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At least 307 records · Page 17Linked to original sources
PubMed2005

Analysis of evolutionary conservation in CD1d molecules among primates.

The hereditary conservation in the genetically encoded CD1D sequences of various primates was analyzed. Genomic CD1D sequences of 17 rhesus macaques with distinct origins, eight Indian and nine Chinese, were examined and differences of only one or two nucleotides were detected and the consensus sequence of rhesus CD1D was determined. CD1D consensus sequences of three African green monkeys (AGMs) and the rhesus monkeys were then compared to study the evolutionary differences among interspecies. The CD1D consensus sequence determined from AGMs apparently differed by seven nucleotides from the rhesus consensus sequence, and nucleotide difference induced only three amino acid changes within Exon3, corresponding to the alpha2 domain of CD1d having a hydrophobic ligand-binding pocket. Such changes in the alpha2 domain may alter the characteristics of the SIV-derived glycolipid/lipid antigens presented by each CD1d molecule to innate natural killer T cells. In addition, the CD1D genomic sequences of three chimpanzees (chimps) were determined. To our surprise, although Exon2 and Exon3 reflecting antigen-binding alpha1 and alpha2 domains in chimps' CD1D were identical to that in humans except one amino acid, three amino acids within Exon4, reflecting alpha3 domain, were distinct from humans, and one of them was identical to those in rhesus and AGM CD1D. On the basis of the findings, the evolutionary relationship of the CD1d molecules among the various primates and their HIV-1/SIV susceptibility will be discussed.

Amino Acid Sequence↗
PubMed1990

Sequence analysis and evolutionary perspectives of ROB-1 beta-lactamase.

The nucleotide sequence of the ROB-1 beta-lactamase gene from Haemophilus influenzae plasmid RRob was determined. The structural gene encodes a polypeptide of 305 amino acids, with an estimated molecular mass of 30,424 for the mature form of the protein. The ROB-1 gene showed low homologies with other beta-lactamases at the nucleic acid level. By using two statistical computer methods, assessment of the extent of similarity between ROB-1 and other known beta-lactamase amino acid sequences suggested that ROB-1 is a class A enzyme. Alignment of class A beta-lactamases with ROB-1 identified conserved residues. The use of a mutation matrix for detecting distance relationships indicated that ROB-1 has higher values and homologies with beta-lactamases of gram-positive bacteria, giving insight into its ancestry and divergence.

Amino Acid Sequence↗
PubMed2006

Neurocontroller analysis via evolutionary network minimization.

This study presents a new evolutionary network minimization (ENM) algorithm. Neurocontroller minimization is beneficial for finding small parsimonious networks that permit a better understanding of their workings. The ENM algorithm is specifically geared to an evolutionary agents setup, as it does not require any explicit supervised training error, and is very easily incorporated in current evolutionary algorithms. ENM is based on a standard genetic algorithm with an additional step during reproduction in which synaptic connections are irreversibly eliminated. It receives as input a successfully evolved neurocontroller and aims to output a pruned neurocontroller, while maintaining the original fitness level. The small neurocontrollers produced by ENM provide upper bounds on the neurocontroller size needed to perform a given task successfully, and can provide for more effcient hardware implementations.

Algorithms↗
PubMed2000

Dimerization and domain swapping in G-protein-coupled receptors: a computational study.

In recent years there has been an increasing number of reports describing G protein-coupled receptor (GPCR) dimerization and heterodimerization. However, the evidence on the nature of the dimers and their role in GPCR activation is inconclusive. Consequently, we present here a review of our computational studies on G protein-coupled receptor dimerization and domain swapping. The studies described include molecular dynamics simulations on receptor monomers and dimers in the absence of ligand, in the presence of an agonist, and in the presence of an antagonist (or more precisely an inverse agonist). Two distinct sequence-based approaches to studying protein interfaces are also described, namely correlated mutation analysis and evolutionary trace analysis. All three approaches concur in supporting the proposal that the dimerization interface includes transmembrane helices 5 and 6. These studies cannot distinguish between domain swapped dimers and contact dimers as the models used were restricted to the helical part of the receptor. However, it is proposed that for the purpose of signalling, the domain swapped dimer and the corresponding contact dimer are equivalent. The evolutionary trace analysis suggests that every GPCR family and subfamily (for which sufficient sequence data is available) has the potential to dimerize through this common functional site on helices 5 and 6. The evolutionary trace results on the G protein are briefly described and these are consistent with GPCR dimerization. In addition to the functional site on helices 5 and 6, the evolutionary trace analysis identified a second functional site on helices 2 and 3. Possible roles for this site are suggested, including oligomerization.

