Somatostatin: aspects of molecular evolution.
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Amino Acid Sequence↗
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[The parameters of the molecular evolution of the 11S globulins of plants].
Nucleotide sequences of cloned cDNA coding for soybean storage protein glycinin and deduced amino acid sequences of basic polypeptides (subfamily II) of glycinin are compared with the amino acid sequences of 11S globulins from other plants. An average number of amino acid substitutions in various evolutionary branches is calculated. A proportional dependence is established between the average number of substitutions per site (the evolutionary distance) and the hypothetical term of divergence of corresponding taxa. The evolution rate of 11S globulins and a term of divergence of the two subfamilies of 11S globulin polypeptides in Fabaceae is estimated.
Amino Acid Sequence↗
[Primary structures of cytochrome P-450's and molecular evolution].
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Amino Acid Sequence↗
[Molecular evolution of proteins with RNA-binding domains].
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Amino Acid Sequence↗
The multiphosphorylation domain of the phosphorylase kinase alpha M and alpha L subunits is a hotspot of differential mRNA processing and of molecular evolution.
We have cloned and sequenced human cDNAs encoding the complete phosphorylase kinase alpha subunit muscle isoform (alpha M). The predicted polypeptide is highly similar to the sequence known from rabbit muscle but lacks a major part of its multiphosphorylation domain, including the main phosphorylation site for cAMP-dependent protein kinase (PKA). Analysis of this region by reverse-transcribed polymerase chain reaction (RT-PCR) in several human and rabbit tissues demonstrates that it is subject to elaborate differential mRNA splicing. Amino acids 1012-1024 of the full-length rabbit sequence, including the major PKA phosphorylation site, and amino acids 1025-1041, which harbor at least one endogenous phosphorylation site, can be deleted from the predicted polypeptide individually or in combination. Molecules lacking one or both of these segments constitute a major part of the alpha M subunit population in many rabbit tissues and constitute the vast majority in all human tissues analyzed. Similar, tissue-dependent differential splicing events could be detected by RT-PCR in the human alpha subunit isoform from liver (alpha L). The expression of the differentially spliced alpha M subtypes differs markedly between corresponding human and rabbit tissues. Sequence divergence in this region is particularly high, not only between the muscle and liver isoforms, but also between alpha M sequences from four different animal species. Moreover, a duplication of the exon encoding the main PKA phosphorylation site was discovered in the mouse. Thus, the multiphosphorylation domain of the phosphorylase kinase alpha subunit isoforms is subject to pronounced structural variation not only between different tissues of one organism via differential splicing, but also in the course of evolution.
Alternative Splicing↗
In vivo molecular evolution reveals biophysical origins of organismal fitness.
In nature, evolution occurs through the continuous adaptation of a population to its environment. At the molecular level, adaptive changes in protein sequence and expression impact organismal fitness and, consequently, dictate population dynamics. Here, we have used a "weak link" method to favor variations in one gene, allowing adaptation to thermostability to be studied in molecular detail as bacteria were grown continuously for approximately 1500 generations. Surprisingly, only six mutant alleles, representing less than 1% of the possible missense mutations, were observed, suggesting a highly constrained molecular landscape during protein evolution. The changes in organismal fitness were linked directly to incremental increases in enzyme stability and activity maxima and corresponded to the narrow temperature ranges where each mutant enjoyed success within the overall population. Thus, continuous evolution of a single gene permits a quantitative approach that extends from the phenotypes of the microbial populations to their underlying biophysical basis.
Adenylate Kinase↗
Temporal scaling of molecular evolution in primates and other mammals.
