Tickle Harbour

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Evolution of Tertiary Structure of Viral RNA Dependent Polymerases

<div><p>Viral RNA dependent polymerases (vRdPs) are present in all RNA viruses; unfortunately, their sequence similarity is too low for phylogenetic studies. Nevertheless, vRdP protein structures are remarkably conserved. In this study, we used the structural similarity of vRdPs to reconstruct their evolutionary history. The major strength of this work is in unifying sequence and structural data into a single quantitative phylogenetic analysis, using powerful a Bayesian approach.</p><p>The resulting phylogram of vRdPs demonstrates that RNA-dependent DNA polymerases (RdDPs) of viruses within <i>Retroviridae</i> family cluster in a clearly separated group of vRdPs, while RNA-dependent RNA polymerases (RdRPs) of dsRNA and +ssRNA viruses are mixed together. This evidence supports the hypothesis that RdRPs replicating +ssRNA viruses evolved multiple times from RdRPs replicating +dsRNA viruses, and <i>vice versa</i>. Moreover, our phylogram may be presented as a scheme for RNA virus evolution. The results are in concordance with the actual concept of RNA virus evolution. Finally, the methods used in our work provide a new direction for studying ancient virus evolution.</p></div

IL-tophat-run

Commands used to map the reads to the reference genome, Larvae sampl

Structure based sequence alignment of vRdPs thumb subdomain.

<p>Alignment of vRdPs is as in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0096070#pone-0096070-g002" target="_blank">Figure 2</a> and <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0096070#pone-0096070-g003" target="_blank">3</a>. Amino acid residues in conserved sequence motifs D and E are highlighted by orange and red frames. Amino acid residues in the conserved structural homomorhps are highlighted the same but lighter colours. hmH homomorph is highlighted in pink.</p

Protein structures of selected vRdPs representatives.

<p>Nine representatives of the selected vRdPs were chosen. Their structures are shown as a ribbon diagram. All molecules are oriented in the same orientation with finger subdomain on the left, the palm on the bottom and the thumb on the right. The catalytic site is positioned in the centre of each molecule and in some protein structures it is enclosed by the finger tips located at the top of each protein structure. Conserved protein structures typical of vRdPs (homomorphs) are highlighted by colours: violet (hmG), dark blue (hmF), dark green (hmA), light green (hmB), yellow (hmC), orange (hmD) red (hmE), and pink (hmH). Molecular rendering in this figure were created with Swiss PDB Viewer.</p

Sample_Larvas_Ixo_all_samples.fastq

FASTQ file with reads from Larvae sample

Phylogenetic tree of vRdPs evolution.

<p>Phylogenetic tree was calculated by an analysis unifying sequence and structure information. Only names of virus species coding vRdPs are listed in the tree. Individual virus species are grouped in genera (blue) and families (red) according actual ICTV virus taxonomy.</p

IG_accepted_hits.bam

BAM file containing the Tophat accepted hits of the Glands sample

Structure based sequence alignment of vRdPs palm subdomain.

<p>Alignment of vRdPs is as in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0096070#pone-0096070-g002" target="_blank">Figure 2</a>. Amino acid residues in conserved sequence motifs F, A, B, and C are highlighted by dark blue, dark green, light green, and yellow frames. Amino acid residues it the conserved structural homomorhps are highlighted the same but lighter colours. The only three 100% conserved amino acid residues in the entire alignment (an arginine residue at position 327 in motif F, an aspartate residue at position 411 in motif, and a glycine residue at position 517 in motif B). The fourth 100% conserved amino acid residue is an aspartate residue in motif C. Despite this aspartate residue is superpostionable in protein structures, it is placed on different position in structure based sequence alignment of protein primary structures thanks to cyclic permutation in IBDV and IPNV RdRPs (see position 397 for birnaviral RdRPs and position 580 for remaining vRdPs).</p

Sample_Glandulas_Ixo_all_samples.fastq

FASTQ file with the reads from Glands sample