title: Structural determinants characteristic to AARS subclasses and tRNA-splicing endonuclease in eukaryotes.
abstract: We compare and analyse the whole set of cytoplasmic, nonorganellar transfer RNA genes from 22 eukaryal genomes. Grouping this whole set into sets of isoacceptors we have elucidated structural elements that are characteristic to individual isoacceptor tRNAs within the subclasses of aminoacyl tRNA synthetases. Further, we have observed structural motifs straddling the exon-intron boundaries, which includes selective occurrence of both symmetric- 3-4-3 and asymmetric-3-4-(4, 5) bulge-helix-bulge-like structural motifs. Among all the tRNA isoacceptors, Ile, Leu, Ser, Pro, Met, Arg, and Tyr harbor BHB-like secondary structures at exon-intron boundaries. The structural signatories at the exon-intron boundaries appear to contribute to the specificity of splice site recognition.
authors.affiliation: Computational Biology Group, Indian Association for the Cultivation of Science, Jadavpur, Calcutta 700032, India. tpbm@iacs.res.in
authors.forename: Bibekanand
authors.initials: B
authors.lastname: Mallick
authors.forename: Zhumur
authors.initials: Z
authors.lastname: Ghosh
authors.forename: Jayprokas
authors.initials: J
authors.lastname: Chakrabarti
mesh_terms: D000818:Animals; D004722:Endoribonucleases / Q000737:chemistry*; D005057:Eukaryotic Cells / Q000201:enzymology*; D006801:Humans; D009690:Nucleic Acid Conformation; D012343:RNA, Transfer / Q000737:chemistry* / Q000235:genetics* / Q000378:metabolism
chemical_list: D012343:RNA, Transfer; D004722:Endoribonucleases; C051012:splicing endonuclease