Genetic divergence between rodent species assessed by using two-dimensional electrophoresis

Proteomic similarity of the Littorinid snails in the evolutionary context

BACKGROUND

The introduction of DNA-based molecular markers made a revolution in biological systematics. However, in cases of very recent divergence events, the neutral divergence may be too slow, and the analysis of adaptive part of the genome is more informative to reconstruct the recent evolutionary history of young species. The advantage of proteomics is its ability to reflect the biochemical machinery of life. It may help both to identify rapidly evolving genes and to interpret their functions.

METHODS

Here we applied a comparative gel-based proteomic analysis to several species from the gastropod family Littorinidae. Proteomes were clustered to assess differences related to species, geographic location, sex and body part, using data on presence/absence of proteins in samples and data on protein occurrence frequency in samples of different species. Cluster support was assessed using multiscale bootstrap resampling and the stability of clustering-using cluster-wise index of cluster stability. Taxon-specific protein markers were derived using IndVal method. Proteomic trees were compared to consensus phylogenetic tree (based on neutral genetic markers) using estimates of the Robinson-Foulds distance, the Fowlkes-Mallows index and cophenetic correlation.

RESULTS

Overall, the DNA-based phylogenetic tree and the proteomic similarity tree had consistent topologies. Further, we observed some interesting deviations of the proteomic littorinid tree from the neutral expectations. (1) There were signs of molecular parallelism in two Littoraria species that phylogenetically are quite distant, but live in similar habitats. (2) Proteome divergence was unexpectedly high between very closely related Littorina fabalis and L. obtusata, possibly reflecting their ecology-driven divergence. (3) Conservative house-keeping proteins were usually identified as markers for cryptic species groups ("saxatilis" and "obtusata" groups in the Littorina genus) and for genera (Littoraria and Echinolittorina species pairs), while metabolic enzymes and stress-related proteins (both potentially adaptively important) were often identified as markers supporting species branches. (4) In all five Littorina species British populations were separated from the European mainland populations, possibly reflecting their recent phylogeographic history. Altogether our study shows that proteomic data, when interpreted in the context of DNA-based phylogeny, can bring additional information on the evolutionary history of species.

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.

From the Macro to the Micro: Gel Mapping to Differentiate between Sporozoites of Two Immunologically Distinct Strains of Eimeria maxima (Strains M6 and Guelph)

Two immunologically distinct strains of E. maxima were examined in this study: the M6 strain and the Guelph strain. The differential expression between the sporozoites of the two strains of E. maxima was determined by image analysis of 100 μg of protein from each strain separated by standard one- and conventional two-dimensional polyacrylamide gel electrophoresis. In addition to differences in both molecular weight and the electrophoretic mobility, differences in the intensity of polypeptide bands for example, GS 136.4 and M6 169 were explored. Pooled gels were prepared from each strain. A representative 2D-PAGE gel spanning a non-linear pH range of 3-10 of E. maxima strain M6 consisted of approximately 694 polypeptide spots with about 67 (9.6%) of the polypeptide spots being unique relative to the other strain. E. maxima strain GS had about 696 discernable polypeptide spots with 69 spots (9.9%) that differed from those of the M6 strain. In-depth characterization of the variable polypeptide spots; unique polypeptide spots (absence or presence) and shared polypeptide spots with modifications may lead to novel vaccine target in the form of multi-component, multi-stage, multi-immunovariant strains, multi-species subunit vaccine, and diagnostic probe for E. maxima.

