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PubMedDate not supplied

Complete structural characterisation of the mammalian and Drosophila TRAF genes: implications for TRAF evolution and the role of RING finger splice variants.

The complete murine TRAF2 gene was obtained using a lambda phage and PCR cloning strategy. The gene was found to consist of ten coding and one 5' non-coding exon spread over 28 kbp of DNA. We also report the basic structure of the human TRAF5 and TRAF6 genes obtained by analysis of the genomic DNA database. Comparison of these three gene structures, along with those previously described for TRAF1, TRAF3 and TRAF4, revealed the evolutionary relationship between the six known mammalian TRAFs. The TRAF1/TRAF2 and TRAF3/TRAF5 gene pairs were found to have arisen from recent independent gene duplications and to share a common ancestral gene. Specific TRAF4 and TRAF6 precursor genes were found to have arisen earlier during evolution, with the divergence of the TRAF6 precursor occuring earliest of all. The Drosophila genome was found to contain three TRAF family genes: dTRAF1, dTRAF6 (dTRAF2) and a previously undescribed member we have designated dTRAF3. TRAF-C domain homology indicated that dTRAF3 is likely to have derived from the common precursor for the TRAF 1, 2, 3 and 5 genes, whilst dTRAF1 and dTRAF6 have derived from the TRAF4 and TRAF6 precursor genes, respectively. The implication of these results for the functional evolution of TRAFs is discussed. Analysis is also presented of the conservation of the TRAF2A molecule, a TRAF2 alternate splice isoform with an extended RING finger domain previously described in mice. TRAF2A was not found to be encoded by the human or rat TRAF2 genes and no other murine TRAF gene was found to produce a similar alternate splice product. We also report that the sequence of murine C57BL/6 TRAF4 differs significantly from the published murine TRAF4 sequence, but appears to represent the actual TRAF4 sequence expressed in many mouse strains.

5' Untranslated Regions↗
PubMed2005

Nonsense-mediated mRNA decay factors act in concert to regulate common mRNA targets.

Nonsense-mediated mRNA decay (NMD) is a surveillance pathway that degrades mRNAs containing nonsense codons, and regulates the expression of naturally occurring transcripts. While NMD is not essential in yeast or nematodes, UPF1, a key NMD effector, is essential in mice. Here we show that NMD components are required for cell proliferation in Drosophila. This raises the question of whether NMD effectors diverged functionally during evolution. To address this question, we examined expression profiles in Drosophila cells depleted of all known metazoan NMD components. We show that UPF1, UPF2, UPF3, SMG1, SMG5, and SMG6 regulate in concert the expression of a cohort of genes with functions in a wide range of cellular activities, including cell cycle progression. Only a few transcripts were regulated exclusively by individual factors, suggesting that these proteins act mainly in the NMD pathway and their role in mRNA decay has not diverged substantially. Finally, the vast majority of NMD targets in Drosophila are not orthologs of targets previously identified in yeast or human cells. Thus phenotypic differences observed across species following inhibition of NMD can be largely attributed to changes in the repertoire of regulated genes.

Animals↗
PubMed2006

Gene duplication and inactivation in the HPRT gene family.

Hypoxanthine phosphoribosyltransferase (HPRT1) is a key enzyme in the purine salvage pathway, and mutations in HPRT1 cause Lesch-Nyhan disease. The studies described here utilized targeted comparative mapping and sequencing, in conjunction with database searches, to assemble a collection of 53 HPRT1 homologs from 28 vertebrates. Phylogenetic analysis of these homologs revealed that the HPRT gene family expanded as the result of ancient vertebrate-specific duplications and is composed of three groups consisting of HPRT1, phosphoribosyl transferase domain containing protein 1 (PRTFDC1), and HPRT1L genes. All members of the vertebrate HPRT gene family share a common intron-exon structure; however, we have found that the three gene groups have distinct rates of evolution and potentially divergent functions. Finally, we report our finding that PRTFDC1 was recently inactivated in the mouse lineage and propose the loss of function of this gene as a candidate genetic basis for the phenotypic disparity between HPRT-deficient humans and mice.

Animals↗
PubMed1993

[The structural and functional classification and evolution of cytokines].

According to the type of secondary structure, cytokines are classified into three categories: alpha-spiral (IFNs-alpha, beta, omega, gamma; ILS-2, 3,4,5,6,7,9; CSFs-G, M, GM, MGF, PDGF), beta-structural (ILs-1 alpha, beta, TNFs-alpha, beta, FGF) and (alpha + beta)-structural proteins (IL-8, IFN-gamma IP-10, PF-4, bTG, GRO, 9E3). According to the type of tertiary structure, alpha-spiral proteins are grouped into IFN- and IL-2-like families and beta-structural ones into IL-1-, and TNF-like families. Two subfamilies can be identified in the IFN-like family. Theoretical and experimental evidence suggests that the genes IFNs are products of divergent or convergent evolution towards the gene of the ancient intracellular protein alpha-prothymosine, which is evolutionally in turn associated with the L7/I1 protein of two ribosomes. It is suggested that the proteins of the immunoglobulin superfamily, including cytokine receptors descended from the ancient proteins of the unicellular organisms molecular shaperons.

