Protein and Peptide Letters - Volume 18, Issue 8, 2011

The small, highly basic nuclear proteins called protamine that package DNA in the sperm of all mammals, most vertebrates and many plant species were discovered nearly 150 years ago. These amazing little proteins have been found to exhibit little structural or functional similarity to any other known chromatin or DNA binding protein. The protamines, which are categorized into two closely related families, protamine P1 and protamine P2, belong to a very limited class of proteins that remain unstructured in solution and do not adopt a conformation until they bind to their intended partner or target. When these proteins are expressed inside the maturing spermatid and delivered into the nucleus, the protamines bind along the entire length of the DNA, displace the majority of the bound chromatin proteins, and globally inactivate the entire elongating spermatid genome. Working in concert with a few remaining sperm specific histones and other proteins retained in sperm chromatin, the genome is deprogrammed and selected male genes are imprinted. This reorganization prepares the sperm genome so it will no longer function as a testis cell and provides a mechanism for the reactivation of a specific subset of genes early after fertilization. Clearly this is a lot of “functionality” to attribute to any protein. However, results from recent biophysical studies suggest the protamines may also perform another function that is not typical of other DNA binding proteins. Upon binding to DNA and condensing it into toroids, the formation of the toroid generates sufficiently large forces inside the nucleus to induce the collapse of the entire spermatid genome, condense the nucleus into a very small volume and perhaps even drive the shaping of the sperm head. The papers presented in this special HOT TOPICS issue on Protamines: Structure and Function review and provide new information and insight into 1) how the protamine proteins evolved and the impact of these changes on chromatin organization, 2) the processing of the protamine P2 precursor and the relationship between incomplete P2 processing and male infertility, 3) the impact of altering the proportion of the two protamines used to package DNA in the sperm cell, 4) the role endocrines play in the histone to protamine transition and chromatin condensation, 5) the forces generated by protamine when it binds to DNA, and 6) the process of protamine removal from DNA when the sperm enters the oocyte. The Kasinsky et al. review, which focuses on the evolution of the protamines, shows that the arginine-rich proteins that comprise the protamine family are likely to have evolved from the lysine-rich histone H1, through a general class of protamine-like proteins to the small, highly basic protamines found in mammalian sperm. One important outcome of this change to arginine-rich protamines, as suggested in this review, is that the evolution of the protein appears to have also led to a change in the pattern of chromatin organization within the nucleus and the development of a lamellar mediated process for generating a highly condensed form of chromatin. At the molecular level, the manner in which the protamines associate with the spermatid's DNA represents an excellent example of the biological self-assembly that is initiated when the protamine molecules, which are synthesized and pumped into the nucleus of the late-stage spermatid, binds to all but a small subset of the haploid genome. Upon binding, the protein neutralizes the negative charge on the phosphodiester backbone of both strands of DNA and functions as the ultimate repressor by shutting down the transcriptional activity of the entire spermatid genome. In addition to the physical compaction of the sperm genome, which contributes directly to the suppression of its genetic activity, the formation of the complex and its compaction also appears to protect the cell's DNA from physical damage and enables the packaging of a large volume of DNA into a small, more hydrodynamic and highly specialized cell nucleus - the sperm head. Two different types of protamine have been isolated from mammalian sperm. Protamine P1, the smaller of the two proteins, is found bound to genomic DNA in the sperm of all mammals. Protamine P2, a slightly larger protein, is found in addition to protamine P1 in the sperm of primates, rodents and a selected subset of other species. As described in the Nanassy et al. review, alterations in the relative proportion of the P1 and P2 protamines in human sperm have a positive correlation with male infertility. While deficiencies of either P1 or P2 have been directly linked to infertility, the cause of the infertility may be related to an indirect effect such as altered histone retention or abnormally established epigenetic marks on developmental gene promoters in the sperm chromatin that ultimately lead to abnormal early embryo development and reduced pregnancy rates.....

Despite their relatively arginine-rich composition, protamines exhibit a high degree of structural variation. Indeed, the primary structure of these histone H1-related sperm nuclear basic proteins (SNBPs) is not random and is the depository of important phylogenetic information. This appears to be the result of their fast rate of evolution driven by positive selection. The way by which the protein variability participates in the transitions that lead to the final highly condensed chromatin organization of spermatozoa at the end of spermiogenesis is not clearly understood. In this paper we focus on the transient chromatin/nucleoplasm patterning that occurs in either a lamellar step or an inversion step during early and mid-spermiogenesis. This takes place in a small subset of protamines in internally fertilizing species of vertebrates, invertebrates and plants. It involves “complex” protamines that are processed, replaced, or undergo side chain modification (such as phosphorylation or disulfide bond formation) during the histone-to-protamine transition. Characteristic features of such patterning, as observed in TEM photomicrographs, include: constancy of the dominant pattern repeat distance λm despite dynamic changes in developmental morphology, bicontinuity of chromatin and nucleoplasm, and chromatin orientation either perpendicular or parallel to the nuclear envelope. This supports the hypothesis that liquid - liquid phase separation by the mechanism of spinodal decomposition may be occurring during spermiogenesis in these species. Spinodal decomposition involves long wave fluctuations of the local concentration with a low energy barrier and thus differs from the mechanism of nucleation and growth that is known to occur during spermiogenesis in internally fertilizing mammals.

