Tempo and mode of mitochondrial DNA evolution in vertebrates at the amino acid sequence level: Rapid evolution in warm-blooded vertebrates

Summary By using complete sequence data of mitochondrial DNAs, three Markov models (Day-hoff, Proportional, and Poisson models) for amino acid substitutions during evolution were applied in maximum likelihood analyses of mitochondrially encoded proteins to estimate a phylogenetic tree depicting human, cow, whale, and murids (mouse and rat), with chicken, frog, and carp as outgroups. A cow/whale clade was confirmed with a more than 99.8% confidence level by any of the three models, but the branching order among human, murids, and the cow/whale clade remained uncertain. It turned out that the Dayhoff model is by far the most appropriate model among the alternatives in approximating the amino acid substitutions of mitochondrially encoded proteins, which is consistent with a previous analysis of a more limited data set. It was shown that the substitution rate of mitochondrially encoded proteins has increased in the order of fishes, amphibians, birds, and mammals and that the rate in mammals is at least six times, probably an order of magnitude, higher than that in fishes. The higher evolutionary rate in birds and mammals than in amphibians and fishes was attributed to relaxation of selective constraints operating on proteins in warm-blooded vertebrates and to high mutation rate of bird and mammalian mitochondrial DNAs.Offprint requests to: M. Hasegawa     

Life-history evolution at the molecular level: adaptive amino acid composition of avian vitellogenins

Avian genomes typically encode three distinct vitellogenin (VTG) egg yolk proteins (VTG1, VTG2 and VTG3), which arose by gene duplication prior to the most recent common ancestor of birds. Analysis of VTG sequences from 34 avian species in a phylogenetic framework supported the hypothesis that VTG amino acid composition has co-evolved with embryo incubation time. Embryo incubation time was positively correlated with the proportions of dietary essential amino acids (EAAs) in VTG1 and VTG2, and with the proportion of sulfur-containing amino acids in VTG3. These patterns were seen even when only semi-altricial and/or altricial species were considered, suggesting that the duration of embryo incubation is a major selective factor on the amino acid composition of VTGs, rather than developmental mode alone. The results are consistent with the hypothesis that the level of EAAs provided to the egg represents an adaptation to the loss of amino acids through breakdown over the course of incubation and imply that life-history phenotypes and VTG amino acid composition have co-evolved throughout the evolutionary history of birds.     

The use of amino acid sequence analysis in assessing evolution

The thirteen year history of assessing evolution by amino acid sequence analysis has made apparent the limitations imposed upon this system by the finite nature of the characters. This finiteness exists on several levels and ultimately expresses itself as parallelism, back mutation and the retention of primitive characters in the sequences of proteins from present day species and the putative ancestral protein chains. Sequence analysis shares these problems with other molecular approaches, but because it is concerned both with the nucleotide substitutions in the genome and with the functional roles of proteins, it has unique advantages. For example, the large fluctuation in the rate of fixation of mutations in a protein's evolution can be detected and used to point out the unreliability of any molecular clock for estimating divergence dates. Moreover, when consideration is given to studies which assign functional significance to specific amino acid sites in a protein, changes in function during the descent of a protein can be appreciated and their significance correlated with organismal evolution.     

Site interdependence attributed to tertiary structure in amino acid sequence evolution

Standard likelihood-based frameworks in phylogenetics consider the process of evolution of a sequence site by site. Assuming that sites evolve independently greatly simplifies the required calculations. However, this simplification is known to be incorrect in many cases. Here, a computational method that allows for general dependence between sites of a sequence is investigated. Using this method, measures acting as sequence fitness proxies can be considered over a phylogenetic tree. In this work, a set of statistically derived amino acid pairwise potentials, developed in the context of protein threading, is used to account for what we call the structural fitness of a sequence. We describe a model combining statistical potentials with an empirical amino acid substitution matrix. We propose such a combination as a useful way of capturing the complexity of protein evolution. Finally, we outline features of the model using three datasets and show the approach's sensitivity to different tree topologies.     

Molecular evolution of protein: Internal homology in the amino acid sequence of calmodulin

Calmodulin is one of the calcium-binding proteins and is distributed widely in eukaryotes. The amino acid sequences were studied of calmodulin taken from bovine brain, scallop (Patinopecten), sea anemone (Metridium senile) and tetrahymena (Tetrahymena pyriformis). One notable feature of the primary structure of calmodulin is its internal homology. It can be subdivided into four domains with similar amino acid sequences. This homology implies that the primary structure of calmodulin has been elongated twice by intragenic duplication. Using this intragenic duplication model, the amino acid sequences of calmodulin from those four species were analyzed in detail. This kind of approach has proved very useful for investigation of the origin and evolution of this protein.     

