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PubMed2006

Distinct specific status of the Korean brown frog, Rana amurensis coreana (Amphibia: Ranidae).

We used morphological and genetic data to assess the taxonomic status of Rana amurensis coreana and R. a. amurensis. Morphological comparisons revealed these two subspecies to be different from each other in size of body, nature of tubercles on dorsal stripe, degree of development in toe webbing, and condition of lateral spots of trunk. They were also different in sequence of mitochondrial 16S rRNA gene, with genetic distance as large as those observed among different species of brown frogs. Therefore, Korean populations previously considered a subspecies of R. amurensis should be regarded as a distinct species (=R. coreana).

Animals↗
PubMedDate not supplied

[Proteomic code].

On the basis of recent fundamentally novel developments in the protein structure a proteomic code is suggested, that would potentially allow to describe sequence, structure, and function of proteins by a spectrum of elementary loop-n-lock units. All major characteristics of the nearly standard units are described, and first five "codons" of the proteomic code are presented with their respective unique sequences, structures, and functions. More such codons are to be discovered, and the general procedure for their identification is described.

Amino Acid Sequence↗
PubMed2004

Comparative analysis of noncoding sequences of orthologous bovine and human gene pairs.

Genomic sequence comparison across species has enabled the elucidation of important coding and regulatory sequences encoded within DNA. Of particular interest are the noncoding regulatory sequences, which influence gene transcriptional and posttranscriptional processes. A phylogenetic footprinting strategy was employed to identify noncoding conservation patterns of 39 human and bovine orthologous genes. Seventy-three conserved noncoding sequences were identified that shared greater than 70% identity over at least 100 bp. Thirteen of these conserved sequences were also identified in the mouse genome. Evolutionary conservation of noncoding sequences across diverse species may have functional significance, and these conserved sequences may be good candidates for regulatory elements.

3' Untranslated Regions↗
PubMed1997

[Molecular evolutionary analysis of GB viruses and hepatitis G virus].

Recently, new blood-transfusion transmissible viruses, called hepatitis G virus(HGV) and GB virus-C(GBV-C), have been reported. It was found that two viruses were independent isolates of the same virus, the genomic structure resembled that of flavivirus family, and GBV-C/HGV was closely related to HCV. To elucidate the evolutionary relationship between hepatitis C virus(HCV) and GBV-C/HGV, we constructed the phylogenetic trees for the putative RNA helicase and the RNA-dependent RNA polymerase regions of the Flaviviridae by UPGMA. The tree showed that HCV was closely related to GB virus-B(GBV-B) and HGV was more nearer to GB virus-A(GBV-A) rather than HCV.

Amino Acid Sequence↗
PubMed1997

Purification and some properties of ribulose 1,5-bisphosphate carboxylases/oxygenases from Acinetobacter sp. strain JC1 and Hydrogenophaga pseudoflava.

Ribulose 1,5-bisphosphate carboxylases/oxygenases (RuBisCOs) of two carboxydobacteria, Acinetobacter sp. strain JC1 and Hydrogenophaga pseudoflava, grown on carbon monoxide were purified and partially characterized. RuBisCO of Acinetobacter sp. JC1 was purified 5-fold in eight steps to homogeneity, with a yield of 1.6%. The final specific activity of the purified enzyme was 39.5 nmol CO2 incorporated per min per mg protein. The molecular weight of the native enzyme was determined to be 520,000. Sodium dodecyl sulfate-gel electrophoresis revealed two nonidentical subunits of molecular weights 53,500 and 15,000. The Km and Vmax for CO2 were 36.7 microM and 296.1 nmol per min per mg protein, respectively, and those for ribulose 1,5-bisphosphate were 3.7 microM and 770 nmol per min per mg protein, respectively. The enzyme of H. pseudoflava was purified 55-fold in eight steps to homogeneity, with a yield of 3.6%. The final specific activity was 304.3 nmol CO2 incorporated per min per mg protein. The molecular weight of the enzyme was estimated to be 505,000. The enzyme was found to have two kinds of nonidentical subunits of molecular weights 51,500 and 14,000. The Km and Vmax for CO2 were found to be 16.4 microM and 777.8 nmol per min per mg protein, respectively, and those for ribulose 1,5-bisphosphate were 0.1 microM and 436.2 nmol per min per mg protein, respectively. The N-terminal amino acid sequences of the large and small subunits of Acinetobacter sp. JC1 enzyme were Ala-Asp-Arg-Trp-Asn-Ala-Gly-Val-IIe-Pro-Tyr-Ala-Glu-Met-Gly and Met-Arg-Ile-Thr-Glu-Gly-Thr-Phe-Ser-Tyr-Leu-Pro-Asp-Phe-Thr, respectively. The sequences of the H. pseudoflava enzyme were Ala-Thr-Lys-Thr-Tyr-Asu-Ala-Gly-Val-Lys-Glu-Tyr-Trp-Ser-Thr and Met-Ser-Met-Gln-Asp-Tyr-His-Ser-Arg-Leu-Ser-Asp-Pro-Ala-Ile, respectively. The peptide map of RuBisCO from Acinetobacter sp. JC1 grown on carbon monoxide was different from that of the bacterium grown on methanol. The two RuBisCOs, however, were found to be identical in N-terminal residue and antigenic property. The RuBisCO of Acinetobacter sp. JC1 was found to share no immunological properties with those of H. pseudoflava, Oligotropha carboxidovorans and Pseudomonas carboxydohydrogena.

