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Nucleic Acids Research Advance Access originally published online on October 27, 2006
Nucleic Acids Research 2006 34(20):6015-6022; doi:10.1093/nar/gkl739
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Nucleic Acids Research, 2006, Vol. 34, No. 20 6015-6022
© 2006 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Genomics

Differential annotation of tRNA genes with anticodon CAT in bacterial genomes

Francisco J. Silva*, Eugeni Belda and Santiago E. Talens

Departament de Genètica, Institut Cavanilles de Biodiversitat i Biologia Evolutiva, Universitat de València Apartat 22085, 46071 Valencia, Spain

*To whom correspondence should be addressed. Tel: +34 963543650; Fax: +34 963543670; Email: francisco.silva{at}uv.es

Received June 26, 2006. Revised September 25, 2006. Accepted September 25, 2006.

We have developed three strategies to discriminate among the three types of tRNA genes with anticodon CAT (tRNAIle, elongator tRNAMet and initiator tRNAfMet) in bacterial genomes. With these strategies, we have classified the tRNA genes from 234 bacterial and several organellar genomes. These sequences, in an aligned or unaligned format, may be used for the identification and annotation of tRNA (CAT) genes in other genomes. The first strategy is based on the position of the problem sequences in a phenogram (a tree-like network), the second on the minimum average number of differences against the tRNA sequences of the three types and the third on the search for the highest score value against the profiles of the three types of tRNA genes. The species with the maximum number of tRNAfMet and tRNAMet was Photobacterium profundum, whereas the genome of one Escherichia coli strain presented the maximum number of tRNAIle (CAT) genes. This last tRNA gene and tilS, encoding an RNA-modifying enzyme, are not essential in bacteria. The acquisition of a tRNAIle (TAT) gene by Mycoplasma mobile has led to the loss of both the tRNAIle (CAT) and the tilS genes. The new tRNA has appropriated the function of decoding AUA codons.


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[Abstract] [Full Text] [PDF]


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