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PubMedDate not supplied

Allele and genotype frequencies of polymorphic FMO3 gene in two genetically distinct populations.

The aims of this study were to analyze flavin-containing monooxygenase 3 (FMO3) polymorphisms and allele and genotype frequencies in 256 Han Chinese and 50 African-American individuals, to compare the allele and genotype frequencies of these populations with those of other world populations. For Han Chinese, genotyping of three common single nucleotide polymorphisms, E158K, V257M and E308G was performed by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP). For African-Americans, genotyping of all coding exons was performed by modified PCR-single strand conformational polymorphism (SSCP). Evolutionary rates of FMO3 were estimated computationally. We found that there were significant differences in allele and genotype frequencies among Han Chinese, African-Americans and other world populations. In Han Chinese, the minor allele frequencies (MAFs) were 0.229 (E158K), 0.203 (V257M) and 0.148 (E308G), respectively. In African-Americans, MAFs were 0.48 (E158K), 0.05 (V257M) and 0 (E308G), respectively. There was rapid evolution during the divergence of primate FMO3. This is the first report comparing FMO alleles and genotypes between Han Chinese and African-Americans. A Han Chinese population database has been established for three gene polymorphisms. The data presented here justify further pharmacogenetic studies for potentially optimizing recommended drug dosages and evaluating relationships with disease processes.

Adult↗
PubMed1996

Membrane exon sequences of the three Xenopus Ig classes explain the evolutionary origin of mammalian isotypes.

We have cloned and sequenced the genes corresponding to the membrane exons of the three immunoglobulin (Ig) heavy chain isotypes (mu, upsilon and chi) of Xenopus. Among membrane Ig (mIg) polypeptides, the transmembrane domain are the most highly conserved. The transmembrane and cytoplasmic domains of Xenopus mIgM are similar to the corresponding domains of all known vertebrate mIgM molecules, supporting the idea that amphibian mu gene is homologous, not just analogous, to the mu gene of higher vertebrates. The membrane forms of the two other Ig isotypes mIgX and mIgY exhibit the specific structure found in all Ig membrane exons, but are not homologous with any specific mammalian non-mu Ig isotype; they are most similar to Xenopus mIgM. Based on the conserved transmembrane domains of Xenopus mIgX, mIgY, we suggest that first the upsilon and later the chi genes arose by duplication from the original mu gene. The transmembrane and the 37-amino-acid-long cytoplasmic domains of Xenopus mIgY have conserved residues found in avian mIgY and mammalian mIgG and mIgE, suggesting that the modern isotypes might share a common ancestor with amphibian mIgY. However, while the sequence similarity between the membrane exons of avian mIgY and mammalian mIgG and IgE is striking, the overall similarity with Xenopus mIgY is very low. Thus, the genes giving rise to Xenopus mIgY and those eventually leading to avian mIgY and mammalian mIgG and mIgE must have diverged early in evolution, probably at the level of the primitive amphibians or before.

Amino Acid Sequence↗
PubMed1985

DO beta: a new beta chain gene in HLA-D with a distinct regulation of expression.

The HLA-D region of the human major histocompatibility complex encodes the genes for the alpha and beta chains of the DP, DQ and DR class II antigens. A cDNA clone encoding a new class II beta chain (designated DO) was isolated from a library constructed from mRNA of a mutant B-cell line having a single HLA haplotype. Complete cDNA clones encoding the four isotypic beta chains of the DR1, DQw1, DPw2 and putative DO antigens were sequenced. The DO beta gene was mapped in the D region by hybridization with DNA of HLA-deletion mutants. DO beta mRNA expression is low in B-cell lines but remains in mutant lines which have lost expression of other class II genes. Unlike other class II genes DO beta is not induced by gamma-interferon in fibroblast lines. The DO beta gene is distinct from the DP beta, DQ beta and DR beta genes in its pattern of nucleotide divergence. The independent evolution and expression of DO beta suggest that it may be part of a functionally distinct class II molecule.