Amino Acid Sequence↗
PubMed2001

Molecular evolution of GH in primates: characterisation of the GH genes from slow loris and marmoset defines an episode of rapid evolutionary change.

Pituitary growth hormone (GH), like several other protein hormones, shows an unusual episodic pattern of molecular evolution in which sustained bursts of rapid change are imposed on long periods of very slow evolution (near-stasis). A marked period of rapid change occurred in the evolution of GH in primates or a primate ancestor, and gave rise to the species specificity that is characteristic of human GH. We have defined more precisely the position of this burst by cloning and sequencing the GH genes for a prosimian, the slow loris (Nycticebus pygmaeus) and a New World monkey, marmoset (Callithrix jacchus). Slow loris GH is very similar in sequence to pig GH, demonstrating that the period of rapid change occurred during primate evolution, after the separation of lines leading to prosimians and higher primates. The putative marmoset GH is similar in sequence to human GH, demonstrating that the accelerated evolution occurred before divergence of New World monkeys and Old World monkeys/apes. The burst of change was confined largely to coding sequence for mature GH, and is not marked in other components of the gene sequence including signal peptide, 5' upstream region and introns. A number of factors support the idea that this episode of rapid change was due to positive adaptive selection. Thus (1) there is no apparent loss of function of GH in man compared with non-primates, (2) after the episode of rapid change the rate of evolution fell towards the slow basal level that is seen for most mammalian GHs, (3) the accelerated rate of substitution for the exons of the GH gene significantly exceeds that for introns, and (4) the amino acids contributing to the hydrophobic core of GH are strongly conserved when higher primate and other GH sequences are compared, and for coding sequences other than that coding for hydrophobic core residues the rate of substitution for non-synonymous sites (K(A)) is significantly greater than that for synonymous sites (K(S)). In slow loris, as in most non-primate mammals, there is no evidence for duplication of the GH gene, but in marmoset, as in rhesus monkey and man, the putative GH gene is one of a cluster of closely related genes.

Animals↗
PubMed2002

Convergent evolution on the molecular level.

Divergence and convergence are two evolutionary processes by which organisms become adapted to their environments. With the advent of molecular biological techniques it is possible to ask if these processes are observed at the molecular level. There are many examples of molecular divergence in which molecular sequence or function change over evolutionary time. There are fewer reports of convergent evolution on the molecular level, and these claims are sometimes controversial. In this paper I discuss the types of convergent molecular evolution, describe the criteria for accepting or rejecting convergence, and give some examples relevant to neurobiology where convergence has been claimed. These include convergent evolution of opsins, gap junction proteins, neurotransmitter receptors, ion channels, and venoms directed against ion channels.

Animals↗
PubMed1987

Uricoteley:its nature and origin during the evolution of tetrapod vertebrates.

The hepatic mechanism for detoxication of ammonia formed during amino acid gluconeogenesis in uricotelic vertebrates requires the intramitochondrial synthesis of glutamine by glutamine synthetase. This glutamine then serves as a precursor of uric acid in the cytosol. The evolutionary development of uricoteley thus required the localization of glutamine synthetase in liver mitochondria. The mechanism for the mitochondrial import of glutamine synthetase in uricotelic vertebrate liver is not yet known. Tortoises, extant relatives of the stem reptiles, possess both the ureotelic and uricotelic hepatic systems. It therefore seems likely that the genetic events allowing the mitochondrial localization of glutamine synthetase in liver occurred in the amniote amphibian ancestors of the stem reptiles. The selection of ureoteley by the theropsids and of uricoteley by the sauropsids were major events in the divergence and subsequent evolution of these two lines. Once established in the sauropsid line, uricoteley has persisted through to the higher reptiles, crocodilians, and birds. Uricoteley was in part responsible for the radiation of the archosaurs during the Triassic as a water-conserving mechanism in the adult, thereby allowing them to invade the arid environments of that period. Contrary to dogma, uricoteley was probably of minor significance in the development of the cleidoic egg. Neither mammalian nor avian embryonic liver tissues catabolize amino acids to any great extent, so it is inappropriate to attribute to them a kind of "waste" nitrogen metabolism.

