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PubMed1980

Primary structures of dehydrogenases. Evolutionary characteristics related to functional aspects; models for isozyme developments and ancestral connections.

This chapter describes known characteristics of evolutionary changes in individual dehydrogenases, as well as possible relationships among this group of enzymes. Data from primary structures are correlated with those from other observations. Variations in the amino acid sequences demonstrate functional properties, and can be interpreted in relation to conformational aspects, subunit arrangements and enzyme stabilities. Different types of isozyme developments have occurred and show functional fixations at various levels. They define isozyme patterns of general significance in protein evolution. Sequence similarities may be found between different segments. They are analyzed in relation to known conformations, subunit sizes, species divergence and genetic mechanisms. A wide-ranging evolutionary model is discussed relating dehydrogenases and some other oligomeric enzymes to a distant, frequently remodelled ancestral building unit of repetitive occurrence.

Alcohol Oxidoreductases↗
PubMed1993

Bioamine receptors: evolutionary and functional variations of a structural leitmotiv.

Bioamines act as neurohormonal messengers through their binding to receptors which belong to the largest membrane protein family known so far: the seven spanning membrane receptors. This class of receptors transmits the effect of agonist binding to intracellular effectors by interacting with an intermediary G-protein. The diversity of receptor subtypes inside the protein family, observed in many animal species, is the result of a long evolutionary process. The tendency to protein diversification depends upon gene duplications and upon the continuous accumulation of mutations. The maintenance of vital functions in organisms, however, strictly requires enough structural conservation to ensure the functionality of the corresponding proteins. Both forces cooperate to ensure the adaptation of organisms to a changing environment. We have reviewed here the main conformational and functional constraints exerted on the structure of the bioamine receptors. They are mainly the transmembrane conformation of the receptors, their ability to bind ligands, to interact with G-proteins and to desensitize. The molecular basis of the biochemical and pharmacological differences used to classify the members of the receptor family have also been examined. Interestingly, this classification is very close to that obtained by the molecular phylogeny methods, used to elucidate the evolutionary relationships between bioamine receptors. However, this latter classification allows to accurately distinguish between different receptor subtypes (paralogous genes) and species homologous (orthologous genes). In addition, the calculation of phylogenetical distances reveals two main periods of diversification: the first one occurred before the separation of arthropods from vertebrates, in the Precambrian, and corresponds to the appearance of the main subtypes of the bioamine receptors. The second one, which occurred about 400 million years ago, might accompany the cephalization of the CNS in vertebrates.

Animals↗
PubMed1986

Methodological problems in evolutionary biology. VII. The species plague.

Various philosophers and evolutionary biologists have recently defended the thesis that species are individuals rather than sets. A decade of debates, however, did not suffice to settle the matter. Conceptual analysis shows that many of the key terms involved ("individuation", "evolutionary species", "spatiotemporal restrictedness", "individual") are ambiguous. Current disagreements should dissolve once this is recognized. Explication of the concepts involved leads to new programs for philosophical research. It could also help biology by showing how extant controversies concerning evolution may have conceptual rather than factual roots.

Animals↗
PubMed1992

Evolutionary dynamics of transposable elements in prokaryotes and eukaryotes.

This paper summarizes some recent theories about the evolution of transposable genetic elements in outbreeding, sexual eukaryotic organisms. The evolutionary possibilities available to self-replicating transposable elements are shown to vary depending on the reproductive biology of the host genome. This effect can be used to explain, in part, the differences in abundance of transposable elements between prokaryotes and eukaryotes. It is argued that the pattern of sexual outbreeding seen in mammals and plants is especially favorable to the spread of transposons. Moreover, because transposon spread is facilitated by zygote formation, the evolutionary origin of sexual conjugation may have been due to selection on transposon-encoded genes. Finally, evidence is also presented that introns could have originated as transposable genetic elements.

Biological Evolution↗
PubMed1994

Estimation of evolutionary distances between nucleotide sequences.

A formal mathematical analysis of the substitution process in nucleotide sequence evolution was done in terms of the Markov process. By using matrix algebra theory, the theoretical foundation of Barry and Hartigan's (Stat. Sci. 2:191-210, 1987) and Lanave et al.'s (J. Mol. Evol. 20:86-93, 1984) methods was provided. Extensive computer simulation was used to compare the accuracy and effectiveness of various methods for estimating the evolutionary distance between two nucleotide sequences. It was shown that the multiparameter methods of Lanave et al.'s (J. Mol. Evol. 20:86-93, 1984), Gojobori et al.'s (J. Mol. Evol. 18:414-422, 1982), and Barry and Hartigan's (Stat. Sci. 2:191-210, 1987) are preferable to others for the purpose of phylogenetic analysis when the sequences are long. However, when sequences are short and the evolutionary distance is large, Tajima and Nei's (Mol. Biol. Evol. 1:269-285, 1984) method is superior to others.

