Mammalian hexokinase 1: Evolutionary conservation and structure to function analysis

We have amplified and sequenced the complete coding region of bovine hexokinase isoenzyme 1 (HK1) from brain RNA with PCR primers selected for sequence conservation. The sequence information was analyzed to evaluate the evolutionary and structure-function relationships among the mammalian and yeast HK isoenzymes. Structure to function analysis identified an unduplicated, invariant N-terminal domain involved in HK1 outer mitochondrial membrane targeting, as well as putative carbohydrate and nucleotide-binding sites in the regulatory and catalytic halves of HK1 essential to enzyme function. The ATP-binding site in the catalytic half of the HK1 protein resembles nucleotide-binding regions from protein kinases, with the single amino acid replacement (lysine to glutamate) in the ATP-binding site of the amino half explaining the loss of HK1 catalytic function in the regulatory domain. Sequence comparisons suggest that the 50-kDa mammalian and yeast glucokinases arose separately in evolution. In addition to providing valuable phylogenetic and structure-function insights, this work provides an efficient strategy for rapid cloning and sequencing of the coding regions for other HKs and related proteins.     

Evolutionary conservation of the linkage between the structural loci for serum albumin and vitamin D binding protein (Gc) in cattle

Summary. Evidence is presented for close genetic linkage between the structural loci for serum albumin and the vitamin D binding protein (Gc) in Belgian Blue and White cattle. Five recombinants were observed in a total of 342 informative offspring. The recombination frequency between the two loci was estimated as 1.5%± 0.9. The observed distribution of the haplotypes deviated from the expected one in the population, probably due to selection and significant linkage disequilibrium.     

Evolutionary conservation of the linkage between the structural loci for serum albumin and vitamin D binding protein (Gc) in cattle

Evidence is presented for close genetic linkage between the structural loci for serum albumin and the vitamin D binding protein (Gc) in Belgian Blue and White cattle. Five recombinants were observed in a total of 342 informative offspring. The recombination frequency between the two loci was estimated as 1.5% +/- 0.9. The observed distribution of the haplotypes deviated from the expected one in the population, probably due to selection and significant linkage disequilibrium.     

Evolutionary conservation of linkage groups: Additional evidence from murid and cricetid rodents

In Mus musculus, family Muridae, the glucosephosphate isomerase (Gpi-1), pink-eyed dilution (p), albinism (c), and -type globin (Hbb) loci are known to be linked in the order Gpi-1-p-c-Hbb. In Rattus norvegicus, another murid rodent, the p, c, and Hbb loci are known to be linked in the same order and with similar recombination frequencies. In Peromyscus maniculatus, family Cricetidae, it was previously known that p and c are linked and by analogy to Mus musculus that linkage group should be bounded by Gpi-1 near p and by a -globin locus near c. Linkage has now been established between Gpi-1 and the Hbe globin locus in Peromyscus. However, the observed recombination frequency in Peromyscus (16.3%) is significantly lower than in Mus, suggesting that perhaps a chromosomal inversion has occurred during the evolutionary divergence of the two rodent families. Linkage relationships were also tested between the Hbc ¹, Hbd ¹, and Hbe ¹ globin variants. Hbc ¹ (presumably an -type globin) segregated independently from Hbd ¹ and Hbe ¹ (presumably -type globins). No recombination was observed between Hbd ¹ and Hbe ¹. Those two globin genes may be alleles at a single locus, although circumstantial evidence suggests that they represent tightly linked duplicate loci.This work was supported by NSF DEB7716104 and by the Committee on Research, UCR.     

Mammalian cytogenetics and conservation of species

The proposition is examined that cytogenetic studies are needed in the conservation of wild captive animals. Several cases of polymorphic species have hybridized to produce infertile offspring. In several gazelle species, this accidental hybridization among look-alike animals has led to the extinction of zoo populations. The suggestion that this is always the result of inbreeding is thus erroneous. Cytogenetic study is also needed in animals that are destined for reintroduction, as accidental release of chromosomally different species is counterproductive to the reestablishment of wild stock. Several examples of mammalian species that have flourished from an extremely small founder stock are here examined to draw attention to the possibility that "inbreeding" is not invariably disadvantageous. The karyotypes of two hybridizing Kobus species with divergent chromosomal numbers are described.     

Evolutionary conservation of domain-domain interactions

Background

Recently, there has been much interest in relating domain-domain interactions (DDIs) to protein-protein interactions (PPIs) and vice versa, in an attempt to understand the molecular basis of PPIs.

Results

Here we map structurally derived DDIs onto the cellular PPI networks of different organisms and demonstrate that there is a catalog of domain pairs that is used to mediate various interactions in the cell. We show that these DDIs occur frequently in protein complexes and that homotypic interactions (of a domain with itself) are abundant. A comparison of the repertoires of DDIs in the networks of Escherichia coli, Saccharomyces cerevisiae, Caenorhabditis elegans, Drosophila melanogaster, and Homo sapiens shows that many DDIs are evolutionarily conserved.

