In silico analysis of 3′-end-processing signals in aspergillus oryzae using expressed sequence tags and genomic sequencing data

DNA Research

Volumn 18, Issue 3, 2011, Pages 189-200

  Tanaka, Mizuki ^a,b   Sakai, Yoshifumi ^a   Yamada, Osamu ^c   Shintani, Takahiro ^a   Gomi, Katsuya ^a  

^a TOHOKU UNIVERSITY   (Japan)

^b JAPAN SOCIETY FOR THE PROMOTION OF SCIENCE   (Japan)

^c NATIONAL RESEARCH INSTITUTE OF BREWING   (Japan)

Author keywords

3 end processing signal; 3 untranslated region (3 UTR); Aspergillus oryzae; polyadenylation signal

Indexed keywords

BINDING PROTEIN; POLYADENYLIC ACID;

3' UNTRANSLATED REGION; ARTICLE; ASPERGILLUS ORYZAE; COMPUTER MODEL; GENE EXPRESSION; GENE SEQUENCE; NUCLEOTIDE SEQUENCE; POLYADENYLATION; PROTEIN CLEAVAGE;

3' UNTRANSLATED REGIONS; ASPERGILLUS ORYZAE; BASE SEQUENCE; COMPUTATIONAL BIOLOGY; EXPRESSED SEQUENCE TAGS; GENOME, FUNGAL;

ASPERGILLUS ORYZAE; MAMMALIA;

EID: 79958855346     PISSN: 13402838     EISSN: 17561663     Source Type: Journal    
DOI: 10.1093/dnares/dsr011     Document Type: Article

References (48)

