de Macêdo Mendes Cayro, Teixeira Diego Gomes, Lima João Paulo Matos Santos, Lanza Daniel Carlos Ferreira
Applied Molecular Biology Lab - LAPLIC, Department of Biochemistry, Federal University of Rio Grande do Norte, Natal, RN, Brazil.
Postgraduate Program in Bioinformatics, Federal University of Rio Grande do Norte, Natal, RN, Brazil.
BMC Struct Biol. 2019 Apr 18;19(1):8. doi: 10.1186/s12900-019-0106-y.
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. 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.
The 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.
The 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.
白斑综合征病毒（WSSV）是一种有包膜的双链DNA病毒，可导致多种虾类死亡，被认为是影响全球对虾养殖的主要病原体之一。该病毒具有约300 kb的复杂基因组，病毒分离株的基因组具有高度同一性。尽管如此，WSSV基因组中的一些可变区存在于编码区，这些推定的蛋白质可能与病毒适应和毒力机制存在某种关系。到目前为止，对这些蛋白质的功能研究较少。在本研究中，对WSSV可变区编码的序列和推定蛋白质进行了电子计算机分析。
电子计算机分析方法能够确定一些序列的变异性，并识别出一些类似于formin同源性2、RNA识别基序、着色性干皮病D组修复解旋酶、血凝素和锚蛋白基序的结构域。从序列中获得的信息以及对二级和三级结构模型的分析表明，其中一些蛋白质可能具有与蛋白质调节/降解、细胞内运输、重组和内体融合事件相关的功能。
生物信息学方法有效地生成了三维模型并识别出结构域，从而能够为ORF wsv129、wsv178、wsv249、wsv463a、wsv477、wsv479、wsv492和wsv497产生的推定多肽提出可能的功能。