Quantitative amino acid compositions at the picomole level using fluorescence scanning

Simple techniques are described for quantitating dansyl amino acids by direct fluoresence scanning and by photo-copying and densitometry. This technique is accurate between 1.0 to 10 × 10^?12 moles with a lower limit of detection around 1 × 10^?14 moles. It is possible to obtain amino acid compositions on very small quantities of peptides and it seems likely that this method will be useful for automatic peptide sequenators which use subtractive dansyl-Edman degradation as a detection procedure.     

Morphological similarity between echinoid taxa as a result of convergent and parallel evolution

Convergence is observed in groups, which are phylogenetically remote. A flat test is typical for some representatives of the order Cassiduloida, such as Jurassic and Early Cretaceous species of the genera Pygurus and Clypeus, and also many Cenozoic «sand dollars,» i.e., echinoids of the order Clypeasteroida. Both usually inhabit coarse sandy grounds of shallow areas. The superorder Spatangacea includes the so-called Echinocorys life form, which is characterized by an oval test with superficial nonpetaloid or subpetaloid ambulacra, marginal or inframarginal periproct, and absence of fascioles. These are the following genera: Early Cretaceous Corthya (family Collyritidae), Late CretaceousLate Paleocene Echinocorys (family Holas-teridae), Paleocene Isaster, Recent Isopatagus (family Isasteridae), Recent Scrippsechinus (family Palaeotro-pidae), and Recent Urechinus (family Urechinidae). In contrast to the majority of spatangaceans with the burrowing mode of life, these genera dwell on the substrate surface. In the Cenozoic, the monobasal apical system appears in some genera of the order Spatangoida, most genera of the order Cassiduloida, all groups of the orders Clypeasteroida and Oligopygoida, and in the genus Echinoneus (order Holectypoida). The paral-lelism is revealed in groups connected by remote relationships. At the end of the Middle Jurassic (Callovian) and, especially, Late Jurassic, the so-called disasterid echinoids (superorder Spatangacea) show a distinct trend to the loss of contact between ocular plates I and V and apices of the posterior ambulacra with the periproct, which are shifted to the anterior part of the apical system (genera Collyrites, Collyropsis, Cyclolam-pas). At the same time, the peristome of some genera was displaced to the anterior margin of the test, which became bilaterally symmetrical in outline. However, in the Jurassic, all spatangaceans remained disasterid echinoids, i.e., had a disjunct apical system, which can be interpreted as a somewhat “abnormal” state. This trend disappeared only at the beginning of the Cretaceous, when “normal” forms with a joint apical system appeared, that is, the families Holasteridae (genera Eoholaster and Holaster, order Holasteroida) and Toxas-teridae (genus Toxaster, order Spatangoida). Interesting examples of synchronous parallelism are provided by the appearance of meridosternous (diasternal) plastron in two collyritid genera (Tetraromania and Corthya) in the Barremian, whereas in the holasterid genus Holaster, this type of plastron apparently appeared in the Valanginian (heterochronous parallelism). The ethmolitic type of the apical system appeared at the end of the Cretaceous and Paleocene at least in five families: Schizasteridae, Paleopneustidae, Brissidae, Spatangidae, and Loveniidae.     

Branched-chain amino acid aminotransferase of Escherichia coli: nucleotide sequence of the ilvE gene and the deduced amino acid sequence

The ilvE gene of the Escherichia coli K-12 ilvGEDA operon, which encodes branched-chain amino acid aminotransferase [EC 2.6.1.42], was cloned. The nucleotide sequence of 1.5 kilobase pairs containing the gene was determined. The coding region of the ilvE gene contained 927 nucleotide residues and could encode 309 amino acid residues. The predicted molecular weight, amino acid composition and the sequence of the N-terminal 15 residues agreed with the enzyme data reported previously (Lee-Peng, F.-C., et al. (1979) J. Bacteriol. 139, 339-345). From the deduced amino acid sequence, the secondary structure was predicted.     

Complete amino acid sequence of human phosphoglycerate kinase. Isolation and amino acid sequence of tryptic peptides

As a part of the elucidation of the complete amino acid sequence of human phosphoglycerate kinase, 46 tryptic peptides, ranging in length from 1 to 26 residues, were isolated and characterized from the reduced and S-carboxymethylated enzyme. The isolated peptides were subjected to sequence analysis by the modified dansyl-Edman degradation procedure and automated Edman degradation technique. The results, together with the data on cyanogen bromide peptides and two additional tryptic peptides from cyanogen bromide peptides reported in the accompanying paper, established the complete amino acid sequence of human erythrocyte phosphoglycerate kinase.     

