title: Nanoarchaeum equitans creates functional tRNAs from separate genes for their 5'- and 3'-halves.
abstract: Analysis of the genome sequence of the small hyperthermophilic archaeal parasite Nanoarchaeum equitans has not revealed genes encoding the glutamate, histidine, tryptophan and initiator methionine transfer RNA species. Here we develop a computational approach to genome analysis that searches for widely separated genes encoding tRNA halves that, on the basis of structural prediction, could form intact tRNA molecules. A search of the N. equitans genome reveals nine genes that encode tRNA halves; together they account for the missing tRNA genes. The tRNA sequences are split after the anticodon-adjacent position 37, the normal location of tRNA introns. The terminal sequences can be accommodated in an intervening sequence that includes a 12-14-nucleotide GC-rich RNA duplex between the end of the 5' tRNA half and the beginning of the 3' tRNA half. Reverse transcriptase polymerase chain reaction and aminoacylation experiments of N. equitans tRNA demonstrated maturation to full-size tRNA and acceptor activity of the tRNA(His) and tRNA(Glu) species predicted in silico. As the joining mechanism possibly involves tRNA trans-splicing, the presence of an intron might have been required for early tRNA synthesis.
authors.affiliation: Department of Molecular Biophysics and Biochemistry, Yale University, 266 Whitney Avenue, New Haven, Connecticut 06520-8114, USA.
authors.forename: Lennart
authors.initials: L
authors.lastname: Randau
authors.forename: Richard
authors.initials: R
authors.lastname: Münch
authors.forename: Michael J
authors.initials: MJ
authors.lastname: Hohn
authors.forename: Dieter
authors.initials: D
authors.lastname: Jahn
authors.forename: Dieter
authors.initials: D
authors.lastname: Söll
mesh_terms: D049148:Aminoacylation; D001483:Base Sequence; D019295:Computational Biology; D019766:Genes, Archaeal / Q000235:genetics*; D020745:Genome, Archaeal; D023281:Genomics; D005975:Glutamate-tRNA Ligase / Q000378:metabolism; D006643:Histidine-tRNA Ligase / Q000378:metabolism; D007438:Introns / Q000235:genetics; D008969:Molecular Sequence Data; D046588:Nanoarchaeota / Q000201:enzymology / Q000235:genetics*; D009690:Nucleic Acid Conformation; D019642:RNA, Archaeal / Q000737:chemistry / Q000235:genetics* / Q000302:isolation & purification / Q000378:metabolism; D012343:RNA, Transfer / Q000737:chemistry / Q000235:genetics* / Q000302:isolation & purification / Q000378:metabolism; D020040:Trans-Splicing / Q000235:genetics*
chemical_list: D019642:RNA, Archaeal; D012343:RNA, Transfer; D005975:Glutamate-tRNA Ligase; D006643:Histidine-tRNA Ligase