Animals↗
PubMed2000

Molecular evolution of the GATA family of transcription factors: conservation within the DNA-binding domain.

The GATA-binding transcription factors comprise a protein family whose members contain either one or two highly conserved zinc finger DNA-binding domains. Members of this group have been identified in organisms ranging from cellular slime mold to vertebrates, including plants, fungi, nematodes, insects, and echinoderms. While much work has been done describing the expression patterns, functional aspects, and target genes for many of these proteins, an evolutionary analysis of the entire family has been lacking. Herein we show that only the C-terminal zinc finger (Cf) and basic domain, which together constitute the GATA-binding domain, are conserved throughout this protein family. Phylogenetic analyses of amino acid sequences demonstrate distinct evolutionary pathways. Analysis of GATA factors isolated from vertebrates suggests that the six distinct vertebrate GATAs are descended from a common ancestral sequence, while those isolated from nonvertebrates (with the exception of the fungal AREA orthologues and Arabidopsis paralogues) appear to be related only within the DNA-binding domain and otherwise provide little insight into their evolutionary history. These results suggest multiple modes of evolution, including gene duplication and modular evolution of GATA factors based upon inclusion of a class IV zinc finger motif. As such, GATA transcription factors represent a group of proteins related solely by their homologous DNA-binding domains. Further analysis of this domain examines the degree of conservation at each amino acid site using the Boltzmann entropy measure, thereby identifying residues critical to preservation of structure and function. Finally, we construct a predictive motif that can accurately identify potential GATA proteins.

Amino Acid Motifs↗
PubMed2004

APE: Analyses of Phylogenetics and Evolution in R language.

UNLABELLED: Analysis of Phylogenetics and Evolution (APE) is a package written in the R language for use in molecular evolution and phylogenetics. APE provides both utility functions for reading and writing data and manipulating phylogenetic trees, as well as several advanced methods for phylogenetic and evolutionary analysis (e.g. comparative and population genetic methods). APE takes advantage of the many R functions for statistics and graphics, and also provides a flexible framework for developing and implementing further statistical methods for the analysis of evolutionary processes. AVAILABILITY: The program is free and available from the official R package archive at http://cran.r-project.org/src/contrib/PACKAGES.html#ape. APE is licensed under the GNU General Public License.

Biological Evolution↗
PubMed1998

Step-wise analysis of polymorphisms in the human dopamine D2 receptor gene.

Evolutionary analysis of neurotransmitter receptor systems has previously focused on interspecies differentiation. Recently, emphasis has shifted to intragenic evolution within a single species and the functional relevance associated with intraspecies variations. For example, multiple polymorphisms have been identified within the human dopamine D2 receptor (DRD2) gene, many of which have been used in clinical association studies. In an attempt to evaluate the intragenic evolution of the DRD2 gene, genotypes from 116 humans were determined using five biallelic markers which reside within a 30 kb span of the DRD2 gene, that are non-polymorphic in other higher order primates. Only seven different haplotypes, out of a theoretical maximum of 32, were present in the study group of 232 chromosomes. Moreover, five of the seven haplotypes accounted for 99% (n = 230/232) of the human haplotypes. A phylogenetic tree was generated from the haplotypic data using a maximum parsimony algorithm. The relationship of the haplotypes within the phylogenetic tree is consistent with a progressive step-wise nucleotide conversion within the human gene. These data indicate that specific haplotypic subtypes of the human DRD2 gene exist within the human population and allow for the possibility that functional differences may exist between the DRD2 subtypes. Therefore, future studies focused on a functional analysis of the entire human DRD2 haplotype, as opposed to individual polymorphisms, may provide important insights into the functional relevance of molecular variations within the human DRD2 gene.

Europe↗
PubMed2005

Evolutionary and structural analysis of the cytochrome c oxidase subunit I (COI) gene from Haematobia irritans, Stomoxys calcitrans and Musca domestica (Diptera: Muscidae) mitochondrial DNA.

