RiceRBP: A database of experimentally identified RNA-binding proteins in Oryza sativa L

Plant Science

Volumn 180, Issue 2, 2011, Pages 204-211

  Morris, Robert T ^a   Doroshenk, Kelly A ^a   Crofts, Andrew J ^a   Lewis, Nicholas ^a   Okita, Thomas W ^a   Wyrick, John J ^a  

^a WASHINGTON STATE UNIVERSITY   (United States)

Author keywords

Database; Oryza sativa; Prolamine; Rice seed; RNA binding protein

Indexed keywords

PLANT RNA; RNA BINDING PROTEIN; VEGETABLE PROTEIN;

ARTICLE; BIOLOGY; COMPUTER INTERFACE; COMPUTER PROGRAM; DNA MICROARRAY; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENETIC DATABASE; GENETICS; HORDEUM; INFORMATION RETRIEVAL; INTERNET; MAIZE; MASS SPECTROMETRY; METABOLISM; METHODOLOGY; PHYLOGENY; PLANT GENOME; PLANT SEED; PROTEIN DATABASE; PROTEIN TERTIARY STRUCTURE; RICE; SORGHUM; WHEAT;

COMPUTATIONAL BIOLOGY; DATABASES, GENETIC; DATABASES, PROTEIN; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, PLANT; GENOME, PLANT; HORDEUM; INFORMATION STORAGE AND RETRIEVAL; INTERNET; MASS SPECTROMETRY; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; ORYZA SATIVA; PHYLOGENY; PLANT PROTEINS; PROTEIN STRUCTURE, TERTIARY; RNA, PLANT; RNA-BINDING PROTEINS; SEEDS; SOFTWARE; SORGHUM; TRITICUM; USER-COMPUTER INTERFACE; ZEA MAYS;

ORYZA SATIVA;

EID: 78650282979     PISSN: 01689452     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.plantsci.2010.08.004     Document Type: Article

References (37)

