A-to-I RNA editing alters less-conserved residues of highly conserved coding regions: Implications for dual functions in evolution

RNA

Volumn 14, Issue 8, 2008, Pages 1516-1525

  Yang, Yun ^a   Lv, Jianning ^a   Gui, Bin ^a   Yin, Heng ^a   Wu, Xiaojie ^a   Zhang, Yaozhou ^b   Jin, Yongfeng ^a,b  

^a ZHEJIANG UNIVERSITY   (China)

^b ZHEJIANG SCI TECH UNIVERSITY   (China)

Author keywords

Insect; Phylogenetic conservation; Protein diversity; RNA editing; Squid

Indexed keywords

AMINO ACID; SHAB POTASSIUM CHANNEL; SYNAPTOTAGMIN I;

AMINO ACID SEQUENCE; ARTICLE; COLEOPTERA; COMPARATIVE STUDY; CULEX PIPIENS; DROSOPHILA MELANOGASTER; EVOLUTION; FLY; HONEYBEE; HYMENOPTERA; INSECT; INVERTEBRATE; LEPIDOPTERA; LOUSE; MOLLUSC; NUCLEOTIDE SEQUENCE; PHYLOGENY; PRIORITY JOURNAL; RNA EDITING; SILKWORM; SQUID; UNINDEXED SEQUENCE;

ADENOSINE; AMINO ACID SEQUENCE; ANIMALS; CONSERVED SEQUENCE; EVOLUTION, MOLECULAR; HUMANS; INOSINE; INSECT PROTEINS; INSECTS; MOLECULAR SEQUENCE DATA; RNA EDITING; SEQUENCE ALIGNMENT; SHAB POTASSIUM CHANNELS;

APIS MELLIFERA; BOMBYX MORI; CEPHALOPODA; COLEOPTERA; CULEX PIPIENS; DIPTERA; DROSOPHILA MELANOGASTER; HEMIPTERA; HEXAPODA; HYMENOPTERA; INVERTEBRATA; LEPIDOPTERA; MOLLUSCA; MYZUS PERSICAE; PEDICULUS HUMANUS; PHTHIRAPTERA; PULEX IRRITANS; TRIBOLIUM CASTANEUM;

EID: 47949099524     PISSN: 13558382     EISSN: 14699001     Source Type: Journal    
DOI: 10.1261/rna.1063708     Document Type: Article

References (50)

