Protamines – histones in disguise

All DNA from yeast to mammals is occupied by histones (H2A, H2B, H3, and H4) and folded into chromatin. Well, not entirely…. Certain types of DNA such as sperm DNA play by their own rules and are actually compacted by proteins other than histones! Most of the paternal DNA in human sperms is compacted with the help of protamines (protamine P1 and P2).  I would still count them as histone-like proteins as protamines are also small (5-8 kDa in size) and basic (but arginine-rich!) proteins and have likely evolved from specialized histones.

During spermatogenesis, human spermatozoa chromatin undergoes a complex chromatin reorganization whereby 85 -90% of histones are replaced by protamine P1 and P2 as part of the pathway to compact the genome into the small nuclear volume of the sperm head. Compared to normal chromatin, sperm DNA is hypercondensated to a volume 1/20ththat of a somatic nucleus. Structural studies of protamines in complex with DNA have been so far largely limited to non-human protamines (e.g. from bull and salmon) and we are unfortunately still lacking a crystallographic structure of a DNA-protamine complex. However, some structural insights were gained by Raman and NMR spectroscopy: The free protamine P1 is unstructured in solution but wraps around the DNA helix in the major groove upon binding to DNA, with one protamine molecule being bound per turn of DNA helix. By doing so, protamines neutralize the negative charges along the phosphodiester backbone of the DNA which enables the DNA to pack close together in form of a toroidal structure. Hydrogen bonds and electrostatic bonds formed between the protamine arginines and the phosphate groups in both DNA strands as well as the formation of disulfide linkage between cysteine residues in protamine molecules lead to a remarkable stability of this nucleo-protamine toroidal structure.Besides this structural aspect, protamines also protect the paternal genome from physical and chemical damage, e.g. from free radicals and nucleases. A miss-ratio between protamine 1 and 2, an abnormal protamine incorporation or protamine-deficiency are linked to infertility and have a huge impact on the sperm quality.

In humans, about 90% of sperm chromatin is formed by these highly compact toroidal nucleo-protamine complexes, however there is also a small but significant fraction (8% of the sperm’s genome) which is still packaged with histones. The localization and function of those retained sperm nucleosomes (which are by the way rich in histone variants and PTMs) are currently a matter of debate: H3-ChIP-Seq on histone-to-protamine replacement-completed sperm reported 2018 in Nature Communications suggests that most of the genes that retain their histone packaging are developmental genes or their regulatory promoters. Thus, it is tempting to speculate that these retained nucleosomes – which display a more dynamic structure than protamine-DNA complexes – may serve to regulate early postfertilization processes and to selectively activate paternal genes in the early embryo. It is worthwhile to mention, that also protamines themselves can carry multiple PTMs. Eleven novel posttranslational modifications including phosphorylation, ubiquitinylation and methylation were identified on protamines (Brunner et al, 2014). Whether these specific PTM combinations might form a “protamine code” similar to the “histone code” and whether these protamine modifications have the potential to regulate gene expression in the embryo remains to be elucidated. But if we take it as faith value that protamines pass on paternal information to the offspring, then this would be an exciting example of transgenerational inheritance!

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