Avatar pre-tRNAs help elucidate the properties of tRNA-splicing endonucleases that produce tRNA from permuted genes

Proceedings of the National Academy of Sciences of the United States of America

Volumn 109, Issue 52, 2012, Pages 21325-21329

  Tocchini Valentini, Giuseppe D ^a   Tocchini Valentini, Glauco P ^a  

^a CNR   (Italy)

Author keywords

Gene duplication; Permuted tRNA genes

Indexed keywords

ENDONUCLEASE; TRANSFER RNA;

3' UNTRANSLATED REGION; 5' UNTRANSLATED REGION; ARTICLE; GENE DUPLICATION; NONHUMAN; PERMUTED TRANSFER RNA GENE; PRIORITY JOURNAL; RNA CLEAVAGE; RNA CONFORMATION; RNA GENE; RNA SPLICING; RNA TRANSCRIPTION;

BASE SEQUENCE; ENDORIBONUCLEASES; GENES; METHANOCOCCACEAE; MOLECULAR SEQUENCE DATA; NUCLEIC ACID CONFORMATION; RNA PRECURSORS; RNA PROCESSING, POST-TRANSCRIPTIONAL; RNA SPLICING; RNA, TRANSFER; SCHIZOSACCHAROMYCES;

ALGAE; ARCHAEA; EUKARYOTA;

EID: 84871824370     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.1219336110     Document Type: Article

References (31)

