masterThesis
Caracterização in silico de orfs variáveis e de regiões regulatórias no genoma do vírus da síndrome da mancha branca (WSSV)
Fecha
2018-11-19Registro en:
MENDES, Cayro de Macêdo. Caracterização in silico de orfs variáveis e de regiões regulatórias no genoma do vírus da síndrome da mancha branca (WSSV). 2018. 79f. Dissertação (Mestrado em Bioinformática) - Instituto Metrópole Digital, Universidade Federal do Rio Grande do Norte, Natal, 2018.
Autor
Mendes, Cayro de Macêdo
Resumen
The white spot syndrome virus (WSSV) is one of the biggest problems facing global
shrimp farming, causing considerable economic losses. The WSSV genome presents
some coding regions that vary between the different isolates. Those regions named
wsv129 (ORF75), wsv178 (ORF94), wsv249 (ORF125), wsv461 / 464 (ORFs 14/15)
and wsv477 / 502 (ORFs 23/24) are possibly involved in virulence mechanisms but
have not been fully characterized functionally so far. The in silico characterization has
been used as a more accessible alternative for prediction and study of the protein
structure that does not have the crystallographic structure available. This work aimed
to characterize in silico the putative proteins encoded by the variable regions of the
WSSV genome, in order to identify possible functions. The variable regions of the
ORs wsv129, wsv178, wsv249 and the clusters formed by the ORs wsv461/464 and
wsv477/502 were analyzed phylogenetically, and structurally. The amino acid
sequences were subjected to remote homologous searches of motifs, conserved
domains, fold recognition and prediction of secondary and tertiary structures. It was
possible to model tertiary structures of protein domains and infer possible functions
for the ORs wsv463a (formin like - regulation of actin filaments), wsv477 (interaction
with RNA - posttranscriptional processes), wsv479 and wsv497 (XPD like - helicase),
wsv 492 (hemagglutinin like signaling, viral docking) and wsv249 (ankyrim repeat and
RING-H2 domains - modulation of Ubiquitin-dependent proteolysis), besides
proposing structural functions for the ORs wsv129 and wsv178 due to their structural
characteristics and charge. It was also possible to detect signatures associated with
nuclear localization signals within the repeating units of the sequences encoded by
the ORs wsv129 and wsv178. In addition to protein structure analyzes, some 100
and 200 nt upstream regulatory regions were prospected for the coding regions and it
was possible to detect some motifs, including a Zinc-Finger binding site, suggesting
the interaction between possible transcription factors. From the results it was
proposed a model of performance for each of the proteins studied.