1. Zhao, J., Hyman, L. and Moore, C. 1999, Formation of mRNA 30 ends in eukaryotes: mechanism, regulation, and interrelationships with other steps in mRNA synthesis, Microbiol. Mol. Biol. Rev., 63, 405-45. (Pubitemid 29264977)
2. Mandel, C.R., Bai, Y. and Tong, L. 2008, Protein factors in pre-mRNA 30-end processing, Cell. Mol. Life Sci., 65, 1099-122.
3. Millevoi, S. and Vagner, S. 2010, Molecular mechanisms of eukaryotic pre-mRNA 30 end processing regulation, Nucleic Acids Res., 38, 2757-74.
4. Graber, J.H., Cantor, C.R., Mohr, S.C. and Smith, T.F. 1999, In slico detection of control signals: mRNA 30- end-processing sequences in diverse species, Proc. Natl Acad. Sci. USA, 96, 14055-60.
5. Graber, J.H., Cantor, C.R., Mohr, S.C. and Smith, T.F. 1999, Genomic detection of new yeast pre-mRNA 30- end-processing signals, Nucleic Acids Res., 27, 888-94. (Pubitemid 29209379)
6. Hu, J., Lutz, C.S., Wilusz, J. and Tian, B. 2005, Bioinformatic identification of candidate cis-regulatory elements involved in human mRNA polyadenylation, RNA, 11, 1485-93. (Pubitemid 41396918)
7. Loke, J.C., Stahlberg, E.A., Stenski, D.G., Haas, B.J., Wood, P.C. and Li, Q.Q. 2005, Complication of mRNA polyadenylation signals in Arabidopsis revealed a new signal element and potential secondary structures, Plant Physiol., 138, 1457-68. (Pubitemid 43142092)
8. Shen, Y., Ji, G., Hass, B.J., et al. 2008, Genome level analysis of rice mRNA 30-end processing signals and alternative polyadenylation, Nucleic Acids Res., 36, 3150-61. (Pubitemid 351737206)
9. Machida, M., Yamada, O. and Gomi, K. 2008, Genomics of Aspergillus oryzae: learning from the history of koji mold and exploration of its future, DNA Res., 15, 173-83.
10. Christensen, T., Woeldike, H., Boel, F., et al. 1988, High level expression of recombinant genes in Aspergillus oryzae, Bio/Technology, 6, 1419-22. (Pubitemid 19015966)
11. Lubertozzi, D. and Keasling, J.D. 2009, Developing Aspergillus as a host for heterologous expression, Biotechnol. Adv., 27, 53-75.
12. Gouka, R.J., Punt, P.J. and van den Hondel, C.A.M.J.J. 1997, Efficient production of secreted proteins by Aspergillus: progress, limitations and prospects, Appl. Microbiol. Biotechnol., 47, 1-11. (Pubitemid 27077292)
13. Tokuoka, M., Tanaka, M., Ono, K., Takagi, S., Shintani, T. and Gomi, K. 2008, Codon optimization increases steady-state mRNA levels in Aspergillus oryzae heterologous gene expression, Appl. Environ. Microbiol., 74, 6538-46.
14. Akao, T., Sano, M., Yamada, O., et al. 2007, Analysis of expressed sequence tags from the fungus Aspergillus oryzae cultured under different conditions, DNA Res., 14, 47-57.
15. Machida, M., Asai, K., Sano, M., et al. 2005, Genome sequencing and analysis of Aspergillus oryzae, Nature, 438, 1157-61. (Pubitemid 41831685)
16. Shen, Y., Liu, Y., Liu, L., Ling, C. and Li, Q.Q. 2008, Unique features of nuclear mRNA poly(A) signals and alternative polyadenylation in Chlamydomonas reinhardtii, Genetics, 179, 167-76.
17. Moore, C.L., Skolnikdavid, H. and Sharp, P.A. 1986, Analysis of RNA cleavage at the Adenovirus-2 L3 polyadenylation site, EMBO J., 5, 1929-38.
18. Sheets, M.D., Ogg, S.C. and Wickens, M.P. 1990, Point mutations in AAUAAA and the poly(A) addition site: effects on the accuracy and efficiency of cleavage and polyadenylation in vitro, Nucleic Acids Res., 18, 5799-805.
19. Chen, F., Macdonald, C.C. and Wilusz, J. 1995, Cleavage site determinants in the mammalian polyadenylation signal, Nucleic Acids Res., 23, 2614-20.
20. Tamano, K., Sano, M., Yamane, N., 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, 139-51.
21. Workman, C.T., Yin, Y., Corcoran, D.L., Ideker, T., Stormo, G.D. and Benos, P.V. 2005, enoLOGOS: a versatile web tool for energy normalized sequence logos, Nucleic Acids Res., 33, W389-92. (Pubitemid 44529949)
22. Van Helden, J., Del Olmo, M. and Perez-Ortin, J.E. 2000, Statistical analysis of yeast genomic downstream sequences reveals putative polyadenylation signals, Nucleic Acids Res., 28, 1000-10. (Pubitemid 30085328)
23. Tatusov, R.L., Federova, N.D., Jackson, J.D., et al. 2003, The COG database: an updated version includes eukaryotes, BMC Bioinformatics, 4, 41-54.
24. Tian, B., Hu, J., Zhang, H. and Lutz, C.S. 2005, A largescale analysis of mRNA polyadenylation of human and mouse genes, Nucleic Acids Res., 33, 201-12. (Pubitemid 40276942)