Molecular clocks are routinely tested for linearity using a relative rate test and routinely calibrated against the geological time scale using a single or average paleontologically determined time of divergence between living taxa. The relative rate test is a test of parallel rate equality, not a test of rate constancy. Temporal scaling provides a test of rates, where scaling coefficients of 1.0 (isochrony) represent stochastic rate constancy. The fossil record of primates and other mammals is now known in sufficient detail to provide several independent divergence times for major taxonomic groups. Molecular difference should scale negatively or isochronically (scaling coefficients less than 1.0) with divergence time: where two or more divergence times are available, molecular difference appears to scale positively (scaling coefficient greater than 1.0). A minimum of four divergence times are required for adequate statistical power in testing the linear model: scaling is significantly nonlinear and positive in six of 11 published investigations meeting this criterion. All groups studied show some slowdown in rates of molecular change over Cenozoic time. The break from constant or increasing rates during the Mesozoic to decreasing rates during the Cenozoic appears to coincide with extraordinary diversification of placental mammals at the beginning of this era. High rates of selectively neutral molecular change may be concentrated in such discrete events of evolutionary diversification.
Amino Acid Sequence↗
Cu,Zn superoxide dismutase from Trematomus bernacchii: functional conservation and erratic molecular evolution in Antarctic teleosts.
In the present study, we describe the purification and molecular characterization of Cu,Zn superoxide dismutase (SOD) from Trematomus bernacchii, a teleost widely distributed in many areas of Antarctica, that plays a pivotal role in the Antarctic food chain. The amino acid and cDNA sequences have been obtained using both biochemical and molecular biology approaches and are compared with Cu,Zn SODs from other fishes. Assessment of the primary sequences highlights that the catalytically important residues are fully conserved in Cu,Zn SOD from T. bernacchii. Phylogenetic analyses performed on Cu,Zn SOD amino acid sequences permit speculation regarding the evolution of this protein. In particular, the data confirms the erratic differentiation of these proteins and concurs with the theory of the "unclock-like" behaviour of Cu,Zn SOD evolution.
Amino Acid Sequence↗
Molecular evolution at subzero temperatures: mitochondrial and nuclear phylogenies of fishes from Antarctica (suborder Notothenioidei), and the evolution of antifreeze glycopeptides.
Most fishes of the perciform suborder Notothenioidei are endemic to the subzero marine waters of Antarctica. A number of remarkable physiological attributes allow them to inhabit this extreme environment; for example, the blood of almost all notothenioid species contains antifreeze glycopeptides. To establish a molecular phylogenetic hypothesis for these fishes, DNA sequences from two mitochondrial genes, portions of the 12S and 16S ribosomal genes (928 base pairs [bp]), were determined for 18 species. These belong to 15 genera in five families of the suborder. The DNA data suggest that two of these families are unnatural groups and consequently that the classification and phylogeny of this suborder is in need of revision. In terms of DNA variation, the Bovichtidae are a distantly related sister group to the other families of the suborder that includes the icefishes, the only vertebrates without hemoglobin. The fishes of the suborder (except the Bovichtidae) seem to have speciated rapidly, forming an adaptive radiation in the Antarctic waters. A phylogenetic analysis of published hemoglobin amino acid sequences for other notothenioid fishes supports these results from mtDNA. On the basis of molecular phylogeny, the evolution of antifreeze glycopeptides was studied. The age of the radiation of notothenioid fishes had been estimated to be at least 38 Mya. However, the level of mtDNA variation detected in notothenioid fishes appears to be too low to agree with this date of origin and might instead suggest a younger age (10-15 Mya). Alternatively, the low level of detected mtDNA variation would agree with the traditional old-age estimate if an extremely slow rate of mtDNA evolution is postulated for this group. This slow-rate hypothesis, if true, could be explained by decreased metabolic rates slowing down the tempo of molecular evolution.
Animals↗
Molecular evolution, adaptive radiation, and geographic diversification in the amphiatlantic family Rapateaceae: evidence from ndhF sequences and morphology.
