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At least 1,063 records · Page 59Linked to original sources
PubMed1995

Molecular evolution of receptors for eicosanoids.

The amino acid sequences of the receptors for various prostaglandins, thromboxane and lipoxin, which belong to the rhodopsin family, were aligned, and a phylogenetic tree was constructed to infer the evolutionary history of the arachidonic acid cascade. The obtained tree suggested that the origin of the cyclooxygenase pathway was different from that of the lipoxygenase pathway. The receptors involved in the cyclooxygenase pathway constructed an independent cluster, but the lipoxin A4 receptor, which is involved in the lipoxygenase pathway, belonged to the cluster of peptide receptors. The primitive form of the cyclooxygenase pathway had been a signal transduction system composed of prostaglandin E2 and its receptor associated with cAMP metabolism.

Amino Acid Sequence↗
PubMed1994

Molecular evolution of magellan, a maize Ty3/gypsy-like retrotransposon.

The magellan transposable element is responsible for a spontaneous 5.7-kb insertion in the maize wx-M allele. This element has the sequence and structural characteristics of a Ty3/gypsy-like retrotransposon. The magellan element is present in all Zea species and Tripsacum andersonii; it is absent, however, in the genomes of all other Tripsacum species analyzed. The genetic distances between magellan elements suggest that this retrotransposon is evolving faster than other Zea nuclear loci. The phylogeny of magellan within Zea and T. andersonii also reveals a pattern of interspecies transfers, resulting in the movement of magellan subfamilies between different species genomes. Interspecific hybridization may be a major mechanism by which this retrotransposon invades and establishes itself in new taxa.

Base Sequence↗
PubMed1994

[Studies on the molecular evolution of apolipoprotein multigene family].

The apolipoprotein genes represent a large family of genes encoding various binding proteins for plasma lipid transport. Because of their long divergence history, it is not known whether and how these genes have evolved through gene duplication from a common ancestor. To test this possibility and reconstruct a reliable phylogenetic tree, a simple method to evaluate the branch length and its divergence time in unrooted parsimony tree under the condition of non-even evolutionary rate was developed. The tree built from the 26 apolipoprotein sequences by above method clearly shows: (1) The common ancestor of ApoA-I ApoA-II, ApoA-IV, ApoE may appear 460 million years ago in an ordovician vertebrate which may be related with the major apolipoprotein LAL1 and LAL2 in Lamprey from the evidence of sequence alignment; (2) The central role of different selection pressure upon the ancestor gene of apolipoprotein made them evolved into different subgroups; (3) The high evolution rate in rodent ApoE molecules may be related with the existence of a large amount of hidden substitutions and the disruption of synonym codon usage clock in their genome; (4) The evolutionary rate of various branches in parsimony tree is significantly different in which the average UEP of ApoA-I, ApoA-IV is 2.0 MY, ApoA-II 1.7MY, ApoE 2.4MY; (5) The receptor domain in ApoE seems to be more conservative than other fragments. These data suggest a long, complex evolutionary history for apolipoprotein genes in which the gene duplication events of different origins took place.

Amino Acid Sequence↗
PubMed1993

Molecular evolution of the human immunoglobulin E response: high incidence of shared mutations and clonal relatedness among epsilon VH5 transcripts from three unrelated patients with atopic dermatitis.

We have analyzed the nucleotide sequences of 19 epsilon VH5 transcripts derived from in vivo isotype switched peripheral blood B cells of three patients with atopic dermatitis. Comparison with the patients' own germline VH5 gene segments revealed that the epsilon transcripts were derived from both functional members of the human VH5 gene family and harbored numerous somatic mutations (range 5-36 per VH5 gene). In two patients, we detected clonally related but diverged transcripts, permitting the construction of a genealogical tree in one patient. We observed a high proportion of shared silent (S) and replacement (R) mutations among epsilon VH5 sequences derived from all three individuals, even among transcripts descending from the two different germline VH5 gene segments. A remarkably high number of these mutations is shared with previously reported VH5 genes encoding antibodies with defined specificities. The shared S mutations, and likely a fraction of the R mutations, appear to mark preferential sites ("hot spots") of somatic hypermutations in human VH5 genes. The distribution of R and S mutations over complementarity determining region and framework regions in the majority of VH regions deviated from that characteristic of antigen-driven immune response. We hypothesize that the V regions of immunoglobulin E-bearing B cells have accumulated "selectively neutral" mutations over extended periods of clonal expansion, resulting in unusual R/S ratios. We propose that the molecular characteristics of the epsilon VH regions in atopic dermatitis may be representative of antigens that recurrently or chronically stimulate the immune system.

