Diversity of tRNA Clusters in the Chloroviruses
Open Access
- 16 October 2020
- Vol. 12 (10), 1173
- https://doi.org/10.3390/v12101173
Abstract
Viruses rely on their host’s translation machinery for the synthesis of their own proteins. Problems belie viral translation when the host has a codon usage bias (CUB) that is different from an infecting virus due to differences in the GC content between the host and virus genomes. Here, we examine the hypothesis that chloroviruses adapted to host CUB by acquisition and selection of tRNAs that at least partially favor their own CUB. The genomes of 41 chloroviruses comprising three clades, each infecting a different algal host, have been sequenced, assembled and annotated. All 41 viruses not only encode tRNAs, but their tRNA genes are located in clusters. While differences were observed between clades and even within clades, seven tRNA genes were common to all three clades of chloroviruses, including the tRNAArg gene, which was found in all 41 chloroviruses. By comparing the codon usage of one chlorovirus algal host, in which the genome has been sequenced and annotated (67% GC content), to that of two of its viruses (40% GC content), we found that the viruses were able to at least partially overcome the host’s CUB by encoding tRNAs that recognize AU-rich codons. Evidence presented herein supports the hypothesis that a chlorovirus tRNA cluster was present in the most recent common ancestor (MRCA) prior to divergence into three clades. In addition, the MRCA encoded a putative isoleucine lysidine synthase (TilS) that remains in 39/41 chloroviruses examined herein, suggesting a strong evolutionary pressure to retain the gene. TilS alters the anticodon of tRNAMet that normally recognizes AUG to then recognize AUA, a codon for isoleucine. This is advantageous to the chloroviruses because the AUA codon is 12–13 times more common in the chloroviruses than their host, further helping the chloroviruses to overcome CUB. Among large DNA viruses infecting eukaryotes, the presence of tRNA genes and tRNA clusters appear to be most common in the Phycodnaviridae and, to a lesser extent, in the Mimiviridae.Keywords
Funding Information
- Office of Experimental Program to Stimulate Competitive Research (1736030)
This publication has 45 references indexed in Scilit:
- Global In-Silico Scenario of tRNA Genes and Their Organization in Virus GenomesViruses, 2019
- Diversity of Viruses Infecting the Green Microalga Ostreococcus lucimarinusJournal of Virology, 2015
- tRNADB-CE: tRNA gene database well-timed in the era of big sequence dataFrontiers in Genetics, 2014
- Genome of Phaeocystis globosa virus PgV-16T highlights the common ancestry of the largest known DNA viruses infecting eukaryotesProceedings of the National Academy of Sciences of the United States of America, 2013
- Evolution of Codon Usage in the Smallest Photosynthetic Eukaryotes and Their Giant VirusesGenome Biology and Evolution, 2013
- Genomic Sequence and Analysis of EhV-99B1, a New Coccolithovirus from the Norwegian FjordsIntervirology, 2012
- Sequence and annotation of the 369-kb NY-2A and the 345-kb AR158 viruses that infect Chlorella NC64AVirology, 2007
- Functional Implication of the tRNA Genes Encoded in the Chlorella Virus PBCV-l GenomeThe Plant Pathology Journal, 2005
- Aminoacylation of tRNAs Encoded by Chlorella Virus CVK2Virology, 1999
- Analysis of 74 kb of DNA Located at the Right End of the 330-kb Chlorella Virus PBCV-1 GenomeVirology, 1997