Amino Acid Sequence↗
PubMedDate not supplied

Exquisite specificity and peptide epitope recognition promiscuity, properties shared by antibodies from sharks to humans.

This review considers definitions of the specificity of antibodies including the development of recent concepts of recognition polyspecificity and epitope promiscuity. Using sets of homologous and unrelated peptides derived from the sequences of immunoglobulin and T cell receptor chains we offer operational definitions of cross-reactivity by investigating correlations of either identities in amino acid sequence, or in hydrophobicity/hydrophilicity profiles with degree of binding in enzyme-linked immunosorbent assays. Polyreactivity, or polyspecificity, are terms used to denote binding of a monoclonal antibody or purified antibody preparation to large complex molecules that are structurally unrelated, such as thyroglobulin and DNA. As a first approximation, there is a linear correlation between degree of sequence identity or hydrophobicity/hydrophilicity and antigenic cross-binding. However, catastrophic interchanges of amino acids can occur where changing of one amino acid out of 16 in a synthetic peptide essentially eliminates binding to certain antibodies. An operational definition of epitope promiscuity for peptides is the case where two peptides show little or no identity in amino acid sequence but bind strongly to the same antibody as shown by either direct binding or competitive inhibition. Analysis of antibodies of humans and sharks, the two most divergent species in evolution to express antibodies and the combinatorial immune response, indicates that the capacity for both exquisite specificity and epitope recognition promiscuity are essential conserved features of individual vertebrate antibodies.

Amino Acid Sequence↗
PubMed1993

MIF protein are theta-class glutathione S-transferase homologs.

MIF proteins are mammalian polypeptides of approximately 13,000 molecular weight. This class includes human macrophage migration inhibitory factor (MIF), a rat liver protein that has glutathione S-transferase (GST) activity (TRANSMIF), and the mouse delayed early response gene 6 (DER6) protein. MIF proteins were previously linked to GSTs by demonstrating transferase activity and observing N-terminal sequence homology with a mu-class GST (Blocki, F.A., Schlievert, P.M., & Wackett, L.P., 1992, Nature 360, 269-270). In this study, MIF proteins are shown to be structurally related to the theta class of GSTs. This is established in three ways. First, unique primary sequence patterns are developed for each of the GST gene classes. The patterns identify the three MIF proteins as theta-like transferase homologs. Second, pattern analysis indicates that GST members of the theta class contain a serine residue in place of the N-terminal tyrosine that is implicated in glutathione deprotonation and activation in GSTs of known structure (Liu, S., et al., 1992, J. Biol. Chem. 267, 4296-4299). The MIF proteins contain a threonine at this position. Third, polyclonal antibodies raised against recombinant human MIF cross-react on Western blots with rat theta GST but not with alpha and mu GSTs. That MIF proteins have glutathione-binding ability may provide a common structural key toward understanding the varied functions of this widely distributed emerging gene family. Because theta is thought to be the most ancient evolutionary GST class, MIF proteins may have diverged early in evolution but retained a glutathione-binding domain.

Amino Acid Sequence↗
PubMed2004

Analysis of protein homology by assessing the (dis)similarity in protein loop regions.

Two proteins are considered to have a similar fold if sufficiently many of their secondary structure elements are positioned similarly in space and are connected in the same order. Such a common structural scaffold may arise due to either divergent or convergent evolution. The intervening unaligned regions ("loops") between the superimposable helices and strands can exhibit a wide range of similarity and may offer clues to the structural evolution of folds. One might argue that more closely related proteins differ less in their nonconserved loop regions than distantly related proteins and, at the same time, the degree of variability in the loop regions in structurally similar but unrelated proteins is higher than in homologs. Here we introduce a new measure for structural (dis)similarity in loop regions that is based on the concept of the Hausdorff metric. This measure is used to gauge protein relatedness and is tested on a benchmark of homologous and analogous protein structures. It has been shown that the new measure can distinguish homologous from analogous proteins with the same or higher accuracy than the conventional measures that are based on comparing proteins in structurally aligned regions. We argue that this result can be attributed to the higher sensitivity of the Hausdorff (dis)similarity measure in detecting particularly evident dissimilarities in structures and draw some conclusions about evolutionary relatedness of proteins in the most populated protein folds.