1. Dreyfuss G., Kim V.N., Kataoka N. Messenger-RNA-binding proteins and the messages they carry. Nat. Rev. Mol. Cell Biol. 2002, 3:195-205.
2. Martin K.C., Ephrussi A. mRNA localization: gene expression in the spatial dimension. Cell 2009, 136:719-730.
3. Crofts A.J., Washida H., Okita T.W., Satoh M., Ogawa M., Kumamaru T., Satoh H. The role of mRNA and protein sorting in seed storage protein synthesis, transport, and deposition. Biochem. Cell Biol. 2005, 83:728-737.
4. Singer R.H RNA zipcodes for cytoplasmic addresses. Curr. Biol. 1993, 3:719-721.
5. Hamada S., Ishiyama K., Sakulsingharoj C., Choi S.B., Wu Y., Wang C., Singh S., Kawai N., Messing J., Okita T.W. Dual regulated RNA transport pathways to the cortical region in developing rice endosperm. Plant Cell 2003, 15:2265-2272.
6. Caudy A.A., Ketting R.F., Hammond S.M., Denli A.M., Bathoorn A.M., Tops B.B., Silva J.M., Myers M.M., Hannon G.J., Plasterk R.H. A micrococcal nuclease homologue in RNAi effector complexes. Nature 2003, 425:411-414.
7. Scadden A.D. The RISC subunit Tudor-SN binds to hyper-edited double-stranded RNA and promotes its cleavage. Nat. Struct. Mol. Biol. 2005, 12:489-496.
8. Sami-Subbu R., Choi S.B., Wu Y., Wang C., Okita T.W. Identification of a cytoskeleton-associated 120kDa RNA-binding protein in developing rice seeds. Plant Mol. Biol. 2001, 46:79-88.
9. Wang C., Washida H., Crofts A.J., Hamada S., Katsube-Tanaka T., Kim D., Choi S.B., Modi M., Singh S., Okita T.W. The cytoplasmic-localized, cytoskeletal-associated RNA binding protein OsTudor-SN: evidence for an essential role in storage protein RNA transport and localization. Plant J. 2008, 55:443-454.
10. Walker N.S, Stiffler N., Barkan A. POGs/PlantRBP: a resource for comparative genomics in plants. Nucleic Acids Res. 2007, 35:D852-856.
11. Crofts A.J., Crofts N., Whitelegge J.P., Okita T.W. Isolation and identification of cytoskeleton-associated prolamine mRNA binding proteins from developing rice seeds. Planta 2010, 231:1261-1276.
12. Doroshenk K.A., Crofts A.J., Morris R.T., Wyrick J.J., Okita T.W. Proteomic analysis of cytoskeleton-associated RNA binding proteins in developing rice seed. J. Proteome Res. 2009, 8:4641-4653.
13. Aranda B., Achuthan P., Alam-Faruque Y., Armean I., Bridge A., Derow C., Feuermann M., Ghanbarian A.T., Kerrien S., Khadake J., Kerssemakers J., Leroy C., Menden M., Michaut M., Montecchi-Palazzi L., Neuhauser S.N., Orchard S., Perreau V., Roechert B., van Eijk K., Hermjakob H. The IntAct molecular interaction database in 2010. Nucleic Acids Res. 2010, 38:D525-531.
14. Tanaka T., Antonio B.A., Kikuchi S., Matsumoto T., Nagamura Y., Numa H., Sakai H., Wu J., Itoh T., Sasaki T., Aono R., Fujii Y., Habara T., Harada E., Kanno M., Kawahara Y., Kawashima H., Kubooka H., Matsuya A., Nakaoka H., Saichi N., Sanbonmatsu R., Sato Y., Shinso Y., Suzuki M., Takeda J., Tanino M., Todokoro F., Yamaguchi K., Yamamoto N., Yamasaki C., Imanishi T., Okido T., Tada M., Ikeo K., Tateno Y., Gojobori T., Lin Y.C., Wei F.J., Hsing Y.I., Zhao Q., Han B., Kramer M.R., McCombie R.W., Lonsdale D., O'Donovan C.C., Whitfield E.J., Apweiler R., Koyanagi K.O., Khurana J.P., Raghuvanshi S., Singh N.K., Tyagi A.K., Haberer G., Fujisawa M., Hosokawa S., Ito Y., Ikawa H., Shibata M., Yamamoto M., Bruskiewich R.M., Hoen D.R., Bureau T.E., Namiki N., Ohyanagi H., Sakai Y., Nobushima S., Sakata K., Barrero R.A., Sato Y., Souvorov A., Smith-White B., Tatusova T., An S., An G., O.Ota S., Fuks G., Fuks G., Messing J., Christie K.R., Lieberherr D., Kim H., Zuccolo A., Wing R.A., Nobuta K., Green P.J., Lu C., Meyers B.C., Chaparro C., Piegu B., Panaud O., Echeverria M. The rice annotation project database (RAP-DB): 2008 update. Nucleic Acids Res. 2008, 36:D1028-1033.
15. Ouyang S., Zhu W., Hamilton J., Lin H., Campbell M., Childs K., Thibaud-Nissen F., Malek R.L., Lee Y., Zheng L., Orvis J., Haas B., Wortman J., Buell C.R. The TIGR rice genome annotation resource: improvements and new features. Nucleic Acids Res. 2007, 35:D883-D887.
16. Kikuchi S., Satoh K., Nagata T., Kawagashira N., Doi K., Kishimoto N., Yazaki J., Ishikawa M., Yamada H., Ooka H., Hotta I., Kojima K., Namiki T., Ohneda E., Yahagi W., Suzuki K., Li C.J., Ohtsuki K., Shishiki T., Otomo Y., Murakami K., Iida Y., Sugano S., Fujimura T., Suzuki Y., Tsunoda Y., Kurosaki T., Kodama T., Masuda H., Kobayashi M., Xie Q., Lu M., Narikawa R., Sugiyama A., Mizuno K., Yokomizo S., Niikura J., Ikeda R., Ishibiki J., Kawamata M., Yoshimura A., Miura J., Kusumegi T., Oka M., Ryu R., Ueda M., Matsubara K., Kawai J., Carninci P., Adachi J., Aizawa K., Arakawa T., Fukuda S., Hara A., Hashizume W., Hayatsu N., Imotani K., Ishii Y., Itoh M., Kagawa I., Kondo S., Konno H., Miyazaki A., Osato N., Ota Y., Saito R., Sasaki D., Sato K., Shibata K., Shinagawa A., Shiraki T., Yoshino M., Hayashizaki Y., Yasunishi A. Collection, mapping, and annotation of over 28,000 cDNA clones from japonica rice. Science 2003, 301:376-379.
