Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2006;34(20):6015-22.
doi: 10.1093/nar/gkl739. Epub 2006 Oct 27.

Differential annotation of tRNA genes with anticodon CAT in bacterial genomes

Francisco J Silva  1 , Eugeni Belda, Santiago E Talens
Affiliations

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.

PubMed Disclaimer

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.
See this image and copyright information in PMC

Similar articles

See all similar articles

Cited by

See all "Cited by" articles

References

    1. Lowe T.M., Eddy S.R. tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res. 1997;25:955–964. - PMC - PubMed
    1. Ardell D.H., Andersson S.G.E. TFAM detects co-evolution of tRNA identity rules with lateral transfer of histidyl-tRNA synthetase. Nucleic Acids Res. 2006;34:893–904. - PMC - PubMed
    1. Grosjean H., Bjork G.R. Enzymatic conversion of cytidine to lysidine in anticodon of bacterial tRNA(lle)—an alternative way of RNA editing. Trends Biochem. Sci. 2004;29:165–168. - PubMed
    1. Agris P.F. Decoding the genome: a modified view. Nucleic Acids Res. 2004;32:223–238. - PMC - PubMed
    1. Soma A., Ikeuchi Y., Kanemasa S., Kobayashi K., Ogasawara N., Ote T., Kato J., Watanabe K., Sekine Y., Suzuki T. An RNA-modifying enzyme that governs both the codon and amino acid specificities of isoleucine tRNA. Mol. Cell. 2003;12:689–698. - PubMed

Publication types