Differential annotation of tRNA genes with anticodon CAT in bacterial genomes - PubMed (original) (raw)

Differential annotation of tRNA genes with anticodon CAT in bacterial genomes

Francisco J Silva et al. Nucleic Acids Res. 2006.

Abstract

We have developed three strategies to discriminate among the three types of tRNA genes with anticodon CAT (tRNA(Ile), elongator tRNA(Met) and initiator tRNA(fMet)) 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 tRNA(fMet) and tRNA(Met) was Photobacterium profundum, whereas the genome of one Escherichia coli strain presented the maximum number of tRNA(Ile) (CAT) genes. This last tRNA gene and tilS, encoding an RNA-modifying enzyme, are not essential in bacteria. The acquisition of a tRNA(Ile) (TAT) gene by Mycoplasma mobile has led to the loss of both the tRNA(Ile) (CAT) and the tilS genes. The new tRNA has appropriated the function of decoding AUA codons.

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Figures

Figure 1

Figure 1

Phenograms of tRNA gene sequences with anticodon CAT. (A) Enterobacteriaceae. (B) Clostridia and Mollicutes. Filled circles show the location of the tRNA genes of a known type from E.coli (eco) and M.capricolum (mcp).

Figure 2

Figure 2

Phenogram of the complete set of tRNA genes with anticodon CAT. Red (tRNAIle), green (tRNAMet) and blue (tRNAfMet). The bar shows the branch length for 2 nt differences. The largest branch at the fMet group corresponds to the mitochondrial tRNA genes.

Figure 3

Figure 3

Three-dimensional plot of TFAM scores for tRNA gene sequences. Positive values show proximity to the profile of a specific tRNA type.

Figure 4

Figure 4

Comparative maps of the region including tilS gene.

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