The genes coding for the cytoskeletal proteins actin and vimentin in warm-blooded vertebrates

Recombinant plasmids were made containing cDNAs synthesized on hamster mRNAs coding for cytoskeletal (beta- or gamma-) actins and for vimentin. Hybridization of the actin probe on restriction digests of one avian and five mammalian DNAs yielded multiple bands; the vimentin probe revealed only one band (accompanied by 2-3 faint bands in some DNAs). The results obtained with the vimentin probe indicate that the corresponding coding sequences: (a) are highly conserved in warm-blooded vertebrates like the actin sequences; (b) have strongly diverged from those coding for other intermediate filament proteins, since hybridization of the vimentin probe does not lead to a diagnostic multiband pattern; and (c) most likely contribute to single gene, in contrast to the sequences coding for other cytoskeletal proteins. Hybridization of the probes on mRNAs from the different sources used showed that the non-coding sequences of both vimentin and actin genes are conserved in length.     

Bendable genes of warm-blooded vertebrates.

It is shown that in the genomes of warm-blooded vertebrates the elevation of genic GC-content is associated with an increase in the bendability of the DNA helix, which is both absolute and relative as compared with random sequences. This trend takes place both in exons and introns, being more pronounced in the latter. At the same time, the free energy of melting (delta G) of exons and introns increases only absolutely with elevation of GC-content, whereas it decreases as compared with random sequences (again, this trend is stronger in the introns). In genes of cold-blooded animals, plants, and unicellular organisms, these regularities are weaker and often not consistent. Generally, there is a negative correlation between bendability and melting energy at any fixed GC-content value. This effect is stronger in the introns. These findings suggest that GC-enrichment of genes in the homeotherm vertebrates can be caused by selection for increased bendability of DNA.     

The compositional transition between the genomes of cold- and warm-blooded vertebrates: codon frequencies in orthologous genes

The genomes of the ancestors of mammals and birds underwent a compositional change in which the gene-richest regions increased their GC levels. Here we investigated this compositional transition by analyzing the levels of G and C in third codon positions, as well as the codon frequencies of orthologous genes from human, chicken and Xenopus. The results may be summed up as follows: (i) GC-poor genes, that did not undergo the compositional transition, showed only minor differences in orthologous sets from Xenopus, human and chicken; this is remarkable in view of the very many nucleotide substitutions that occurred over the long evolutionary times separating these species; (ii) GC-rich genes, that underwent the compositional transition, showed large differences between Xenopus and warm-blooded vertebrates, but not between chicken and human. In other words, the independent changes that occurred in avian and mammalian genes, on the average, were the same.     

Evolutionary relationships between rat and mouse chromosomes

Trypsin banded karyotypes of rat and mouse chromosomes were analyzed for banding pattern similarities. Apparently identical banding patterns were found, covering about 40% of the genome of each species. Predictions are made as to what gene loci are located on specific rat chromosomes. The problem of the relationship between the genetic content of a chromosome and its banding pattern is discussed.     

Evolutionary history of the Rh blood group-related genes in vertebrates

Rh and its homologous Rh50 gene products are considered to form heterotetramers on erythrocyte membranes. Rh protein has Rh blood group antigen sites, while Rh50 protein does not, and is more conserved than Rh protein. We previously determined both Rh and Rh50 gene cDNA coding regions from mouse and rat, and carried out phylogenetic analyses. In this study, we determined Rh50 gene cDNA coding regions from African clawed frog and Japanese medaka fish, and examined the long-term evolution of the Rh blood group and related genes. We constructed the phylogenetic tree from amino acid sequences. Rh50 genes of African clawed frog and Japanese medaka fish formed a cluster with mammalian Rh50 genes. The gene duplication time between Rh and Rh50 genes was estimated to be about 510 million years ago based on this tree. This period roughly corresponds to the Cambrian, before the divergence between jawless fish and jawed vertebrates. We also BLAST-searched an amino acid sequence database, and the Rh blood group and related genes were found to have homology with ammonium transporter genes of many organisms. Ammonium transporter genes can be classified into two major groups (amt alpha and amt beta). Both groups contain genes from three domains (bacteria, archaea, and eukaryota). The Rh blood group and related genes are separated from both amt alpha and beta groups.     

