Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-Universidad Politécnica de Valencia, CPI, Ed 8E, Camino de Vera s/n, 46022 Valencia, Spain.
Virus Res. 2011 Jan;155(1):274-82. doi: 10.1016/j.virusres.2010.10.022. Epub 2010 Oct 25.
The genomic structure of Pelargonium line pattern virus (PLPV), a tentative member of a proposed new genus within the family Tombusviridae, has been recently determined. However, little is known about the genetic variability and population structure of this pathogen. Here, we have investigated the heterogeneity of PLPV isolates from different origins by sequence analysis of a 1817nt fragment encompassing the movement (p7 and p9.7) and coat protein genes as well as flanking segments including the complete 3' untranslated region. We have evaluated the selective pressures operating on both viral proteins and RNA genome in order to assess the relative functional and/or structural relevance of different amino acid or nucleotide sites. The results of the study have revealed that distinct protein domains are under different selective constraints and that maintenance of certain primary and/or secondary structures in RNA regulatory sequences might be an important factor limiting viral heterogeneity. We have also performed covariation analyses to uncover potential dependencies among amino acid sites of the same protein or of different proteins. The detection of linked amino acid substitutions has permitted to draw a putative network of intra- and interprotein interactions that are likely required to accomplish the different steps of the infection cycle. Finally, we have obtained phylogenetic trees that support geographical segregation of PLPV sequences.
最近确定了 Pelargonium 线图案病毒 (PLPV) 的基因组结构，PLPV 是拟议的 Tombusviridae 科新属中的一个暂定成员。然而，人们对这种病原体的遗传变异和种群结构知之甚少。在这里，我们通过对包含运动 (p7 和 p9.7) 和外壳蛋白基因以及侧翼片段 (包括完整的 3'非翻译区) 的 1817nt 片段的序列分析，研究了来自不同起源的 PLPV 分离株的异质性。我们评估了对病毒蛋白和 RNA 基因组起作用的选择压力，以评估不同氨基酸或核苷酸位点的相对功能和/或结构相关性。研究结果表明，不同的蛋白质结构域受到不同的选择限制，并且 RNA 调节序列中某些一级和/或二级结构的维持可能是限制病毒异质性的一个重要因素。我们还进行了共变分析，以揭示同一蛋白质或不同蛋白质中氨基酸位点之间的潜在依赖性。检测到关联的氨基酸取代允许绘制一个假定的蛋白质内和蛋白质间相互作用网络，这些相互作用可能是完成感染周期不同步骤所必需的。最后，我们获得了支持 PLPV 序列地理分离的系统发育树。