This work describes the molecular characterization of the cytochrome c oxidase subunit I (COI) gene of the mitochondrial DNA from three species of great medical and veterinary importance: the horn fly, Haematobia irritans, the stable fly, Stomoxys calcitrans and the house fly, Musca domestica (Diptera: Muscidae) (Linnaeus). The nucleotide sequence in all species was 1536 bp in size and coded for a 512 amino acid peptide. The nucleotide bias for an A+T-rich sequence is linked to three features: a high A+T content throughout the entire gene, a high A+T content in the third codon position, and a predominance of A+T-rich codons. An anomalous TCG (serine) start codon was identified. Comparative analysis among members of the Muscidae, Scatophagidae, Calliphoridae and Drosophilidae showed high levels of nucleotide sequence conservation. Analysis of the divergent amino acids and COI protein topologies among these three Muscidae species agreed with the evolutionary model suggested for the insect mitochondrial COI protein. The characterization of the structure and evolution of this gene could be informative for further evolutionary analysis of dipteran species.

Amino Acids↗
PubMed2006

The GH3 family in plants: genome wide analysis in rice and evolutionary history based on EST analysis.

The GH3 gene family in Arabidopsis, implicated in hormonal homeostasis through the conjugation of indolacetic and jasmonic acids to amino acids, is involved in a broad range of plant growth and development processes. In this work, the analysis of the GH3 family in the genome of Oryza sativa identified 13 hypothetical ORFs. EST analysis and RT-PCR assays demonstrated that 12 of them were active genes. An extensive EST analysis of the GH3 family performed on 26 plant species was used to estimate the minimum number of GH3 genes en each one. The data indicated that the members of the GH3 family progressively increased in the different plant divisions from Chlorophyta (0), Bryophyta (3), and Coniferophyta (4), to Magnoliophyta (7-19). Phylogenetic analyses showed a high degree of conservation between Arabidopsis and rice GH3 proteins and, in general, in the plant kingdom. The data revealed a homology clustering consistent with the functional classification of the Arabidopsis proteins, since most of the 110 sequences analyzed grouped into 2 main clusters, corresponding to the Arabidopsis functional groups I (jasmonic acid adenylation) and II (indolacetic acid adenylation). And additional cluster including group III (non-adenylation ability) was exclusively composed of proteins from Arabidopsis thaliana, Brassica napus and Gossypium hirsutum.

Evolution, Molecular↗
PubMed2002

Gene family phylogenetics: tracing protein evolution on trees.

How have proteins taken on the remarkable diversity of biochemical and physiological functions necessary to create and maintain complex organisms? The majority of proteins are organized hierarchically into families and superfamilies, reflecting an ancient and continuing process of gene duplication and divergence. The techniques of molecular phylogenetics, developed to recover the nested hierarchy of taxa from character information in their gene sequences, can also reconstruct the evolutionary relationships among genes and provide a conceptual foundation for comparative evolutionary analysis of proteins and their functions. In this review, I outline the application of phylogenetic approaches to issues in gene family studies, beginning with the inference of phylogeny and the assessment of the two types of homology by which genes in a family can be related: orthology (common descent from a cladogenetic event) and paralogy (common descent from a gene duplication event). I show how the phylogenetic approach makes possible novel kinds of comparative analysis, including detection of exon shuffling, reconstruction of the evolutionary diversification of gene families, tracing of evolutionary change in protein function at the amino acid level, and prediction of structure-function relationships. A marriage of the principles of phylogenetic systematics with the copious sequence data being generated by molecular biology and genomics promises unprecedented insights into the nature of biological organization and the historical processes that created it.

Animals↗
PubMed2004

Isolation, characterization, and evolutionary divergence of mouse RNase 6: evidence for unusual evolution in rodents.