1. Athanasiadis, A., Rich, A., and Maas, S. 2004. Widespread A-to-I RNA editing of Alu-containing mRNAs in the human transcriptome. PLoS Biol. 2: e391. doi: 10.1371/journal.pbio.0020391.
2. Baro, D.J., Cole, C.L., Zarrin, A.R., Hughes, S., and Harris-Warrick, R.M. 1994. Shab gene expression in identified neurons of the pyloric network in the lobster stomatogastric ganglion. Receptors Channels 2: 193-205.
3. Bass, B.L. 2002. RNA editing by adenosine deaminases that act on RNA. Annu. Rev. Biochem. 71: 817-846.
4. Bhalla, T., Rosenthal, J.J., Holmgren, M., and Reenan, R. 2004. Control of human potassium channel inactivation by editing of a small mRNA hairpin. Nat. Struct. Mol. Biol. 11: 950-956.
5. Blow, M., Futreal, P.A., Wooster, R., and Stratton, M.R. 2004. A survey of RNA editing in human brain. Genome Res. 14: 2379-2387.
6. Bommert, K., Charlton, M.P., DeBello, W.M., Chin, G.J., Betz, H., and Augustine, G.J. 1993. Inhibition of neurotransmitter release by C2-domain peptides implicates synaptotagmin in exocytosis. Nature 363: 163-165.
7. Bratt, E. and Ohman, M. 2003. Coordination of editing and splicing of glutamate receptor pre-mRNA. RNA 9: 309-318.
8. Butler, A., Wei, A.G., Baker, K., and Salkoff, L. 1989. A family of putative potassium channel genes in Drosophila. Science 243: 943-947.
9. Covello, P.S. and Gray, M.W. 1989. RNA editing in plant mitochondria. Nature 341: 662-666.
10. Flomen, R., Knight, J., Sham, P., Kerwin, R., and Makoff, A. 2004. Evidence that RNA editing modulates splice site selection in the 5-HT2C receptor gene. Nucleic Acids Res. 32: 2113-2122.
11. Grauso, M., Reenan, R.A., Culetto, E., and Sattelle, D.B. 2002. Novel putative nicotinic acetylcholine receptor subunit genes, Dα5, Dα6 and Dα7, in Drosophila melanogaster identify a new and highly conserved target of adenosine deaminase acting on RNA-mediated A-to-I pre-mRNA editing. Genetics 160: 1519-1533.
12. Gray, M.W. and Covello, P.S. 1993. RNA editing in plant mitochondria and chloroplasts. FASEB J. 7: 64-71.
13. Gualberto, J.M., Lamattina, L., Bonnard, G., Weil, J.H., and Grienenberger, J.M. 1989. RNA editing in wheat mitochondria results in the conservation of protein sequences. Nature 341: 660-662.
14. Higuchi, M., Maas, S., Single, F.N., Hartner, J., Rozov, A., Burnashev, N., Feldmeyer, D., Sprengel, R., and Seeburg, P.H. 2000. Point mutation in an AMPA receptor gene rescues lethality in mice deficient in the RNA-editing enzyme ADAR2. Nature 406: 78-81.
15. Hoopengardner, B., Bhalla, T., Staber, C., and Reenan, R. 2003. Nervous system targets of RNA editing identified by comparative genomics. Science 301: 832-836.
16. Jepson, J.E. and Reenan, R.A. 2007. RNA editing in regulating gene expression in the brain. Biochim. Biophys. Acta (in press). doi: 10.1016/j.bbagrm.2007.11.009.
17. Jin, Y., Tian, N., Cao, J., Liang, J., Yang, Z., and Lv, J. 2007. RNA editing and alternative splicing of the insect nAChR subunit α6 transcript: Evolutionary conservation, divergence, and regulation. BMC Evol. Biol. 7: 98.
18. Jones, A.K., Grauso, M., and Sattelle, D.B. 2005. The nicotinic acetylcholine receptor gene family of the malaria mosquito, Anopheles gambiae. Genomics 85: 176-187.
19. Jones, A.K., Raymond-Delpech, V., Thany, S.H., Gauthier, M., and Sattelle, D.B. 2006. The nicotinic acetylcholine receptor gene family of the honey bee, Apis mellifera. Genome Res. 16: 1422-1430.
20. Kawahara, Y., Zinshteyn, B., Chendrimada, T.P., Shiekhattar, R., and Nishikura, K. 2007a. RNA editing of the microRNA-151 precursor blocks cleavage by the Dicer-TRBP complex. EMBO Rep. 8: 763-769.
21. Kawahara, Y., Zinshteyn, B., Sethupathy, P., Iizasa, H., Hatzigeorgiou, A.G., and Nishikura, K. 2007b. Redirection of silencing targets by adenosine-to-inosine editing of miRNAs. Science 315: 1137-1140.
22. Keegan, L.P., Brindle, J., Gallo, A., Leroy, A., Reenan, R.A., and O'Connell, M.A. 2005. Tuning of RNA editing by ADAR is required in Drosophila. EMBO J. 24: 2183-2193.
23. Kim, D.D., Kim, T.T., Walsh, T., Kobayashi, Y., Matise, T.C., Buyske, S., and Gabriel, A. 2004. Widespread RNA editing of embedded alu elements in the human transcriptome. Genome Res. 14: 1719-1725.
24. Knight, S.W. and Bass, B.L. 2002. The role of RNA editing by ADARs in RNAi. Mol. Cell 10: 809-817.