Adult↗
PubMed1997

Molecular evolution of the tet(M) gene in Gardnerella vaginalis.

Five clinical isolates of Gardnerella vaginalis known to carry the tetracycline resistance determinant Tet M were examined by hybridization and nucleotide sequencing. Four of the strains carried tet(M) genes with identical sequences. The two versions of the tet(M) gene found in G. vaginalis did not show complete identity with other published tet(M) sequences, but showed mosaic structures with regions of homology to tet(M) gene sequences from Tn916, Tn1545 and the American type plasmid found in Neisseria gonorrhoeae. Hybridization studies showed that all isolates carried the tet(M) gene on a single HindII restriction fragment of variable length. No evidence was found for the presence of sequences homologous to the transposition functions of Tn916.

Base Sequence↗
PubMed1998

Characterization and molecular evolution of a vertebrate hyaluronan synthase gene family.

The three mammalian hyaluronan synthase (HAS) genes and the related Xenopus laevis gene, DG42, belong to a larger evolutionarily conserved vertebrate HAS gene family. We have characterized additional vertebrate HAS genes from chicken (chas2 and chas3) and Xenopus (xhas2, xhas3, and a unique Xenopus HAS-related sequence, xHAS-rs). Genomic structure analyses demonstrated that all vertebrate HAS genes share at least one exon-intron boundary, suggesting that they evolved from a common ancestral gene. Furthermore, the Has2 and Has3 genes are identical in structure, suggesting that they arose by a gene duplication event early in vertebrate evolution. Significantly, similarities in the genomic structures of the mouse Has1 and Xenopus DG42 genes strongly suggest that they are orthologues. Northern analyses revealed a similar temporal expression pattern of HAS genes in developing mouse and Xenopus embryos. Expression of mouse Has2, Has3, and Xenopus Has1 (DG42) led to hyaluronan biosynthesis in transfected mammalian cells. However, only mouse Has2 and Has3 expressing cells formed significant hyaluronan-dependent pericellular coats in culture, implying both functional similarities and differences among vertebrate HAS enzymes. We propose that vertebrate hyaluronan biosynthesis is regulated by a comparatively ancient gene family that has arisen by sequential gene duplication and divergence.

Amino Acid Sequence↗
PubMed1990

Rapid molecular evolution of wild type 3 poliovirus during infection in individual hosts.

A panel of nine neutralizing monoclonal antibodies was used to analyse the antigenic properties of 188 plaque-purified type 3 poliovirus strains from 17 faecal specimens, derived from eight people during a 2 month observation period. Most poliovirus specimens consisted of a mixture of antigenically distinct variants and the composition of the mixture was found to change between sequential specimens in many individuals, indicating antigenic evolution. Thirty-five strains representing different antigenic patterns were selected for partial sequencing of genomic RNA. Mutations leading to amino acid substitutions, as well as silent mutations, were seen at and close to the known antigenic sites. The frequency of silent mutations was used to estimate the evolutionary potential of the virus. The largest difference in silent changes between strains isolated from one person was 0.8%, which corresponds to a minimum of about 60 mutations per genome within a period of 3 weeks. The observed incidence of silent mutations between isolates from different persons was usually between 0.8 and 2%. These figures agree with the previously reported overall mutation rates of poliovirus, determined by other methods.

Amino Acid Sequence↗
PubMed1996

Chloroplast and mitochondrial genomes from a liverwort, Marchantia polymorpha--gene organization and molecular evolution.