Computational Biology↗
PubMed1993

Isolation of a cDNA for chicken liver 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase.

A chicken liver cDNA for 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase was isolated from a Lambda ZAP2 phage library. The chicken liver cDNA codes for a protein that has 89.1, 88.4 and 88.0% amino acid identity with the human, rat and bovine liver isoforms, respectively. The kinetic properties of the rat and chicken liver enzymes, purified to homogeneity after expression in E. coli, were different including negative cooperativity for ATP binding and inhibition by Mg2+ for the chicken liver 6-phosphofructo-2-kinase but not for the rat liver kinase. Differences in the beta-loop ATP signature sequences in the chicken and rat liver kinase domains may explain the kinetic differences and represent the major divergence in the evolution of the enzyme from birds to mammals.

Adenosine Triphosphate↗
PubMed1999

Cloning and analysis of the gene for the human puromycin-sensitive aminopeptidase.

The gene encoding the human puromycin-sensitive aminopeptidase (PSA) has been cloned and characterized. The human PSA gene is composed of 23 exons and 22 introns and spans approximately 40 kb of chromosome 17 at the interval 17q12-21. An analysis of the 5' end of the human PSA transcript reveals that the translational start site corresponds to nt 210 of the human PSA cDNA, as suggested by RT-PCR, 5' RACE, and computer analysis of expressed sequence tags. A comparison of the exon/exon boundaries of the human PSA gene with those of the human aminopeptidase N (APN) gene shows little conservation, suggesting that the two genes, which are closely related in protein sequence, diverged early during evolution.

Amino Acid Sequence↗
PubMedDate not supplied

Structural proteins involved in emergence of microbial aerial hyphae.

Filamentous fungi and filamentous bacteria (i.e., the streptomycetes) belong to different kingdoms that diverged early in evolution. Yet, they adopted similar lifestyles. After a submerged feeding mycelium has been established, hyphae grow into the air and form aerial structures from which (a)sexual spores can develop. These spores are dispersed and can give rise to a new mycelium. Some of the key processes involved in the formation of aerial hyphae by these microbes appear to be very similar. In both cases molecules that lower the surface tension are secreted into the aqueous environment, thereby enabling hyphae to grow into the air. Aerial hyphae are then covered with a hydrophobic film. In fungi, this film is characterized by a mosaic of parallel rodlets, while similar rodlets have also been observed on aerial structures of filamentous bacteria. Although the erection of aerial hyphae in both filamentous fungi and filamentous bacteria is dependent upon (poly)peptides that are structurally unrelated, they can, at least partially, functionally substitute for each other.

Bacterial Proteins↗
PubMed1993

The human glutamate dehydrogenase gene family: gene organization and structural characterization.

Glutamate dehydrogenase is a mitochondrially located, key metabolic enzyme. In addition to its general metabolic role, GLUD is important in neurotransmission. Significant alterations in GLUD enzymatic activity have been associated with certain neurodegenerative human disorders. Although a single species of human GLUD cDNA molecule has been identified so far, both genomic DNA Southern and cytogenetic analyses have indicated the presence of a GLUD gene family. Screening of a human genomic lambda-phage library with the GLUD cDNA, led us to the isolation of several clones divided into five structurally distinct contigs. We have confirmed the presence of all GLUD-specific sequences in the human genome by detailed genomic Southern analysis. This study allowed the identification of the entire functional GLUD gene, named GLUD1. The GLUD1 gene is about 45 kb long and it is organized into 13 exons. Its nucleotide sequence, exon-intron boundaries, and transcription start sites were determined. Potential binding sites for various regulatory factors such as Sp1, AP-1, and AP-2 were recognized at the promoter region of the gene. The members of the other contigs showed an organization clearly different from GLUD1. Two distinct GLUD-specific gene loci, termed GLUDP2 and GLUDP3, possibly represent truncated pseudogenes. Their high degree of similarity to GLUD1 is limited to the region surrounding exons 2, 3, and 4. Finally, two additional GLUD-specific genomic sequences, termed GLUDP4 and GLUDP5, are structurally similar with the 3' part of the GLUD cDNA sequence. These loci probably represent truncated GLUD pseudogenes generated by retrotransposition. The data presented here suggest that all human GLUD pseudogenes have diverged recently in evolution.