25. Kung, S.S., Wu, Y.M., and Chow, W.Y. 1996. Characterization of two fish glutamate receptor cDNA molecules: Absence of RNA editing at the Q/R site. Brain Res. Mol. Brain Res. 35: 119-130.
26. Laurencikiene, J., Kallman, A.M., Fong, N., Bentley, D.L., and Ohman, M. 2006. RNA editing and alternative splicing: The importance of co-transcriptional coordination. EMBO Rep. 7: 303-307.
27. Lev-Maor, G., Sorek, R., Levanon, E.Y., Paz, N., Eisenberg, E., and Ast, G. 2007. RNA-editing-mediated exon evolution. Genome Biol. 8: R29. doi: 10.1186/gb-2007-8-2-r29.
28. Levanon, E.Y., Eisenberg, E., Yelin, R., Nemzer, S., Hallegger, M., Shemesh, R., Fligelman, Z.Y., Shoshan, A., Pollock, S.R., Sztybel, D., et al. 2004. Systematic identification of abundant A-to-I editing sites in the human transcriptome. Nat. Biotechnol. 22: 1001-1005.
29. Maas, S., Patt, S., Schrey, M., and Rich, A. 2001. Underediting of glutamate receptor GluR-B mRNA in malignant gliomas. Proc. Natl. Acad. Sci. 98: 14687-14692.
30. Maas, S., Rich, A., and Nishikura, K. 2003. A-to-I RNA editing: Recent news and residual mysteries. J. Biol. Chem. 278: 1391-1394.
31. Mikoshiba, K., Fukuda, M., Moreira, J.E., Lewis, F.M., Sugimori, M., Niinobe, M., and Llinas, R. 1995. Role of the C2A domain of synaptotagmin in transmitter release as determined by specific antibody injection into the squid giant synapse preterminal. Proc. Natl. Acad. Sci. 92: 10703-10707.
32. Mulligan, R.M., Chang, K.L., and Chou, C.C. 2007. Computational analysis of RNA editing sites in plant mitochondrial genomes reveals similar information content and a sporadic distribution of editing sites. Mol. Biol. Evol. 24: 1971-1981.
33. Nakhost, A., Houeland, G., Blandford, V.E., Castellucci, V.F., and Sossin, W.S. 2004. Identification and characterization of a novel C2B splice variant of synaptotagmin I. J. Neurochem. 89: 354-363.
34. Ohlson, J., Pedersen, J.S., Haussler, D., and Ohman, M. 2007. Editing modifies the GABA(A) receptor subunit α3. RNA 13: 698-703.
35. Palladino, M.J., Keegan, L.P., O'Connell, M.A., and Reenan, R.A. 2000. A-to-I pre-mRNA editing in Drosophila is primarily involved in adult nervous system function and integrity. Cell 102: 437-449.
36. + channels with altered functional properties. Neuron 19: 711-722.
37. Reenan, R.A. 2005. Molecular determinants and guided evolution of species-specific RNA editing. Nature 434: 409-413.
38. + channel regulates subunit tetramerization. Neuron 34: 743-757.
39. Rueter, S.M., Dawson, T.R., and Emeson, R.B. 1999. Regulation of alternative splicing by RNA editing. Nature 399: 75-80.
40. Scadden, A.D. and Smith, C.W. 2001. RNAi is antagonized by A → I hyperediting. EMBO Rep. 2: 1107-1111.
41. Schoft, V.K., Schopoff, S., and Jantsch, M.F. 2007. Regulation of glutamate receptor B pre-mRNA splicing by RNA editing. Nucleic Acids Res. 35: 3723-3732.
42. Sugden, A.M., Jasny, B.R., Culotta, E., and Pennisi, E. 2003. Charting the evolutionary history of life. Science 300: 1691.
43. Tian, N., Wu, X., Zhang, Y., and Jin, Y. 2008. A-to-I editing sites are a genomically encoded G: Implications for the evolutionary significance and identification of novel editing sites. RNA 14: 211-216.
44. Tillich, M., Funk, H.T., Schmitz-Linneweber, C., Poltnigg, P., Sabater, B., Martin, M., and Maier, R.M. 2005. Editing of plastid RNA in Arabidopsis thaliana ecotypes. Plant J. 43: 708-715.
45. Tonkin, L.A. and Bass, B.L. 2003. Mutations in RNAi rescue aberrant chemotaxis of ADAR mutants. Science 302: 1725.
46. Tonkin, L.A., Saccomanno, L., Morse, D.P., Brodigan, T., Krause, M., and Bass, B.L. 2002. RNA editing by ADARs is important for normal behavior in Caenorhabditis elegans. EMBO J. 21: 6025-6035.
47. Vissel, B., Royle, G.A., Christie, B.R., Schiffer, H.H., Ghetti, A., Tritto, T., Perez-Otano, I., Radcliffe, R.A., Seamans, J., Sejnowski, T., et al. 2001. The role of RNA editing of kainate receptors in synaptic plasticity and seizures. Neuron 29: 217-227.
48. Wang, Q., Khillan, J., Gadue, P., and Nishikura, K. 2000. Requirement of the RNA editing deaminase ADAR1 gene for embryonic erythropoiesis. Science 290: 1765-1768.
49. Yang, W., Chendrimada, T.P., Wang, Q., Higuchi, M., Seeburg, P.H., Shiekhattar, R., and Nishikura, K. 2006. Modulation of microRNA processing and expression through RNA editing by ADAR deaminases. Nat. Struct. Mol. Biol. 13: 13-21.
50. Zuker, M. 2003. Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res. 31: 3406-3415.