Ammonia↗
PubMed2002

Progress in bioinformatics and the importance of being earnest.

In silico biology has gathered momentum as, worldwide, scientists have united in a common quest to sequence, store and analyse complete genomes. This year, a pivotal achievement of this cooperative endeavour was realised in the release of a public draft of the human genome, and with it the promises to improve our understanding of diverse aspects of biology and to yield a healthier future with safe personalized medicines. Key to these goals will be the need to elucidate and characterise the genes and gene products encoded not just in the human genome, but in many genomes. These tasks are underpinned by the concepts and processes of genome and gene/protein evolution, regulation of gene expression, mechanisms of protein folding, the manifestation of protein function, and so on, all of which must be understood in the context of complex, dynamic biological systems. Our use of computers to model such concepts and systems must be placed in the context of the current limits of our understanding of them:- it is important to recognise, for example, that we don't have a common understanding either of what constitutes a gene or a protein function; we can't invariably say that a particular sequence or fold has arisen via divergent or convergent evolution; and we don't fully understand the rules of protein folding. Accepting what we can't do in silico is essential in appreciating what we can do. Without this understanding, it is easy to be misled, as notions of what particular computational approaches can achieve are sometimes rather optimistic. There are valuable lessons to be learned here from the field of Artificial Intelligence, principal among which is the realisation that capturing and representing complex knowledge is time consuming, expensive and hard. Thus, we argue here that if bioinformatics is to tackle biological complexity in earnest, it would be wise to absorb the experience distilled from decades of artificial intelligence research, and to approach the road ahead with caution, rigour and pragmatism.

Artificial Intelligence↗
PubMedDate not supplied

Developmental mechanisms of threshold evolution in a polyphenic beetle.

Polyphenic development is thought to play a pivotal role in the origin of morphological novelties. However, little is known about how polyphenisms evolve in natural populations, the developmental mechanisms that may mediate such evolution, and the consequences of such modification for patterns of morphological variation. Here we examine the developmental mechanisms of polyphenism evolution in highly divergent natural populations of the dung beetle, Onthophagus taurus. Males of this species express two alternative morphologies in response to larval feeding conditions. Favorable conditions cause males to grow larger than a threshold body size and to develop a pair of horns on their heads. Males that encounter relatively poor conditions during larval life do not reach this threshold size and remain hornless. Exotic populations of O. taurus have diverged dramatically in body size thresholds in less than 40 years since introduction to new habitats, resulting in the expression of highly divergent and novel horn length-body size scaling relationships in these populations. Here we show that larvae of populations that have evolved a larger threshold body size (1) have to accumulate greater mass to become competent to express the horned morph, (2) require more time to complete the final instar, (3) are less sensitive to the juvenile hormone (JH) analogue methoprene, and (4) exhibit a delay in the sensitive period for methoprene relative to other developmental events. JH has been shown previously to control horn expression in this species. Our results show that threshold evolution may be mediated via changes in the degree and timing of sensitivity to JH and may result in correlated changes in the dynamics and duration of larval development. Strain-specific differences in JH sensitivity have previously been demonstrated in other insects. However, to the best of our knowledge this is the first demonstration that changes in the timing of the sensitive period for JH may play an equally important role in the evolution of novel thresholds. We discuss our findings in the context of the developmental regulatory mechanisms that underlie polyphenic development and use our results to explore the consequences of, and constraints on, polyphenism evolution in nature.

Animals↗
PubMed1998

A mitochondrial-like chaperonin 60 gene in Giardia lamblia: evidence that diplomonads once harbored an endosymbiont related to the progenitor of mitochondria.

Diplomonads, parabasalids, as represented by trichomonads, and microsporidia are three protist lineages lacking mitochondria that branch earlier than all other eukaryotes in small subunit rRNA and elongation factor phylogenies. The absence of mitochondria and plastids in these organisms suggested that they diverged before the origin of these organelles. However, recent discoveries of mitochondrial-like heat shock protein 70 and/or chaperonin 60 (cpn60) genes in trichomonads and microsporidia imply that the ancestors of these two groups once harbored mitochondria or their endosymbiotic progenitors. In this report, we describe a mitochondrial-like cpn60 homolog from the diplomonad parasite Giardia lamblia. Northern and Western blots reveal that the expression of cpn60 is independent of cellular stress and, except during excystation, occurs throughout the G. lamblia life cycle. Phylogenetic analyses position the G. lamblia cpn60 in a clade that includes mitochondrial and hydrogenosomal cpn60 proteins. The most parsimonious interpretation of these data is that the cpn60 gene was transferred from the endosymbiotic ancestors of mitochondria to the nucleus early in eukaryotic evolution, before the divergence of the diplomonads and trichomonads from other extant eukaryotic lineages. A more complicated explanation requires that these genes originated from distinct alpha-proteobacterial endosymbioses that formed transiently within these protist lineages.

