The origin of the ADAR gene family and animal RNA editing

BMC Evolutionary Biology

Volumn 15, Issue 1, 2015, Pages

  Grice, Laura F ^a   Degnan, Bernard M ^a  

^a UNIVERSITY OF QUEENSLAND   (Australia)

Author keywords

A to I editing; Adenosine deaminase acting on RNA (ADAR); Ctenophore; Domain architecture; Domain evolution; Evolution; Metazoa; RNA editing; Sponge

Indexed keywords

EVOLUTIONARY BIOLOGY; METAZOAN; RNA;

ANIMALIA; BILATERIA; CTENOPHORA (COELENTERATES); MAMMALIA; METAZOA; VERTEBRATA;

ADENOSINE DEAMINASE; RNA BINDING PROTEIN;

ANIMAL; CHEMISTRY; GENETICS; METABOLISM; MOLECULAR EVOLUTION; PHYLOGENY; RNA EDITING;

ADENOSINE DEAMINASE; ANIMALS; EVOLUTION, MOLECULAR; PHYLOGENY; RNA EDITING; RNA-BINDING PROTEINS;

EID: 84923876827     PISSN: None     EISSN: 14712148     Source Type: Journal    
DOI: 10.1186/s12862-015-0279-3     Document Type: Article

References (28)

1. Simpson L. RNA editing. Annu Rev Neurosci. 1996;19:27-52.
2. Gott JM, Emeson RB. Functions and mechanisms of RNA editing. Annu Rev Genet. 2000;34:499-531.
3. Bass BL, Weintraub H. An unwinding activity that covalently modifies its double-stranded RNA substrate. Cell. 1988;55:1089-98.
4. Wagner RW, Smith JE, Cooperman BS, Nishikura K. A double-stranded RNA unwinding activity introduces structural alterations by means of adenosine to inosine conversions in mammalian cells and Xenopus eggs. Proc Natl Acad Sci U S A. 1989;86:2647-51.
5. Nishikura K. Functions and regulation of RNA editing by ADAR deaminases. Annu Rev Biochem. 2010;79:321-49.
6. Jantsch MF, Ohman M. RNA editing by adenosine deaminases that act on RNA (ADARs). In: Göringer HU, editor. RNA Editing. Berlin: Springer Verlag; 2008. p. 51-84.
7. Scadden ADJ, Smith CW. RNAi is antagonized by A → I hyper-editing. EMBO Rep. 2001;2:1107-11.
8. Samuel CE. Adenosine deaminases acting on RNA (ADARs) are both antiviral and proviral dependent on the virus. Virology. 2011;411:180-93.
9. Athanasiadis A, Rich A, Maas S. Widespread A-to-I RNA editing of Alu-containing mRNAs in the human transcriptome. PLoS Biol. 2004;2:e391.
10. Ng SK, Weissbach R, Ronson GE, Scadden ADJ. Proteins that contain a functional Z-DNA-binding domain localize to cytoplasmic stress granules. Nucleic Acids Res. 2013;41:9786-99.
11. Rueter SM, Dawson TR, Emeson RB. Regulation of alternative splicing by RNA editing. Nature. 1999;399:75-80.
12. Solomon O, Oren S, Safran M, Deshet-Unger N, Akiva P, Jacob-Hirsch J, et al. Global regulation of alternative splicing by adenosine deaminase acting on RNA (ADAR). RNA. 2013;19:591-604.
13. Gerber A. Tad1p, a yeast tRNA-specific adenosine deaminase, is related to the mammalian pre-mRNA editing enzymes ADAR1 and ADAR2. EMBO J. 1998;17:4780-9.
14. Jin Y, Zhang W, Li Q. Origins and evolution of ADAR-mediated RNA editing. IUBMB Life. 2009;61:572-8.
15. Keegan LP, McGurk L, Palavicini JP, Brindle J, Paro S, Li X, et al. Functional conservation in human and Drosophila of Metazoan ADAR2 involved in RNA editing: loss of ADAR1 in insects. Nucleic Acids Res. 2011;39:7249-62.
16. Moroz LL, Kocot KM, Citarella MR, Dosung S, Norekian TP, Povolotskaya IS, et al. The ctenophore genome and the evolutionary origins of neural systems. Nature. 2014;510:109-14.
17. Melcher T, Maas S, Herb A, Sprengel R, Higuchi M, Seeburg PH. RED2, a brain-specific member of the RNA-specific adenosine deaminase family. J Biol Chem. 1996;271:31795-8.
18. Ryan JF, Pang K, Schnitzler CE, Nguyen A-D, Moreland RT, Simmons DK, et al. The genome of the ctenophore Mnemiopsis leidyi and its implications for cell type evolution. Science. 2013;342:1242592.
19. Srivastava M, Simakov O, Chapman J, Fahey B, Gauthier MEA, Mitros T, et al. The Amphimedon queenslandica genome and the evolution of animal complexity. Nature. 2010;466:720-6.
20. Grimson A, Srivastava M, Fahey B, Woodcroft BJ, Chiang HR, King N, et al. Early origins and evolution of microRNAs and Piwi-interacting RNAs in animals. Nature. 2008;455:1193-7.
21. Degnan BM, Vervoort M, Larroux C. Early evolution of metazoan transcription factors. Curr Opin Genet Dev. 2009;19:591-9.
22. Richards GS, Degnan BM. The dawn of developmental signaling in the Metazoa. Cold Spring Harb Symp Quant Biol. 2009;74:81-90.
23. Eddy SR. Profile hidden Markov models. Bioinformatics. 1998;14:755-63.
24. Altschul SF, Madden TL, Schäffer AA, Zhang J, Zhang Z, Miller W, et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 1997;25:3389-402.
25. Punta M, Coggill PC, Eberhardt RY, Mistry J, Tate J, Boursnell C, et al. The Pfam protein families database. Nucleic Acids Res. 2011;40:D290-301.
26. Li W, Godzik A. Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences. Bioinformatics. 2006;22:1658-9.
27. Huang Y, Niu B, Gao Y, Fu L, Li W. CD-HIT Suite: a web server for clustering and comparing biological sequences. Bioinformatics. 2010;26:680-2.
28. Thacker RW, Hill AL, Hill MS, Redmond NE, Collins AG, Morrow CC, et al. Nearly complete 28S rRNA gene sequences confirm new hypotheses of sponge evolution. Integr Comp Biol. 2013;53:373-87.