Yang Chu-Wen
Department of Microbiology, Soochow University, Shih-Lin, Taipei, Taiwan, Republic of China.
PLoS One. 2012;7(6):e38637. doi: 10.1371/journal.pone.0038637. Epub 2012 Jun 8.
Protein-protein interactions through short linear motifs (SLiMs) are an emerging concept that is different from interactions between globular domains. The SLiMs encode a functional interaction interface in a short (three to ten residues) poorly conserved sequence. This characteristic makes them much more likely to arise/disappear spontaneously via mutations, and they may be more evolutionarily labile than globular domains. The diversity of SLiM composition may provide functional diversity for a viral protein from different viral strains. This study is designed to determine the different SLiM compositions of ribonucleoproteins (RNPs) from influenza A viruses (IAVs) from different hosts and with different levels of virulence. The 96 consensus sequences (regular expressions) of SLiMs from the ELM server were used to conduct a comprehensive analysis of the 52,513 IAV RNP sequences. The SLiM compositions of RNPs from IAVs from different hosts and with different levels of virulence were compared. The SLiM compositions of 845 RNPs from highly virulent/pandemic IAVs were also analyzed. In total, 292 highly conserved SLiMs were found in RNPs regardless of the IAV host range. These SLiMs may be basic motifs that are essential for the normal functions of RNPs. Moreover, several SLiMs that are rare in seasonal IAV RNPs but are present in RNPs from highly virulent/pandemic IAVs were identified.The SLiMs identified in this study provide a useful resource for experimental virologists to study the interactions between IAV RNPs and host intracellular proteins. Moreover, the SLiM compositions of IAV RNPs also provide insights into signal transduction pathways and protein interaction networks with which IAV RNPs might be involved. Information about SLiMs might be useful for the development of anti-IAV drugs.
通过短线性基序（SLiMs）进行的蛋白质-蛋白质相互作用是一个新兴概念，与球状结构域之间的相互作用不同。SLiMs在短（三到十个残基）且保守性较差的序列中编码一个功能性相互作用界面。这一特性使得它们更有可能通过突变自发出现/消失，并且它们在进化上可能比球状结构域更不稳定。SLiM组成的多样性可能为来自不同病毒株的病毒蛋白提供功能多样性。本研究旨在确定来自不同宿主、具有不同毒力水平的甲型流感病毒（IAV）核糖核蛋白（RNP）的不同SLiM组成。利用ELM服务器中SLiMs的96个共有序列（正则表达式）对52,513个IAV RNP序列进行全面分析。比较了来自不同宿主、具有不同毒力水平的IAV的RNP的SLiM组成。还分析了来自高毒力/大流行IAV的845个RNP的SLiM组成。无论IAV宿主范围如何，在RNP中总共发现了292个高度保守的SLiMs。这些SLiMs可能是RNP正常功能所必需的基本基序。此外，还鉴定出了一些在季节性IAV RNP中罕见但存在于高毒力/大流行IAV的RNP中的SLiMs。本研究中鉴定出的SLiMs为实验病毒学家研究IAV RNP与宿主细胞内蛋白质之间的相互作用提供了有用的资源。此外，IAV RNP的SLiM组成也为深入了解IAV RNP可能参与的信号转导途径和蛋白质相互作用网络提供了线索。有关SLiMs的信息可能有助于抗IAV药物的开发。
