Exploring tRNA gene cluster in archaea

Morgado, Sérgio; Vicente, Ana Carolina Paulo

doi:10.1590/0074-02760180348

Cited by 5 publications

(4 citation statements)

References 31 publications

(42 reference statements)

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“…Besides, some tRNA genes occurring in these viruses are organized in clusters comprising up to dozens of tRNA genes [ 2 , 4 , 11 , 12 , 13 , 14 , 15 , 16 ]. Interestingly, such tRNA gene organization is particularly common in mitochondrial genomes [ 17 , 18 , 19 ], but large clusters have been observed in the three domains of life ( Archaea , Bacteria and Eukarya ) [ 16 , 20 , 21 , 22 , 23 , 24 , 25 ]. Studies indicate that the presence of tRNA genes in virus genomes would be to compensate for differences in codon and/or amino acid usage between virus and hosts, favoring an efficient protein synthesis and/or expanding the host range [ 2 , 4 ].…”

Section: Introductionmentioning

confidence: 99%

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

Morgado

Vicente

2019

Viruses

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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.

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Section: Introductionmentioning

confidence: 99%

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

Morgado

Vicente

2019

Viruses

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“…Two NC64A chloroviruses, PBCV-1 and CVK2, also have the interesting property of clustered tRNA genes (Lee et al, 2005;Nishida et al 1999). Clusters of tRNA genes are found in some bacteriophage (Morgado and Vicente, 2019), as well as in a small percentage of organisms from all three domains of life (Bermudez-Santana et al, 2010;Morgado and Vicente, 2018, 2019a. Clusters of tRNA-genes have also been reported in mitochondria and plastids (Abe et al, 2014;Fan et al, 2017;Freidrich et al, 2012).…”

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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“…Two NC64A chloroviruses, PBCV-1 and CVK2, were reported to have the interesting property of clustered tRNA genes [ 8 , 9 ]. Clusters of tRNA genes are found in a small percentage of organisms from all three domains of life [ 1 , 17 , 18 , 19 ]. tRNA-gene clusters have also been reported to occur in mitochondria and plastids [ 2 , 20 , 21 ].…”

Section: Introductionmentioning

confidence: 99%

Diversity of tRNA Clusters in the Chloroviruses

Duncan

Dunigan

Etten

2020

Viruses

View full text Add to dashboard Cite

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.

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Exploring tRNA gene cluster in archaea

Cited by 5 publications

References 31 publications

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

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

Diversity of tRNA Clusters in the Chloroviruses

Diversity of tRNA Clusters in the Chloroviruses

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