During spermiogenesis, human sperm undergo a dramatic reorganization of the chromatin in which canonical histones are replaced by two types of protamines, protamine 1 (P1) and protamine (P2). P1 and P2 are expressed approximately at a 1:1 ratio in healthy men. Alteration of this ratio is associated with male infertility. Patients with an abnormal P1/P2 ratio generally exhibit diminished semen quality, lower fertilization ability, and lower pregnancy rates when undergoing in vitro fertilization. Many studies have reported an elevated incidence of abnormal P1/P2 ratios in infertile men compared to fertile controls, and have evaluated the relationship between infertility and abnormal protamination; however, no prospective study has investigated the normal range of the P1/P2 ratio in men from the general population. Here, we report a P1/P2 reference range of 0.54 to 1.43 in a fertile, normozoospermic population. This rather wide normal range of P1/P2 led us to the conclusion that abnormal protamination is more likely indicative of other perturbations during spermatogenesis than the underlying mechanism to cause infertility. Alternatively, protamine expression may act as a checkpoint mechanism and thus be indirectly related to semen quality.

Protamine 2 (P2) is synthesised as a precursor protein (pre-P2) which by proteolysis is processed to generate the mature components of the protamine 2 family of proteins (HP2, HP3 and HP4). In infertile patients, abnormal processing of the protamine 2 precursors has been suggested by the detection of an increased presence of precursor forms. However, the presence of small detectable amounts of precursor proteins has been demonstrated also in normal sperm samples, although the variation of pre-P2 in individual human sperm cells had not yet been explored. In the present manuscript we perform a mini-review describing what is known about protamine 2 precursors and P2 processing. In addition, we by immunofluorescence demonstrate the existence of a marked variation in the presence and abundance of pre-P2 in individual sperm cells.

During spermiogenesis, the elongating rat spermatid chromatin undergoes a gradual process of condensation which is initiated in the round spermatids at “step 7” of cytodifferentation in stage VII and extending to elongated spermatids at “step 19” of cytodifferentiation in stage VIII. The mechanism of chromatin condensation in the elongating spermatids is an elaborate process that encompasses several biochemical and biological aspects culminating in the deposition of protamine in DNA grooves. The protamination of sperm chromatin involves expression and storage of proteins involved in condensation, removal and degradation of nuclear histones and their replacement by transition proteins and protamine 1, transcriptional silencing and DNA repair, reduction of nuclear volume, repackaging of protaminated chromatin in torroids and development of a characteristic head shape and perforatorium. A study was undertaken in my laboratory to delineate the role of follicle stimulating hormone (FSH) and testosterone in the condensation of nuclear chromatin in the elongating spermatids of sexually competent rat. Towards this end, sexually competent male Holtzmann rats were treated with 20 mg/Kg/d per os (oral supplementum) of cyproterone acetate and 3 mg/Kg/d i.p (intra peritoneal) of fluphenazine decanoate to induce a functional deficiency in either testosterone or FSH. In both rat models, membrane-impermeable CMA3 fluorescent dye uptake assay for GC-rich prospective sites of DNA protamination, was indicative of insufficiency of protamine 1 in spermatozoa taken from caput epididymides of treated rats whereas a fluorescent TUNEL assay indicated the presence of nicked chromatin strands only in protamine-deficient spermatozoa derived from caput epididymides of fluphenazine-treated rats with functional deficiency of FSH. Western blotting of acid-soluble sperm basic proteins had confirmed the near absence of protamine 1 in treated rat spermatozoa in both models. Electron Microscopic evaluation too revealed fine ultrastructural changes in the nuclear membrane of cyproterone acetate as well as fluphenazine decanoate treated spermatozoa derived from caput epididymides. Electrophoretic analysis of caput sperm nuclear basic proteins substantiated the observations at cellular level and revealed a pattern of abnormal persistence of acid-soluble nuclear basic proteins in both rat models, the levels being more prominent in fluphenazine treated rats. Our studies suggest that adequate levels of both FSH and testosterone could be essential during the stages of spermatidal condensation and led us to hypothesize the existence of an endocrine-regulated molecular mechanism for histone to protamine transition and maintenance of chromatin integrity during chromatin condensation in the testis during spermiogenesis.

Single molecule studies of protamine-DNA interactions have characterized the kinetics of protamine binding to DNA and the morphology of the toroidal subunits that comprise sperm chromatin. The results provided by these studies are reviewed, the advantage of using single molecule techniques is discussed, and the implications of the results to the structure, kinetics of toroid formation, and stability of the DNA-protamine complex are described. New measurements of DNA condensation forces induced by the binding of protamine to DNA are also presented. These forces induce a significant tension in constrained segments of DNA and may contribute to the reduction in volume and shaping of the maturing spermatid cell nucleus.

