Viral mRNAs: evolution and structure-function relashionships

病毒的高进化率是免疫逃逸的主要因素，也是疫苗开发的主要障碍。关于氨基酸突变导致耐药性的证据正在迅速增加。同时，由于需要保持稳定的蛋白质结构和功能，序列多样性受到限制。与一般认为蛋白质的氨基酸序列仅决定其表达、折叠和功能相反，有报道称沉默突变和mRNA结构也可以影响蛋白质的功能。到目前为止，病毒rna的结构-功能关系在很大程度上仍未被研究。最近RNA结构测定的实验和计算方法的改进，以及完全测序的病毒基因组的大量增加，现在允许第一次系统地尝试组织病毒编码RNA结构的折叠空间，以便了解碱基配对模式如何限制遗传多样性并最终影响发病机制。该提案的主要目标是研究病毒基因组如何在其结构组织的不同水平上传递功能信息，特别关注RNA二级结构。将基于序列和结构特征对序列进行聚类。一个病毒结构数据库将生成使用基于系统发育，热力学和序列分析的一整套计算方法。通过大规模的序列比较、结构预测和聚类，将在一级和二级结构水平上同时分析病毒的进化，从而深入了解影响氨基酸序列的rna水平选择压力。将创建一个病毒RNA基序的综合目录，以及它们在确定病毒突变稳健性和将差异序列多样性与临床结果联系起来方面的作用。我们将研究RNA结构元件形成的进化和生物学因素，这些RNA结构元件对基因组包装、复制、蛋白质表达、与宿主细胞内机制的相互作用以及逃避宿主防御系统至关重要。我们将研究为什么有些病毒有明确的二级结构，而另一些则没有，以及这些结构在毒力、组织趋向性、宿主适应和种间传播中起什么作用。我们希望了解RNA结构的数量是如何增强或抑制基因表达的，并最终得出修改基因序列的方法，以优化二级结构的含量，从而提高表达水平。从长远来看，我们设想以定期更新公共资源的形式创建病毒mRNA结构元素纲要。

The high rate of viral evolution is a major factor in immune escape and the main obstacle for the development of vaccines. A quickly growing body of evidence on amino acid mutations leading to drug resistance is available. At the same time sequence diversity is restricted by the need to preserve stable protein structure and function. Contrary to the general belief that the amino acid sequence of a protein solely determines its expression, folding, and function, reports have started to emerge that silent mutations and mRNA structure can also exert influence on protein function. So far structure-function relationships in viral RNAs remain largely uninvestigated. Recent improvements of experimental and computational methods for RNA structure determination as well as the massive increase of completely sequenced viral genomes allow now for a first systematic attempt to organize the fold space of coding RNA structures in viruses in order to understand how base paring patterns constrain genetic diversity and ultimately influence pathogenesis. The main goal of the proposal is to investigate how viral genomes convey functional information at different levels of their structural organization, with a special focus on RNA secondary structure. Sequences will be clustered based on both sequence and structural features. A viral structurome database will be generated using a whole battery of computational methods based on phylogenetics, thermodynamics, and sequence analysis. A simultaneous analysis of viral evolution both at the level of primary and secondary structure will be conducted by large-scale sequence comparison, structure prediction, and clustering, providing insights into RNA-level selection pressure affecting amino-acid sequences. A comprehensive catalog of viral RNA motifs will be created, and their role in determining mutational robustness of viruses and linking differential sequence diversity to clinical outcome examined. We will study evolutionary and biological factors underlying the formation of RNA structure elements important for genome packaging, replication, protein expression, interaction with the host intracellular machinery, and evading the host defense systems. We will investigate why some viruses have clearly defined secondary structures while others do not, and what role such structures play in virulence, tissue tropism, host adaptation, and inter-species transmission. We hope to understand how the amount of RNA structure enhances or represses gene expression and ultimately to derive recipes for modifying gene sequences in order to optimize secondary structure content and hence expression level. In the long run we envisage creation of a compendium of viral mRNA structural elements in form of a regularly updated public resource.