Rapid Evolution of Sperm Chromatin Remodeling Proteins in Primates

Spermatogenesis requires both the remodeling and condensation of chromatin, a process facilitated by the sequential replacement of histones with sperm-specific DNA binding proteins. First, the transition nuclear proteins 1 and 2 (TNP1, TNP2) act to replace the sperm-specific histones, then they are themselves replaced by protamine 1 (PRM1) and, in some species, protamine 2 (PRM2). It has been theorized that changes to these chromatin-remodeling proteins may affect an organism’s sperm formation, and thus reproductive success. While studies have found that PRM1 evolves rapidly, with evidence of positive selection on the human lineage, and that PRM2 has also evolved rapidly in some groups, the evolutionary rates of the TNPs have not been reported. Our research therefore compares the rates and patterns of evolution of the genes that encode the proteins in the protamine locus (Prm1, Prm2, Prm3, and Tnp2) and Tnp1, which is on a different chromosome. To do this, we have utilized NCBI databases and their BLAST tools to retrieve sequences of these five genes from diverse mammalian species, with an emphasis on the primates. We have obtained gene sequences of 25 primate species of known phylogenetic relationship, and aligned them against each other using the molecular analysis software package MEGA7. From these alignments, we were able to both characterize the overall consensus sequence for each protein and analyze interspecies differences. We also produced expanded alignments including other mammalian sequences, so that we may compare them to the primates. Our analyses suggest a few patterns of evolution within the genes that encode our proteins of interest. In general, the genes in the protamine locus appear to have experienced more rapid evolution than Tnp1, which appears to be highly conserved in most species studied, with the notable exception of the gorilla, where it appears to be an expressed pseudogene. Surprisingly, Tnp2 has evolved so rapidly that its sequences were difficult to align across some species, even within the primates. This rapid evolution appears to be due primarily to repeat sequence expansion and contraction, rather than to simple point mutations. Prm1 and Prm2, though also experiencing relatively rapid evolution (mostly at a point mutational level), exhibit conservation of certain positions, including characteristic cysteine residues and arginine stretches. Similar to Tnp2, Prm3 shows dramatic evolution due to repeat expansions. In rodents and primates, there is a 12-nucleotide expansion that encodes a 4-amino acid repeat near the Nterminus; in addition, all mammals show a simple repeat region that encodes a stretch of glutamate residues. We note that proteins encoded at the protamine locus have evolved more rapidly in the hominoids than in the Old World monkeys. Our study of these sequences using the alignments and sequence analysis tools has led us to theorize that the evolution of the protamine locus is not only in rapid in nature, but characterized by several repeat expansion areas, indicative of non-B DNA motifs that are known to be mutagenic. We believe that the possibility of non-B DNA mutagenesis driving the rapid evolution of the protamine locus merits further study, because this implies that these proteins evolved quickly due to mutational drive, rather than to positive selection, as previously suggested by several authors. If true, this has broad implications for the study of molecular evolution, in general