the unfolded protein response. PLoS Biol., 2, 1208-1223.
43. Arvas, M., Pakula, T., Lanthaler, K., Saloheimo, M., Valkonen, M., Suortti, T., Robson, G. and Penttila, M. (2006) Common features and interesting differences in transcriptional responses to secretion stress in the fungi Trichoderma reesei and Saccharomyces cerevisiae. BMC Genomics, 7, 32.
44. Pakula, T.M., Laxell, M., Huuskonen, A., Uusitalo, J., Saloheimo, M. and Penttila, M. (2003) The effects of drugs inhibiting protein secretion in the filamentous fungus Trichoderma reesei-Evidence for down-regulation of genes that encode secreted proteins in the stressed cells. J. Biol. Chem., 278, 45011-45020.
45. Al-Sheikh, H., Watson, A.J., Lacey, G.A., Punt, P.J., MacKenzie, D.A., Jeenes, D.J., Pakula, T., Penttila, M., Alcocer, M.J.C. and Archer, D.B. (2004) Endoplasmic reticulum stress leads to the selective transcriptional downregulation of the glucoamylase gene in Aspergillus niger. Mol. Microbiol., 53, 1731-1742.
46. Sims, A.H., Gent, M.E., Lanthaler, K., Dunn-Coleman, N.S., Oliver, S.G. and Robson, G.D. (2005) Transcriptome analysis of recombinant protein secretion by Aspergillus nidulans and the unfolded-protein response in vivo. Appl. Environ. Microbiol., 71, 2737-2747.