Interspecies immunologic cross-reactivity of mammalian sperm basic proteins

The species uniqueness of the sperm basic nuclear proteins (SBNPs) of mammals is in sharp contrast to the highly conserved function of those proteins, to mediate extreme condensation of the sperm chromatin. Despite their molecular uniqueness, however, the SBNPs of all eutherian mammals share certain characteristics: low molecular weight, high percentage of arginine and cysteine residues and, in the final step of chromatin condensation, extensive SS cross-linking. By radioimmunoassay, we have demonstrated that rabbit antiserum to mouse SBNP is reactive with purified mouse SBNP and mouse sperm and is cross-reactive with purified bull SBNP and sperm of bull, rat, rabbit, dog and man. The immunologically cross-reactive sites, therefore, may represent the homologous regions of the various species of SBNPs that serve the function of chromatin condensation. Immunologic reactivity was displayed only by sperm made to swell by treatment with 2-mercaptoethanol. Unswollen sperm were not reactive, confirming previous observations by immunofluorescence [1] indicating that reduction of SS bonds is necessary to render the antigenic sites of SBNP available for immunologic recognition, and suggesting that formation of SS bonds within that protein may be a molecular mechanism of antigen sequestration in vivo.     

The amino acid composition of mammalian and bacterial cells

Summary High performance liquid chromatography was used to analyze the amino acid composition of cells. A total of 17 amino acids was analyzed. This method was used to compare the amino acid compositions of the following combinations: primary culture and established cells, normal and transformed cells, mammalian and bacterial cells, andEscherichia coli andStaphylococcus aureus. The amino acid compositions of mammalian cells were similar, but the amino acid compositions ofEscherichia coli andStaphylococcus aureus differed not only from mammalian cells, but also from each other. It was concluded that amino acid composition is almost independent of cell establishment and cell transformation, and that the amino acid compositions of mammalian and bacterial cells differ. Thus, it is likely that changes in amino acid composition due to cell transformation or species differences between mammalian cells are negligible compared with the differences between mammalian and bacterial cells, which are more distantly related.     

Unique amino acid composition of proteins in halophilic bacteria

The amino acid compositions of proteins from halophilic archaea were compared with those from non-halophilic mesophiles and thermophiles, in terms of the protein surface and interior, on a genome-wide scale. As we previously reported for proteins from thermophiles, a biased amino acid composition also exists in halophiles, in which an abundance of acidic residues was found on the protein surface as compared to the interior. This general feature did not seem to depend on the individual protein structures, but was applicable to all proteins encoded within the entire genome. Unique protein surface compositions are common in both halophiles and thermophiles. Statistical tests have shown that significant surface compositional differences exist among halophiles, non-halophiles, and thermophiles, while the interior composition within each of the three types of organisms does not significantly differ. Although thermophilic proteins have an almost equal abundance of both acidic and basic residues, a large excess of acidic residues in halophilic proteins seems to be compensated by fewer basic residues. Aspartic acid, lysine, asparagine, alanine, and threonine significantly contributed to the compositional differences of halophiles from meso- and thermophiles. Among them, however, only aspartic acid deviated largely from the expected amount estimated from the dinucleotide composition of the genomic DNA sequence of the halophile, which has an extremely high G+C content (68%). Thus, the other residues with large deviations (Lys, Ala, etc.) from their non-halophilic frequencies could have arisen merely as "dragging effects" caused by the compositional shift of the DNA, which would have changed to increase principally the fraction of aspartic acid alone.     

Identification of proteins in sequence databases from amino acid composition data.

Having obtained the amino acid composition of a protein, chemists and molecular biologists may wish to identify the protein from this data alone. In general such data will have errors associated with them and the length of the protein may be known only approximately or not at all. In this paper a method is described which enables searching of protein sequence databases for sequences or fragments of sequences which have a composition similar to the one being sought. Such searches are generally quite discriminating as shown by the examples provided. This method has been implemented as part of the computer program Scrutineer and is being freely distributed. It is simple to use.     

The broken-stick model for amino acid composition in proteins

Summary The relative abundances among the amino acids, which are functionally similar to one another, were explained by random partition of a unit interval.     

Deoxyribonucleoproteins of herring sperm nuclei. I. Chemical composition

The chemical composition of deoxyribonucleoproteins from herring sperm nuclei was analyzed and the results are summarized as follows: 1. Chemical analysis of nuclear proteins and nucleic acids revealed that arginine/P molar ratio in herring sperm nuclei is unity but the ratio of arginine residues in protamine to phosphorus in the total DNA is 0.86. 2. The deoxyribonucleoproteins were isolated and their composition showed that about 14% of the total DNA in herring sperm nuclei is free from protamine and is bound with nonprotamine proteins in the weight ratio of nonprotamine proteins to DNA of 0.25-0.30. The remaining 86% of the total DNA is combined mainly with protamine and a small amount of nonprotamine proteins; the weight ratios of protamine and nonprotamine proteins to DNA are 0.75 and 0.08, respectively. In the latter complex, the molar ratio of arginine residues in protamine to phosphorus in DNA is unity.     

The amino acid composition of proteins: a method of analysis.

Four quasiloglinear models are proposed for describing relationships between the amino acid composition of proteins and the structure of the genetic code. The models allow estimation of base frequencies in all three codon positions and can be used to investigate “interactions” between any two codon positions. The estimation procedure proposed by Ohta and Kimura (Genetics64 (1970), 387–395) is discussed and using two of the proposed quasiloglinear models an analysis of the amino acid composition of human cytochrome c is presented. The analysis suggests that of the six codons which code for leucine (CUU, CUC, CUA and CUG) do not occur in human cytochrome c.     