During late stages of spermatogenesis in mammals, most histones bound to DNA are replaced by protamines (PRM), which results in formation of supercondensed and genetically inert sperm chromatin. At fertilization, mature spermatozoon penetrates oocyte and chromatin is remodeled “back” from nucleoprotamine to nucleohistone state. While being crucial for activation of male genome and ultimately for initiation of embryonic development, this process is poorly studied, especially in humans. Data on model animals concerning PRM to histones exchange post fertilization are few and contradictory. As direct experimentation with human embryos is impossible due to ethical, legal and technical reasons, we evaluate the timing and mode of PRM removal in a heterologous ICSI system using hamster ova injected with human sperm. Localization of human PRM 1 and 2 in hybrid zygotes was established using immunofluorescence. We observed a marked zygote to zygote variability in male pronuclei size for any time point post ICSI and demonstrated that PRM removal correlates with the developing pronuclei area rather than time after injection. Overall, the disappearance of protamines from sperm is rather rapid and most likely completed within 1 hr. We propose that the critical characteristic influencing PRM removal after heterologous fertilization is the intrinsic heterogeneity of the human sperm population. The same yet unexplored variance may be one of the reasons for canceled, delayed or aberrant early embryonic development during natural or artificial fertilization in humans.

This is report of mutational analysis of higher plant 5'-methylthioadenosine nucleosidase (MTAN). We identified and characterized the gene encoding yellow lupine (Lupinus luteus) MTAN (LlMTAN). The role of active site amino acids residues Glu24, Phe134, Glu188 and Asp211 was analyzed by site-directed mutagenesis. The Glu24Gln and Asp211Asn substitutions completely abolished the enzyme activity. The Glu188Gln mutant showed only trace activity toward 5'-methylthioadenosine. These results indicate that these three amino acid residues are necessary for enzyme activity. Furthermore, as the result of replacement of Phe134 by less bulky leucine, LlMTAN acquired the ability to bind and hydrolyze S-adenosylhomocysteine. We also analyzed the sequence of the LlMTAN promoter region. It appeared that there may be a direct link between LlMTAN expression regulation and sulfate metabolism.

The development of a stable L-BDH chimera was attempted by exchanging whole domains between two native structural analogs, L-BDH and meso-BDH, because the S-configuration specificity of L-BDH is valuable from the standpoint of its application but its activity is unstable, whereas meso-BDH is stable. The domain chimeras obtained indicated that the leaf-like structures constituting three domains were likely to be mainly associated with chiral recognition, and the fourth domain, the basic domain, is likely to be mainly associated with enzyme stability. A combination of the leaf domains of L-BDH and the basic domain of meso-BDH attained a sufficient level of practical use as an artificial L-BDH chimera, because the resulting enzyme had both stability and S-configuration specificity. However, the levels of stability and specificity were slightly lower than those of the respective enzymes from which they were derived.

Signal peptides recognition by bioinformatics approaches is particularly important for the efficient secretion and production of specific proteins. We concentrate on developing an integrated fuzzy Fisher clustering (IFFC) and designing a novel classifier based on IFFC for predicting secretory proteins. IFFC provides a powerful optimal discriminant vector calculated by fuzzy intra-cluster scatter matrix and fuzzy inter-cluster scatter matrix. Because the training samples and test samples are processed together in IFFC, it is convenient for users to employ their own specific samples of high reliability as training data if necessary. The cross-validation results on some benchmark datasets indicate that the fuzzy Fisher classifier is quite promising for signal peptide prediction.

Based on B cell epitope predictions, a recombinant antigen with multiple epitopes from four Hepatitis C Virus fragments (C, NS3, NS4 and NS5) were engineered. The recombinant gene was then highly expressed in E. coli. The nonmodified and C-terminal-modified recombinant proteins were used for coating and biotin labeling, respectively, to establish the double-antigen sandwich ELISA. Ten positive reference samples confirmed by the CHIRON RIBA HCV 3.0 SIA kit were detected positive, Forty one plasma samples were positive among samples from 441 volunteers, which indicated that the recombinant antigen could readily react well with plasma HCV antibody. As critical reagents of double-antigen sandwich ELISA, the recombinant multi-epitope antigen and the C-terminal-modified and biotin-conjugated antigen show good antigenicity. In this study, we provide a simple approach to produce multiple epitopes within one recombinant protein in order to avoid the costly expression of less-effective pools of multiple proteins, which is the conventional strategy of diagnostic antigen production for HCV antibody detection.

The O-acyl isopeptide method has recently gained attention as an efficient protocol for the synthesis of ‘difficult sequence‘ peptides. Herein, synthesis of three oligopeptides of different length, a pentapeptide Gly-Leu-Leu-Ser-Val, a heptapeptide fragment 285-291 of transmembrane (M7-24-T40) Ala-Val-Leu-Ser-Leu-Pro-Leu and a decapeptide, Gly- Leu-Leu-Ser-Val-Leu-Gly-Ser-Val-Ala were demonstrated in solution phase by employing O-acyl isopeptide method. The peptides were established through an efficient pH triggered intramolecular O→N acyl migration under physiological conditions. The reactions were clean and complete in appreciable length of time.