17. Satoh K, Doi K., Nagata T., Kishimoto N., Suzuki K., Otomo Y., Kawai J., Nakamura M., Hirozane-Kishikawa T., Kanagawa S., Arakawa T., Takahashi-Iida J., Murata M., Ninomiya N., Sasaki D., Fukuda S., Tagami M., Yamagata H., Kurita K., Kamiya K., Yamamoto M., Kikuta A., Bito T., Fujitsuka N., Ito K., Kanamori H., Choi I.R., Nagamura Y., Matsumoto T., Murakami K., Matsubara K., Carninci P., Hayashizaki Y., Kikuchi S. Gene organization in rice revealed by full-length cDNA mapping and gene expression analysis through microarray. PLoS One 2007, 2:e1235.
18. Sayers E.W., Barrett T., Benson D.A., Bryant S.H., Canese K., Chetvernin V., Church D.M., DiCuccio M., Edgar R., Federhen S., Feolo M., Geer L.Y., Helmberg W., Kapustin Y., Landsman D., Lipman D.J., Madden T.L., Maglott D.R., Miller V., Mizrachi I., Ostell J., Pruitt K.D., Schuler G.D., Sequeira E., Sherry S.T., Shumway M., Sirotkin K., Souvorov A., Starchenko G., Tatusova T.A., Wagner L., Yaschenko E., Ye J. Database resources of the national center for biotechnology information. Nucleic Acids Res. 2009, 37:D5-15.
19. The UniProt Consortium The universal protein resource (UniProt). Nucleic Acids Res. 2009, 37:D169-D174.
20. Hulo N., Bairoch A., Bulliard V., Cerutti L., Cuche B.A., de Castro E., Lachaize C., Langendijk-Genevaux P.S., Sigrist C.J. The 20 years of PROSITE. Nucleic Acids Res. 2008, 36:D245-D249.
21. Horton P., Park K.J., Obayashi T., Fujita N., Harada H., Adams-Collier C.J., Nakai K. WoLF PSORT: protein localization predictor. Nucleic Acids Res. 2007, 35:W585-W587.
22. Deluca T.F., Wu I.H., Pu J., Monaghan T., Peshkin L., Singh S., Wall D.P. Roundup: a multi-genome repository of orthologs and evolutionary distances. Bioinformatics 2006, 22:2044-2046.
23. Berglund A.C., Sjolund E., Ostlund G., Sonnhammer E.L. InParanoid 6: eukaryotic ortholog clusters with inparalogs. Nucleic Acids Res. 2008, 36:D263-D266.
24. Dong Q., Schlueter S.D., Brendel V. PlantGDB, plant genome database and analysis tools. Nucleic Acids Res. 2004, 32:D354-D359.
25. Lin H, Ouyang S., Egan A., Nobuta K., Haas B.J., Zhu W., Gu X., Silva J.C., Meyers B.C., Buell C.R. Characterization of paralogous protein families in rice. BMC Plant Biol. 2008, 8:18.
26. Edgar R.C. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 2004, 32:1792-1797.
27. Guindon S., Gascuel O. A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst. Biol. 2003, 52:696-704.
28. Letunic I, Bork P. Interactive Tree Of Life (iTOL): an online tool for phylogenetic tree display and annotation. Bioinformatics 2007, 23:127-128.
29. Price M.N., Dehal P.S., Arkin A.P. FastTree: computing large minimum evolution trees with profiles instead of a distance matrix. Mol. Biol. Evol. 2009, 26:1641-1650.
30. Jiao Y., Tausta S.L., Gandotra N., Sun N., Liu T., Clay N.K., Ceserani T., Chen M., Ma L., Holford M., Zhang H.Y., Zhao H., Deng X.W., Nelson T. A transcriptome atlas of rice cell types uncovers cellular, functional and developmental hierarchies. Nat. Genet. 2009, 41:258-263.
31. Kenan D.J, Query C.C., Keene J.D. RNA recognition: towards identifying determinants of specificity. Trends Biochem. Sci. 1991, 16:214-220.
32. Siomi H., Matunis M.J., Michael W.M., Dreyfuss G. The pre-mRNA binding K protein contains a novel evolutionarily conserved motif. Nucleic Acids Res. 1993, 21:1193-1198.
33. Burd C.G., Dreyfuss G. Conserved structures and diversity of functions of RNA-binding proteins. Science 1994, 265:615-621.
34. Washida H., Sugino A., Messing J., Esen A., Okita T.W. Asymmetric localization of seed storage protein RNAs to distinct subdomains of the endoplasmic reticulum in developing maize endosperm cells. Plant Cell Physiol. 2004, 45:1830-1837.
35. Washida H., Sugino A., Kaneko S., Crofts N., Sakulsingharoj C., Kim D., Choi S.B., Hamada S., Ogawa M., Wang C., Esen A., Higgins T.J., Okita T.W. Identification of cis-localization elements of the maize 10-kDa delta-zein and their use in targeting RNAs to specific cortical endoplasmic reticulum subdomains. Plant J. 2009, 60:146-155.
36. Kumamaru T., Ogawa M., Satoh H., Okita T.W. Protein body biogenesis in cereal endosperms. Endosperm 2007, 141-158. Springer-Verlag, Berlin Heidelberg. O.A. Olsen (Ed.).
37. Morris R.T., O'Connor T.R., Wyrick J.J. Osiris: an integrated promoter database for Oryza sativa L. Bioinformatics 2008, 24:2915-2917.