The evolution of the ribonuclease A (RNase A) vertebrate-specific enzyme family is interesting in that specific gene lineages appear to be responding to unique selective pressures in wildly diverse manners to generate proteins that are capable of reducing the infectivity of viruses, killing systemic pathogens, and inducing the growth of blood vessels all while maintaining the signature motifs of a ribonuclease. In this paper, we present the DNA sequence and gene structure of Mus musculus RNase 6 and examine the expression pattern and enzymatic activity of the recombinant protein. M. musculus RNase 6 has a limited expression pattern compared to human RNase 6 and is an efficient ribonuclease, with a catalytic efficiency 17-fold higher than that of human protein. Evolutionary analysis reveals that RNase 6 was subject to unusual evolutionary forces (dN/dS = 1.2) in an ancestral rodent lineage before the separation of Mus and Rattus. However, more recent evolution of rodent RNase 6 has been relatively conserved, with an average dN/dS of 0.66. These data suggest that the ancestral rodent RNase 6 was subject to accelerated evolution, resulting in the conserved modern gene, which most likely plays an important role in mouse physiology.

Amino Acid Sequence↗
PubMed2004

An evolutionary and molecular analysis of Bmp2 expression.

The coding regions of many metazoan genes are highly similar. For example, homologs to the key developmental factor bone morphogenetic protein (BMP) 2 have been cloned by sequence identity from arthropods, mollusks, cnidarians, and nematodes. Wide conservation of protein sequences suggests that differential gene expression explains many of the vast morphological differences between species. To test the hypothesis that the regulatory mechanisms controlling this evolutionarily ancient and critical gene are conserved, we compared sequences flanking Bmp2 genes of several species. We identified numerous conserved noncoding sequences including some retained because the fish lineage separated 450 million years ago. We tested the function of some of these sequences in the F9 cell model system of Bmp2 expression. We demonstrated that both mouse and primate Bmp2 promoters drive a reporter gene in an expression pattern resembling that of the endogenous transcript in F9 cells. A conserved Sp1 site contributes to the retinoic acid responsiveness of the Bmp2 promoter, which lacks a classical retinoic acid response element. We have also discovered a sequence downstream of the stop codon whose conservation between humans, rodents, deer, chickens, frogs, and fish is striking. A fragment containing this region influences reporter gene expression in F9 cells. The conserved region contains elements that may mediate the half-life of the Bmp2 transcript. Together, our molecular and evolutionary analysis has identified new regulatory elements controlling Bmp2 expression.

Animals↗
PubMed1996

Coracoacromial ligament function: a phylomorphic analysis.

Various morphologic parameters of the coracoacromial region were quantified for five hominoid genera to examine the evolutionary development of the coracoacromial ligament (CAL) and its significance and relationship to shoulder function. No evolutionary correlation within the family Hominoidea was found for several calculated parameters obtained from osseous dimensions and CAL length. However, from an evolutionary analysis of the order Anthropoidea, it appears that the CAL is not solely a vestigial structure in humans but rather represents a stage in the development of the hominoid shoulder with the function of providing increased mechanical stability to the superior bony vault.

Animals↗
PubMed1993

Antigenicities of Group I and II hepatitis C virus polypeptides--molecular basis of diagnosis.

Comparative nucleotide sequence studies on the putative NS3 and NS4 regions of the genomes of hepatitis C viruses (HCV) have revealed that there are at least two groups of HCV, group I and group II. The cDNA clone E, corresponding to a boundary between the NS3 and NS4 (NS3-4) region of the group II HCV genome, encodes antigens that react to antibodies specific to group II HCV (Tsukiyama-Kohara et al. (1991) Virus Genes 5, 243-254). To understand the molecular basis of the group-specific antigenicity of HCV peptides, the predicted amino acid sequences around the NS3-4 region of our group II HCV cDNAs were compared with those of other HCV isolates. The analysis revealed the presence of group-specific amino acids in this peptide region. Evolutionary analysis of nucleotide sequences within this region of these HCV isolates also led to the same classification. A similar result was obtained by sequence analysis of cloned cDNAs corresponding to the core region. A cDNA of the group II HCV core region was prepared by polymerase chain reaction from the cDNA synthesized with group II-specific primer complementary to the NS3-4 region. The products directed by the cDNA of the core region did not have group-specific antigenicity. The NS3 peptide region also appeared not to carry group-specific antigens. Our results indicate that most HCV isolates can be classified into either group I or II, and that the existence of two groups of HCV does not disturb HCV diagnosis as long as core and/or NS3 peptides are used to detect HCV antibodies.

Amino Acid Sequence↗