Acinetobacter↗
PubMed1997

Amino acid sequence homology of factor C produced by Streptomyces griseus with regulatory proteins of zinc finger type.

Factor C is a regulatory protein produced by Streptomyces griseus 45H. Factor C-like antigen can be detected in the most diverse species examined. It is also present in human serum with an average of 219.4 U/ml of narrow dispersion. The level of factor C-like antigen shows an increase in the sera of patients with different hepatic disorders (341 U/ml), some values being 3-7 times higher than normal (600-1500 U/ml). Correlation was found between the elevated antigen levels and the amount of the bilirubin in the sera of patients with liver cirrhosis. Amino acid sequence homology was found between factor C and zinc finger motifs of several known DNA binding proteins. In fact, factor C was successfully bound to and eluted from a Zn2+ affinity column. Our data show that factor C is probably a zinc finger type DNA binding protein.

Amino Acid Sequence↗
PubMed1982

Saccharomyces cerevisiae contains a complex multigene family related to the major heat shock-inducible gene of Drosophila.

Saccharomyces cerevisiae contains a family of genes related to the major heat shock-induced gene of Drosophila (hsp 70). Two members of the multigene family (YG100 and YG101) were isolated. The primary DNA sequences of more than one-half of the protein-encoding regions of YG100 and YG101 were determined and compared with the Drosophila hsp 70 gene sequence; the predicted amino acid sequences were 72 and 64% homologous to the sequence of the Drosophila hsp 70 protein, respectively. The predicted amino acid sequences of the yeast genes were 65% homologous. Our results demonstrate a striking sequence conservation of hsp 70-related sequences in evolution. Hybridization of the S. cerevisiae genes to total S. cerevisiae DNA indicated that the multigene family consists of approximately 10 members. Hybridization of labeled RNAs from heat-shocked and control cells suggested that, like transcription of the Drosophila hsp 70 gene, transcription of YG100 or a closely related gene is enhanced after heat shock. However, the amount of RNA sequences homologous to YG101 was reduced after heat shock. A multigene family related to the hsp 70 gene exists in Drosophila; transcription of some members is induced by heat shock, whereas transcription of others is not. Our results suggest that S. cerevisiae, like Drosophila, contains a multigene family of hsp 70-related sequences under complex transcriptional regulation and that the differential control, as well as the nucleotide sequence, has been highly conserved in evolution.

Amino Acid Sequence↗
PubMed1999

Relationship of the CCA sequence of tRNA with the early evolutional aspect of aminoacyl-tRNA synthetases.

The CCA sequence is common to the 3'-ends of all tRNAs. We investigated the requirement of the CCA sequence in aminoacylation with the cognate aminoacyl-tRNA synthetases (aaRSs) and several interesting conclusions could be drawn. In tRNAs belonging to the class I aaRSs, decreased aminoacylation activities resulted from the substitution of A76 with a pyrimidine, whereas in tRNAs belonging to the class II aaRSs, decreased aminoacylation activities resulted from the substitution with guanine. The results suggest that aminoacylation of proto-tRNA might have started through the direct hydrophobic (or stacking) interaction between the large, hydrophobic amino acid residue (now utilizing a class I aaRS) of aminoacyl-AMP and the 3'-terminal adenine. The shorter distance between the adenine and the 2'-OH position than the 3'-OH position, and the bulkiness and hydrophobicity of amino acids may be important reasons why class I aaRSs select the 2'-OH position in aminoacylation. Molecular mechanics-based conformation modeling also indicated that the resulting positioning of the adenine and the amino acid residue of 2'-aminoacyl-adenosine for large amino acid is in the vicinity. In contrast, in the case of small amino acids (with class II aaRSs) which would not be able to use the hydrophobic interaction, a protein enzyme might have participated in the aminoacylation reaction from an early stage. The active-site folds of aaRSs belonging to each class reflect the history of evolution: typical nucleotide-binding fold (Rossman fold) in the case of class I aaRSs, and primitive fold which is found also among the family of nonribosomal peptide synthetases in the case of class II aaRSs.