Proteomics in evolutionary ecology: linking the genotype with the phenotype

The study of the proteome (proteomics), which includes the dynamics of protein expression, regulation, interactions and its function, has played a less prominent role in evolutionary and ecological investigations in comparison with the study of the genome and transcriptome. There are, however, a number of arguments suggesting that this situation should change. First, the proteome is closer to the phenotype than the genome or the transcriptome, and as such may be more directly responsive to natural selection, and thus closely linked to adaptation. Second, there is evidence of a low correlation between protein and transcript expression levels across genes in many different organisms. Finally, there have been some recent important technological improvements in proteomics methods that make them feasible, practical and useful to address a wide range of evolutionary questions even in nonmodel organisms. The different proteomic methods, their limitations and problems when interpreting empirical data are described and discussed. In addition, the proteomic literature pertaining to evolutionary ecology is reviewed with examples, and potential applications of proteomics in a variety of evolutionary contexts are outlined. New proteomic research trends such as the study of posttranslational modifications and protein-protein interactions, as well as the combined use of the different -omics approaches, are discussed in relation to the development of a more functional and integrated perspective, needed for achieving a more comprehensive knowledge of evolutionary change.

Screening trematodes for novel intervention targets: a proteomic and immunological comparison of Schistosoma haematobium, Schistosoma bovis and Echinostoma caproni

With the current paucity of vaccine targets for parasitic diseases, particularly those in childhood, the aim of this study was to compare protein expression and immune cross-reactivity between the trematodes Schistosoma haematobium, S. bovis and Echinostoma caproni in the hope of identifying novel intervention targets. Native adult parasite proteins were separated by 2-dimensional gel electrophoresis and identified through electrospray ionisation tandem mass spectrometry to produce a reference gel. Proteins from differential gel electrophoresis analyses of the three parasite proteomes were compared and screened against sera from hamsters infected with S. haematobium and E. caproni following 2-dimensional Western blotting. Differential protein expression between the three species was observed with circa 5% of proteins from S. haematobium showing expression up-regulation compared to the other two species. There was 91% similarity between the proteomes of the two Schistosoma species and 81% and 78·6% similarity between S. haematobium and S. bovis versus E. caproni, respectively. Although there were some common cross-species antigens, species-species targets were revealed which, despite evolutionary homology, could be due to phenotypic plasticity arising from different host-parasite relationships. Nevertheless, this approach helps to identify novel intervention targets which could be used as broad-spectrum candidates for future use in human and veterinary vaccines.

Analysis of two-dimensional protein patterns from developmental stages of the potato cyst-nematode,Globodera rostochiensis

Two-dimensional polyacrylamide gel electrophoresis was used to examine the differences in total protein composition between two motile stages and two sedentary stages of the potato cyst-nematode,Globodera rostochiensis. Using a sensitive silver stain, 542 reproducible protein spots were distinguished. A list of these spots is presented, showing their apparent molecular weights, estimated isoelectric points, and occurrences in the different developmental stages. When the protein patterns were compared, 401 spots were found to change their presence or size in one or more of the four developmental stages. It is therefore estimated that during the post-embryonic development ofG. rostochiensis, 74% of the polypeptides undergo modulation of their synthesis, or are affected by protein degradation or modification. In the motile stages several abundant proteins were present, which disappeared or decreased in concentration in the sedentary stages. Some of these proteins are presumably muscle proteins, and their modulation may illustrate the degeneration of body-wall musculature in the sedentary stages. It is concluded that the potato cyst-nematode has a very dynamic protein metabolism.

Genetic variability of the marine mussel Mytilus galloprovincialis assessed using two-dimensional electrophoresis

Two-dimensional electrophoresis (2-DE) has been used to measure the degree of genetic variability of the marine mussel Mytilus galloprovincialis. Genetic polymorphisms were detected in 33 of a total of 86 polypeptides scored among the most abundant proteins from foot samples in 38 individuals. Estimates of average heterozygosity were 0.101+/-0.018 and 0.114+/-0.021 in a natural and a cultured population, respectively, from the NW of the Iberian Peninsula. These are the highest estimates of average heterozygosity reported by 2-DE in an animal species to date. We consider that these data throw open the question of the level of genetic variability detectable by two-dimensional electrophoresis. Multilocus genotype data were used to infer haplotypic frequencies by means of the EM algorithm in order to detect linkage disequilibrium between loci coding abundant proteins. Significant associations were found in 22.7% of the 406 two-locus pairs analysed. Also, clusters of loci in which all pairwise combinations exhibit statistically significant associations were detected and physical linkage between some of these loci is postulated from the linkage disequilibrium data.