Isolation and amino acid sequence of cyclophilin

Cyclophilin, a specific cyclosporin A-binding protein has been purified to homogeneity from human spleen and bovine thymus cytosol. Purification of bovine and human cyclophilin was achieved by large scale molecular filtrations, Matrex Blue A affinity chromatography, preparative isoelectric focusing, phenyl-Sepharose chromatography, and weak cation exchange high performance liquid chromatography. Major and minor bovine and human cyclophilin isoforms were identified and found to have an apparent molecular weight of 17,000 and very similar amino acid compositions. The complete amino acid sequence of the major bovine cyclophilin isoform (163 residues, Mr 17,737) was determined from analysis of peptides derived by endoproteinase lysine C and cyanogen bromide cleavage and an NH2-terminal sequence of the intact protein. The first 72 NH2-terminal residues of the major human cyclophilin isoform were also determined and found to be identical to bovine cyclophilin. A computer search of cyclophilin with the National Biomedical Research Foundation database (3,182 protein sequences) did not detect any significant homologies. Cyclophilin represents a new class of abundant, highly conserved cytosolic proteins that probably play an important role in the regulation of T lymphocyte activation and proliferation.     

X-ray crystallography and the amino acid sequence of lysozyme

Certain parts of the amino acid sequence of hen's-egg lysozyme were reinvestigated. The parts in question are those in which X-ray-crystallographic data were used to decide between the two reported versions of the sequence that were based on chemical data. We conclude that the X-ray evidence, in the main, led to the correct choice between the sequences.     

Evolutionary process of amino acid biosynthesis in Corynebacterium at the whole genome level

Corynebacterium glutamicum, which is the closest relative of Corynebacterium efficiens, is widely used for the large scale production of many kinds of amino acids, particularly glutamic acid and lysine, by fermentation. Corynebacterium diphtheriae, which is well known as a human pathogen, is also closely related to these two species of Corynebacteria, but it lacks such productivity of amino acids. It is an important and interesting question to ask how those closely related bacterial species have undergone such significant functional differentiation in amino acid biosynthesis. The main purpose of the present study is to clarify the evolutionary process of functional differentiation among the three species of Corynebacteria by conducting a comparative analysis of genome sequences. When Mycobacterium and Streptomyces were used as out groups, our comparative study suggested that the common ancestor of Corynebacteria already possessed almost all of the gene sets necessary for amino acid production. However, C. diphtheriae was found to have lost the genes responsible for amino acid production. Moreover, we found that the common ancestor of C. efficiens and C. glutamicum have acquired some of genes responsible for amino acid production by horizontal gene transfer. Thus, we conclude that the evolutionary events of gene loss and horizontal gene transfer must have been responsible for functional differentiation in amino acid biosynthesis of the three species of Corynebacteria.     

Completion of the amino acid sequence of papain

Papain was inhibited with bromo[2-(14)C]acetic acid, the tertiary structure of the inhibited enzyme was unfolded and the disulphide bridges were reduced with mercaptoethanol and aminoethylated. Digestion with trypsin gave a radioactive peptide consisting of residues 18-58 inclusive and containing therefore the sequence of the thirteen unknown residues 29-41 in the primary sequence of papain. This peptide was digested with pepsin to give a radioactive peptide consisting of residues 18-47, which after digestion with 0.4m-hydrochloric acid gave a radioactive peptide consisting of residues 24-43 inclusive. Further digestion with 6m-hydrochloric acid gave peptides that were used to determine the sequence: Ser-Ala-Val-Val-Thr-Ile-Glx-Gly-Ile-Ile-Lys-Ile-Arg for the residues 29-41, so completing the amino acid sequence of papain.     

A case of convergent evolution of nucleic acid binding modules

Divergent evolution can explain how many proteins containing structurally similar domains, which perform a variety of related functions, have evolved from a relatively small number of modules or protein domains. However, it cannot explain how protein domains with similar, but distinguishable, functions and similar, but distinguishable, structures have evolved. Examples of this are the RNA-binding proteins containing the RNA-binding domain (RBD), and a newly established protein group, the cold-shock domain (CSD) protein family. Both protein domains contain conserved RNP motifs on similar single-stranded nucleic acid-binding surfaces. Apart from the RNP motifs, which have a similar function, the two families show little similarity in topology or amino acid sequence. This can be considered an interesting example of convergent evolution at the molecular level. Previously, a β-sheet surface was found to interact with RNA in non-homologous proteins from yeast, phage and man, revealing that this mode of RNA binding may be a widely recurring theme.