Abstract
BackgroundWhite Spot Syndrome Virus (WSSV) is an enveloped double-stranded DNA virus which causes mortality of several species of shrimp, being considered one of the main pathogens that affects global shrimp farming. This virus presents a complex genome of ~ 300 kb and viral isolates that present genomes with great identity. Despite this conservation, some variable regions in the WSSV genome occur in coding regions, and these putative proteins may have some relationship with viral adaptation and virulence mechanisms. Until now, the functions of these proteins were little studied. In this work, sequences and putative proteins encoded by WSSV variable regions were characterized in silico.ResultsThe in silico approach enabled determining the variability of some sequences, as well as the identification of some domains resembling the Formin homology 2, RNA recognition motif, Xeroderma pigmentosum group D repair helicase, Hemagglutinin and Ankyrin motif. The information obtained from the sequences and the analysis of secondary and tertiary structure models allow to infer that some of these proteins possibly have functions related to protein modulation/degradation, intracellular transport, recombination and endosome fusion events.ConclusionsThe bioinformatics approaches were efficient in generating three-dimensional models and to identify domains, thereby enabling to propose possible functions for the putative polypeptides produced by the ORFs wsv129, wsv178, wsv249, wsv463a, wsv477, wsv479, wsv492, and wsv497.
Highlights
White Spot Syndrome Virus (WSSV) is an enveloped double-stranded DNA virus which causes mortality of several species of shrimp, being considered one of the main pathogens that affects global shrimp farming
White Spot Syndrome Virus (WSSV) is an enveloped double-stranded DNA virus recognized for its great impact on global shrimp farming and for the complexity of its ~ 300 kb genome [1]
Available nucleotide sequences corresponding to the variable regions from WSSV different isolates were retrieved from GenBank and subjected to a multiple alignment through MAFFT [16], and some adjustments were made by manual editing
Summary
Characterization results with highest confidence levels based on the evaluation of the protein models are presented . ORF wsv463a The ORF wsv463a, a putative coding sequence located in wsv461/wsv464 cluster (Fig. 1a), presented a proline rich domain located in an unfolded portion of the predicted protein (positions 99–159) and a larger domain similar to the Formin Homology 2 (FH2) between positions 170–508 (Fig. 1b). Wsv129 has two types of repeat units, the most frequent having 45 bp and a 57 bp ORF wsv129 Secondary structure predictions revealed small transmembrane helices in the N-terminal region (positions 50–72) which coincide with a structured region of the wsv129 predicted protein (Fig. 3a). ORF wsv178 Small transmembrane helices were predicted in the N-terminal region of wsv178 putative product (positions 7–29) coinciding with the unique folded region of the protein (Fig. 3b). The characterization by remote homology and fold recognition revealed that the first 300 residues of the N-terminal region correspond to a Ankyrin repeat (ANK) motif (Fig. 3d and Additional file 7). A RING-H2 was detected immediately next to the Ankyrin domain located between positions 310–357 of the protein (Fig. 3c, e), which has the Cys-X2-Cys-X(9–39)-Cys-X(1–3)-His-X(2–3)-His-X2-Cys-X (4–48)-Cys-X2-Cys pattern, where “X” comprises any amino acid
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