Experimental Confirmation of a Whole Set of tRNA Molecules in Two Archaeal Species
Based on the genomic sequences for most archaeal species, only one tRNA gene (isodecoder) is predicted for each triplet codon. This observation promotes analysis of a whole set of tRNA molecules and actual splicing patterns of interrupted tRNA in one organism. The entire genomic sequences of two Cr...
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| Format: | Article |
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MDPI AG
2015-01-01
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| Series: | International Journal of Molecular Sciences |
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| Online Access: | http://www.mdpi.com/1422-0067/16/1/2187 |
| _version_ | 1811322584728338432 |
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| author | Yoh-ichi Watanabe Yutaka Kawarabayasi |
| author_facet | Yoh-ichi Watanabe Yutaka Kawarabayasi |
| author_sort | Yoh-ichi Watanabe |
| collection | DOAJ |
| description | Based on the genomic sequences for most archaeal species, only one tRNA gene (isodecoder) is predicted for each triplet codon. This observation promotes analysis of a whole set of tRNA molecules and actual splicing patterns of interrupted tRNA in one organism. The entire genomic sequences of two Creanarchaeota, Aeropyrum pernix and Sulfolobus tokodaii, were determined approximately 15 years ago. In these genome datasets, 47 and 46 tRNA genes were detected, respectively. Among them, 14 and 24 genes, respectively, were predicted to be interrupted tRNA genes. To confirm the actual transcription of these predicted tRNA genes and identify the actual splicing patterns of the predicted interrupted tRNA molecules, RNA samples were prepared from each archaeal species and used to synthesize cDNA molecules with tRNA sequence-specific primers. Comparison of the nucleotide sequences of cDNA clones representing unspliced and spliced forms of interrupted tRNA molecules indicated that some introns were located at positions other than one base 3' from anticodon region and that bulge-helix-bulge structures were detected around the actual splicing sites in each interrupted tRNA molecule. Whole-set analyses of tRNA molecules revealed that the archaeal tRNA splicing mechanism may be essential for efficient splicing of all tRNAs produced from interrupted tRNA genes in these archaea. |
| first_indexed | 2024-04-13T13:38:47Z |
| format | Article |
| id | doaj.art-20dd4c5147274dfb95b51007c3f98ef2 |
| institution | Directory Open Access Journal |
| issn | 1422-0067 |
| language | English |
| last_indexed | 2024-04-13T13:38:47Z |
| publishDate | 2015-01-01 |
| publisher | MDPI AG |
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| series | International Journal of Molecular Sciences |
| spelling | doaj.art-20dd4c5147274dfb95b51007c3f98ef22022-12-22T02:44:42ZengMDPI AGInternational Journal of Molecular Sciences1422-00672015-01-011612187220310.3390/ijms16012187ijms16012187Experimental Confirmation of a Whole Set of tRNA Molecules in Two Archaeal SpeciesYoh-ichi Watanabe0Yutaka Kawarabayasi1University of Tokyo, Graduate School of Medicine, Hongo 7-3-1, Bunkyo-ku, Tokyo 113-0033, JapanKyushu University, Faculty of Agriculture, Hakozaki 6-10-1, Fukuoka 812-8581, JapanBased on the genomic sequences for most archaeal species, only one tRNA gene (isodecoder) is predicted for each triplet codon. This observation promotes analysis of a whole set of tRNA molecules and actual splicing patterns of interrupted tRNA in one organism. The entire genomic sequences of two Creanarchaeota, Aeropyrum pernix and Sulfolobus tokodaii, were determined approximately 15 years ago. In these genome datasets, 47 and 46 tRNA genes were detected, respectively. Among them, 14 and 24 genes, respectively, were predicted to be interrupted tRNA genes. To confirm the actual transcription of these predicted tRNA genes and identify the actual splicing patterns of the predicted interrupted tRNA molecules, RNA samples were prepared from each archaeal species and used to synthesize cDNA molecules with tRNA sequence-specific primers. Comparison of the nucleotide sequences of cDNA clones representing unspliced and spliced forms of interrupted tRNA molecules indicated that some introns were located at positions other than one base 3' from anticodon region and that bulge-helix-bulge structures were detected around the actual splicing sites in each interrupted tRNA molecule. Whole-set analyses of tRNA molecules revealed that the archaeal tRNA splicing mechanism may be essential for efficient splicing of all tRNAs produced from interrupted tRNA genes in these archaea.http://www.mdpi.com/1422-0067/16/1/2187archaeatRNAtRNA geneinterrupted genegenomecDNAintronsplicingendonuclease |
| spellingShingle | Yoh-ichi Watanabe Yutaka Kawarabayasi Experimental Confirmation of a Whole Set of tRNA Molecules in Two Archaeal Species International Journal of Molecular Sciences archaea tRNA tRNA gene interrupted gene genome cDNA intron splicing endonuclease |
| title | Experimental Confirmation of a Whole Set of tRNA Molecules in Two Archaeal Species |
| title_full | Experimental Confirmation of a Whole Set of tRNA Molecules in Two Archaeal Species |
| title_fullStr | Experimental Confirmation of a Whole Set of tRNA Molecules in Two Archaeal Species |
| title_full_unstemmed | Experimental Confirmation of a Whole Set of tRNA Molecules in Two Archaeal Species |
| title_short | Experimental Confirmation of a Whole Set of tRNA Molecules in Two Archaeal Species |
| title_sort | experimental confirmation of a whole set of trna molecules in two archaeal species |
| topic | archaea tRNA tRNA gene interrupted gene genome cDNA intron splicing endonuclease |
| url | http://www.mdpi.com/1422-0067/16/1/2187 |
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