Diversity of tRNA Clusters in the Chloroviruses
| Autor: | James L. Van Etten, David D. Dunigan, Garry A. Duncan |
|---|---|
| Rok vydání: | 2020 |
| Předmět: |
0301 basic medicine
food.ingredient viruses lcsh:QR1-502 Genome Viral Cyanobacteria codon usage bias (CUB) Genome Article lcsh:Microbiology chemistry.chemical_compound 03 medical and health sciences algal viruses food RNA Transfer Chlorovirus Virology Phycodnaviridae Mimiviridae Codon Codon Usage Gene Phylogeny Genetics Host Microbial Interactions biology Viral translation Genetic Variation biology.organism_classification 030112 virology tRNAs tRNA clusters 030104 developmental biology Infectious Diseases chloroviruses chemistry Multigene Family Codon usage bias Transfer RNA Lysidine GC-content |
| Zdroj: | Viruses Volume 12 Issue 10 Viruses, Vol 12, Iss 1173, p 1173 (2020) |
| ISSN: | 1999-4915 |
| DOI: | 10.3390/v12101173 |
| Popis: | Viruses rely on their host&rsquo 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&rsquo 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&ndash 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. |
| Databáze: | OpenAIRE |
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