Entropy based analysis of vertebrate sperm protamines sequences: evidence of potential dityrosine and cysteine-tyrosine cross-linking in sperm protamines

Abstract

Background: Spermatogenesis is the process by which germ cells develop into spermatozoa in the testis. Sperm protamines are small, arginine-rich nuclear proteins which replace somatic histones during spermatogenesis, allowing a hypercondensed DNA state that leads to a smaller nucleus and facilitating sperm head formation. In eutherian mammals, the protamine-DNA complex is achieved through a combination of intra-and intermolecular cysteine cross-linking and possibly histidine-cysteine zinc ion binding. Most metatherian sperm protamines lack cysteine but perform the same function. This lack of dicysteine cross-linking has made the mechanism behind metatherian protamines folding unclear. Results: Protamine sequences from UniProt's databases were pulled down and sorted into homologous groups. Multiple sequence alignments were then generated and a gap weighted relative entropy score calculated for each position. For the eutherian alignments, the cysteine containing positions were the most highly conserved. For the metatherian alignment, the tyrosine containing positions were the most highly conserved and corresponded to the cysteine positions in the eutherian alignment. Conclusions: High conservation indicates likely functionally/structurally important residues at these positions in the metatherian protamines and the correspondence with cysteine positions within the eutherian alignment implies a similarity in function. One possible explanation is that the metatherian protamine structure relies upon dityrosine cross-linking between these highly conserved tyrosines. Also, the human protamine P1 sequence has a tyrosine substitution in a position expecting eutherian dicysteine cross-linking. Similarly, some members of the metatherian Planigales genus contain cysteine substitutions in positions expecting plausible metatherian dityrosine cross-linking. Rare cysteine-tyrosine cross-linking could explain both observations.

Male Infertility and Oxidative Stress: A Focus on the Underlying Mechanisms

“…Sperm DNA is partially protected from damage by virtue of its highly condensed state, achieved via the extensive replacement of nuclear histones with small basic proteins, protamines, that neutralize the negative changes present on the DNA backbone to permit a high level of compaction. In addition, human sperm protamines contain cysteine residues that promote the further condensation of the sperm chromatin via the formation of extensive inter- and intra-molecular disulphide, and rarely, cysteine-tyrosine, bridges [ 164 ]. However, this strategy is not completely effective because human spermatozoa have been recognized for some time to contain high levels of oxidative DNA damage [ 28 , 165 , 166 ].…”

Exploring Structures and Dynamics of Protamine Molecules through Molecular Dynamics Simulations

“…Last, we examine the possibility of intramolecular bond formation through cysteine–cysteine or cysteine–tyrosine linkages in mammalian P1 protamines. Although our attention is primarily on cysteine pairs for intramolecular disulfide bonding, a potential cysteine–tyrosine crosslink has been proposed recently in some mammalian protamines . Hence, we include one cysteine–tyrosine pair (labeled:6:14Y, where “Y” refers to tyrosine) in human P1 in our analysis.…”

“…Thus, despite human and bull P1 protamines having similar lengths and numbers of arginine residues, the arrangements of the arginines along these sequences are very different. Third, eutherian P1 protamine sequences can be separated into a central domain (residues ∼13 to 42), that has been hypothesized to be the DNA-binding region, and flanking regions. , Both bull and human P1 protamines fit this model, as the central domain region of each sequence contains the long clusters of consecutive arginines, while all of the arginines in the flanking regions are singles or instances of only two consecutive arginines. In contrast, the arginine clusters in salmon protamine occur throughout the sequence.…”

“…Specifically, we examine one fish (salmon) and two mammalian (bull P1 and human P1) protamines, three protamines that are frequently used in experimental studies. One of the key differences between fish and mammalian protamines is that mammalian protamines contain cysteine residues and, therefore, can form intra- and intermolecular disulfide bonds. ,,, The formation of intramolecular disulfide bonds has been associated with hairpin loop structures in mammalian protamines. , As disulfide bond patterns in protamines have not been firmly established, we used our simulations to examine the relationship between protamine sequences, hairpin loop structures, and the possibility of intramolecular bond formation. First, we observed that all three protamines adopt compact structures (i.e., structures with low R s values) that were commonly associated with the formation of long-lasting hairpin loops.…”

Antimicrobial Peptides with pH-Dependent Activity and Alkaline Optima: Their Origins, Mechanisms of Action and Potential Applications

“…However, surprisingly, the only major marine AMPs with alkaline optima so far reported appear to be protamine, which was first shown to possess antimicrobial properties in the 1930s when it was found to inactivate the Vaccinia virus 203 . It is now known that protamine comprises a diverse family of small arginine-rich proteins found in eukaryotic spermatic cells 204,205 that are particularly abundant in those of fish [206][207][208] , where these peptides are known as salmine in the case of salmon, and clupeine in that of herrings 204,205 . Enhanced efficacy against a broad range of bacteria under alkaline conditions as been demonstrated for salmine A1 from the salmon, Salmo salar 209,210 , and clupeine Z from the herrings, Clupea pallasii 211 and Clupea harengus 212 .…”