Genome-wide computational identification of WG/GW Argonaute-binding proteins in Arabidopsis

Nucleic Acids Research

Volumn 38, Issue 13, 2010, Pages 4231-4245

  Karlowski, Wojciech M ^a   Zielezinski, Andrzej ^a   Carrère, Julie ^b   Pontier, Dominique ^b   Lagrange, Thierry ^b   Cooke, Richard ^b  

^a ADAM MICKIEWICZ UNIVERSITY   (Poland)

^b UNIVERSITÉ DE PERPIGNAN   (France)

Author keywords

[No Author keywords available]

Indexed keywords

ARABIDOPSIS PROTEIN; ARGONAUTE PROTEIN; PROTEIN GW; PROTEIN WG; RNA BINDING PROTEIN; UNCLASSIFIED DRUG;

ALGORITHM; AMINO ACID COMPOSITION; ARABIDOPSIS; ARTICLE; BINDING SITE; CONTROLLED STUDY; EXPRESSED SEQUENCE TAG; GENE LOCUS; GENE SEQUENCE; GENOME ANALYSIS; NONHUMAN; NUCLEOTIDE SEQUENCE; PLANT GENETICS; PREDICTION; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN BINDING; PROTEIN DOMAIN; PROTEIN FUNCTION; PROTEIN MOTIF;

AMINO ACID MOTIFS; AMINO ACID SEQUENCE; ARABIDOPSIS; ARABIDOPSIS PROTEINS; BINDING SITES; CONSERVED SEQUENCE; GENOME, PLANT; GENOMICS; MOLECULAR SEQUENCE DATA; MULTIGENE FAMILY; PROTEIN STRUCTURE, TERTIARY;

ARABIDOPSIS; MAMMALIA;

EID: 77955254815     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkq162     Document Type: Article

References (51)

