The probability of electrophoretic idendity of proteins as a function of amino acid divergence

MOLECULAR GENETIC-DISTANCE ESTIMATES AMONG THE URSIDAE AS INDICATED BY ONE- AND TWO-DIMENSIONAL PROTEIN ELECTROPHORESIS

Evolutionary relationships among eight species of Ursidae (including the giant panda) relative to two Procyonidae species (raccoon and red panda) were estimated based on the extent of electrophoretic variation of 289 radiolabelled fibroblast proteins resolved by two-dimensional gel electrophoresis and among 44 isozyme loci resolved by one-dimensional electrophoresis. Allelic differences among these species were converted to genetic distances, and phenetic trees were constructed. In addition, the electrophoretic data were coded as unit characters, and minimum-length trees were derived based on the Wagner method using maximum parsimony. Regardless of the tree-building method employed, the data sets agreed on the following branching sequence: between 22.4 and 32.3 million years (MY) ago, the ancestors of the procyonids and the ursids split into two lineages. Within 10 MY, the red panda split from the line that led to the raccoon. An ancestor of the giant panda split from the ursid line 18-22 MY ago, and the South American spectacled bear split from the line leading to ursine bears 10.5-15.0 MY B.P. A group of six closely related ursine bears (brown bear, polar bear, Asiatic black bear, Malayan sun bear, American black bear, and sloth bear) diverged from a common ancestor during the past 4-8 MY. Much of this ursine radiation was not resolved by our results, with the exception of a recent (2-3 MY B.P.) divergence of brown bear and polar bear. The topological concordance of the data sets from one- and two-dimensional electrophoresis supports the usefulness of these procedures for evolutionary inference and provides additional precision to the reconstruction of divergence nodes of this carnivore group.

A Mixed Model of Mutation for Electrophoretic Identity of Proteins within and between Populations

A model which is a mixture of the model of infinite alleles and the Ohta-Kimura model of stepwise mutation has been proposed for the study of eletcrophoretic variants in natural populations. Mutations which alter the mobility of a protein are divided into two classes: stepwise mutations and nonstepwise mutations. It is assumed that stepwise mutations follow the Ohta-Kimura model while nonstepwise mutations follow the infinite allele model. It is then shown that even if the proportion of nonstepwise mutations is only 5%, with the other 95% stepwise mutations, the effective number of alleles given by the present model is considerably larger than that given by the Ohta-Kimura model of stepwise mutation. The result has also been applied to study Nei's genetic distance.

The influence of site-specificity of single amino acid substitutions on electrophoretic separation of yeast iso-1-cytochrome c

This study dealt with the ability of non-denaturing gel electrophoresis to separate iso-1-cytochrome c with single amino acid replacements isolated from revertants of various cyc1 nonsense mutants of the yeast Saccharomyces cerevisiae. A total of 28 different iso-1-cytochromes c with single amino acid substitutions of one of seven amino acids at six positions were examined on nondenaturing polyacrylamide gels at pH 4.8. Each of these iso-1-cytochromes c exhibited 1 of 16 distinct electrophoretic mobilities. We could distinguish the majority of iso-1-cytochromes c, even those having the same replacement at different sites and those having different replacements that resulted in the same net charge. These results provide confirmation of the importance of site-specific effects on the electrophoretic mobility, and presumably other properties, of proteins differing in sequence by as little as one amino acid. They demonstrate that nondenaturing electrophoresis is able to separate the majority of, but not all, proteins differing by single amino acids.

A molecular phylogeny of the hominoid primates as indicated by two-dimensional protein electrophoresis

A molecular phylogeny for the hominoid primates was constructed by using genetic distances from a survey of 383 radiolabeled fibroblast polypeptides resolved by two-dimensional electrophoresis (2DE). An internally consistent matrix of Nei genetic distances was generated on the basis of variants in electrophoretic position. The derived phylogenetic tree indicated a branching sequence, from oldest to most recent, of cercopithecoids (Macaca fascicularis), gibbon-siamang, orangutan, gorilla, and human-chimpanzee. A cladistic analysis of 240 electrophoretic characters that varied between ape species produced an identical tree. Genetic distance measures obtained by 2DE are largely consistent with those generated by other molecular procedures. In addition, the 2DE data set appears to resolve the human-chimpanzee-gorilla trichotomy in favor of a more recent association of chimpanzees and humans.