Phylogenetic relationships and intraspecific variations of loaches of the genus Lefua (Balitoridae, Cypriniformes)

Three nominal species are known in East Asian balitorid loaches of the genus Lefua, i.e. L. echigonia, L. nikkonis, and L. costata. Lefua echigonia, with large morphological variations was recently separated into two groups, L. echigonia including the holotype and L. sp., based on morphological and ecological traits. We performed protein and DNA analyses to elucidate phylogenetic relationships among loaches of the genus Lefua and to settle the taxonomic status of L. sp. We also investigated intraspecific variations in L. echigonia s. str. to shed light on the process of formation of freshwater fish fauna in Japan. Protein analyses using two-dimensional gel electrophoresis showed that genetic distances between L. sp. and L. echigonia s. str. and between L. sp. and L. nikkonis were as large as that between L. echigonia s. str. and L. nikkonis. DNA analyses of the mitochondrial D-loop region showed that L. sp. and L. echigonia s. str. were monophyletic, respectively, while neither L. nikkonis nor L. costata was monophyletic and these species formed together a clade. The results supported the specific status of L. sp. and proposed reevaluation of the taxonomic status of L. nikkonis and L. costata. DNA analyses also showed that L. sp. was more closely related to L. echigonia s. str. than to the L. nikkonis-L. costata complex, and four local populations were distinguished in L. echigonia s. str. Distribution patterns of the four local populations of L. echigonia s. str. in Japan were approximately congruent with those of the medaka, Oryzias latipes, suggesting that differentiation in the two distantly related fishes have a common historical background.

Distance indices in a comparison between the A, D, I and R genomes of the Triticeae tribe

Two-dimensional gel electrophoresis of shoot proteins was used to study the relationships between Triticum, Secale, and Hordeum. A high level of polymorphism was found among the 1275 spots scored: only 198 spots were found common to all. But, under the hypothesis that only allelic variations were observed, the mean number of alleles per locus was only two. Phenograms were built from different distance indices. All of them showed Triticum genomes A and D close to each other, Hordeum far from the Triticum cluster, and Secale at an intermediate position. A discussion on the use of various distance indices is presented.

Quantification of silver-stained proteins resolved by two-dimensional electrophoresis: genetic variability as related to abundance and solubility in two maize lines

Relative abundance and solubility of proteins from etiolated coleoptiles of maize were investigated using two-dimensional electrophoresis (2-D PAGE). Automatic quantification of silver-stained polypeptides on replicate 2-D gels made it possible to test the linearity of the relationship between spot integrated optical density and protein amount in the range from 15 micrograms to 135 micrograms per gel, in two inbred lines. A linear response was found for more than 60% of the spots in each genotype. When a linear response was found in both lines for a given spot, the slope values were similar in 94% of the cases, indicating the reliability of silver staining for polypeptide quantification. The parameters of the curves allowed the definition of protein classes of different abundances that could be compared for genetic variability between the two lines. From a comparison between standard 2-D patterns (trichloroacetic acid-acetone extracted proteins) and patterns obtained from Tris buffer extracted proteins, it appeared that 92% of the proteins visualized in the standard gels were soluble. No difference in genetic variability, either qualitative or quantitative, was evidenced between the various classes of abundance, or between soluble and insoluble proteins.