Amino Acid Sequence↗
PubMed1986

Molecular evolution of the carbonic anhydrase genes: calculation of divergence time for mouse carbonic anhydrase I and II.

A cDNA clone in pBR322 that cross-hybridizes with a mouse carbonic anhydrase form II (CAII) probe has been sequenced and identified as mouse carbonic anhydrase form I (CAI). The 1224-base-pair clone encodes the entire 260-amino-acid protein and appears to contain an Alu-like element in the 3' untranslated region. The deduced amino acid sequence exhibits 77% homology to human CAI and contains 17 of the 20 residues that are considered unique to and invariant for all mammalian CAI isozymes. The results of a detailed comparison of the nucleic acid sequences spanning the coding regions of mouse CAI and rabbit CAI have been used to calibrate an evolutionary clock for the carbonic anhydrases (CAs). These data have been applied to a comparison of the mouse CAI and CAII nucleic acid sequences to calculate the divergence time between the two genes. The divergence-time calculation provides the first estimation of the evolutionary relationship between CAs based entirely on nucleotide sequence comparison.

Amino Acid Sequence↗
PubMed1996

The gene for a subunit of an ABC-type heme transporter is transcribed together with the gene for subunit 6 of NADH dehydrogenase in rice mitochondria.

We previously identified a chloroplast-derived (ct-derived) sequence of 32 base pairs (bp) in rice mitochondrial DNA that includes a part (30 bp; psitrnI) of a gene for isoleucine tRNA (CAU) of the chloroplast. Analyzing the ct-derived psitrnI, we found that an open reading frame (orf240), which was homologous to the gene for a subunit of an ATP-binding cassette-type (ABC-type) heme transporter, namely helC, of Rhodobacter capsulatus, and a gene for subunit 6 of NADH dehydrogenase (nad6) were located upstream of and downstream from the ct-derived psitrnI, respectively. Northern-blot hybridization and analysis by reverse transcription-polymerase chain reaction (RT-PCR) revealed that both orf240 and nad6 were co-transcribed in rice mitochondria. An analysis of PCR-amplified fragments of the region of orf240/nad6 from the DNA of some Gramineae suggests that the arrangement of orf240/nad6 was generated in the mitochondrial genome of the genus Oryza during evolution after its divergence from the other Gramineae. Most of the transcripts of orf240 are edited, with a change from cytidine to uridine, at 35 positions. Editing of the RNA changes 33 amino-acid residues among the 240 encoded amino-acid residues, suggesting that the orf240 gene is functional in rice mitochondria.

ATP-Binding Cassette Transporters↗
PubMed1997

Profile of numbers of sequence differences among V-genes coding for the variable regions of T cell receptor for antigen alpha and beta chains.

When human T cell receptor for antigen (TCR) alpha chain V-genes were compared pair-wise, the numbers of nucleotide differences showed a characteristic distribution; most were in the range of 100 to 200 differences out of a total of about 300 bases. The same distribution was observed for mouse TCR alpha chains. Even more interesting was that comparing human alpha chains and mouse alpha chains gave essentially the same nucleotide difference pattern. It is inferred from the large number of differences and from the nonspecificity of trans-species (human and mouse) nucleotide sequence differences of TCR V-genes that TCR alpha chains probably diverged early during evolution. The same feature was also observed for human and mouse TCR beta chains, although the alpha and beta chain V-genes were distinct. This evolutionary preservation could be of vital importance to the fidelity of the complicated trimolecular interactions among TCR alpha and beta chains, the processed peptide, and the major histocompatibility complex (MHC) class I or II molecules.