The complete nucleotide sequence of chloroplast DNA (121,025 basepairs, bp) from a liverwort, Marchantia polymorpha, has made clear the entire gene organization of the chloroplast genome. Quite a few genes encoding components of photosynthesis and protein synthesis machinery have been identified by comparative computer analysis. We also identified the complete nucleotide sequence of the liverwort mitochondrial DNA and deduced 96 possible genes in the sequence of 186,608 bp. The complete nucleotide sequence from chloroplast DNA comprises twenty introns (19 group II and 1 group I) in 18 different genes. One of the chloroplast group II introns separated the ribosomal protein gene in the trans-position. The mitochondrial genome also has thirty-two introns (25 group II and 7 group I) in the coding regions of 17 genes. From the evolutionary point of view, we describe the origin of organellar introns which gave the evidence for their vertical and horizontal transfers and their intragenic propagation, and RNA editing which was apparently lacking in the liverwort chloroplast and mitochondrial genomes.

Amino Acid Sequence↗
PubMed2004

Molecular evolution of FtsZ protein sequences encoded within the genomes of archaea, bacteria, and eukaryota.

The FtsZ protein is a polymer-forming GTPase which drives bacterial cell division and is structurally and functionally related to eukaryotic tubulins. We have searched for FtsZ-related sequences in all freely accessible databases, then used strict criteria based on the tertiary structure of FtsZ and its well-characterized in vitro and in vivo properties to determine which sequences represent genuine homologues of FtsZ. We have identified 225 full-length FtsZ homologues, which we have used to document, phylum by phylum, the primary sequence characteristics of FtsZ homologues from the Bacteria, Archaea, and Eukaryota. We provide evidence for at least five independent ftsZ gene-duplication events in the bacterial kingdom and suggest the existence of three ancestoral euryarchaeal FtsZ paralogues. In addition, we identify "FtsZ-like" sequences from Bacteria and Archaea that, while showing significant sequence similarity to FtsZs, are unlikely to bind and hydrolyze GTP.

Amino Acid Sequence↗
PubMed1994

The molecular evolution of the alcohol dehydrogenase and alcohol dehydrogenase-related genes in the Drosophila melanogaster species subgroup.

The DNA sequences of the Adh genes of three members of the Drosophila melanogaster species subgroup have been determined. This completes the Adh sequences of the eight species of this subgroup. Two species, D. yakuba and D. teissieri, possess processed Adh pseudogenes. In all of the species of the subgroup, a gene of unknown function, Adhr, is located about 300 bp 3' to Adh. Although this gene is experiencing a higher rate of synonymous substitution than Adh, it is more constrained at the amino acid level. Phylogenetic relationships between all eight members of the melanogaster subgroup have been analyzed using a variety of methods. All analyses suggested that the D. yakuba and D. teissieri pseudogenes have a single common ancestor, rather than evolving independently in each species, and that D. melanogaster is the sister species to D. simulans, D. sechellia, and D. mauritiana. The evolutionary relationships of the latter three species remain equivocal.

Alcohol Dehydrogenase↗
PubMed1995

Nucleotide sequences and the molecular evolution of the DMA and DMB genes of the bovine major histocompatibility complex.

cDNA clones encoding the bovine major histocompatibility complex (MHC) class II DM alpha- and beta-chains were isolated and characterized. The BoLA-DMA cDNA clone, MA7, encoded a primary translated product of 260 amino acids, which included a signal peptide of 26 amino acids and a mature polypeptide of 234 amino acids. The BoLA-DMB cDNA clone, MB6, encoded a primary translated product of 262 amino acids, with a signal peptide of 18 amino acids and a mature polypeptide of 244 amino acids. Comparison of the sequences and construction of a phylogenetic tree revealed that both clones are more closely related to human and mouse DM genes than to genes for conventional bovine class II alpha- and beta-chains. Thus, since the bovine DMA and DMB genes are so different from other class II sequences and show evidence of strong conservation (> 70%) among the bovine, mouse and human homologues, it seems likely that each of these cDNA clones encodes a functional product, which might perform an important function, as previously established in studies in mouse and man.

Amino Acid Sequence↗
PubMed1994

Molecular evolution of the period gene in Drosophila athabasca.