Polymorphism of pepper (Capsicum annuum L.) seed proteins studied by two-dimensional electrophoresis with immobilized pH gradients: methodical and genetic aspects

A population of ten morphologically similar inbred lines of pepper (Capsicum annuum L.) has been investigated for polymorphism of seed proteins by two-dimensional (2-D) electrophoresis with immobilized pH gradients. To reveal as much variation as possible, both the water- and the urea/detergent-soluble protein fraction were electrophoretically analyzed and subsequently visualized by silver staining. The 2-D patterns were subjected to computer analysis to be able to establish genetic variation. A high number of the seed proteins were found to be variable as to presence/absence: these were 68 out of 184 reproducible water-soluble proteins and 34 out of 419 reproducible urea/detergent-soluble proteins. Comparison of the 2-D data of the water-soluble and the urea/detergent-soluble proteins, which represent the biggest part of all extractable seed proteins, showed that both protein fractions have proteins in common, but the variable proteins found in both fractions were non-identical. The difference of variability scored in both solubility fractions was discussed. Genetic distances between all pairs of inbred pepper lines were calculated and a genetic tree was constructed. A correlation analysis was carried out to correct for genetic linkage and for secondary modifications, to have a more proper estimate of genetic distances. In both cases the dendrograms showed two distinct genetic groups of five inbred lines. This electrophoretic study was done in order to utilize the genetic distance data in breeding for heterosis. The genetic distance data presented will be used to validate the assumption that there is a higher chance to achieve better hybrid performance when the genetic distance between the parents is as great as possible.(ABSTRACT TRUNCATED AT 250 WORDS)

The distribution and spreading of rare variants in the histone multigene family of Drosophila melanogaster

We surveyed the distribution of rare variant restriction sites within and among histone gene arrays of Drosophila melanogaster using restriction fragment length polymorphism (RFLP) analysis. Seventy-three naturally occurring arrays were digested with restriction enzymes that had no recognition sites in the published histone sequence. Of the arrays surveyed, 68.5% had at least two nonconsensus restriction sites present as indicated by the presence of a small band or bands on the autoradiographs. These bands were almost always the length of a single repeat in the histone multigene family or a multiple of this length. In arrays with more than one band, intensity of the bands almost always decreased with increasing size. This shows that within these arrays variant restriction sites were predominantly located on adjacent repeats. If these bands are caused by spreading of variant sites, as is most likely, then variants spread along the array as an inverse function of distance. Overall, if a sequence spread it had a 92% probability of ending up in its nearest neighbor. This pattern may result from the noncontiguous nature of the histone family.

A combined classical genetic and high resolution two-dimensional electrophoretic approach to the assessment of the number of genes affecting hybrid male sterility in Drosophila simulans and Drosophila sechellia

We have attempted to estimate the number of genes involved in postzygotic reproductive isolation between two closely related species, Drosophila simulans and Drosophila sechellia, by a novel approach that involves the use of high resolution two-dimensional gel electrophoresis (2DE) to examine testis proteins in parents, hybrids and fertile and sterile backcross progenies. The important results that have emerged from this study are as follows: (1) about 8% of about 1000 proteins examined showed divergence (presence/absence) between the two species; (2) by tracing individual proteins in parental, hybrid and backcross males, we were able to associate the divergent proteins with different chromosomes and found that most divergent proteins are associated with autosomes and very few with X chromosome, Y chromosome and cytoplasm; (3) when proteins showing both quantitative and qualitative differences between the two species were examined in F1 hybrid males, most (97.4%) proteins were expressed at levels between the two parents and no sign of large scale changes in spot density was observed. All the proteins observed in the two parental species were present in F1 hybrid males except two species-specific proteins that may be encoded (or regulated) by sex chromosomes; (4) when different fertile and sterile backcross male testes were compared, a few D. sechellia-specific proteins were identified to be consistently associated with male sterility. These results along with the observation that a large proportion (23.6%) of first generation backcross males were fertile show that hybrid male sterility between D. simulans and D. sechellia involves a relatively small number of genes. Role of large scale genetic changes due to general genome incompatibility is not supported. The results also suggest that the large effect of X chromosome on hybrid male sterility is not due to higher divergence of X chromosome than autosomes.