Animals↗
PubMed2005

Conservation of novel Mahya genes shows the existence of neural functions common between Hymenoptera and Deuterostome.

Honeybees have been shown to exhibit cognitive performances that were thought to be specific to some vertebrates. However, the molecular and cellular mechanisms of such cognitive abilities of the bees have not been understood. We have identified a novel gene, Mahya, expressed in the brain of the honeybee, Apis mellifera, and other Hymenoptera. Mahya orthologues are present in Deuterostomes but are absent or highly diverged in nematodes and, intriguingly, in two dipteran insects (fruit fly and mosquito) and Lepidoptera (silk moth). Mahya genes encode novel secretory proteins with a follistatin-like domain (Kazal-type serine/threonine protease inhibitor domain and EF-hand calcium-binding domain), two immunoglobulin domains, and a C-terminal novel domain. Honeybee Mahya is expressed in the mushroom bodies and antennal lobes of the brain. Zebra fish Mahya orthologues are expressed in the olfactory bulb, telencephalon, habenula, optic tectum, and cerebellum of the brain. Mouse Mahya orthologues are expressed in the olfactory bulb, hippocampus, and cerebellum of the brain. These results suggest that Mahya may be involved in learning and memory and in processing of sensory information in Hymenoptera and vertebrates. Furthermore, the limited existence of Mahya in the genomes of Hymenoptera and Deuterostomes supports the hypothesis that the genes typically represented by Mahya were lost or highly diverged during the evolution of the central nervous system of specific Bilaterian branches under the specific selection and subsequent adaptation associated with different ecologies and life histories.

Animals↗
PubMed2002

Sec20p-interacting proteins (Tip20p, Ufe1p) in the retrograde secretory pathway of the fungal pathogen Candida albicans.

Sec20p is an essential Type-II membrane protein of the human fungal pathogen Candida albicans, which is thought to be involved in mediating retrograde vesicle traffic from the Golgi to the endoplasmic reticulum (ER). Using an epitope-tagged Sec20p we obtained evidence for its localization in ER membranes, which is consistent with its proposed role in an ER-tSNARE complex. Two genes encoding potential interaction partners for Sec20p, Tip20p and Ufe1p, were identified in genomic sequences of C. albicans; these show 18% and 27% identity, respectively, to homologues in Saccharomyces cerevisiae. An interaction between the cytoplasmic domain of Sec20p and Tip20p was demonstrated by two-hybrid analysis; in addition, Tip20p was found to form homodimers. Interaction between Sec20p and Tip20p in vivo was verified by co-immunoprecipation experiments. CaUFE1, which encodes a potential ER-tSNARE, was able to complement a thermosensitive ufe1 mutation in S. cerevisiae, suggesting functional conservation between the two fungal proteins. Thus, although the sequences of some components of the ER-tSNARE complex have diverged considerably during evolution, it appears that they have retained similar functions in C. albicans and S. cerevisiae.

Amino Acid Sequence↗
PubMed1992

Species diversity of neuronectin and cytotactin expression patterns in the vertebrate central nervous system.