Mutagenicity testing on non-selectively cloned Chinese hamster ovary cells with the protein-mapping method

Chemical mutagenesis was studied on Chinese hamster ovary cells by protein mapping. Cell cultures were treated with methylnitrosourea and the cells were cloned in non-selective media. The proteins of single clones were separated by 2-dimensional electrophoresis and analysed for qualitative (electrophoretic mobility) and quantitative (staining intensity; presence/absence) changes in the protein patterns. The investigation included 26 clones derived from treated cells and 26 control clones. The total number of gene loci tested was calculated from the number of protein spots analysed: it amounted to about 33 800. The protein patterns revealed 2 alterations defined as qualitative variant proteins. No alteration of this type was found in the control group. The frequency of quantitative variant proteins was increased by more than 100% compared with the control group. Our results and theoretical considerations suggest that the cellular concentration of single proteins offers a sensitive parameter for mutagenicity testing.

Genetic variation in natural populations: problem of electrophoretically cryptic alleles

Electrophoretic studies have shown that the average frequency of heterozygous loci per individual is about 12% in Drosophila and other invertebrates and about 6% in vertebrates. It is estimated that only about two-thirds of all amino acid substitutions change net electric charge; hence, a large fraction of all genetic variation may be undetected by electrophoresis. Peptide mapping of 11 independent alleles coding for alcohol dehydrogenase in Drosophila melanogaster has uncovered one cryptic variant; thus, the frequency of electrophoretically cryptic variation is apparently low, about 9% in this sample. Nevertheless, with a simple model it is shown that this degree of cryptic variation, if it is typical of other loci, would substantially change our current estimates of genetic variation: the average heterozygosity would increase from about 12% to about 25% for invertebrates and from about 6% to 21% for vertebrates. A variety of techniques--including sequential electrophoresis and heat or urea denaturation--have been used by various investigators to detect electrophoretically cryptic variation. These techniques appear to be less effective than peptide mapping for detecting cryptic variation, but, like peptide mapping, they suggest that standard electrophoresis may detect most of the protein variation present in natural populations. The charge-state model of protein variation proposes that the "alleles" detected by electrophoresis are extremely diverse classes consisting of many electrophoretically cryptic alleles. The alcohol dehydrogenase peptide-mapping results are inconsistent with the charge-state model.

Comparison of the larval serum proteins of Drosophila melanogaster using one and two-dimensional peptide mapping

Immunological data, amino acid composition, and coordinate control during development suggest that the alpha, beta and gamma subunits of the major protein of Drosophila larval serum (LSP-1) are coded for by genes which evolved by replications of an ancestral gene followed by mutation. In order to test this hypothesis, and to study the relationship of these genes with that coding for the second major larval serum protein subunits. One-dimensional maps generated by three different proteases showed many similarities among these proteins. Two-dimensional peptide mapping of the methionine-containing tryptic peptides showed that half of these peptides are common to all four larval serum protein subunits, and that about two-thirds are common to the three LSP-1 subunits. These observations show that the LSP-1 subunits are more closely related to each other than any is to LSP-2, and supported the initial suggestion that the proteins are homologous. Because the genes for the LSP-1 subunits are each located on a different chromosome, the LSP-1 subunits are a suitable system for investigating the evolution and dispersal of related genes, and trans control in eukaryotes.

Composite stepwise mutation model under the neutral mutation hypothesis

As an extension of the conventional ("Ohta-Kimura") stepwise mutation model, a new model is proposed. In this model, it is assumed that each charge state ("electromorph") is represented by K alleles and that a mutation changes an allele either by one step in the charge space or to one of the other members of the identical electromorph. It is shown that the net genetic variability within a population is similar to that predicted by the infinite-allele model ("Kimura-Crow" model) rather than to that predicted by the stepwise mutation model, and the K-dependence of genetic variability is rather weak when K greater than or equal to 2 and the effective population size is not much greater than the reciprocal of mutation rate. The results are compared with the recent observations at the xanthine dehydrogenase locus in Drosophila pseudoobscura.

Estimating total genic diversity in the house mouse

In a survey of variation in both electrophoretic charge and thermostability at 14 structural loci in 40 strains of Mus musculus, 27 electromorphs (polypeptides differing in electrophoretic charge) and 20 thermomorphs (polypeptides differing in thermostability) were found. Electrophoresis detected 11 new variants within thermomorphs, and the heat denaturation technique detected four new variants within electromorphs. From these data, and making the assumption that both techniques are independent of each other, it is estimated that the actual total number of alleles at the 14 loci is 53, or an average of 3.79 per locus (1.96 per electromorph), and that electrophoresis apparently detects one-third of the variants, thus describing about 50% of the alleles at structural gene loci in the house mouse.

