放线菌是有重大医学和经济价值的微生物资源类群，目前放线菌门的系统分类框架主要依赖于对16S rRNA基因的序列分析。由于16S rRNA基因的局限性，没有明确的标准界定不同的分类单元，而且几大分支之间的进化关系也没有解决。基因组序列为寻找不同微生物特有的分子标记提供了丰富资源，可用来研究微生物系统发育与分类。本项目提出利用目前海量的基因组序列,寻找放线菌门下不同分类单元特有的蛋白序列,为不同分类单元的定义和划分提供新的分子标记,并根据它们的分布规律研究不同单元之间的进化关系，从而修订完善放线菌门的系统分类框架。并依据蛋白结构提供的线索对放线菌特有蛋白之一SCO1997进行功能鉴定，证实其功能是否与蛋白酶体这一重要的蛋白水解机器有关。本项目可为放线菌系统发育研究提供新的分子依据，并以SCO1997为例揭示放线菌特有蛋白在细胞中的功能，两方面的研究结果将加快对放线菌生物学特征的认知与功能应用。

Actinobacteria is one of the most important microbial groups with great medical and economic significance. To date, the phylogeny and taxonomic framework of Actinobacteria phylum is mainly based on the sequence analysis of 16S rRNA gene. However, due to the limitation of 16S rRNA gene, it has proven difficult to delimit different taxonomic ranks of prokaryotes in definitive terms. Genome sequences provide rich resource for identifying molecular markers that are specific for different microbial groups and which can aid in understanding microbial phylogeny and taxonomy. We propose to study the phylogeny of Actinobacteria phylum by analyzing whole proteins that are limited to particular groups of organisms. These markers will be used to define and circumscribe different taxonomic ranks within Actinobacteria, and their distribution pattern in different species can be used to infer the evolutionary relationships of different clades. In this way, a more reliable and accurate phylogenetic framework will be achieved for the Actinobacteria phylum. Additionally, based on the protein structural information, we propose to carry out functional studies on one of the Actinobacteria-specific proteins SCO1997 to determine its functional relationship with 20S Proteasome, which is very important cellular proteolytic machine. The proposed project will provide novel molecular makers for understanding the phylogeny of Actinobacteria, and also the functional characterization of protein SCO1997 will shed light on the cellular role of Actinobacteria-specific proteins. Finally, the results from these two aspects will expedite our understanding and bioprospecting of the unique biological features of Actinobacteria.