Transfer RNA genes and their significance to codon usage in the Pseudomonas aeruginosa lamboid bacteriophage D3.
Using tRNAscan-SE and FAStRNA we have identified four tRNA genes in the delayed early region of the bacteriophage D3 genome (GenBank accession No. AF077308). These are specific for methionine (AUG), glycine (GGA), asparagine (AAC), and threonine (ACA). The D3 Thr- and Gly-tRNAs recognize codons, which are rarely used in Pseudomonas aeruginosa and presumably, influence the rate of translation of phage proteins. BLASTN searches revealed that the D3 tRNA genes have homology to tRNA genes from Gram-positive bacteria. Analysis of codon usage in the 91 ORFs discovered in D3 indicates patterns of codon usage reminiscent of Escherichia coli or P. aeruginosa.
Kropinski
A M
AM
Department of Microbiology and Immunology, Queen's University, Kingston, ON, Canada. kropinsk@post.queensu.ca
Sibbald
M J
MJ
D001435:Bacteriophages / Q000235:genetics*; D001483:Base Sequence; D003062:Codon / Q000235:genetics; D004926:Escherichia coli / Q000235:genetics; D016679:Genome, Viral; D008969:Molecular Sequence Data; D016366:Open Reading Frames / Q000235:genetics; D011550:Pseudomonas aeruginosa / Q000821:virology*; D012345:RNA, Transfer, Amino Acid-Specific / Q000235:genetics*; D012349:RNA, Transfer, Asp / Q000737:chemistry / Q000235:genetics; D012353:RNA, Transfer, Gly / Q000737:chemistry / Q000235:genetics; D012358:RNA, Transfer, Met / Q000737:chemistry / Q000235:genetics; D012363:RNA, Transfer, Thr / Q000737:chemistry / Q000235:genetics; D012367:RNA, Viral / Q000235:genetics*
D003062:Codon; D012345:RNA, Transfer, Amino Acid-Specific; D012349:RNA, Transfer, Asp; D012353:RNA, Transfer, Gly; D012358:RNA, Transfer, Met; D012363:RNA, Transfer, Thr; D012367:RNA, Viral