Base Sequence↗
PubMed1992

Evolutionary origin of a Kunitz-type trypsin inhibitor domain inserted in the amyloid beta precursor protein of Alzheimer's disease.

The Kunitz-type protease inhibitor is one of the serine protease inhibitors. It is found in blood, saliva, and all tissues in mammals. Recently, a Kunitz-type sequence was found in the protein sequence of the amyloid beta precursor protein (beta APP). It is known that beta APP accumulates in the neuritic plaques and cerebrovascular deposits of patients with Alzheimer's disease. Collagen type VI in chicken also has an insertion of a Kunitz-type sequence. To elucidate the evolutionary origin of these insertion sequences, we constructed a phylogenetic tree by use of all the available sequences of Kunitz-type inhibitors. The tree shows that the ancestral gene of the Kunitz-type inhibitor appeared about 500 million years ago. Thereafter, this gene duplicated itself many times, and some of the duplicates were inserted into other protein-coding genes. During this process, the Kunitz-type sequence in the present beta APP gene diverged from its ancestral gene about 270 million years ago and was inserted into the gene soon after duplication. Although the function of the insertion sequences is unknown, our molecular evolutionary analysis shows that these insertion sequences in beta APP have an evolutionarily close relationship with the inter-alpha-trypsin inhibitor or trypstatin, which inhibits the activity of tryptase, a novel membrane-bound serine protease in human T4+ lymphocytes.

Alzheimer Disease↗
PubMed1992

Early evolutionary relationships among known life forms inferred from elongation factor EF-2/EF-G sequences: phylogenetic coherence and structure of the archaeal domain.

Phylogenies were inferred from both the gene and the protein sequences of the translational elongation factor termed EF-2 (for Archaea and Eukarya) and EF-G (for Bacteria). All treeing methods used (distance-matrix, maximum likelihood, and parsimony), including evolutionary parsimony, support the archaeal tree and disprove the "eocyte tree" (i.e., the polyphyly and paraphyly of the Archaea). Distance-matrix trees derived from both the amino acid and the DNA sequence alignments (first and second codon positions) showed the Archaea to be a monophyletic-holophyletic grouping whose deepest bifurcation divides a Sulfolobus branch from a branch comprising Methanococcus, Halobacterium, and Thermoplasma. Bootstrapped distance-matrix treeing confirmed the monophyly-holophyly of Archaea in 100% of the samples and supported the bifurcation of Archaea into a Sulfolobus branch and a methanogen-halophile branch in 97% of the samples. Similar phylogenies were inferred by maximum likelihood and by maximum (protein and DNA) parsimony. DNA parsimony trees essentially identical to those inferred from first and second codon positions were derived from alternative DNA data sets comprising either the first or the second position of each codon. Bootstrapped DNA parsimony supported the monophyly-holophyly of Archaea in 100% of the bootstrap samples and confirmed the division of Archaea into a Sulfolobus branch and a methanogen-halophile branch in 93% of the bootstrap samples. Distance-matrix and maximum likelihood treeing under the constraint that branch lengths must be consistent with a molecular clock placed the root of the universal tree between the Bacteria and the bifurcation of Archaea and Eukarya. The results support the division of Archaea into the kingdoms Crenarchaeota (corresponding to the Sulfolobus branch and Euryarchaeota). This division was not confirmed by evolutionary parsimony, which identified Halobacterium rather than Sulfolobus as the deepest offspring within the Archaea.

Amino Acid Sequence↗
PubMed1995

Different evolutionary histories of kringle and protease domains in serine proteases: a typical example of domain evolution.

With the aim of elucidating the evolutionary processes of the kringle and protease domains in serine proteases which are involved with the system of blood coagulation and fibrinolysis, we constructed phylogenetic trees for the kringle and protease domains, separately, by use of amino acid sequence data. The phylogenetic trees constructed clearly showed that the topologies were different between the kringle and protease domains. Because both domains are coded by single peptides of serine proteases, this strongly suggests that the kringle and protease domains must have undergone different evolutionary processes. Thus, these observations imply that serine proteases evolve in a way such that each domain is a unit of evolution, exemplifying a typical mode of domain evolution. A possible relationship between the domain evolution and the exon shuffling theory is also discussed from the viewpoint of gene evolution.