Amino Acyl-tRNA Synthetases↗
PubMed1990

Characterization of chicken octamer-binding proteins demonstrates that POU domain-containing homeobox transcription factors have been highly conserved during vertebrate evolution.

The DNA sequence motif ATTTGCAT (octamer) or its inverse complement has been identified as an evolutionarily conserved element in the promoter region of immunoglobulin genes. Two major DNA-binding proteins that bind in a sequence-specific manner to the octamer DNA sequence have been identified in mammalian species--a ubiquitously expressed protein (Oct-1) and a lymphoid-specific protein (Oct-2). During characterization of the promoter region of the chicken immunoglobulin light chain gene, we identified two homologous octamer-binding proteins in chicken B cells. When the cloning of the human gene for Oct-2 revealed it to be a member of a distinct family of homeobox genes, we sought to determine if the human Oct-2 cDNA could be used to identify homologous chicken homeobox genes. Using a human Oct-2 homeobox-specific DNA probe, we were able to identify 6-10 homeobox-containing genes in the chicken genome, demonstrating that the Oct-2-related subfamily of homeobox genes exists in avian species. Low-stringency screening of a chicken embryonic cDNA library allowed us to clone one of these genes. DNA sequence analysis revealed it to be the chicken homologue of the human Oct-1 gene. The predicted protein sequence of the chicken Oct-1 gene demonstrated that the gene for Oct-1 has been highly conserved during vertebrate evolution with an overall 96% amino acid sequence identity between the chicken and human proteins. The previously described POU domain (termed POU for its presence in the Pit-1, Oct-1/Oct-2, and Unc-86 genes) and homeobox domain are 100% conserved between the two protein products. Together, our data show that the POU-containing subfamily of homeobox genes have been highly conserved during vertebrate evolution, apparently as a result of selection for their DNA-binding and transcriptional regulatory properties.

Amino Acid Sequence↗
PubMed1996

Adaptive evolution of lysozyme: changes in amino acid sequence, regulation of expression and gene number.

Adaptive evolution of lysozyme has involved remodelling of amino acid sequences and changes in patterns of gene expression and in gene number. Following an outline of the phenomena likely to be indicative of adaptive evolution and how one can assess them, this chapter focuses on four cases in which lysozyme c has been recruited as a digestive enzyme in the stomachs of creatures needing to retrieve nutrients from microorganisms in fermented food. For each case-ruminant artiodactyls, leaf-eating monkeys, a leaf-eating bird, and fruit flies-the factors likely to be of primary importance in lysozyme's adaptation are examined. Additional examples of apparent adaptation for digestion or antimicrobial defense in animals as diverse as mice, moths, and molluscs are summarized. This chapter considers also the case of three internally clustered residues which among galliform bird lysozymes c occur either as Thr 40, Ile 55, and Ser 91 (TIS) or as Ser 40, Val 55, and Thr 91 (SVT). Reconstruction and testing of six possible intermediate proteins and development of the concept of a neutral corridor of protein traits are described.

Adaptation, Physiological↗
PubMed2003

Sequencing the chimpanzee genome: insights into human evolution and disease.

Large-scale sequencing of the chimpanzee genome is now imminent. Beyond the inherent fascination of comparing the sequence of the human genome with that of our closest living relative, this project is likely to yield tangible scientific benefits in two areas. First, the discovery of functionally important mutations that are specific to the human lineage offers a new path towards medical benefits. Second, chimpanzee-human comparisons are likely to yield molecular insights into how new biological characteristics evolve--findings that might be relevant throughout the tree of life.

Animals↗
PubMed1997

Interspecific and intraspecific comparisons of the period locus in the Drosophila willistoni sibling species.

The period (per) locus has received much attention in molecular evolution studies because it is one of the best studied "behavioral genes" and because it offers insight into the evolution of repetitive sequences. We studied most of the coding region of per in Drosophila willistoni and confirmed previously observed patterns of conservation and divergence among distantly related species. Five regions are so highly diverged that they cannot be aligned, whereas a region encompassing the PAS domain is very conserved. Structural and nucleotide polymorphism patterns in the willistoni group are not the same as those observed in previously studied species. We sequenced the region homologous to the highly polymorphic threonine-glycine repeat of D. melanogaster in multiple strains of D. willistoni, as well as in other members of willistoni group, and found an unusual amount of conservation in this region. However, the next nonconserved region downstream in the sequence is quite variable and polymorphic for the number of repeated glycines. The glycine codon usage is significantly different in this glycine repeat as compared to other parts of the gene. We were able to plot the directionality of change in the glycine repeat region onto a phylogeny and find that the addition of glycines is the general trend with the diversification of the willistoni group.