We measured nucleotide variability within and between the three semispecies of the Drosophila athabasca complex, at the period (per) gene by using a polymerase chain reaction-based four-cutter restriction-enzyme analysis. The levels of polymorphism varied considerably between the three semispecies. Our results for per, combined with previous data for X-linked allozymes, suggest that the X chromosome in the western-northern semispecies is less variable than expected under an equilibrium-neutral model. Both the pattern of divergence between the semispecies and a cladistic clustering of per haplotypes support the previously hypothesized grouping of eastern A and eastern B as the two most recently diverged semispecies. A 21-bp in-frame segment in the region of per which shares sequence similarity with the neuronal development gene single minded is deleted in all eastern A and eastern B flies examined but is present in all of the western-northern flies and all other published per sequences. Despite these hints that there may be significant differences at the per gene between the semispecies, especially the western-northern group versus the two eastern groups, there is no compelling evidence that per is involved in the mating song differences between the semispecies.

Animals↗
PubMed1985

Diversity in the germline antibody repertoire. Molecular evolution of the T15 VN gene family.

The T15 heavy chain variable region (VH) gene family in BALB/c mice includes four elements each greater than 88% homologous with the other. One of these elements, V1, encodes virtually all of the VH regions in BALB/c antiphosphorylcholine antibodies, while another element, V3, is a pseudogene and cannot be transcribed or translated. We have examined the structural features of this VH gene family in other mouse strains and, in particular, have cloned and sequenced the alleles of these gene segments present in B10.P mice. Each of the four B10.P sequences can be matched with its allelic counterpart in BALB/c mice. This represents the first successful analysis of allelism in antibody variable region gene segments. The V1B10.P allele, like its BALB/c counterpart, encodes most of the known phosphorylcholine binding heavy chains from C37BL/6 mice. Similarly, the V3B10.P gene segment is a pseudogene like V3BALB, although only two of four abnormalities present in the BALB/c allele are also present in the B10.P allele. Careful analysis of the specific substitutions observed in the T15 VH gene family suggests that environmental selection for functional combining regions contributes significantly to the pattern of variation in the germline antibody repertoire. In addition, evidence is presented supporting frequent gene conversion events in the divergence of antibody genes.

Alleles↗
PubMed1995

Synthetic inducible biological response amplifiers (SIBRAs): rational peptides at the crossroads between molecular evolution and structure-based drug design.

The present study proposes a novel type of synthetic chimaeric polypeptides potentially useful in the therapy of various diseases. The prototype peptide termed 'synthetic inducible biological response amplifier' (SIBRA) would comprise a ligand-binding site, a DNA-binding region, a trans-activating domain as well as strings of residues ensuring bioavailability and targeting to specific compartments such as the cell nucleus. These domains would be selected from cellular proteins, artificially tailored to a SIBRA and further modified towards a molecule with both in vivo and intracellular activity. Since proposed to resemble a host molecule with autoregulatory properties, a SIBRA would be activated upon exposure to a defined environmental stimulus and amplify host responses appropriate for this stimulus. Proteins would accumulate that share functional domains with the administered SIBRA and have a positive autoregulatory capacity. The latter may involve the interaction of the induced protein with the promoter of its gene resulting in a direct positive autoregulatory loop or require the induction of intermediary proteins that eventually upregulate the production of SIBRA-like host proteins. Since the ligand-binding site of a SIBRA is rationally designed to target a pathogenic protein, SIBRAs could be regarded as the product of an artificial acceleration and refinement of strategies intrinsic to the immune system.

Biological Availability↗
PubMed1990

Molecular evolution of ubiquitous beta-lactamases towards extended-spectrum enzymes active against newer beta-lactam antibiotics.

Production of beta-lactamases, and of the plasmid-encoded TEM- and SHV-type enzymes in particular, is the most common mechanism of resistance against beta-lactam antibiotics in Gram-negative bacteria. The two ubiquitous types of enzyme have a large spectrum of activity and preferentially hydrolyse the penicillins as well as some first- and second-generation cephalosporins. Recently, point mutations in the corresponding genes have been observed, apparently selected for, in the clinical setting, by originally 'beta-lactamase-stable' third-generation cephalosporins or by monobactams, which fall into the substrate range of the mutant or 'extended-spectrum' beta-lactamases. The point mutations are clustered in three areas, each adjacent to one of the seven evolutionarily conserved boxes described by Joris et al. (1988). The substituted amino acids at positions 102 (adjacent to the alpha-3 helix), 162 (adjacent to the alpha-7 helix) and 235, 236 and 237 (on the beta-3 strand) are located in close proximity to the active-site cavity and are thought to open up novel enzyme-substrate interactions, involving, in particular, the oxyimino moieties of the newer beta-lactam compounds.