Two extracellular matrix proteins of brain tissue, neuronectin (NEC1) and cytotactin (CT), are disulfide-bonded multimers of M(r) 180,000-250,000 subunits. The previously known distribution of these molecules is, however, very different. Human NEC1 is found throughout the white matter of rostral segments of the adult central nervous system (CNS) but not in rostral gray matter or in caudal CNS segments, including the cerebellum. In contrast, CT is absent or expressed at a low level in the adult chicken cerebrum but highly expressed in the cerebellum. Despite these differences in distribution, results obtained with antibodies that recognize NEC1 and CT in several vertebrate species indicate that these molecules are identical or at least closely related: (1) alpha NEC1 antibodies recognize proteins affinity-purified with CT-binding proteoglycan; (2) proteins recognized by alpha NEC1 and alpha CT antibodies in cells constitutively expressing the molecules, cells in which expression is induced by growth factors and phorbol ester and cells treated with tunicamycin (to block glycosylation) are identical in subunit composition and mobility on SDS gels; (3) the removal of NEC1 from culture supernatants by immunoprecipitation removes all molecules reactive with alpha CT antibodies and vice versa; (4) immunoblots of brain extracts with alpha NEC1 and alpha CT antibodies yield identical results. Having demonstrated the structural similarity between NEC1 and CT, we reexamined their distribution in the CNS. Surprisingly, the temporal and spatial distribution pattern of NEC1/CT varied greatly among species. Immunohistochemical and immunoblot experiments with adult human CNS tissues revealed significant levels of NEC1/CT in rostral but not caudal segments. In contrast, in cows and pigs the molecule is found throughout the CNS. Adult rat and mouse brains show regionally restricted expression of NEC1/CT in several areas of the cerebrum--distinct from those showing NEC1/CT in the human--and in the molecular layer of the cerebellum. Tests with fetal and newborn tissues revealed that CNS development in humans, cows and pigs is not accompanied by the marked decline in NEC1/CT levels or the changes in subunit composition found in the chicken CNS. The marked species diversity in temporospatial expression patterns suggests that intrinsic and/or extrinsic elements controlling the expression of NEC1/CT have diverged during vertebrate evolution.

Animals↗
PubMed1995

Chicken beta B1 crystallin: gene sequence and evidence for functional conservation of promoter activity between chicken and mouse.

The complete sequence was determined for the chicken beta B1-crystallin gene and 2.2 kbp of its 5' flanking region; the chicken gene was then compared to its rat ortholog. Although both have a 5' non-coding exon followed by 5 protein coding exons, the chicken gene is only 2.2 kbp while the rat gene is 13.6 kpb due to longer introns. The coding exons of the chicken beta B1-crystallin gene, like those of the rat and other beta-crystallin genes, each correspond to one of the four 'Greek key' motifs of the encoded protein. The only obvious similarity between the 5' flanking sequences of the chicken and rat beta B1-crystallin gene is associated with the TATA box. A CR1 repetitive element is present at positions -559 to -730 of the chicken beta B1-crystallin gene. In vivo footprinting using dimethyl sulfate/ligation mediated PCR showed that the PL-1 (-116/-102), PL-2 (-90/-76), OL-2 (-75/-68) and OL-1 (-125/-118) control elements identified previously (Roth et al. (1991) Mol. Cell. Biol. 11, 1488-1499) bind proteins within the chromatin of cultured embryonic chicken lens cells. Both -2448/+30 and -434/+30 promoter fragments from the chicken beta B1-crystallin gene directed lens-specific CAT gene expression in a copy number and position independent manner in transgenic mice. These data indicate that the structure and lens-specific expression of this gene are highly conserved although, like other crystallin genes, the 5' flanking sequences have diverged appreciably during evolution.

Amino Acid Sequence↗
PubMed1987

The immunoglobulins of carcharhine sharks: a comparison of serological and biochemical properties.

The immunoglobulins of three carcharhine sharks were isolated from serum by means of salt precipitation and gel chromatography. The Galapagos shark (Carcharhinus galapagensis), the sandbar shark (Carcharhinus plumbeus) and the tiger shark (Galeocerdo cuvieri) each contained high molecular weight (18S) and low molecular weight (7S) IgM-like molecules as the major serum immunoglobulins. Both within and between species 18S and 7S immunoglobulins closely resemble each other in antigenic character, polypeptide chain composition, chain mass, amino acid composition, carbohydrate content and amino-terminal sequence. These results suggest that the immunoglobulins of carcharhine sharks have undergone little structural divergence during their evolution.

Amino Acid Sequence↗