Genomic and Expression Analysis of Spermatid Nuclear Transition Proteins in 12 Sequenced Drosophila species

The current study was aimed at analyzing conserved domains found in spermatid nuclear transition proteins (SNTPs) in the original 12 sequenced species of Drosophila. SNTPs facilitate the process of transforming chromatin from a histone-based nucleosome structure to a protamine-based structure during spermatogenesis. The sperm nuclei specific transition-like protein (Tpl^94D) in D. melanogaster was used as a reference sequence in this work. NCBI open reading frame (ORF) finder (PSI-BLAST) was used to obtain sequences from the NCBI Ref-Seq database. A rigorous bioinformatics analysis of the amino acid content indicated that Tpl^94D orthologs are only present within melanogaster subgenus (D. simulans, D. sechellia, D. erecta, and D. yakuba), D. ananassae, and D. pseudoobscura, but absent in D. persmilis, D. willistoni, and Drosophila subgenus (D. mojavensis, D. virilis, and D. grimshawi). Differential gene expression (DGE) analysis was conducted on testes and ovaries next generation transcriptome data (RNA-Seq) found in D. melanogaster, D. simulans, D. yakuba, D. ananassae, and D. pseudoobscura. DGE showed high expression of the Tpl^94D orthologs in the testes. NIH Isoform Two-Step Analysis (IUTA) was used to identify D. melanogaster Tpl^94D isoform A had a higher expression than D. melanogaster Tpl^94D isoform B in D. melanogaster’s testes. Functional analyses of the orthologs revealed a conserved high mobility group (HMG) box/DNA-binding domain present in both the Tpl^94D orthologs and Drosophila protamine-like protein orthologs (MST35Ba/MST35Bb). Our work suggests that Drosophila Tpl^94D orthologs should be classified as their own SNTPs group.