Evolutionary relationships of the carbamoylphosphate synthetase genes

Carbamoylphosphate is a common intermediate in the metabolic pathways leading to the biosynthesis of arginine and pyrimidines. The amino acid sequences of all available proteins that catalyze the formation of carbamoylphosphate were retrieved from Genbank and aligned to estimate their mutual phylogenetic relations. In gram-negative bacteria carbamoylphosphate is synthesized by a two-subunit enzyme with glutamiriase and carbamoylphosphate synthetase (CPS) activity, respectively. In gram-positive bacteria and lower eukaryotes this two-subunit CPS has become dedicated to arginine biosynthesis, while in higher eukaryotes the two subunits fused and subsequently lost the glutaminase activity. The CPS dedicated to pyrimidine synthesis is part of a multifunctional enzyme (CPS II), encoding in addition dihydroorotase and aspartate transcarbamoylase. Evidence is presented to strengthen the hypothesis that the two kinas subdomains of all CPS isozymes arose from a duplication of an ancestral gene in the progenote. A further duplication of the entire CPS gene occurred after the divergence of the plants and before the divergence of the fungi from the eukaryotec root, generating the two isoenzymes involved in either the synthesis of arginine or that of pyrimidines. The mutation rate was found to be five- to tenfold higher after the duplication than before, probably reflecting optimization of the enzymes for their newly acquired specialized function. We hypothesize that this duplication arose from a need for metabolic channeling for pyrimidine biosynthesis as it was accompanied by the tagging of the CPS gene with the genes for dihydroorotase and aspartate transcarbamoylase, and as the duplication occurred independently also in gram-positive bacteria. Analysis of the exon-intron organization of the two kinase subdomains in CPS I and II suggests that ancient exons may have comprised approx. 19 amino acids, in accordance with the prediction of the intron-early theory. Correspondence to: M.J.B. van den Hoff     

Evolutionary relationships between reptiles inferred from the comparison of their ITS2 sequences

The reptile phylogeny is poorly studied, and many existing hypotheses are controversial. In this study, the ITS2 regions of 43 species of lizards, snakes, turtles, and crocodiles were cloned and sequenced in addition to eight ITS2 sequences of amphibians, reptiles, and birds already present in the database. The ITS2 of reptiles, similarly to other vertebrates, contain short conserved (consensus) regions, alternating with variable regions (DI, DII, and DIII), which are potentially capable of forming stable secondary structures. These functionally neutral rDNA regions, separating the consensus regions, are substantially different in size, as well as in the primary and secondary structure. Sequences of the ITS2 variable regions were aligned using the GeneBee Molecular Biology Server software program with subsequent automated construction of prescribed trees. The trees for all three variable regions were highly similar, enabling certain conclusions on the evolutionary history of reptiles.     

Evolutionary relationships between the t and H-2 haplotypes in the house mouse

Thirty-three mouse strains carrying t haplotypes were typed with a large battery of monoclonal and polyclonal antibodies specific for class I and class II antigens controlled by the H-2 complex. Among these t haplotypes were representatives of the six complementation groups defined previously and of eight new groups defined by us recently. The typing resulted in the identification of the H-2 haplotypes of these strains and of their alleles at K, D, A, and E loci. Nineteen of the 33 strains proved to carry a mutation that prevents the expression of the E molecule on the cell surface. All H-2 haplotypes of the t strains are related in terms of sharing certain antigenic determinants, most of which have not, as yet, been found in inbred strains or in wild mice that do not carry t haplotypes. According to the degree of serological relatedness, the haplotypes can be arranged into a pedigree presumably reflecting the evolutionary history of the t chromosomes. The ancestral t chromosome from which the 33 chromosomes derive was presumably present in the mouse population before the divergence of the Mus musculus and Mus domesticus species. The E° mutation, too, is apparently ancient because it occurs in different branches of the evolutionary tree.     

Evolutionary dynamics of the immunoglobulin heavy chain variable region genes in vertebrates

Immunoglobulin heavy chains are polypeptides encoded by four genes: variable (IGHV), joining (IGHJ), diversity (IGHD), and constant (IGHC) region genes. The number of IGHV genes varies from species to species. To understand the evolution of the IGHV multigene family, we identified and analyzed the IGHV sequences from 16 vertebrate species. The results show that the numbers of functional and nonfunctional IGHV genes among different species are positively correlated. The number of IGHV genes is relatively stable in teleosts, but the intragenomic sequence variation is generally higher in teleosts than in tetrapods. The IGHV genes in tetrapods can be classified into three phylogenetic clans (I, II, and III). The clan III and/or II genes are relatively abundant, whereas clan I genes exist in small numbers or are absent in most species. The genomic organization of clan I, II, and III IGHV genes varies considerably among species, but the entire IGHV locus seems to be conserved in the subtelomeric or near-centromeric region of chromosome. The presence or absence of specific IGHV clan members and the lineage-specific expansion and contraction of IGHV genes indicate that the IGHV locus continues to evolve in a species-specific manner. Our results suggest that the evolution of IGHV multigene family is more complex than previously thought and that several factors may act synergistically for the development of antibody repertoire. Electronic supplementary materials The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Evolutionary transitions between mechanisms of sex determination in vertebrates