Two-dimensional protein electrophoretic analysis of postponed aging in Drosophila

Five populations of Drosophila melanogaster that had been selected for postponed aging were compared with five control populations using two-dimensional protein gel electrophoresis. The goals of the study were to identify specific proteins associated with postponed aging and to survey the population genetics of the response to selection. A total of 321 proteins were resolvable per population; these proteins were scored according to their intensity. The resulting data were analyzed using resampling, combinatoric, and maximum parsimony methods. The analysis indicated that the populations with postponed aging were different from their controls with respect to specific proteins and with respect to the variation between populations. The populations selected for postponed aging were more heterogeneous between populations than were the control populations. Maximum parsimony trees separate the selected populations, as a group, from their controls, thereby exhibiting a homoplastic pattern.

Molecular evolution and phylogeny of the Drosophila virilis species group as inferred by two-dimensional electrophoresis

Systematic relationship among the 12 species of the Drosophila virilis species group, and Drosophila robusta, were investigated by the use of two-dimensional electrophoresis (2-DE). A total of 389 protein characters (about 200 loci) were scored and analyzed both phylogenetically and phenetically. The resulting phylogeny was found to be largely concordant with the current views of evolution among these species based on other independent morphological, chromosomal, electrophoretic, and immunological data sets, although some notable differences were observed. The 2-DE data also appeared to be useful for constructing a molecular clock to date the absolute times of divergence among the species. It appears from this analysis that the evolution of the major clades within the species group occurred about 20 million years ago. Previous suggestions that the rate of molecular evolution was different between the virilis and montana phylads was not confirmed. The technique of 2-DE seems to be an excellent tool for reconstructing phylogenies and should be particularly valuable for examining relatively closely related species.

Genetic differentiation of Drosophila melanogaster populations as assessed by two-dimensional electrophoresis

Seven populations of Drosophila melanogaster, representing a worldwide distribution, were compared using two-dimensional protein gel electrophoresis. A total of 611 protein spots was scored, which probably represent a sample of over 500 loci that were surveyed. Of the protein spots scored, 521 spots were found to be invariant, but another 90 spots were found to be variable among the populations. Of these variable protein spots, 12 were found to be present in only one population. All the populations, except one, had at least one protein spot restricted to itself. However, the Japanese population had by far the most, with five protein spots restricted to this one population, which has been observed in previous studies of private alleles in oriental populations. The mean genetic similarity (F) found among the seven populations was 0.965, with a range of between 0.956 and 0.977. This is similar to previous reports of lower variation found in population genetic surveys using two-dimensional electrophoresis. It was found that the historical relationships among these populations was somewhat congruent with the geographic distribution of the populations, but as in previous studies, it was not exactly coincident.

Comparisons of genetic variability detected among mouse blood proteins using one- and two-dimensional electrophoreses

Comparisons of the sensitivities of one-dimensional (1D) and two-dimensional (2D) electrophoreses to detect genetic variability have generally shown that the 2D approach appears to be two- to five-fold less sensitive than conventional 1D approaches. Concerns about the validity of this conclusion have arisen because such comparisons have involved mainly enzymic proteins in 1D approaches versus a complex mixture of soluble proteins in most 2D analyses. Comparisons involving the absolute number of variants detected, using 1D and 2D sodium dodecyl sulfate (SDS)-polyacrylamide gel electrophoresis (PAGE), denatured mouse blood proteins isolated from C3HeB/FeJ and C57B1/6J inbred strains of mice, and highly sensitive silver staining, indicate that the latter uncovers at least as much variability as the former. Although the relative percentage of variable bands (1D SDS-PAGE) was greater than the relative percentage of variable spots (2D SDS-PAGE) when proteins of intact erythrocytes were surveyed, both techniques uncovered approximately equal percentages of variable proteins when the mouse erythrocyte proteins were partitioned into membrane and lysate components. Therefore, the simpler 1D SDS-PAGE was found to be as effective as 2D SDS-PAGE in detecting protein variability. Since 1D SDS-PAGE separates proteins primarily on the basis of molecular weight and to a lesser degree on other primary protein sequence alterations, much of the variability observed by 2D SDS-PAGE may be due to these same features and unit charge differences may not play a significant role in detecting variability in the proteins studied. This differs from enzymic proteins, where such charge differences appear to be responsible for much of the variability. This study also indicated that decreasing the number of proteins in samples (membranes and lysates vs whole erythrocytes) increased the ability of both of these techniques to resolve differences. Mating studies indicated that most of the differences detected with both techniques were inherited and were not artifacts.