Amino Acid Sequence↗
PubMed1981

Similar amino acid sequences: chance or common ancestry?

The systemic comparison of every newly determined amino acid sequence with all other known sequences may allow a complete reconstruction of the evolutionary events leading to contemporary proteins. But sometimes the surviving similarities are so vague that even computer-based sequence comparisons procedures are unable to validate relationships. In other cases similar sequences may appear in totally alien proteins as a result of mere chance or, occasionally, by the convergent evolution of sequences with special properties.

Amino Acid Sequence↗
PubMed1991

Incipient mitochondrial evolution in yeasts. II. The complete sequence of the gene coding for cytochrome b in Saccharomyces douglasii reveals the presence of both new and conserved introns and discloses major differences in the fixation of mutations in evolution.

We have determined the complete sequence of the mitochondrial gene coding for cytochrome b in Saccharomyces douglasii. The gene is 6310 base-pairs long and is interrupted by four introns. The first one (1311 base-pairs) belongs to the group ID of secondary structure, contains a fragment open reading frame with a characteristic GIY ... YIG motif, is absent from Saccharomyces cerevisiae and is inserted in the same site in which introns 1 and 2 are inserted in Neurospora crassa and Podospora anserina, respectively. The next three S. douglasii introns are homologous to the first three introns of S. cerevisiae, are inserted at the same positions and display various degrees of similarity ranging from an almost complete identity (intron 2 and 4) to a moderate one (intron 3). We have compared secondary structures of intron RNAs, and nucleotide and amino acid sequences of cytochrome b exons and intron open reading frames in the two Saccharomyces species. The rules that govern fixation of mutations in exon and intron open reading frames are different: the relative proportion of mutations occurring in synonymous codons is low in some introns and high in exons. The overall frequency of mutations in cytochrome b exons is much smaller than in nuclear genes of yeasts, contrary to what has been found in vertebrates, where mitochondrial mutations are more frequent. The divergence of the cytochrome b gene is modular: various parts of the gene have changed with a different mode and tempo of evolution.

Amino Acid Sequence↗
PubMed1997

Molecular phylogeny and evolution of the neurotrophins from monotremes and marsupials.

We have investigated the phylogenetic relationships of monotremes and marsupials using nucleotide sequence data from the neurotrophins; nerve growth factor (NGF), brain-derived neurotrophic factor (BDNF), and neurotrophin-3 (NT-3). The study included species representing monotremes, Australasian marsupials and placentals, as well as species representing birds, reptiles, and fish. PCR was used to amplify fragments encoding parts of the neurotrophin genes from echidna, platypus, and eight marsupials from four different orders. Phylogenetic trees were generated using parsimony analysis, and support for the different tree structures was evaluated by bootstrapping. The analysis was performed with NGF, BDNF, or NT-3 sequence data used individually as well as with the three neurotrophins in a combined matrix, thereby simultaneously considering phylogenetic information from three separate genes. The results showed that the monotreme neurotrophin sequences associate to either therian or bird neurotrophin sequences and suggests that the monotremes are not necessarily related closer to therians than to birds. Furthermore, the results confirmed the present classification of four Australasian marsupial orders based on morphological characters, and suggested a phylogenetic relationship where Dasyuromorphia is related closest to Peramelemorphia followed by Notoryctemorphia and Diprotodontia. These studies show that sequence data from neurotrophins are well suited for phylogenetic analysis of mammals and that neurotrophins can resolve basal relationships in the evolutionary tree.

Amino Acid Sequence↗
PubMed2004

Covarion structure in plastid genome evolution: a new statistical test.

Covarion models of molecular evolution allow the rate of evolution of a site to vary through time. There are few simple and effective tests for covarion evolution, and consequently, little is known about the presence of covarion processes in molecular evolution. We describe two new tests for covarion evolution and demonstrate with simulations that they perform well under a wide range of conditions. A survey of covarion evolution in sequenced plastid genomes found evidence of covarion drift in at least 26 out of 57 genes. Covarion evolution is most evident in first and second codon positions of the plastid genes, and there is no evidence of covarion evolution in third codon positions. Therefore, the significant covarion tests are likely due to changes in the selective constraints of amino acids. The frequency of covarion evolution within the plastid genome suggests that covarion processes of evolution were important in generating the observed patterns of sequence variation among plastid genomes.

Codon↗