Sex in many organisms is a dichotomous phenotype--individuals are either male or female. The molecular pathways underlying sex determination are governed by the genetic contribution of parents to the zygote, the environment in which the zygote develops or interaction of the two, depending on the species. Systems in which multiple interacting influences or a continuously varying influence (such as temperature) determines a dichotomous outcome have at least one threshold. We show that when sex is viewed as a threshold trait, evolution in that threshold can permit novel transitions between genotypic and temperature-dependent sex determination (TSD) and remarkably, between male (XX/XY) and female (ZZ/ZW) heterogamety. Transitions are possible without substantive genotypic innovation of novel sex-determining mutations or transpositions, so that the master sex gene and sex chromosome pair can be retained in ZW-XY transitions. We also show that evolution in the threshold can explain all observed patterns in vertebrate TSD, when coupled with evolution in embryonic survivorship limits.     

Evolutionary dynamics of the ABCA chromosome 17q24 cluster genes in vertebrates

ABCA is a subfamily of ATP-binding-cassette (ABC) transporter genes. In this subfamily, it was found that five ABCA genes cluster in a head-to-tail pattern in the human and mouse genomes, but only one was found in fish. To understand better the evolution of this cluster of genes, we screened 11 vertebrate genome sequences and newly identified 28 ABCA cluster genes. Comparative genomic analysis reveals that the ABCA5 gene is relatively evolutionarily conserved. In contrast, the repertoires of the other ABCA genes in this cluster diverge tremendously among species, which is due mainly to postspeciation duplications. In addition, maximum likelihood analysis reveals that positive selection is acting on the paralogous genes ABCA6 and Abca8a, suggesting that these two genes have possibly acquired new functions after duplication. Because most eukaryotic ABC proteins integrate into the cytoplasmic membrane and transport a wide range of substrates across it, we conjecture that newly duplicated ABCA cluster genes are under diversifying selection for the ability to recognize a diverse array of substrates.     

Evolutionary conservation of expression profiles between human and mouse orthologous genes

Mouse models are often used to study human genes because it is believed that the expression and function are similar for the majority of orthologous genes between the two species. However, recent comparisons of microarray data from thousands of orthologous human and mouse genes suggested rapid evolution of gene expression profiles under minimal or no selective constraint. These findings appear to contradict non-array-based observations from many individual genes and imply the uselessness of mouse models for studying human genes. Because absolute levels of gene expression are not comparable between species when the data are generated by species-specific microarrays, use of relative mRNA abundance among tissues (RA) is preferred to that of absolute expression signals. We thus reanalyze human and mouse genome-wide gene expression data generated by oligonucleotide microarrays. We show that the mean correlation coefficient among expression profiles detected by different probe sets of the same gene is only 0.38 for humans and 0.28 for mice, indicating that current measures of expression divergence are flawed because the large estimation error (discrepancy in expression signal detected by different probe sets of the same gene) is mistakenly included in the between-species divergence. When this error is subtracted, 84% of human-mouse orthologous gene pairs show significantly lower expression divergence than that of random gene pairs. In contrast to a previous finding, but consistent with the common sense, expression profiles of orthologous tissues between species are more similar to each other than to those of nonorthologous tissues. Furthermore, the evolutionary rate of expression divergence and that of coding sequence divergence are found to be weakly, but significantly positively correlated, when RA and the Euclidean distance are used to measure expression-profile divergence. These results highlight the importance of proper consideration of various estimation errors in comparing the microarray data between species.     

Evolutionary origin of sex-related genes in the mouse brain

With the aim of elucidating the evolutionary process of sexual dimorphism in the brain at the molecular level, we conducted genomic comparisons of a set of genes expressed in a sexually different manner in the mouse brain with all genes from other species of eukaryotes. First, seventeen protein-coding genes whose levels of mRNA expression in the brain differed between male and female mice have been known according to the currently available microarray data, and we designated these genes operationally as "sex-related genes in the mouse brain". Next, we estimated the time when these sex-related genes in the mouse brain emerged in the evolutionary process of eukaryotes by examining the presence or absence of the orthologues in the 26 eukaryotic species whose genome sequences are available. As a result, we found that the ten sex-related genes in the mouse brain emerged after the divergence of urochordates and mammals whereas the other seven sex-related genes in the mouse brain emerged before the divergence of urochordates and mammals. In particular, five sex-related genes out of the ten genes in the mouse brain emerged just before the appearance of bony fish which have phenotypic sexual dimorphism in the brain. Interestingly, three of these five sex-related genes that emerged during this period were classified into the "protein binding" function category. Moreover, all of these three genes were expected to have the functions that are related to cell-cell communications in the brain according to the gene expression patterns and/or functional information of these genes. These findings suggest that the orthologues of the sex-related genes in the mouse brain that emerged just before the divergence of bony fish might have essential roles in the evolution of the sexual dimorphism in the brain forming protein-protein interactions.     