Conclusion

Our results indicate that different organisms use the same 'building blocks' for PPIs, suggesting that the functionality of many domain pairs in mediating protein interactions is maintained in evolution.     

Evolutionary dynamics of self-incompatibility alleles in Brassica

Self-incompatibility in Brassica entails the rejection of pollen grains that express specificities held in common with the seed parent. In Brassica, pollen specificity is encoded at the multipartite S-locus, a complex region comprising many expressed genes. A number of species within the Brassicaceae express sporophytic self-incompatibility, under which individual pollen grains bear specificities determined by one or both S-haplotypes of the pollen parent. Classical genetic and nucleotide-level analyses of the S-locus have revealed a dichotomy in sequence and function among S-haplotypes; in particular, all class I haplotypes show dominance over all class II haplotypes in determination of pollen specificity. Analysis of an evolutionary model that explicitly incorporates features of the Brassica system, including the class dichotomy, indicates that class II haplotypes may invade populations at lower rates and decline to extinction at higher rates than class I haplotypes. This analysis suggests convergence to an evolutionarily persistent state characterized by the maintenance in high frequency of a single class II haplotype together with many class I haplotypes, each in low frequency. This expectation appears to be consistent with empirical observations of high frequencies of relatively few distinct recessive haplotypes.     

Evolutionary conservation of domain-domain interactions

Background  

Recently, there has been much interest in relating domain-domain interactions (DDIs) to protein-protein interactions (PPIs) and vice versa, in an attempt to understand the molecular basis of PPIs.     

Evolutionary conservation of microtubule-capture mechanisms

The dynamic nature of microtubules allows them to search the three-dimensional space of the cell. But what are they looking for? During cellular morphogenesis, microtubules are captured at sites just under the plasma membrane, and this polarizes the microtubule array and associated organelles. Recent data indicate that the signalling pathways that are involved in regulating the different microtubule cortical interactions are not only conserved between species, but also that they function in diverse processes.     

Functional Divergence and Evolutionary Turnover in Mammalian Phosphoproteomes

Protein phosphorylation is a key mechanism to regulate protein functions. However, the contribution of this protein modification to species divergence is still largely unknown. Here, we studied the evolution of mammalian phosphoregulation by comparing the human and mouse phosphoproteomes. We found that 84% of the positions that are phosphorylated in one species or the other are conserved at the residue level. Twenty percent of these conserved sites are phosphorylated in both species. This proportion is 2.5 times more than expected by chance alone, suggesting that purifying selection is preserving phosphoregulation. However, we show that the majority of the sites that are conserved at the residue level are differentially phosphorylated between species. These sites likely result from false-negative identifications due to incomplete experimental coverage, false-positive identifications and non-functional sites. In addition, our results suggest that at least 5% of them are likely to be true differentially phosphorylated sites and may thus contribute to the divergence in phosphorylation networks between mouse and humans and this, despite residue conservation between orthologous proteins. We also showed that evolutionary turnover of phosphosites at adjacent positions (in a distance range of up to 40 amino acids) in human or mouse leads to an over estimation of the divergence in phosphoregulation between these two species. These sites tend to be phosphorylated by the same kinases, supporting the hypothesis that they are functionally redundant. Our results support the hypothesis that the evolutionary turnover of phosphorylation sites contributes to the divergence in phosphorylation profiles while preserving phosphoregulation. Overall, our study provides advanced analyses of mammalian phosphoproteomes and a framework for the study of their contribution to phenotypic evolution.     

Evolutionary Conservative and Species-Specific Antigenic Determinants of Mammalian Thyroglobulins

Evolutionary conservative and species-specific epitopes of thyroglobulins (Tg) from different mammalian species were studied using panel of 20 monoclonal antibodies (mAb) raised in our laboratory and recognizing 16 antigen determinants on human Tg molecule. Cross-reactivity of mAb with preparations of purified mammalian Tg from other species was studied by the method of indirect enzyme-linked immunosorbent assay (ELISA). Interaction of mAb with Tg in histological sections of thyroid gland tissue was studied by direct immunofluorescence assay using mAb conjugated with fluorescein isothiocyanate (FITC). Since certain Tg epitopes lose their ability to bind mAb after fixation and paraffin embedding, only 12 out of 20 mAb turned out to be suitable for detection of Tg in the tissue sections. The obtained data have allowed establishing that four human Tg epitopes are species-specific. Meanwhile, six human Tg epitopes are shared with bovine Tg epitopes, seven epitopes with porcine Tg, four with rat, and two with mouse Tg. Each Tg of two species (cat and dog) has three common epitopes with human Tg.     

长江流域的生物多样性及其与经济协调发展的对策

长江流域的生物多样性及其与经济协调发展的对策陈家宽李博（武汉大学生命科学学院,武汉４３００７２）吴千红（复旦大学生命科学学院,上海２００４３３）众所周知,生物多样性（ｂｉｏｄｉｖｅｒｓｉｔｙ）是当代国际社会日益关注的重大问题之一。生物多样性是人类赖以...     