1. Mulder, N.J. and Apweiler, R. (2008) The InterPro database and tools for protein domain analysis. Current Protocols in Bioinformatics, Chapter 2, Unit 2.7.
2. Finn, R.D., Tate, J., Mistry, J., Coggill, P.C., Sammut, S.J., Hotz, H.- R., Ceric, G., Forslund, K., Eddy, S.R., Sonnhammer, E.L.L. et al. (2008) The Pfam protein families database. Nucleic Acids Res., 36, D281-D288.
3. Pontier, D., Yahubyan, G., Vega, D., Bulski, A., Saez-Vasquez, J., Hakimi, M.-A., Lerbs-Mache, S., Colot, V. and Lagrange, T. (2005) Reinforcement of silencing at transposons and highly repeated sequences requires the concerted action of two distinct RNA polymerases IV in Arabidopsis. Genes Dev., 19, 2030-2040.
4. Herr, A.J., Jensen, M.B., Dalmay, T. and Baulcombe, D.C. (2005) RNA polymerase IV directs silencing of endogenous DNA. Science, 308, 118-120.
5. Onodera, Y., Haag, J.R., Ream, T., Nunes, P.C., Pontes, O. and Pikaard, C.S. (2005) Plant nuclear RNA polymerase IV mediates siRNA and DNA methylation-dependent heterochromatin formation. Cell, 120, 613-622.
6. Kanno, T., Huettel, B., Mette, M.F., Aufsatz, W., Jaligot, E., Daxinger, L., Kreil, D.P., Matzke, M. and Matzke, A.J. (2005) Atypical RNA polymerase subunits required for RNA-directed DNA methylation. Nat. Genet., 37, 761-765.
7. Ream, T.S., Haag, J.R., Wierzbicki, A.T., Nicora, C.D., Norbeck, A.D., Zhu, J.-K., Hagen, G., Guilfoyle, T.J., Pasa-Tolić, L. and Pikaard, C.S. (2009) Subunit compositions of the RNA-silencing enzymes Pol IV and Pol V reveal their origins as specialized forms of RNA polymerase II. Mol. Cell, 33, 192-203.
8. Huang, L., Jones, A.M.E., Searle, I., Patel, K., Vogler, H., Hubner, N.C. and Baulcombe, D.C. (2009) An atypical RNA polymerase involved in RNA silencing shares small subunits with RNA polymerase II. Nat. Struct. Mol. Biol., 16, 91-93.
9. He, X.-J., Hsu, Y.-F., Pontes, O., Zhu, J., Lu, J., Bressan, R.A., Pikaard, C., Wang, C.-S. and Zhu, J.-K. (2009) NRPD4, a protein related to the RPB4 subunit of RNA polymerase II, is a component of RNA polymerases IV and V and is required for RNA-directed DNA methylation. Genes Dev., 23, 318-330.
10. Lahmy, S., Pontier, D., Cavel, E., Vega, D., El-Shami, M., Kanno, T. and Lagrange, T. (2009) PolV(PolIVb) function in RNA-directed DNA methylation requires the conserved active site and an additional plant-specific subunit. Proc. Natl Acad. Sci. USA, 106, 941-946.
11. El-Shami, M., Pontier, D., Lahmy, S., Braun, L., Picart, C., Vega, D., Hakimi, M.-A., Jacobsen, S.E., Cooke, R. and Lagrange, T. (2007) Reiterated WG/GW motifs form functionally and evolutionarily conserved ARGONAUTE-binding platforms in RNAi-related components. Genes Dev., 21, 2539-2544.
12. Zilberman, D., Cao, X., Johansen, L.K., Xie, Z., Carrington, J.C. and Jacobsen, S.E. (2004) Role of Arabidopsis ARGONAUTE4 in RNA-directed DNA methylation triggered by inverted repeats. Curr. Biol., 14, 1214-1220.
13. Qi, Y., He, X., Wang, X.J., Kohany, O., Jurka, J. and Hannon, G.J. (2006) Distinct catalytic and non-catalytic roles of ARGONAUTE4 in RNA-directed DNA methylation. Nature, 443, 1008-1012.
14. Vaucheret, H. (2008) Plant ARGONAUTES. Trends Plant Sci, 13, 350-358.
15. Altschul, S.F., Madden, T.L., Schaffer, A.A., Zhang, J., Zhang, Z., Miller, W. and Lipman, D.J. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res, 25, 3389-3402.
16. Eystathioy, T., Chan, E.K.L., Tenenbaum, S.A., Keene, J.D., Griffith, K. and Fritzler, M.J. (2002) A phosphorylated cytoplasmic autoantigen, GW182, associates with a unique population of human mRNAs within novel cytoplasmic speckles. Mol. Biol. Cell, 13, 1338-1351.
17. Eulalio, A., Behm-Ansmant, I., Schweizer, D. and Izaurralde, E. (2007) P-body formation is a consequence, not the cause, of RNA-mediated gene silencing. Mol. Cell. Biol., 27, 3970-3981.
18. Gibbings, D.J., Ciaudo, C., Erhardt, M. and Voinnet, O. (2009) Multivesicular bodies associate with components of miRNA effector complexes and modulate miRNA activity. Nat. Cell. Biol., 11, 1143-1149.
19. Eulalio, A., Helms, S., Fritzsch, C., Fauser, M. and Izaurralde, E. (2009) A C-terminal silencing domain in GW182 is essential for miRNA function. RNA, 15, 1067-1077.
20. Lazzaretti, D., Tournier, I. and Izaurralde, E. (2009) The C-terminal domains of human TNRC6A, TNRC6B, and TNRC6C silence bound transcripts independently of Argonaute proteins. RNA, 15, 1059-1066.
21. Takimoto, K., Wakiyama, M. and Yokoyama, S. (2009) Mammalian GW182 contains multiple Argonaute-binding sites and functions in microRNA-mediated translational repression. RNA, 15, 1078-1089.
22. Behm-Ansmant, I., Rehwinkel, J., Doerks, T., Stark, A., Bork, P. and Izaurralde, E. (2006) mRNA degradation by miRNAs and GW182 requires both CCR4:NOT deadenylase and DCP1:DCP2 decapping complexes. Genes Dev., 20, 1885-1898.
23. Schneider, M.D., Najand, N., Chaker, S., Pare, J.M., Haskins, J., Hughes, S.C., Hobman, T.C., Locke, J. and Simmonds, A.J. (2006) Gawky is a component of cytoplasmic mRNA processing bodies required for early Drosophila development. J. Cell. Biol., 174, 349-358.
24. Eulalio, A., Tritschler, F. and Izaurralde, E. (2009) The GW182 protein family in animal cells: new insights into domains required for miRNA-mediated gene silencing. RNA, 15, 1433-1442.