Evolutionary relationships of class II major-histocompatibility-complex genes in mammals

The major histocompatibility complex (MHC) class II molecule consists of noncovalently associated alpha and beta chains. In mammals studied so far, the class II MHC can be divided into a number of regions, each containing one or more alpha-chain genes (A genes) and beta-chain genes (B genes), and it has been known for some time that orthologous relationships exist between genes in corresponding regions from different mammalian species. A phylogenetic analysis of DNA sequences of class II A and B genes confirmed these relationships; but no such orthologous relationship was observed between the B genes of mammals and those of birds. Thus, the class II regions have diverged since the separation of birds and mammals (approximately 300 Mya) but before the radiation of the placental mammalian orders (60-80 Mya). Comparison of the phylogenetic trees for A and B genes revealed an unexpected characteristic of DP-region genes: DPB genes are most closely related to DQB genes, whereas DPA chain genes are most closely related to DRA-chain genes. Thus, the DP region seems to have originated through a recombinational event which brought together a DQB gene and a DRA gene (perhaps approximately 120 Mya). The 5' untranslated region of all class II genes includes sequences which are believed to be important in regulating class II gene expression but which are not conserved in known pseudogenes. These sequences are conserved to an extraordinary degree in the human DQB1 gene and its mouse homologue A beta 1, suggesting that regulation of expression of this locus may play a key role in expression of the entire class II MHC.     

ID sequences in the genes of three brain-specific proteins

We characterized the brain-specific gene coding for rat S-100 protein beta-subunit and found three "brain identifier (ID)" elements, which have been proposed to regulate the gene expression in rat brain. The nucleotide sequences of these elements corresponded well with that of the consensus ID element and were clearly different from those of "ID-like" elements in rat beta B1-crystallin gene, etc. ID elements were also observed in the flanking regions of rat neuron-specific enolase and cholecystokinin genes, which were expressed in the neuronal cells. Direct repeats were observed in the regions flanking ID elements.     

Molecular cloning of actin genes in Trichomonas vaginalis and phylogeny inferred from actin sequences

The parasitic protozoan Trichomonas vaginalis is known to contain the ubiquitous and highly conserved protein actin. A genomic library and a cDNA library have been screened to identify and clone the actin gene(s) of T. vaginalis. The nucleotide sequence of one gene and its flanking regions have been determined. The open reading frame encodes a protein of 376 amino acids. The sequence is not interrupted by any introns and the promoter could be represented by a 10 bp motif close to a consensus motif also found upstream of most sequenced T. vaginalis genes. The five different clones isolated from the cDNA library have similar sequences and encode three actin proteins differing only by one or two amino acids. A phylogenetic analysis of 31 actin sequences by distance matrix and parsimony methods, using centractin as outgroup, gives congruent trees with Parabasala branching above Diplomonadida.     

Evolutionary relationships of the classes of major histocompatibility complex genes

A number of hypotheses have been proposed to account for the evolutionary origin of the classes of major histocompatibility complex (MHC) genes of vertebrates. According to one hypothesis the class II MHC evolved first, whereas another hypothesis holds that the class I MHC originated first as a result of a recombination between an immunoglobulin-like C-domain and the peptide-binding domain of an HSP70 heat-shock protein. A phylogenetic tree of C-domains from MHC and related molecules supports a relationship between the class II MHC chain and ₂-microglobulin and between the class II MHC -chain and the class I chain. If this phylogeny is correct, the hypothesis that class I MHC evolved by recombination with HSP70 is less parsimonious than the hypothesis that class II evolved first. Furthermore, when MHC peptide-binding domains are simultaneously aligned with HSP70 domains and with V-domains from members of the immunoglobulin superfamily, they are slightly more similar to the latter than to the former; and the class II ₁ and ₁ domains show much greater similarity to each other than would be expected if they evolved from separate HSP70 domains. Thus, most evidence supports the hypothesis that the ancestral MHC molecule had a class II-like structure.     

Evolution conservatively of SCAR DNA localization in genome isochores of warm-blooded vertebrates

In meiotic prophase I, chromatin fibrils attached to the lateral elements of the synaptonemal complexes form loops. Synaptonemal complex associated regions of DNA (SCARs DNA) are a family of genomic DNA sequences tightly associated with the synaptonemal complex; they are located at the chromatin loop basements. Isochore compositional fractions of the human and chicken genomes were used as 32P labeled probes for hybridization with SCAR DNA isolated previously from the spermatocyte nuclei of the golden hamster Mesocricetus auratus. Nucleotide sequences similar to the golden hamster’s SCAR DNA were found in human and chicken genome isochores. The localization of SCAR DNA in isochore compartments of the examined genomes was established to be evolutionary conservative.