Rapateaceae (16 genera, approximately 100 species) is largely restricted to the tepuis and sandplains of the Guayana Shield in northern South America, with Maschalocephalus endemic to West Africa. The family has undergone extensive radiation in flower form, leaf shape, habit, and habitat. To analyze the evolution of these distributions and traits, we derived a molecular phylogeny for representatives of 14 genera, based on sequence variation in the chloroplast-encoded ndhF gene. The lowland subfamily Rapateoideae is paraphyletic and includes the largely montane subfamily Saxofridericioideae as a monophyletic subset. Overall, the morphological/anatomical data differ significantly from ndhF sequences in phylogenetic structure, but show a high degree of concordance with the molecular tree in three of four tribes. Branch lengths are consistent with the operation of a molecular clock. Maschalocephalus diverges only slightly from other Monotremae: it is the product of relatively recent, long-distance dispersal, not continental drift--only its habitat atop rifted, nutrient-poor sandstones is vicariant. The family appears to have originated approximately 65 Mya in inundated lowlands of the Guayana Shield, followed by: (1) wide geographic spread of lowland taxa along riverine corridors; (2) colonization of Amazonian white-sand savannas in the western Shield; (3) invasion of tepui habitats with frequent speciation, evolution of narrow endemism, and origin of hummingbird pollination in the western Shield; and (4) reinvasion of lowland white-sand savannas. The apparent timing of speciation in the Stegolepis alliance about 6-12 Mya occurred long after the tepuis began to be dissected from each other as the Atlantic rifted approximately 90 Mya. Given the narrow distributions of most montane taxa, this suggests that infrequent long-distance dispersal combined with vicariance accounts for speciation atop tepuis in the Stegolepis alliance.
Adaptation, Physiological↗
Different patterns in molecular evolution of the Triticeae.
A huge part of the genomes of most Triticeae species is formed by different families of repetitive DNA sequences. In this paper the phylogenetic distribution of two major classes of the repeats, retrotransposons and tandemly organized DNA sequences, are considered and compared with the evolution of gene-rich regions and generally accepted Triticeae phylogenetic relationships. In Hordeum, LTR-containing retrotransposons are dispersed along the chromosomes and are consistent with the existing picture of the phylogeny of Hordeum. Another retrotransposon class, LINEs, have evolved independently from LTR-retrotransposons. Different retrotransposon classes appear to have competed for genome space during the evolution of Hordeum. Another class of repeats, tandemly organized DNA sequences, tends to cluster at the functionally important regions of chromosomes, centromeres and telomeres. The distribution of a number of tandem DNA families in Triticeae is not congruent with generally accepted phylogenetic relationships. While natural selection is the dominant factor determining the structure of genic regions we suggest that the contribution of random events is important in the evolution of repetitive DNA sequences. The interplay of stochastic processes, molecular drive, and selection determines the structure of chromosomal regions, notably at centromeres and telomeres, stabilizing and differentiating species-specific karyotypes. Thus, the evolution of these regions may occur largely independently of the evolution of gene-rich regions.
Blotting, Southern↗
Molecular evolution of H6 influenza viruses from poultry in Southeastern China: prevalence of H6N1 influenza viruses possessing seven A/Hong Kong/156/97 (H5N1)-like genes in poultry.
The A/teal/Hong Kong/W312/97 (H6N1) influenza virus and the human H5N1 and H9N2 influenza viruses possess similar genes encoding internal proteins, suggesting that H6N1 viruses could become novel human pathogens. The molecular epidemiology and evolution of H6 influenza viruses were characterized by antigenic and genetic analyses of 29 H6 influenza viruses isolated from 1975 to 1981 and 1997 to 2000. Two distinct groups were identified on the basis of their antigenic characteristics. Phylogenetic analysis revealed that all H6N1 viruses isolated from terrestrial poultry in 1999 and 2000 are closely related to A/teal/Hong Kong/W312/97 (H6N1), and the nucleotide sequences of these viruses and of A/Hong Kong/156/97 (H5N1) were more than 96% homologous. The hemagglutinin (HA) of the 1999 and 2000 terrestrial viruses does not have multiple basic amino acids at the site of cleavage of HA1 to HA2; however, a unique insertion of aspartic acid in HA1 between positions 144 and 145 (H3 numbering) was found. The neuraminidase of these terrestrial H6N1 viruses has a deletion of 19 amino acids characteristic of A/Hong Kong/156/97 (H5N1). Evolutionary analysis suggested that these H6N1 viruses coevolved with A/quail/Hong Kong/G1/97-like H9N2 viruses and became more adapted to terrestrial poultry. These terrestrial 1999 and 2000 A/teal/Hong Kong/W312/97 (H6N1)-like viruses, along with the H9N2 viruses, could have been involved in the genesis of the pathogenic H5N1 influenza viruses of 1997. The presence of H6N1 viruses in poultry markets in Hong Kong that possess seven of the eight genes of the A/Hong Kong/156/97 (H5N1) virus raises the following fundamental questions relevant to influenza pandemic preparedness: could the pathogenic H5N1 virus reemerge and could the H6N1 viruses directly cross the species barrier to mammals?