25. Jakymiw, A., Pauley, K.M., Li, S., Ikeda, K., Lian, S., Eystathioy, T., Satoh, M., Fritzler, M.J. and Chan, E.K.L. (2007) The role of GW/P-bodies in RNA processing and silencing. J. Cell Sci, 120, 1317-1323.
26. Ding, L., Spencer, A., Morita, K. and Han, M. (2005) The developmental timing regulator AIN-1 interacts with miRISCs and may target the argonaute protein ALG-1 to cytoplasmic P bodies in C. elegans. Mol. Cell, 19, 437-447.
27. Ding, X.C. and Grosshans, H. (2009) Repression of C. elegans microRNA targets at the initiation level of translation requires GW182 proteins. EMBO J., 28, 213-222.
28. Bies-Etheve, N., Pontier, D., Lahmy, S., Picart, C., Vega, D., Cooke, R. and Lagrange, T. (2009) RNA-directed DNA methylation requires an AGO4-interacting member of the SPT5 elongation factor family. EMBO Rep, 10, 649-654.
29. He, X.-J., Hsu, Y.-F., Zhu, S., Wierzbicki, A.T., Pontes, O., Pikaard, C.S., Liu, H.-L., Wang, C.S., Jin, H. and Zhu, J.-K. (2009) An effector of RNA-directed DNA methylation in arabidopsis is an ARGONAUTE 4- and RNA-binding protein. Cell, 137, 498-508.
30. Partridge, J.F., DeBeauchamp, J.L., Kosinski, A.M., Ulrich, D.L., Hadler, M.J. and Noffsinger, V.J.P. (2007) Functional separation of the requirements for establishment and maintenance of centromeric heterochromatin. Mol. Cell, 26, 593-602.
31. Till, S., Lejeune, E., Thermann, R., Bortfeld, M., Hothorn, M., Enderle, D., Heinrich, C., Hentze, M.W. and Ladurner, A.G. (2007) A conserved motif in argonaute-interacting proteins mediates functional interactions through the Argonaute PIWI domain. Nat. Struct. Mol. Biol., 14, 897-903.
32. Bednenko, J., Noto, T., Desouza, L., Siu, K., Pearlman, R., Mochizuki, K. and Gorovsky, M. (2009) Two GW repeat proteins interact with the tetrahymena argonaute and promote genome rearrangement. Mol. Cell. Biol., 29, 5020-5030.
33. Arabidopsis Genome Initiative. (2000) Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature, 408, 796-815.
34. Cooke, R., Raynal, M., Laudié, M., Grellet, F., Delseny, M., Morris, P.C., Guerrier, D., Giraudat, J., Quigley, F., Clabault, G. et al. (1996) Further progress towards a catalogue of all Arabidopsis genes: analysis of a set of 5000 non-redundant ESTs. Plant J., 9, 101-124.
35. Seki, M., Narusaka, M., Kamiya, A., Ishida, J., Satou, M., Sakurai, T., Nakajima, M., Enju, A., Akiyama, K., Oono, Y. et al. (2002) Functional annotation of a full-length Arabidopsis cDNA collection. Science, 296, 141-145.
36. Schoof, H. and Karlowski, W.M. (2003) Comparison of rice and Arabidopsis annotation. Curr. Opin. Plant Biol., 6, 106-112.
37. R Development Core Team. (2009) R: A Language and Environment for Statistical Computing, R Foundation for Statistical Computing, Vienna, Austria.
38. Hollander, M. and Wolfe, D. (1999) Nonparametric Statistical Methods. 2nd edn. Wiley-Interscience, John Wiley & Sons, Inc., Hoboken, NJ. 787 pp.
39. Eitoku, M., Sato, L., Senda, T. and Horikoshi, M. (2008) Histone chaperones: 30 years from isolation to elucidation of the mechanisms of nucleosome assembly and disassembly. Cell. Mol. Life Sci., 65, 414-444.
40. Sims, R.J. 3rd, Belotserkovskaya, R. and Reinberg, D. (2004) Elongation by RNA polymerase II: the short and long of it. Genes Dev., 18, 2437-2468.
41. Dalmay, T., Horsefield, R., Braunstein, T.H. and Baulcombe, D.C. (2001) SDE3 encodes an RNA helicase required for post-transcriptional gene silencing in Arabidopsis. EMBO J., 20, 2069-2078.
42. Katoh, K. and Toh, H. (2008) Recent developments in the MAFFT multiple sequence alignment program. Brief. Bioinformatics, 9, 286-298.
43. Hutvagner, G. and Simard, M.J. (2008) Argonaute proteins: key players in RNA silencing. Nat. Rev. Mol. Cell. Biol., 9, 22-32.
44. Kaplan, C.D., Morris, J.R., Wu, C. and Winston, F. (2000) Spt5 and spt6 are associated with active transcription and have characteristics of general elongation factors in D. melanogaster. Genes Dev., 14, 2623-2634.
45. Ardehali, M.B., Yao, J., Adelman, K., Fuda, N.J., Petesch, S.J., Webb, W.W. and Lis, J.T. (2009) Spt6 enhances the elongation rate of RNA polymerase II in vivo. EMBO J, 28, 1067-1077.
46. Höck, J., Weinmann, L., Ender, C., Rüdel, S., Kremmer, E., Raabe, M., Urlaub, H. and Meister, G. (2007) Proteomic and functional analysis of Argonaute-containing mRNA-protein complexes in human cells. EMBO Rep., 8, 1052-1060.
47. Haussecker, D., Cao, D., Huang, Y., Parameswaran, P., Fire, A.Z. and Kay, M.A. (2008) Capped small RNAs and MOV10 in human hepatitis delta virus replication. Nat. Struct. Mol. Biol., 15, 714-721.
48. Kuzniar, A., van Ham, R.C., Pongor, S. and Leunissen, J.A. (2008) The quest for orthologs: finding the corresponding gene across genomes. Trends Genet, 24, 539-551.
49. Zeng, C.J.T., Lee, Y.-R.J. and Liu, B. (2009) The WD40 repeat protein NEDD1 functions in microtubule organization during cell division in Arabidopsis thaliana. Plant Cell, 21, 1129-1140.
50. Lau, C.-k., Bachorik, J.L. and Dreyfuss, G. (2009) Gemin5-snRNA interaction reveals an RNA binding function for WD repeat domains. Nat. Struct. Mol. Biol., 16, 486-491.
51. Smith, T.F. (2008) Diversity of WD-repeat proteins. Subcell. Biochem, 48, 20-30.