Characterization of coccidial proteins by two-dimensional sodium dodecyl sulphate-polyacrylamide gel electrophoresis

Two dimensional sodium dodecyl sulphate-polyacrylamide gel electrophoresis (2D SDS-PAGE) has been used to produce 'fingerprint' maps of the proteins from each of the 7 species of Eimeria which infect the chicken. All 7 species could be identified from their array of polypeptides but few differences were detected between strains of the same species. Alterations to the polypeptide array associated with the stage of sporulation of the oocysts were observed. Iodination of sporozoites, 2D SDS-PAGE, autoradiography and immunoblotting techniques were combined to identify polypeptides with a surface moiety and those which were antigenic.

Is the polymorphism of protein amounts related to phenotypic variability? A comparison of two-dimensional electrophoresis data with morphological traits in maize

The hypothesis that the quantitative variations in gene product levels could be a more important basis for morphological and adaptative change than the classical qualitative variability revealed by electrophoretic techniques was studied by comparing five maize lines from three sets of variables: (i) qualitative variations of proteins (presence/absence) revealed by two-dimensional polyacrylamide gel electrophoresis (2D PAGE), at a physiological seedling stage; (ii) quantitative variations in proteins (spots more or less intense) revealed by 2D PAGE, at the same physiological stage; (iii) general combining abilities of fourteen heritable, morphological or agronomical characters measured at various juvenile and adult stages. Distances between lines were defined, based on qualitative and quantitative variations of proteins. These distances do not appear to be correlated and do not give the same patterns of divergence between lines, as shown by principal coordinate analyses. Mahalanobis distances computed from the general combining abilities of the morphological characters are significantly correlated (r=0.75) to quantitative but not to qualitative distances. The comparison of the first planes of the principal coordinate analyses performed on the three kinds of distances clearly confirms this finding. Our results are discussed in connection with the possible genetic meaning of the two molecular distances and with the hypothesis that regulatory processes are primarily implicated in morphological variation.

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.

Qualitative and quantitative variability in different classes of proteins: comparison of mouse and rat

Proteins of membranes and cytosols were extracted from the livers and brains of mice (inbred strain DBA/6J) and rats (inbred strain DA/Han) and separated by two-dimensional electrophoresis (2-DE). The 2-DE patterns were compared with regard to qualitative (spot position) and quantitative (spot intensity) characteristics of the proteins of these two species. The following results were obtained: Brain had more (higher percentage) conservative proteins (proteins found in both mice and rats) than liver; plasma membranes had more conservative proteins than the cytosols; organ-unspecific proteins contained more conservative proteins than relatively organ-specific proteins; the pattern of distribution of genetic variability among different classes of proteins represented by findings 1-3 was the same for the qualitative and quantitative characteristics of the proteins; and some observations indicated that quantitative variability occurred more frequently among proteins than did qualitative variability. Our conclusion is that regulatory sequences in the DNA (regulatory genes) are subjected to functional constraints that differ in strength among different classes of proteins by the same ratios as the constraints acting on the structural genes. The overall effect of the selective pressure is, however, less stringent for regulatory genes than for structural genes. The results obtained here by comparing two different species are very similar to previous results we obtained by studying different subspecies (inbred strains of the mouse). From this finding arises a new concept: the study of molecular evolution on the basis of different classes of proteins. Our results were compared with data from the literature that were obtained in part from studies on cultured cells. The comparison suggested that cultured cells have lost their tissue-specific proteins, and so generate predominantly extremely conservative proteins.

