Global In-Silico Scenario of tRNA Genes and Their Organization in Virus Genomes
Open Access
- 21 February 2019
- Vol. 11 (2), 180
- https://doi.org/10.3390/v11020180
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
Funding Information
- Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (001)
This publication has 55 references indexed in Scilit:
- A Multivalent Adsorption Apparatus Explains the Broad Host Range of Phage phi92: a Comprehensive Genomic and Structural AnalysisJournal of Virology, 2012
- Giant virus with a remarkable complement of genes infects marine zooplanktonProceedings of the National Academy of Sciences of the United States of America, 2010
- New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies: Assessing the Performance of PhyML 3.0Systematic Biology, 2010
- Comparative Genomic Analysis of 60 Mycobacteriophage Genomes: Genome Clustering, Gene Acquisition, and Gene SizeJournal of Molecular Biology, 2010
- Complete Genome of the Broad-Host-Range Erwinia amylovora Phage ΦEa21-4 and Its Relationship to Salmonella Phage Felix O1Applied and Environmental Microbiology, 2009
- Viral adaptation to host: a proteome‐based analysis of codon usage and amino acid preferencesMolecular Systems Biology, 2009
- Phage T4 SegB protein is a homing endonuclease required for the preferred inheritance of T4 tRNA gene region occurring in co-infection with a related phageNucleic Acids Research, 2008
- Patterns of Evolution in the Unique tRNA Gene Arrays of the Genus EntamoebaMolecular Biology and Evolution, 2007
- Causes for the intriguing presence of tRNAs in phagesGenome Research, 2007
- Cytoscape: A Software Environment for Integrated Models of Biomolecular Interaction NetworksGenome Research, 2003