Bioinformatics Approaches In The Study Of Spermatogenesis Associated Proteomes For Human And Macaque

Currently, infertility has become a common disease in modern society, and male factor constitutes about60%of human infertility directly or indirectly. On the other hand, there is a lack of contraceptive drugs for men, and men contribute only14%to contraception. Spermatogenesis is a complex process occurred in testis and is important for normal male fertility, thus the study of spermatogenesis is both important in biological and clinical science. To better understand the process and regulation of spermatogenesis, it is necessary to study the composition and roles of genes associated with spermatogenesis. In testis, there is a low correlation between the expression levels of transcripts and proteins, and there are lots of testis specific genes expressed in testis. Thus, proteomics may be helpful in the study of spermatogenesis.Based on high-resolution and high-throughput liquid chromatography tandem mass spectrometry, we identified7400and4461proteins in human testis and sperm respectively, we also identified297N-linked glycoproteins which contains556modified sites in human sperm. We identified9078and2552proteins in macaque testis and sperm respectively. In the present study, we mainly performed functional annotation and prediction on these proteins and sites based on bioinformatics approaches.First, we systematically analyzed the chromosomal distribution of testis and sperm genes of human and macaque, we also identified a list of retrogenes which escaped from chromosome X and located in autosomal. Based on semi-quantification, we compared the expression levels of the homologous genes of human and macaque. We found that evolutionary conserved proteins have higher expression levels. As macaque genes are mainy annotated baed on prediction or homology inference, we provided directly protein evidence for these predicted proteins. Based on GO and KEGG analysis, we systematically annotated the biological functions of the protein coding genes derived from these proteomes. We summarized their functions and related biological processes in the levels of spermatogenesis and sperm function. To further scan for biomarkers for male infertility and cancer, we annotated the reproductive phenotypes related with these genes. By comparison analysis with CT gene, testis specific genes and secreted proteins encoding genes, we screened candidate biomarkes and discussed their potential clinicla application.Compare to men, male macaques have higher pressure of sperm competition. Under sperm competition, macaque produces faster sperm than human. We compared positively selected genes in human and macaque sperm and identified specific genes and corresponding positively selected sites in macaque branch. Based on enrichment analysis, we found that these genes are prone to located in mitochondria and flagella and highly associated with male infertility. We provided molecular basis for explaining the differences of phenotypes under different pressure of sperm competition.Finally, we performed preliminary structural analysis on N-linked glycosylation sites in human sperm. To study the locations and features of these sits in the levels of protein sequence and three-dimensional structure will help us further understand the roles of these sites.Based on bioinformatics approaches, we systematically annotated the biological functions of proteins associated with spermatogenesis. We provided the molecular basis for expalining the processes of sperm competition. We also analyzed the structral features of glycosylated sites in human sperm. Our study provided candidate biomarkers for the diagnosis and therapy of male infertility, as well as the development of contraceptive drugs.