Evolutionary ecology and the conservation of biodiversity

Studies on evolving interactions among species and the coevolutionary process have suggested that the conservation of biodiversity requires a broad geographic perspective, if the `interaction biodiversity' of the earth is to be conserved with its species diversity. Continued maintenance of the geographic mosaic of specialization, defense and population structure appears to be crucial to the coevolutionary process and the long-term persistence of some interspecific interactions.     

Evolutionary conservation of the folding nucleus

Here, we present statistical analysis of conservation profiles in families of homologous sequences for nine proteins whose folding nucleus was determined by protein engineering methods. We show that in all but one protein (AcP) folding nucleus residues are significantly more conserved than the rest of the protein. Two aspects of our study are especially important: (i) grouping of amino acid residues into classes according to their physical-chemical properties and (ii) proper normalization of amino acid probabilities that reflects the fact that evolutionary pressure to conserve some amino acid types may itself affect concentration of various amino acid types in protein families. Neglect of any of those two factors may make physical and biological "signals" from conservation profiles disappear.     

Evolutionary conservation of protein vibrational dynamics

The aim of the present work is to study the evolutionary divergence of vibrational protein dynamics. To this end, we used the Gaussian Network Model to perform a systematic analysis of normal mode conservation on a large dataset of proteins classified into homologous sets of family pairs and superfamily pairs. We found that the lowest most collective normal modes are the most conserved ones. More precisely, there is, on average, a linear correlation between normal mode conservation and mode collectivity. These results imply that the previously observed conservation of backbone flexibility (B-factor) profiles is due to the conservation of the most collective modes, which contribute the most to such profiles. We discuss the possible roles of normal mode robustness and natural selection in the determination of the observed behavior. Finally, we draw some practical implications for dynamics-based protein alignment and classification and discuss possible caveats of the present approach.     

Noncytopathic replication of Venezuelan equine encephalitis virus and eastern equine encephalitis virus replicons in Mammalian cells

Venezuelan equine encephalitis (VEE) and eastern equine encephalitis (EEE) viruses are important, naturally emerging zoonotic viruses. They are significant human and equine pathogens which still pose a serious public health threat. Both VEE and EEE cause chronic infection in mosquitoes and persistent or chronic infection in mosquito-derived cell lines. In contrast, vertebrate hosts infected with either virus develop an acute infection with high-titer viremia and encephalitis, followed by host death or virus clearance by the immune system. Accordingly, EEE and VEE infection in vertebrate cell lines is highly cytopathic. To further understand the pathogenesis of alphaviruses on molecular and cellular levels, we designed EEE- and VEE-based replicons and investigated their replication and their ability to generate cytopathic effect (CPE) and to interfere with other viral infections. VEE and EEE replicons appeared to be less cytopathic than Sindbis virus-based constructs that we designed in our previous research and readily established persistent replication in BHK-21 cells. VEE replicons required additional mutations in the 5' untranslated region and nsP2 or nsP3 genes to further reduce cytopathicity and to become capable of persisting in cells with no defects in alpha/beta interferon production or signaling. The results indicated that alphaviruses strongly differ in virus-host cell interactions, and the ability to cause CPE in tissue culture does not necessarily correlate with pathogenesis and strongly depends on the sequence of viral nonstructural proteins.     

Three new HLA-G alleles and their linkage disequilibria with HLA-A

Three new allelic forms of the HLA-G DNA sequence (HLA-G*II, HLA-G*III, and HLA-G*IV) have been identified. With the HLA-G*I sequence (previously designated HLA 6.0) as a reference, HLA-G*II shows a silent (G A) mutation at the third base of codon 57, HLA-G*III bears a non-synonymous (A T), but conservative, (Thr Ser) substitution at the first base of codon 31, and HLA-G*IV shows two silent substitutions: (A T) at the third base of codon 107 and (G A) at the third base of codon 57. A rapid method of singling out each allele on genomic DNA has been developed by using polymerase chain reaction amplification followed by restriction endonuclease treatment. Also, more or less strong linkage disequilibria has been found between most HLA-A alleles and either HLA-G*I or *II, both being the most prevalent alleles in the population, with a genotypic frequency of 0.55 and 0.38, respectively; HLA-G*III is very rare and HLA-G*IV has a genotypic frequency of 0.07. An evolutive classification of HLA-A alleles results according to their association with either HLA-G*I or HLA-G*II, which does not correlate with the classical serological cross-reacting groups classification. The finding of a strong and selective A/G linkage disequilibria with most HLA-A alleles, together with the existence of less frequent random A/G associations, may suggest that there exist in different haplotypes true and varied A/G genetic distances (and not a recombinational hotspot). It may be inferred from preliminary data that in primates HLA-A/G haplotypes bearing G*II may have appeared later than those bearing G*I.The nucleotide sequence data reported in this paper have been submitted to the GenBank and EMBL nucleotide sequence databases and have been assigned the following accession numbers: EMBL-X60983 (HLA-G*II), GenBank-M99048 (HLA-G*III), and GenBank-L07784 (HLA-G*IV).The contribution to this paper by P. Morales and A. Corell is equal, and the order of authorship is arbitrary. Correspondence to: A. Arnaiz-Villena.