25. Edwalds-Gilbert, G., Veraldi, K.L. and Milcarek, C. 1997, Alternative poly(A) site selection in complex transcription units: means to an end?, Nucleic Acids Res., 25, 2547-61. (Pubitemid 27298148)
26. Pesole, G., Mignone, F., Gissi, C., Grillo, G., Licciulli, F. and Liuni, S. 2001, Structural and functional features of eukaryotic mRNA untranslated regions, Gene, 276, 73-81. (Pubitemid 32925261)
27. Kuersten, S. and Goodwin, E.B. 2003, The power of the 30 UTR: translational control and development, Nat. Rev. Genet., 4, 626-37. (Pubitemid 36917504)
28. Mazumder, B., Seshadri, V. and Fox, P.L. 2003, Translational control by the 30-UTR: the ends specify the means, Trends Biochem. Sci., 28, 91-8. (Pubitemid 36165138)
29. Kozak, M. 2004, How strong is the case for regulation of the initiation step of translation by elements at the 30 end of eukaryotic mRNAs?, Gene, 343, 41-54. (Pubitemid 39551028)
30. Bartel, D.P. 2009, MicroRNAs: target recognition and regulatory functions, Cell, 136, 215-233.
31. Kebaara, B.W. and Atkin, A.L. 2009, Long 30-UTRs target wild-type mRNAs for nonsense-mediated mRNA decay in Saccharomyces cerevisiae, Nucleic Acids Res., 37, 2771-8.
32. Morozov, I.Y., Martinez, M.G., Jones, M.G. and Caddick, M.X. 2000, A defined sequence within the 30 UTR of the areA transcript is sufficient to mediate nitrogen metabolite signaling via accelerated deadenylation, Mol. Microbiol., 37, 1248-57.
33. Caddick, M.X., Jones, M.G., van Tonder, J.M., et al. 2006, Opposing signals differentially regulate transcript stability in Aspergillus nidulans, Mol. Microbiol., 62, 509-19. (Pubitemid 44477238)
34. Wickens, M., Bernstein, D.S., Kimble, J. and Parker, R. 2002, A PUF family portrait: 30 UTR regulation as a way of life, Trends Genet., 18, 150-7. (Pubitemid 34164641)
35. Barreau, C., Paillard, L. and Osborne, B. 2006, AU-rich elements and associated factors: are there unifying principles?, Nucleic Acids Res., 33, 7138-50.
36. Vasudevan, S. and Peltz, S.W. 2001, Regulated AREmediated mRNA decay in Saccharomyces cerevisiae, Mol. Cell, 7, 1191-200. (Pubitemid 32607353)
37. Puig, S., Askeland, E. and Thiele, D. 2005, Coordinated remodeling of cellular metabolism during iron deficiency through targeted mRNA degradation, Cell, 120, 99-110. (Pubitemid 40094606)
38. Jackson, J.S., Houshmandi, S.S., Leban, F.L. and Olivas, W.M. 2004, Recruitment of the Puf3 protein to its mRNA target for regulation of mRNA decay in yeast, RNA, 10, 1625-36. (Pubitemid 39288196)
39. Dong, H., Deng, Y., Chen, J., et al. 2007, An exploration of 30-end processing signals and their tissue distribution in Oryza sativa, Gene, 389, 107-13. (Pubitemid 46186779)
40. Wickens, M. and Stephenson, P. 1984, Role of the conserved AAUAAA sequence: for AAUAAA point mutations prevent messenger RNA 30 end formation, Science, 226, 1045-51. (Pubitemid 15217822)
41. Guo, Z., Russo, P., Yun, D.F., Butler, J.S. and Sherman, F. 1995, Redundant 30 end-forming signals for the yeast CYC1 mRNA, Proc. Natl. Acad. Sci. USA, 92, 4211-14.
42. Graber, J.H., McAllister, G.D. and Smith, T.F. 2002, Probabilistic prediction of Saccharomyces cerevisiae mRNA 3'-processing sites, Nucleic Acids Res., 30, 1851-58. (Pubitemid 34679764)
43. Venkataraman, K., Brown, K.M. and Gilmartin, G.M. 2005, Analysis of a noncanonical poly(A) site reveals a tripartite mechanism for vertebrate poly(A) site recognition, Genes Dev., 19, 1315-27. (Pubitemid 41003021)
44. Nedea, E., He, X., Kim, M., et al. 2003, Organization and function of APT, a subcomplex of the yeast cleavage and polyadenylation factor involved in the formation of mRNA and small nucleolar RNA 3'-ends, J. Biol. Chem., 278, 33000-10. (Pubitemid 37055745)
45. Kessler, M.M., Henry, M.F., Shen, E., et al. 1997, Hrp1, a sequence-specific RNA-binding protein that shuttles between the nucleus and the cytoplasm, is required for mRNA 30-end formation in yeast, Genes Dev., 11, 2545-56. (Pubitemid 27438835)
46. Pérez-Cañadillas, J.M. 2006, Grabbing the message: structural basis of mRNA 30 UTR recognition by Hrp1, EMBO J., 25, 3167-78. (Pubitemid 44106767)
47. Dichtl, B., Blank, D., Sadowski, M., Hubner, W., Weiser, S. and Keller, W. 2002, Yhh1p/Cft1p directly links poly(A) site recognition and RNA polymerase II transcription termination, EMBO J., 21, 4125-35. (Pubitemid 34857444)
48. Hunt, A.G., Xu, R., Addepalli, B., et al. 2008, Arabidopsis mRNA polyadenylation machinery: comprehensive analysis of protein-protein interactions and gene expression profiling, BMC Genomics, 9, 220.