Preparative separation and amino acid composition of neurofilament triplet proteins

Abstract: Intact neurofilaments were isolated from bovine spinal cord white matter, washed by sedimentation in 0.1 m -NaCl, and extracted with 8 m -urea. Solubilized neurofilament triplet proteins of molecular weights approximately 68,000 (P68), 150,000 (P150), and 200,000 (P200) were purified by preparative electrophoresis, using an LKB 7900 Uniphor apparatus. The method provides for an enhanced yield of purified protein and has markedly reduced admixture of electrophoresed protein with acrylamide and associated protein contaminants. Amino acid compositions of the purified neurofilament triplet proteins are reported and compared.     

Persistent biases in the amino acid composition of prokaryotic proteins

Correspondence analysis of 28 proteomes selected to span the entire realm of prokaryotes revealed universal biases in the proteins' amino acid distribution. Integral Inner Membrane Proteins always form an individual cluster, which can then be used to predict protein localisation in unknown proteomes, independently of the organism's biotope or kingdom. Orphan proteins are consistently rich in aromatic residues. Another bias is also ubiquitous: the amino acid composition is driven by the G + C content of the first codon position. An unexpected bias is driven, in many proteomes, by the AAN box of the genetic code, suggesting some functional biochemical relationship between asparagine and lysine. Less-significant biases are driven by the rare amino acids, cysteine and tryptophan. Some allow identification of species-specific functions or localisation such as surface or exported proteins. Errors in genome annotations are also revealed by correspondence analysis, making it useful for quality control and correction.     

On the diversity of sperm basic proteins in the vertebrates: V. Cytochemical and amino acid analysis in Squamata, Testudines, and Crocodylia

The variability of sperm basic proteins in representatives of three reptilian orders, Squamata, Testudines, and Crocodylia, has been examined by cytochemistry, acid-urea polyacrylamide gel electrophoresis, and amino acid analysis of amidoblack-stained bands. Snakes contain type 3B intermediate sperm basic proteins by cytochemical criteria. Electrophoresis of basic proteins from epididymis chromatin as well as from testis and ductus deferens cell suspensions shows two fast-moving bands in the vicinity of herring protamine. These proteins are triprotamines containing about 27 mol % arginine, along with lysine and histidine. Lizards have type 1 protamines in their sperm nuclei cytochemically and also show a two-banded electrophoretic pattern similar to that of snakes. However, these proteins are triprotamines, similar to those in snakes with 25 mol % arginine. It may be that these are testis-specific proteins of the spermatid stage in lizards since a cytochemical transition can be observed from type 3A intermediate proteins in spermatids of testis to type 1 protamine in mature sperm of ductus deferens. Turtles contain type 3A intermediate sperm basic proteins cytochemically and basic proteins from epididymis chromatin display both a prominent band and a minor band close to, but slightly slower than, the two bands for snakes and lizards. Amino acid analysis of these bands shows that these basic proteins are also triprotamines but with a higher level of arginine, about 48 mol %, than that in snake and lizard sperm proteins. Basic proteins from epididymis chromatin of a single Mississippi alligator show three main bands moving close to the bands of snakes, lizards, and turtles. These proteins have amino acid compositions typical for triprotamines, with 28-39 mol % arginine. The data indicate that the sperm basic proteins of representatives of 25 species in three reptilian orders are very similar, in contrast to the diversity of sperm protein types found in frogs (Kasinsky, Huang, Kwauk, Mann, Sweeney, and Yee: J. Exp. Zool., 203:109-126, '78; Kasinsky, Huang, Mann, Roca, and Subirana: J. Exp. Zool., 234:33-46, '85a). This appears to be part of a macroevolutionary trend from diversity of sperm basic proteins in frogs to relative constancy in reptiles (Kasinsky, Mann, Pickerill, Gutovich, and Byrd, Jr.:J. Cell Biol., 91:1879, '81; Kasinsky, Mann, Lemke, and Huang: In: Chromosomal Proteins and Gene Expression, Plenum Press, New York, pp. 333-352, '85b). We present the hypothesis that one factor for such a trend resides in the fact that fertilization is internal in reptiles but external in anurans.     

Effects of metabolic rate and sperm competition on the fatty‐acid composition of mammalian sperm

The sperm membrane is a key structure affecting sperm function and thus reproductive success. Spermatozoa are highly specialized and differentiated cells that undergo a long series of processes in the male and female reproductive tracts until they reach the site of fertilization. During this transit, the sperm membrane is prone to damage such as lipid peroxidation. The characteristics and performance of the sperm membrane are strongly determined by the fatty‐acid composition of membrane phospholipids. Polyunsaturated fatty‐acids (PUFAs) are the most prone to lipid peroxidation. Lipid peroxidation and other types of oxidative damage increase with higher metabolism and with higher levels of sperm competition due to the increased ATP production to fuel higher sperm velocities. Consequently, we hypothesized that, in order to avoid oxidative damage, and the ensuing impairment of sperm function, sperm cells exhibit a negative relationship between PUFA content and mass‐specific metabolic rate (MSMR). We also hypothesized that higher sperm competition leads to a reduction in the proportion of sperm PUFAs. We performed a comparative study in mammals and found that high MSMR and high levels of sperm competition both promote a decrease in the proportion of PUFAs that are more prone to lipid peroxidation. The negative relationship between MSMR and these PUFAs in sperm cells is surprising, because a positive relationship is found in all other cell types so far investigated. Our results support the idea that the effects of MSMR and sperm competition on sperm function can operate at very different levels.