Amino Acid Sequence↗
PubMed1994

Evolutionary implications of the family of 14-3-3 brain protein homologs in Arabidopsis thaliana.

The GF14 family of proteins in Arabidopsis thaliana consists of a homologous group of polypeptides ranging in size from approximately 27 kDa to approximately 32 kDa. As a group, GF14 proteins are also homologous to a family of mammalian proteins most commonly referred to as 14-3-3 proteins. Several distinct and different biochemical activities have been historically attributed to the various isoforms of the mammalian 14-3-3 proteins. These data present the possibility that the various activities are performed by functionally distinct lineages of the gene family. Here we present phylogenetic analyses based on the derived amino acid sequences of five GF14 isoforms expressed in Arabidopsis suspension-cultured cells. A high degree of sequence integrity is apparent in the various Arabidopsis isoforms, and the overall structures of the plant forms are quite conserved with regard to the structures of the known mammalian forms. These gene phylogenies indicate no evolutionary conservation of specific isoform lineages within both plants and animals. Rather, the evolutionary history of this protein appears to be characterized by a separate radiation of plant and animal forms from a common ancestral sequence. Even though the plant and animal forms have evolved independently since that ancestral split, large domains are conserved in both major lineages.

14-3-3 Proteins↗
PubMed1991

The dynamical attainability of ESS in evolutionary games.

In this paper, the attainability of ESS of the evolutionary game among n players under the frequency-independent selection is studied by means of a mathematical model describing the dynamical development and a concept of stability (strongly determined stability). It is assumed that natural selection and small mutations cause the phenotype to change gradually in the direction of fitness increasing. It is shown that (1) the ESS solution is not always evolutionarily attainable in the evolutionary dynamics, (2) in the game where the interaction between two species is completely competitive, the Nash solution is always attainable, and (3) one of two species may attain the state of minimum fitness as a result of evolution. The attainability of ESS is also examined in two game models on the sex ratio of wasps and aphids in light of our criterion of the attainability of ESS.

Animals↗
PubMed1992

Phylogenetic analysis of the thiolase family. Implications for the evolutionary origin of peroxisomes.

The thiolase family is a widespread group of proteins present in prokaryotes and three cellular compartments of eukaryotes. This fact makes this family interesting in order to study the evolutionary process of eukaryotes. Using the sequence of peroxisomal thiolase from Saccharomyces cerevisiae recently obtained by us and the other known thiolase sequences, a phylogenetic analysis has been carried out. It shows that all these proteins derived from a primitive enzyme, present in the common ancestor of eubacteria and eukaryotes, which evolved into different specialized thiolases confined to various cell compartments. The evolutionary tree obtained is compatible with the endosymbiotic theory for the origin of peroxisomes.

Acetyl-CoA C-Acetyltransferase↗
PubMed1992

Evolutionary relationships among the primate Mhc-DQA1 and DQA2 alleles.

The variation of the Mhc-DQA1 and DQA2 loci of ten different primate species (hominoids and Old World monkeys) was studied in order to obtain an insight in the processes that generate polymorphism of major histocompatibility complex (Mhc) class II genes and to establish the evolutionary relationships of their alleles. To that end nucleotide sequences of 36 Mhc class II DQA1 and seven DQA2 second exons were determined and phylogenetic trees that illustrate their evolutionary relationships were constructed. We demonstrate the existence of four primate Mhc-DQA1 allele lineages, two of which probably existed before the separation of the ancestors of the hominoids and Old World monkeys (approximately 22-28 million years ago). Mhc-DQA2 sequences were found only in the hominoid species and showed little diversity. We found no evidence for a major contribution of recombinational events to the generation of allelic diversity of the primate Mhc-DQA1 locus. Instead, our data suggest that the primate Mhc-DQA1 and DQA2 loci are relatively stable entities that mutated primarily as a result of point mutations.

Alleles↗
PubMed1984

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 E0 mutation, too, is apparently ancient because it occurs in different branches of the evolutionary tree.

Animals↗
PubMed1985

Handicapped individua in evolutionary processes.

Usually, when considering an evolutionary development, the fittest individua and their successful mutations receive most attention. The less fit ones, existing due to selection-mutation equilibria, are regarded, as an inevitable waste. It appears that these handicapped individua play an important role in evolution, as they make escapes from evolutionary traps possible. It is concluded that crucial improvements come from mutations of mutants. The implications seem to account to some extent for the observed speed and mode of evolution. An appropriate stochastic model is introduced, numerical experiments reported and results discussed.