Animals↗
Origin and molecular evolution of receptor tyrosine kinases with immunoglobulin-like domains.
Receptor tyrosine kinases (RTKs) are involved in the control of fundamental cellular processes in metazoans. In vertebrates, RTK could be grouped in distinct classes based on the nature of their cognate ligand and modular composition of their extracellular domain. RTK with immunoglobulin-like domains (IG-like RTK) encompass several RTK classes and have been found in early metazoans, including sponges. Evolution of IG-like RTK is characterized by extended molecular and functional diversification, which prompted us to study their evolutionary history. For that purpose, a nonredundant data set including annotated protein sequences of IG-like RTK (n = 85) was built, representing 19 species ranging from sponges to humans. Phylogenetic trees were generated from alignment of conserved regions using maximum likelihood approach. Molecular phylogeny strongly suggests that IG-like RTK diversification occurred according to a complex scenario. In particular, we propose that specific cis duplications of a common ancestor to both platelet-derived growth factor receptor (class III) and vascular endothelial growth factor receptor (class V) families preceded two trans duplications. In contrast, other IG-like RTK genes, like Musk and PTK7, apparently did not evolve by duplications, whereas fibroblast growth factor receptors (class IV) evolved through two rounds of trans duplications. The proposed model of IG-like RTK evolution is supported by high bootstrap values and by the clustering of genes encoding class III and class V RTKs at specific chromosomal locations in mouse and human genomes.
Animals↗
A distinct subclass of mammalian striated myosins: structure and molecular evolution of "superfast" or masticatory myosin heavy chain.
"Superfast" or masticatory myosin is the molecular motor in the powerful and specialized jaw-closing muscles of carnivores, folivores, and frugivores. This myosin presumably underpins the unusual high force and moderate shortening velocity of muscle fibers expressing it. Here, we report the cloning and sequencing of the cDNA encoding the full-length masticatory myosin heavy chain (MyHC) from cat temporalis muscle. This was obtained by immunoscreening a cDNA expression library and RACE-PCR (rapid amplification of cDNA ends-PCR). Sequence comparisons at the DNA and amino acid levels show that masticatory MyHC has less than 70% homology to known striated MyHCs, compared with 87-96% between other mammalian fast isoforms themselves. Nucleotide substitution rates at the nonsynonymous sites between masticatory MyHC and other mammalian striated MyHCs are considerably higher than between these striated MyHCs themselves. Phylogenetic analysis revealed that masticatory MyHC diverged from invertebrate MyHC before the avian cardiac MyHC subclass and the mammalian fast/developmental and slow/cardiac MyHC subclasses. Masticatory MyHC is thus a distinct new subclass of vertebrate striated myosins. The early divergence from invertebrate MyHC, combined with immunochemical evidence of its expression in reptilian and shark jaw-closing muscles, suggests that masticatory MyHC evolved in early gnathostomes, driven by benefits derived from powerful jaw closure. During the mammalian radiation, some taxa continued to express it, while others adapted to new types of food and eating habits by replacing masticatory MyHC with more appropriate isoforms normally found in limb and cardiac muscles.
Animals↗
Molecular evolution of nuclear genes in Cupressacea, a group of conifer trees.
