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

Morgado, Sérgio; Vicente, Ana Carolina Paulo

doi:10.3390/v11020180

Cited by 40 publications

(45 citation statements)

References 54 publications

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“…In the genome of AAS21, 29 genes coding for tRNA ( Supplementary Table S5) together with protein-encoding genes compose a cluster of genes, which is about 14 kb in length ( Figure 2). As it was observed in many lytic viruses, tRNA genes usually form clusters, especially in genomes harboring more than 15 tRNAs [24]. The vast majority (30 out of 32) of protein-encoding genes present in this cluster are genes coding for hypothetical (11) or unique (19) proteins with no reliable identity to database entries.…”

Section: Resultsmentioning

confidence: 98%

“…In addition, endonuclease V and two HNH endonucleases, encoded by ORF101, ORF104, and ORF117, respectively, are present within the aforementioned cluster of genes. The HNH endonucleases belong to the family of the homing endonuclease that act as a mobile element, and, thus, are supposed to play a role of dissemination of tRNA gene clusters among related organisms [24,25]. The presence of tRNA genes in virus genomes could be associated with numerous functions.…”

Section: Resultsmentioning

confidence: 99%

“…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.…”

Section: Resultsmentioning

confidence: 99%

See 2 more Smart Citations

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

Šimoliūnienė

Truncaitė

Petrauskaitė

et al. 2020

Viruses

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A novel cold-adapted siphovirus, vB_PagS_AAS21 (AAS21), was isolated in Lithuania using Pantoea agglomerans as the host for phage propagation. AAS21 has an isometric head (~85 nm in diameter) and a non-contractile flexible tail (~174 × 10 nm). With a genome size of 116,649 bp, bacteriophage AAS21 is the largest Pantoea-infecting siphovirus sequenced to date. The genome of AAS21 has a G+C content of 39.0% and contains 213 putative protein-encoding genes and 29 genes for tRNAs. A comparative sequence analysis revealed that 89 AAS21 open reading frames (ORFs) code for unique proteins that have no reliable identity to database entries. In total, 63 AAS21 ORFs were functionally annotated, including those coding for the proteins responsible for virion morphogenesis, phage-host interactions, and DNA metabolism. Proteomic analysis led to the experimental identification of 19 virion proteins, including 11 that were predicted by bioinformatics approaches. Based on comparative phylogenetic analysis, AAS21 cannot be assigned to any genus currently recognized by ICTV and may represents a new branch of viruses within the family Siphoviridae.

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Section: Resultsmentioning

confidence: 98%

Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

See 1 more Smart Citation

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

Šimoliūnienė

Truncaitė

Petrauskaitė

et al. 2020

Viruses

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“…Viruses strongly depend on the translational machinery of the host for the expression of their own proteins and, ultimately, their replication. For instance, given the small size of most viral genomes, no or very few tRNA genes are generally autonomously encoded 5 . In terms of codon usage, it has indeed been shown that bacteriophages are specifically adapted to their microbial hosts 6,7 .…”

Section: Introductionmentioning

confidence: 99%

Translational adaptation of human viruses to the tissues they infect

Hernandez‐Alias

Schaefer

Serrano

2020

Preprint

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Viruses need to hijack the translational machinery of the host cell for a productive infection to happen. However, given the dynamic landscape of tRNA pools among tissues, it is unclear whether different viruses infecting different tissues have adapted their codon usage toward their tropism. Here, we collect the coding sequences of over 500 human-infecting viruses and determine that tropism explains changes in codon usage. Using an in silico model of translational efficiency, we validate the correspondence of the viral codon usage with the translational machinery of their tropism. In particular, we propose that the improved translational adaptation to the upper respiratory airways of the pandemic agent SARS-CoV-2 coronavirus could enhance its transmissibility. Furthermore, this correspondence is specifically defined in early viral proteins, as upon infection cells undergo reprogramming of tRNA pools that favors the translation of late counterparts.

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“…However, some viruses have genes that help adapt to the host's CUB in favor of their own CUB by encoding tRNAs. These include large dsDNA viruses infecting eukaryotic organisms (see Morgado and Vicente, 2019 for an extensive list) and…”

Section: Introductionmentioning

confidence: 99%

Diversity of tRNA Clusters in the Chloroviruses

Duncan

Dunigan

Etten

2020

Preprint

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ABSTRACTViruses 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 with differences in the GC content between the host/virus genome. Here, we evaluate 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 of three different algal hosts have been sequenced, assembled and annotated. All 41 viruses not only encode tRNAs, but their tRNA genes are located in clusters. One tRNA gene was common to all three clades of chloroviruses, while differences were observed between clades and even within clades. By comparing the codon usage of one chlorovirus algal host, whose 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. In addition, 39/41 chloroviruses encode a putative lysidine synthase, which alters the anticodon of tRNAmet that normally recognizes AUG to recognize the codon AUA, a codon for isoleucine. This is advantageous to the viruses because the AU-rich codon AUA is 12-13 times more common in the chloroviruses than their host. Evidence is presented that supports the concept that chlorovirus tRNA clusters were acquired prior to events that separated them into the three clades.IMPORTANCEChloroviruses are members of a group of giant viruses that infect freshwater green algae around the world. More than 40 chloroviruses have been sequenced and annotated. In order to propagate efficiently, chloroviruses with low GC content must overcome the high GC content and codon usage bias (CUB) of their hosts. We provide support for one mechanism by which viruses can overcome host CUB. Specifically, the chloroviruses examined herein encode tRNAs whose cognate codons are common in the viruses but not in the host. Virus-encoded tRNAs that recognize AU-rich codons enable more efficient protein synthesis, thus enhancing viral propagation. The tRNA genes are located in clusters and the original tRNA gene cluster was acquired by the most recent common ancestor of the four chlorovirus clades. Furthermore, we show some conservation among all clades, but also substantial variation between and within clades, demonstrating the dynamics of viral evolution.

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

Cited by 40 publications

References 54 publications

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

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

Translational adaptation of human viruses to the tissues they infect

Diversity of tRNA Clusters in the Chloroviruses

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