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DNA Research Advance Access originally published online on February 23, 2006
DNA Research 2005 12(6):403-416; doi:10.1093/dnares/dsi023
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© The Author 2006. Kazusa DNA Research Institute
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use, please contact journals.permissions@oxfordjournals.org

Characterization of a Whole Set of tRNA Molecules in an Aerobic Hyper-thermophilic Crenarchaeon, Aeropyrum pernix K1

Syuji Yamazaki1, Hisashi Kikuchi1 and Yutaka Kawarabayasi2,*

1National Institute of Technology and Evaluation 2-49-10 Nishihara, Shibuya, Tokyo 151-0066, Japan
2National Institute of Advanced Industrial Science and Technology (AIST) Higashi 1-1, Tsukuba, Ibaraki 305-8566, Japan

The tRNA molecule has an important role in translation, the function of which is to carry amino acids to the ribosomes. It is known that tRNA is transcribed from tRNA genes, some of which, in Eukarya and Archaea, contain introns. A computational analysis of the complete genome of Aeropyrum pernix K1 predicted the presence of 14 intron-containing tRNA genes. To elucidate whether these introns are actually processed in living cells and what mechanism detects the intron regions, cDNAs for premature and mature forms of the tRNA molecules transcribed from the intron-containing tRNA genes in the model aerobic acidothermophilic crenarchaeon, A. pernix K1 were identified and analyzed. A comparison between the nucleotide sequences of these two types of cDNAs indicated that the intron regions of the tRNA molecules were indeed processed in A. pernix K1 living cells. Some cDNA clones showed that the actual splicing positions were different from those predicted by computational analysis. However, the bulge–helix–bulge structure, which has been previously identified in exon–intron boundaries of archaeal tRNA genes, was evident in all boundary regions confirmed in this work. These results indicate that the generally described mechanism for tRNA processing in Archaea is utilized for processing the intron region of the tRNA molecules in A. pernix K1.

Key words: tRNA; intron; splicing; bulge–helix–bulge structure; genome; Crenarchaeon; Aeropyrum pernix K1

*To whom correspondence should be addressed. Tel: +81-29-861-6040, Fax: +81-29-861-6423, Email: kawarabayasi.yutaka{at}aist.go.jp

Communicated by Michio Oishi


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