Comparison of codon usage in mycobacteriophages with and without tRNAs in their genomes
© Gill and Rinehart; licensee BioMed Central Ltd. 2013
Published: 22 October 2013
Mycobacterium smegmatis is a soil bacterium. Over 448 mycobacteriophages specific for M. smegmatis have been sequenced and grouped into clusters of related genomes based on the similarity of their products and genome organization . Eighty-one of these sequenced phage genomes contain at least one tRNA.
Materials and methods
To determine which codons may require expression of phage tRNAs, Figure 1 plot regions for phages containing tRNA (red) that show frequencies in excess of those not containing tRNA (blue) have been circled in magenta. Only a few codons meet this criteria: ACT, ATG, CAG***, CGT, GAC**, GAG*, TAC, TAT, TGG. A significant number of mycobacteriophages lay outside the non-tRNA phage boundaries for codons CAG, GAC and GAG, therefore, these phages may be dependent on internally coded tRNAs.
- Hatfull GF: Mycobacteriophages: genes and genomes. Annu Rev Microbiol. 2010, 64: 331-356. 10.1146/annurev.micro.112408.134233.View ArticlePubMedGoogle Scholar
- Benson DA, Karsch-Mizrachi I, Clark K, Lipman DJ, Ostel J, Sayers EW: GenBank. Nucleic Acids Res. 2012, 40 (Database issue): D48-D53.PubMed CentralView ArticlePubMedGoogle Scholar
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