Biological Evolution↗
PubMed1985

Evolutionary conservation of fragile sites induced by 5-azacytidine and 5-azadeoxycytidine in man, gorilla, and chimpanzee.

Lymphocyte cultures from man, gorilla, and chimpanzee were treated with 5-azacytidine and 5-azadeoxycytidine. These cytidine analogues induce common fragile sites in the chromosome bands 1q42 and 19q13 of man. A rare fragile site is induced by 5-azadeoxycytidine in the band 1q24. The optimum conditions required for inducing these new fragile sites were determined by a series of experiments. The common fragile site in human chromosome 1q42 also exists in the gorilla and chimpanzee in the homologous band 1p32. The fragile site in human chromosome 19q13 was demonstrated in the gorilla in the homologous chromosome band 20q13. These are the first examples found of evolutionary highly conserved fragile sites in homologous chromosome bands in related primate species. The interaction between 5-azacytidine, 5-azadeoxycytidine, and chromosomal DNA; the evolutionary conservation of genes located within or closely adjacent to the fragile sites in the chromosome 1 of Hominoidea; and the phylogenetic origin of the two new common fragile sites are discussed.

Animals↗
PubMed1985

Evolutionary implications of features of aromatic amino acid biosynthesis in the genus Acinetobacter.

Key enzymes of aromatic amino acid biosynthesis were examined in the genus Acinetobacter. Members of this genus belong to a suprafamilial assemblage of Gram-negative bacteria (denoted Superfamily B) for which a phylogenetic tree based upon oligonucleotide cataloging of 16S rRNA exists. Since the Acinetobacter lineage diverged at an early evolutionary time from other lineages within Superfamily B, an examination of aromatic biosynthesis in members of this genus has supplied important clues for the deduction of major evolutionary events leading to the contemporary aromatic pathways that now exist within Superfamily B. Together with Escherichia coli, Pseudomonas aeruginosa and Xanthomonas campestris, four well-spaced lineages have now been studied in comprehensive detail with respect to comparative enzymological features of aromatic amino acid biosynthesis. A. calcoaceticus and A. lwoffii both possess two chorismate mutase isozymes: one a monofunctional isozyme (chorismate mutase-F), and the other (chorismate mutase-P) a component of a bifunctional P-protein (chorismate mutase-prephenate dehydratase). While both P-protein activities were feedback inhibited by L-phenylalanine, the chorismate mutase-P activity was additionally inhibited by prephenate. Likewise, chorismate mutase-F was product inhibited by prephenate. Two isozymes of 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase were detected. The major isozyme (greater than 95%) was sensitive to feedback inhibition by L-tyrosine, whereas the minor isozyme was apparently insensitive to allosteric control. Prephenate dehydrogenase and arogenate dehydrogenase activities were both detected, but could not be chromatographically resolved. Available evidence favors the existence of a single dehydrogenase enzyme, exhibiting substrate ambiguity for prephenate and L-arogenate.(ABSTRACT TRUNCATED AT 250 WORDS)

Acinetobacter↗
PubMed1976

Evolutionary oscillation in prebiology: igneous activity and the origins of life.

The processes of chemical evolution are responsible for the origin of life. Three such processes have special importance: oscillation, creation, and competition. An oscillation from one kind of environment to another provides a mechanism for instituting processes that can only take place under conditions far removed from equilibrium. Oscillating evolutionary processes are likely to have played an important part in the origin of life. It is a mistake to assume that life originated in any one environment. It did not arrive in a moment of time. It was the result of a long period of chemical evolution during which it passed through a variety of environments. Biopoesis took place in an environment in which a variety of different kinds of protolife were assembled and concentrated. One essential form of protolife involved in these processes is the protocell. The experiments of Fox suggest that the creation of protocells involves violent oscillations of temperature and hydration. Igneous activity is especially characterised by oscillating conditions. Volcanic eruptions consist of violent changes from one extreme condition to another. Temperatures, pressure, phase, concentration and hydration all oscillate violently, and are subject to shock pulses of many kinds. Protolife may well have passed through extremes of environment for wider that those that life itself can sustain. The most probable environment for the assembly of the various forms of protolife would be on mudbanks forming either at the mouth of streams draining regions of active vulcanicity, or round the edge of hot volclanic pools. In this situation one could fins concentrated not only the various stands of protolife necessary for the final act of biopoesis, but also perbiologically formed nutrients necessary as for the first eobionts. As soon as the first protocells start to grow, they start to compete with each other, and so initiate a new additional evolutionary process, that of natural selection. Only after such competition has been initiated is life itself likely to be established"20

Biological Evolution↗