Testing hypotheses for the presence of tRNA genes in mycobacteriophage genomes

Abstract

The presence of tRNA genes in bacteriophages has been explained on the basis of codon usage (tRNA genes are retained in the phage genome if they correspond to codons more common in the phage than in its host) or amino acid usage (independent of codon, the amino acid corresponding to the retained tRNA gene is more common in the phage genome than in the bacterial host). The existence of a large database of sequenced mycobacteriophages, isolated on the common host Mycobacterium smegmatis, allows us to test the above hypotheses as well as explore other hypotheses for the presence of tRNA genes. Our analyses suggest that amino acid rather than codon usage better explains the presence of tRNA genes in mycobacteriophages. However, closely related phages that differ in the presence of tRNA genes in their genomes are capable of lysing the common bacterial host and do not differ in codon or amino acid usage. This suggests that the benefits of having tRNA genes may be associated with either growth in the host or the ability to infect more hosts (i.e., host range) rather than simply infecting a particular host.

Beyond the Limits: tRNA Array Units in Mycobacterium Genomes

“…In some species from this genus, there are multiple tandem arrays of clustered tRNA genes containing up to five tRNA genes (Tawari et al, 2008 ). Contrasting with the regular organization and distribution of tRNA genes in the genomes, large tRNA gene clusters, presenting high number and density (i.e., tRNA/kb), have been observed in some prokaryote and bacteriophage genomes (Green and Vold, 1993 ; Bailly-Bechet et al, 2007 ; Hatfull et al, 2010 ; Pope et al, 2011 , 2014 ; Puerto-Galán and Vioque, 2012 ; Delesalle et al, 2016 ; Alamos et al, 2017 ). Concerning the presence of large tRNA clusters in bacteria, a recent large-scale genome survey characterized an abundance of tRNA array units mainly in Firmicutes and few other low GC Gram-positive bacteria phyla.…”

Discovering the Molecular Determinants of Phaeobacter inhibens susceptibility to Phaeobacter phage MD18

“…These tRNA genes corresponded to codons which were significantly enriched in the Phaeobacter phage MD18 genome compared to codons without a corresponding tRNA gene (Figure 2A) (p = 6.4 x 10 -5 , Wilcox rank sum test). Phage genomes frequently encode tRNA genes, which facilitate the translation of phage transcripts in host bacteria (22)(23)(24). Another assumption of phage genome evolution is that phage codon usage adapts to resemble that of their bacterial hosts (23,24).…”

Pantoea agglomerans-Infecting Bacteriophage vB_PagS_AAS21: A Cold-Adapted Virus Representing a Novel Genus within the Family Siphoviridae

“…The presence of tRNA genes in virus genomes could be associated with numerous functions. Various studies indicated that tRNA genes in viral genomes could be used to compensate for differences in codon and/or amino acid usage between virus and its hosts, resulting in an efficient protein synthesis and/or expansion of the host range [24][25][26][27]. Thus, keeping in mind a significantly lower G+C content (39.0%) of the bacteriophage AAS21 DNA compared to that (52-55%) observed for Pantoea spp., it might be speculated that a large number of tRNAs present in the genome of AAS21 are necessary to optimize a translation process.…”