人程序化死亡分子5(PDCD5)核酸和蛋白质序列的数据发掘

In silico data mining of the human programmed cell death 5 (PDCD5) sequences

目的 :以程序化死亡分子 5 (PDCD5 )为靶分子 ,对其核酸与蛋白质序列进行生物信息学分析 ,为PDCD5功能的实验研究提供基础 ,同时也为人类功能基因的生物信息学分析提供新的技术路线。方法 :利用数据库相似性搜索、同源物结构比较、表达谱分析和查询基因“邻居”等技术进行数据发掘和数据综合分析。结果 :发现人PDCD5在 12号和 5号染色体上分别存在返座假基因 (retropseudogene) ,小鼠 1号染色体也存在小鼠PDCD5cDNA的返座假基因。热自养甲烷杆菌的PDCD5同源物、泛素及核糖体蛋白S13具有与人PDCD5相似的折叠方式。线虫的PDCD5同源物、泛素及IAP(inhibitorofapoptosisproteins)分子等在表达谱拓扑图上属于同一基因簇成员 ,该基因簇与生物合成和蛋白质合成相关。PDCD5同源物在多个基因组中与多种核糖体蛋白相邻。结论 :PDCD5存在 2个拷贝的假基因。PDCD5除参与细胞凋亡外 ,预测还与泛素有功能相关性 ,并可能参与蛋白质的翻译调控。

Objective:To lay foundation for the functional studies of programmed cell death 5 ( PDCD5 ) and develop new technical pathway for bioinformatics analysis of human functional genes. Methods:Using PDCD5 as the target molecule, intensive bioinformatics analysis of the nucleic acid and protein sequences were conducted. Data mining and comprehensive analysis by sequence against database similarity searching, ortholog structure comparison, expression profile analysis and gene “neighbor” listing were performed. Results: Two human putative pseudogenes on chromosomes 12 and 5, and one mouse putative pseudogene on chromosome 1 were identified. The methanobacterium thermoautotrophicum ortholog was classified as the same fold as ubiquitin and ribosomal protein S13. The C. elegans ortholog, ubiquitin and IAP (inhibitor of apoptosis proteins) belonged to the same expression profile cluster. This cluster was related to biosynthesis and protein synthesis. PDCD5 orthologs in various genomes were adjacent to various ribosomal proteins on the chromosome. Conclusion: The human genome contains at least two processed pseudogenes of PDCD5 . Besides the relationship with cell apoptosis, PDCD5 is predicted to have functional relationship with ubiquitin and participate in the translation regulation.