We surveyed the molecular evolutionary characteristics of 11 nuclear genes from 10 conifer trees belonging to the Taxodioideae, the Cupressoideae, and the Sequoioideae. Comparisons of substitution rates among the lineages indicated that the synonymous substitution rates of the Cupressoideae lineage were higher than those of the Taxodioideae. This result parallels the pattern previously found in plastid genes. Likelihood-ratio tests showed that the nonsynonymous-synonymous rate ratio did not change significantly among lineages. In addition, after adjustments for lineage effects, the dispersion indices of synonymous and nonsynonymous substitutions were considerably reduced, and the latter was close to 1. These results indicated that the acceleration of evolutionary rates in the Cupressoideae lineage occurred in both the nuclear and plastid genomes, and that generally, this lineage effect affected synonymous and nonsynonymous substitutions similarly. We also investigated the relationship of synonymous substitution rates with the nonsynonymous substitution rate, base composition, and codon bias in each lineage. Synonymous substitution rates were positively correlated with nonsynonymous substitution rates and GC content at third codon positions, but synonymous substitution rates were not correlated with codon bias. Finally, we tested the possibility of positive selection at the protein level, using maximum likelihood models, assuming heterogeneous nonsynonymous-synonymous rate ratios among codon (amino acid) sites. Although we did not detect strong evidence of positively selected codon sites, the analysis suggested that significant variation in nonsynonymous-synonymous rate ratio exists among the sites. The most likely sites for action of positive selection were found in the ferredoxin gene, which is an important component of the apparatus for photosynthesis.
Base Sequence↗
Molecular evolution of the brain of chordates.
The molecular basis of regionalisation and patterning of the developing brain is an area of current intense interest. Members of the Otx, Pax-2/5/8 and Hox gene families appear to play important roles in these processes in vertebrates, but functional divergence and genetic redundancy arising from gene duplication events obscures our view of the roles played by these genes during the evolution of vertebrate brains. Determination of the ancestral gene copy number in chordates through molecular phylogenetics, accompanied by gene expression analysis in all three chordate subphyla (vertebrates, cephalochordates and urochordates) may distinguish between ancestral and derived expression domains and give clues to the roles played by these genes in chordate ancestors. Application of this comparative approach indicates evolutionary homologous brain regions (fore-/midbrain, isthmus/cerebellum and hindbrain) in chordates and supports homology of the frontal eye of cephalochordates to the paired eyes of vertebrates.
Animals↗
Neutral theory of molecular evolution.
DNA sequence data are generally interpreted as favouring Kimura's neutral theory but not without dissent and often with a great deal of controversy with respect to molecular clocks, DNA polymorphism, adaptive evolution, and gene genealogy. Although the theory serves as a guiding principle, many issues concerning mutation, recombination, and selection remain unsettled. Of particular importance is the need for more knowledge about the function and structure of molecules.
Adaptation, Biological↗
Molecular evolution of the GapC gene family in Amsinckia spectabilis populations that differ in outcrossing rate.
Molecular evolutionary analysis of the glyceraldehyde 3-phosphate dehydrogenase (GapC) gene family was conducted in the plant genus Amsinckia (Boraginaceae), a group that exhibits marked variation in the mating system. GapC genes in this group differ from those of Arabidopsis thaliana in terms of both intron size and number. Phylogenetic and Southern hybridization analyses suggest the presence of multiple GapC loci, each defined by a set of base substitutions that are in strong linkage disequilibrium. One species of Amsinckia, A. spectabilis, was studied in some detail. This species consists of selfing (A. s. spectabilis) and outcrossing (A. s. microcarpa) varieties. Two selfing populations and one outcrossing population sample were analyzed in detail for variation at one of the members of this gene family. GapC3. A reduction in number of GapC3 haplotypes and level of genetic diversity was observed in the selfing populations of A. spectabilis. GapC3 in the outcrossing population (but not the two selfing populations) exhibited a significant departure from neutrality in the direction of an excess of singletons. These results are discussed in the context of forces acting on sequence evolution in populations with different mating systems.
Amsinckia↗