Amino Acid Sequence↗
PubMed1988

Molecular evolution of lytic enzymes of Streptococcus pneumoniae and its bacteriophages.

A 2.9-kilobase Acc I fragment of the DNA of the pneumococcal bacteriophage Cp-1, containing the cpl gene, hybridizes with the lytA gene encoding the pneumococcal amidase. The nucleotide sequence of the cpl gene of Cp-1, encoding a muramidase (CPL), has been determined. The 3' regions of the cpl and lytA coding sequences show considerable nucleotide sequence homology and the carboxyl-terminal domains of the deduced amino acid sequences of these lysins are quite similar: 73 of the carboxyl-terminal 142 amino acid residues are identical, and of the 69 substitutions, 55 are conservative. Comparisons between CPL, the pneumococcal amidase, and the muramidase of the fungus Chalaropsis sp. (an enzyme that also degrades the pneumococcal cell wall) strongly suggest that the carboxyl-terminal domains of CPL and of the amidase might be responsible for the specific recognition of choline-containing cell walls, as well as for the noncompetitive inhibition of the catalytic activity of these enzymes by the pneumococcal lipoteichoic acid or by high concentrations of choline. In addition, the active center of these enzymes should be located in their amino-terminal domains. Our results suggest an evolutionary relationship between phage and host lysins.

Amidohydrolases↗
PubMed1988

Molecular evolution of streptococcal M protein: cloning and nucleotide sequence of the type 24 M protein gene and relation to other genes of Streptococcus pyogenes.

The structural gene for the type 24 M protein of group A streptococci has been cloned and expressed in Escherichia coli. The complete nucleotide sequence of the gene and the 3' and 5' flanking regions was determined. The sequence includes an open reading frame of 1,617 base pairs encoding a pre-M24 protein of 539 amino acids and a predicted Mr of 58,738. The structural gene contains two distinct tandemly reiterated elements. The first repeated element consists of 5.3 units, and the second contains 2.7 units. Each element shows little variation of the basic 35-amino-acid unit. Comparison of the sequence of the M24 protein with the sequence of the M6 protein (S. K. Hollingshead, V. A. Fischetti, and J. R. Scott, J. Biol. Chem. 261:1677-1686, 1986) indicates that these molecules have are conserved except in the regions coding for the antigenic (type specific) determinant and they have three regions of homology within the structural genes: 38 of 42 amino acids within the amino terminal signal sequence, the second repeated element of the M24 protein is found in the M6 molecule at the same position in the protein, and the carboxy terminal 164 amino acids, including a membrane anchor sequence, are conserved in both proteins. In addition, the sequences flanking the two genes are strongly conserved.

Amino Acid Sequence↗
PubMed1976

Molecular evolution of the polypeptide hormones.

Any biological function is at least bimolecular and its evolution therefore is at least dual, with variations in two lines of molecules. The hormone specificity results from a particular fit between the three-dimensional structure of the agent and that of the receptor but, because receptors are not known at the structural level, a discussion on the evolution of the polypeptide hormones is mainly limited to the possible progressive changes of the latter. As for other proteins (enzymes, oxygen carriers etc.) two degrees of complexity can be distinguished according to whether the hormone comprises one or several polypeptide chains. Protein assembly can bring new biological properties, each subunit playing a particular role. In this case, the 'internal' evolution (chain-chain interactions) overlaps the 'external' evolution (hormone-receptor contacts). The 'monomeric' hormones present the following problems: evolution of the prohormone and of the converting enzyme (for insulin), duplication and differentiation of two lines of hormones either by amino acid substitutions (neurohypophysial hormones and neurophysins) or by substitutions and size modifications (corticotropin and lipotropin), duplication and fusion leading to internal homology in the single polypeptide chain (somatotropin, prolactin, placental lactogen). The 'dimeric' hormones lead to several problems: successive duplications giving different subunits, selective associations between subunits, unequal rates of evolution of the subunits, the function of each subunit (lutropin, follitropin, thyrotropin, choriogonadotropin). An attempt is made to integrate the evolution of polypeptide hormones in the frame of the evolution of proteins.

Amino Acid Sequence↗