Global In-Silico Scenario of tRNA Genes and Their Organization in Virus Genomes

Abstract

Viruses are known to be highly dependent on the host translation machinery for their protein synthesis. However, tRNA genes are occasionally identified in such organisms, and in addition, few of them harbor tRNA gene clusters comprising dozens of genes. Recently, tRNA gene clusters have been shown to occur among the three domains of life. In such a scenario, the viruses could play a role in the dispersion of such structures among these organisms. Thus, in order to reveal the prevalence of tRNA genes as well as tRNA gene clusters in viruses, we performed an unbiased large-scale genome survey. Interestingly, tRNA genes were predicted in ssDNA (single-stranded DNA) and ssRNA (single-stranded RNA) viruses as well in many other dsDNA viruses of families from Caudovirales order. In the latter group, tRNA gene clusters composed of 15 to 37 tRNA genes were characterized, mainly in bacteriophages, enlarging the occurrence of such structures within viruses. These bacteriophages were from hosts that encompass five phyla and 34 genera. This in-silico study presents the current global scenario of tRNA genes and their organization in virus genomes, contributing and opening questions to be explored in further studies concerning the role of the translation apparatus in these organisms.

Keywords: bacteriophages; codons; host range; ssDNA; ssRNA; tRNA gene; tRNA gene cluster; translation apparatus; virus.

Figure 1

Correlations between tRNA gene number and genome length. (A) Correlation between the total number of tRNA genes in each genome and their length (Spearman’s correlation coefficients: R = 0.5, p = 10⁻¹⁶). (B) Correlation between the number of clustered tRNA genes and the genome length of viruses carrying tRNA gene clusters (Spearman’s correlation coefficients: R = −0.49, p = 10⁻¹⁵).

Figure 2

Codon patterns of the tRNA gene clusters. The heatmap shows the tRNA gene copy number (codons and isotypes) of each tRNA gene cluster. The background color of the labels is associated with each tRNA gene cluster group (indicated by the red labels or shown in Figure S1). The yellow background labels represent the Cellulophaga phages with the same tRNA gene cluster group. Genomes having identical codon pattern were collapsed, represented by the bold label. A larger version of this figure is provided in Figure S4.