1. Randau L, Söll D (2008) Transfer RNA genes in pieces. EMBO Rep 9(7):623-628. (Pubitemid 351927682)
2. Randau L, Pearson M, Söll D (2005) The complete set of tRNA species in Nanoarchaeum equitans. FEBS Lett 579(13):2945-2947. (Pubitemid 40725271)
3. Randau L, Münch R, Hohn MJ, Jahn D, Söll D (2005) Nanoarchaeum equitans creates functional tRNAs from separate genes for their 5′- and 3′-halves. Nature 433(7025):537-541. (Pubitemid 40204312)
4. Fujishima K, et al. (2009) Tri-split tRNA is a transfer RNA made from 3 transcripts that provides insight into the evolution of fragmented tRNAs in archaea. Proc Natl Acad Sci USA 106(8):2683-2687.
5. Soma A, et al. (2007) Permuted tRNA genes expressed via a circular RNA intermediate in Cyanidioschyzon merolae. Science 318(5849):450-453. (Pubitemid 47614530)
6. Lowe TM, Eddy SR (1997) tRNAscan-SE: A program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res 25(5):955-964. (Pubitemid 27298263)
7. Altman S, Kirsebom L, Talbot S (1993) Recent studies of ribonuclease P. FASEB J 7(1):7-14. (Pubitemid 23034007)
8. Schürer H, Schiffer S, Marchfelder A, Mörl M (2001) This is the end: Processing, editing and repair at the tRNA 3′-terminus. Biol Chem 382(8):1147-1156.
9. Maruyama S, Sugahara J, Kanai A, Nozaki H (2010) Permuted tRNA genes in the nuclear and nucleomorph genomes of photosynthetic eukaryotes. Mol Biol Evol 27(5):1070-1076.
10. Tocchini-Valentini GD, Fruscoloni P, Tocchini-Valentini GP (2005) Coevolution of tRNA intron motifs and tRNA endonuclease architecture in Archaea. Proc Natl Acad Sci USA 102(43):15418-15422. (Pubitemid 41528072)
11. Tocchini-Valentini GD, Fruscoloni P, Tocchini-Valentini GP (2005) Structure, function, and evolution of the tRNA endonucleases of Archaea: An example of subfunctionalization. Proc Natl Acad Sci USA 102(25):8933-8938. (Pubitemid 40881056)
12. Heinonen TY, Schnare MN, Young PG, Gray MW (1987) Rearranged coding segments, separated by a transfer RNA gene, specify the two parts of a discontinuous large subunit ribosomal RNA in Tetrahymena pyriformis mitochondria. J Biol Chem 262(6):2879-2887.
13. Keiler KC, Shapiro L, Williams KP (2000) tmRNAs that encode proteolysis-inducing tags are found in all known bacterial genomes: A two-piece tmRNA functions in Caulobacter. Proc Natl Acad Sci USA 97(14):7778-7783. (Pubitemid 30460724)
14. Williams KP (2002) Descent of a split RNA. Nucleic Acids Res 30(9):2025-2030. (Pubitemid 34537600)
15. Chan PP, Cozen AE, Lowe TM (2011) Discovery of permuted and recently split transfer RNAs in Archaea. Genome Biol 12(4):R38.
16. Goodman HM, Olson MV, Hall BD (1977) Nucleotide sequence of a mutant eukaryotic gene: The yeast tyrosine-inserting ochre suppressor SUP4-o. Proc Natl Acad Sci USA 74(12):5453-5457.
17. Valenzuela P, Venegas A, Weinberg F, Bishop R, Rutter WJ (1978) Structure of yeast phenylalanine-tRNA genes: An intervening DNA segment within the region coding for the tRNA. Proc Natl Acad Sci USA 75(1):190-194. (Pubitemid 8290476)
18. Castronova E (2001) Virtual worlds: A first-hand account of market and society on the cyberian frontier. CEsifo working paper no. 618. Available at http://papers.ssrn.com/sol3/papers.cfm?abstract-id=294828. Accessed November 19, 2012.
19. Abelson J, Trotta CR, Li H (1998) tRNA splicing. J Biol Chem 273(21):12685-12688. (Pubitemid 28246818)
20. Tocchini-Valentini GP, Baldi MI, Gandini-Attardi D, Mattoccia E (1993) Cleavage site recognition by the tRNA splicing endoribonuclease. Gene 135(1-2):93-97. (Pubitemid 24042940)
21. Reyes VM, Abelson J (1988) Substrate recognition and splice site determination in yeast tRNA splicing. Cell 55(4):719-730.
22. Di Nicola Negri E, et al. (1997) The eucaryal tRNA splicing endonuclease recognizes a tripartite set of RNA elements. Cell 89(6):859-866.
23. Attardi DG, Margarit I, Tocchini-Valentini GP (1985) Structural alterations in mutant precursors of the yeast tRNALeu3 gene which behave as defective substrates for a highly purified splicing endoribonuclease. EMBO J 4(12):3289-3297.
24. Fruscoloni P, Baldi MI, Tocchini-Valentini GP (2001) Cleavage of non-tRNA substrates by eukaryal tRNA splicing endonucleases. EMBO Rep 2(3):217-221. (Pubitemid 32273300)
25. Fabbri S, et al. (1998) Conservation of substrate recognition mechanisms by tRNA splicing endonucleases. Science 280(5361):284-286. (Pubitemid 28178071)
26. Kjems J, Jensen J, Olesen T, Garrett RA (1989) Comparison of transfer RNA and ribosomal RNA intron splicing in the extreme thermophile and archaebacterium Desulfurococcus mobilis. Can J Microbiol 35(1):210-214. (Pubitemid 19093363)
27. Marck C, Grosjean H (2003) Identification of BHB splicing motifs in intron-containing tRNAs from 18 archaea: Evolutionary implications. RNA 9(12):1516-1531. (Pubitemid 37463477)
28. Trotta CR, et al. (1997) The yeast tRNA splicing endonuclease: A tetrameric enzyme with two active site subunits homologous to the archaeal tRNA endonucleases. Cell 89(6):849-858. (Pubitemid 27513511)
29. Paushkin SV, Patel M, Furia BS, Peltz SW, Trotta CR (2004) Identification of a human endonuclease complex reveals a link between tRNA splicing and pre-mRNA 3′ end formation. Cell 117(3):311-321. (Pubitemid 38534538)
30. Tocchini-Valentini GD, Fruscoloni P, Tocchini-Valentini GP (2011) Evolution of introns in the archaeal world. Proc Natl Acad Sci USA 108(12):4782-4787.
31. Yu WP, Brenner S, Venkatesh B (2003) Duplication, degeneration and subfunctionalization of the nested synapsin-Timp genes in Fugu. Trends Genet 19(4):180-183. (Pubitemid 36398417)