The 5S and 5.8S ribosomal RNA sequences of Tetrahymena thermophila and T. pyriformis

The nucleotide sequences of the 5S rRNAs of Tetrahymena thermophila and two strains of T. pyriformis have been determined to be identical. The 5.8S rRNA sequences have also been determined; these sequences correct several errors in an earlier report. The 5.8S rRNAs of the two species differ at a single position. The sequencing results indicate that the species are of recent common ancestry. Molecular evidence that has been interpreted in the past as suggestive of an ancient divergence has been reviewed and found to be consistent with a T. pyriformis complex radiation beginning approximately 30-40 million years ago.

Population distribution of the human vitamin D binding protein: anthropological considerations

The polymorphism of the serum vitamin D binding protein (DBP) in humans is based on the existence of three common alleles, Gc1F, Gc1S, and Gc2, and 84 rare alleles. The geographical distribution of Gc1F, Gc1S, and Gc2 alleles shows north to south clines, together with a balanced equilibrium between the Gc1F or Gc1S allele frequency and the Gc2 frequency. The distribution of the FST values shows high variability within a geographical area. For European and North Asiatic groups, the FST values are the lowest observed, and the reason may be a long process of homogenization. Aboriginal populations from Australia and New Guinea and groups from both North Africa and South America show the greatest heterogeneity of their allele frequencies. Systematic factors such as genetic drift and selection may account for this distribution. In contrast with the three main DBP alleles, the distribution of the rare alleles corresponds to patterns of human migrations that occurred during prehistoric and historic periods. Thus, the rare mutants are of particular relevance to anthropological and genetical investigations.

The polymorphism of the vitamin D-binding protein (Gc); isoelectric focusing in 3 M urea as additional method for identification of genetic variants

Since the last report numerous new DBP (Gc) variants have been observed; at present a total of 84 different mutants can be distinguished. Several of them have similar electrophoretic mobilities and/or isoelectric points of conventional isoelectric focusing (IEF). IEF in polyacrylamide gels in the presence of 3 M urea is a convenient and efficient method for the detection of hidden variation.

Genetic variation in proteins: comparison of one-dimensional and two-dimensional gel electrophoresis

Two proteins with known characteristics on one-dimensional gels were studied by two-dimensional electrophoresis to compare the sensitivities of the two methods in detecting genetic variation. Two-dimensional electrophoresis was found to be less sensitive than several types of one-dimensional gels in distinguishing variants of both proteins. Denaturation of proteins in urea in the two-dimensional method makes it possible to distinguish closely related proteins that differ from each other by units of charge. Many more types of variation in protein sequences can be distinguished on one-dimensional gels in the absence of denaturants. The estimates of heterozygosity based on two-dimensional gels are lower than those based on other methods, at least in part, because of the limited types of sequence differences that can be detected on two-dimensional gels. The application of two-dimensional electrophoresis to the measurement of genetic variation and to the detection of new mutations should be made carefully, in view of the limited sensitivity of the method in finding differences in sequence.

Molecular evolution, intracellular organization, and the quinary structure of proteins

High-resolution two-dimensional polyacrylamide gel electrophoresis shows that at least half of 370 denatured polypeptides from hamster cells and human cells are indistinguishable in terms of isoelectric points and molecular weights. Molecular evolution may have been more conservative for this set of proteins than sequence studies on soluble proteins have implied. This may be a consequence of complexities of intracellular organization and the numerous macromolecular interactions in which most polypeptides participate. It is suggested that the term "quinary structure" be used to refer to macromolecular interactions that are transient in vivo. Such interactions will not be evident from the composition of purified proteins, but they may constitute an important source of constraints on changes in primary structure.