Unimodality, symmetry and the step-state hypothesis of electrophoretic variation in natural populations

The population frequency distributions of electromorphs of polymorphic loci, when ordered by electrophoretic mobility, tend strongly and significantly to be both unimodal and symmetrical. Such distributions are predicted by all step-change models and their generality in published data can be construed as supportive of the step-change hypothesis. On the other hand, unimodality and symmetry might also be due to artifactual "unit perception" biases that affect the interpretation and reporting of electrophoretic data. In any case, it appears that perceived electromorphs are highly heterogeneous.

Patterns of molecular variation. I. Interspecific comparisons of electromorphs in the Drosophila mulleri complex

The average mobility of electromorphs at an enzyme locus in a single population was defined as the weighted average mobility of the electromorphs in that population, where the electromorph frequencies are the weights. A derivative distance measure was defined whose taxonomic utility was determined in the Drosophila mulleri species complex. Most of the variation in this metric was at the interspecific level, primarily among clusters of sibling species. The electromorphs of some loci were equally and regularly spaced, while those of other loci were less regular in their spacing. Overall, these minor perturbations from regular spacing did not noticeably detract from the taxonomic utility of average mobility, and cluster analysis yielded the same taxonomic relationships as more conventional nonmolecular treatments. On the other hand, electromorph spacing may be related to functional constraints on the enzyme molecules. Some possible implications of the results for the modes of selection during evolution of the different enzymes are discussed.

The charge-state model of protein polymorphism in natural populations

Routine electrophoretic surveys for genetic variation in natural populations depend primarily upon detecting differences in the net charge carried by a protein. We have calculated the proportion of base substitutions which would yield an electrophoretically detectable mutant protein, and the relative mutation rates among different chare classes, under a variety of simplifying assumptions. These calculations indicate that: (i) only 25 per cent of all single base mutations would lead to a charge change on a protein molecule. (ii) five distinct classes of electrophoretic variants can be generated from a specified protein by single base substitutions. (iii) the relative mutation rates differ markedly among the different charge classes which can be generated by single base substitutions. The estimates of the proportion of electrophoretically detectable mutant proteins and relative mutation rates among charge classes were relatively robust to changes in assumptions concerned with the kind and site of base substitutions and the amino acid composition of the protein.

Protein mapping by combined isoelectric focusing and electrophoresis of mouse tissues. A novel approach to testing for induced point mutations in mammals

The protein-mapping method which combines isoelectric focusing in acrylamide gel and gel electrophoresis was previously used mainly for the separation of plant proteins and human serum proteins. We investigated with this technique soluble proteins of mouse tissues (whole embryos, the liver of fetal and adult mice, kidneys) and the proteins of mouse serum. The technique was tested under a number of different conditions to find those best for our purpose; they may represent some general improvements in the method. The protein patterns show high resolution and excellent reproducibility. About 275 spots were found for fetal liver, about 230 for whole embryos (day 14 p.c.) and about 100 for serum. The fact that a high number of protein spots can be evaluated by a single and comparatively simple experiment suggests that this method may be useful as an assay system for induced point mutations. The protein patterns demonstrated are compared and discgs of dominant lethal examinations after acute and subacute application of these three substances.

Distribution of allelic frequencies in a finite population under stepwise production of neutral alleles

A formula for the distribution of allelic frequencies in a finite population is derived assuming stepwise production of multiple alleles. Monte Carlo experiments were performed to check the validity of the formula, and excellent agreement was obtained between theoretical distribution and experimental results. The formula should be useful for analyzing genetic variability in natural populations that can be detected by electrophoretic methods.

An electrophoretic variant of beta-galactosidase with altered catalytic properties in a patient with GM1 gangliosidosis

In nine patients with GM1 gangliosidosis, liver ganglioside GM1 beta-galactosidase (EC 3.2.1.23) activity ranged from less than 0.01% to 0.05% of normal. In a tenth patient's liver, much higher activity was found (0.5% of normal). In this patient the residual enzyme had the same molecular weight as beta-galactosidase A, the major form of beta-galactosidase of normal human liver. No activity was found that corresponded to beta-galactosidase B, the minor form of human liver beta-galactosidase. On starch gel electrophoresis, the patient's enzyme migrated less anodally than normal beta-galactosidase A, both before and after treatment with neuraminidase. Beta-Galactosidase from the patient had a Km that was higher then normal; 5-fold higher with ganglioside GM1 and 2-fold higher with 4-methylumbelliferyl beta-galactoside. The patient's enzyme crossreacted immunologically with normal beta-galactosidase A and had about 100-fold more antigenic activity per unit catalytic activity than the normal enzyme. The results indicate that in this patient a beta-galactosidase A protein with altered charge and altered catalytic properties was present in relatively normal amounts, the first electrophoretic variant reported for a patient with a lysosomal hydrolase deficiency.