Amino Acid Sequence↗
PubMed2003

Four functionally distinct C-type natriuretic peptides found in fish reveal evolutionary history of the natriuretic peptide system.

Natriuretic peptides (NPs) are major cardiovascular and osmoregulatory hormones in vertebrates. Although tetrapods generally have three subtypes, atrial NP (ANP), B-type NP (BNP), and C-type NP (CNP), some teleosts lack BNP, and sharks and hagfish have only one NP. Thus, NPs have diverged during fish evolution, possibly reflecting changes in osmoregulatory systems. In this study, we found, by cDNA cloning, four distinct CNPs (1 through 4) in the medaka (Oryzias latipes) and puffer fish (Takifugu rubripes), although to our knowledge no more than two CNPs have been isolated from a vertebrate species. Predicted mature CNP-1 was most similar, and CNP-4 was most dissimilar, to mammalian CNPs. However, synthetic CNP-4 most potently activated OlGC1, a medaka CNP-specific receptor (NPR-B) expressed in cultured cells, whereas CNP-1 and CNP-3 most activated OlGC7 and OlGC2, two medaka homologues of the ANP/BNP receptor (NPR-A), respectively. Linkage mapping in medaka followed by comparative genomic analyses among fishes and humans located four CNP genes in separate medaka chromosomes corresponding to human chromosomes 1, 2, 12, and 17. From conserved synteny, the following evolutionary history of NPs was evoked: (i) four CNP genes were generated by chromosomal duplications before the divergence of elasmobranchs; (ii) the CNP-3 gene generated ANP and BNP genes through tandem duplication before the divergence of tetrapods and teleosts; (iii) CNP-1 and -2 genes were retained in the teleost lineage but not in the tetrapod lineage; (iv) the CNP-3 gene disappeared from the tetrapod lineage after divergence of amphibians; and (v) the CNP-4 gene is retained in humans as CNP.

Amino Acid Sequence↗
PubMed2006

Supernetwork identifies multiple events of plastid trnF(GAA) pseudogene evolution in the Brassicaceae.

The occurrence of nonfunctional trnF pseudogenes has been rarely described in flowering plants. However, we describe the first large-scale supernetwork for the Brassiccaeae built from gene trees for 5 loci (adh, chs, matK, trnL-F, and ITS) and report multiple independent origins for trnF pseudogenes in crucifers. The duplicated regions of the original trnF gene are comprised of its anticodon domain and several other highly structured motifs not related to the original gene. Length variation of the trnL-F intergenic spacer region in different taxa ranges from 219 to 900 bp as a result of differences in pseudocopy number (1-14). It is speculated that functional constraints favor 2-3 or 5-6 copies, as found in Arabidopsis and Boechera. The phylogenetic distribution of microstructural changes for the trnL-F region supports ancient patterns of divergence in crucifer evolution for some but not all gene loci.

Brassicaceae↗
PubMed1999

A highly conserved 3-methylhistidine modification is absent in yeast actin.

To identify a protein histidine methyltransferase from Saccharomyces cerevisiae, we examined purified actin for the presence of the highly conserved 3-methylhistidine residue at position 73 by amino acid analysis of the whole protein and by amino acid analysis and mass spectrometry of the corresponding tryptic fragment. Surprisingly, we found that His-73 is not modified. A similar lack of modification was also found in actin from the yeast Candida albicans, while rabbit muscle actin revealed the expected 3-methylhistidine residue. Phylogenetic analysis of actin sequences suggests that this modification was introduced in evolution after the divergence of yeast from higher eukaryotic organisms, including unicellular eukaryotes such as Acanthamoeba, Dictyostelium, and Physarum, whose actins contain 3-methylhistidine. Our methodology for the analytical determination of 3-methylhistidine in actin offers an improved approach for investigating histidine methylation in proteins.

Actins↗
PubMed2005

A divergent cellular role for the FUSED kinase family in the plant-specific cytokinetic phragmoplast.

The FUSED (FU) Ser/Thr protein kinase family has a key role in the hedgehog signaling pathway known to control cell proliferation and patterning in fruit flies and humans . The genomes of Arabidopsis thaliana and rice each encode a single Fu ortholog, but their role is unknown. Here, we show that cytokinesis-defective mutants, which we named two-in-one (tio), result from mutations in Arabidopsis Fu. Phenotypic analysis of tio mutants reveals an essential role for TIO in conventional modes of cytokinesis in plant meristems and during male gametogenesis. TIO also has a key role in nonconventional modes of cytokinesis (cellularization) during female gametogenesis. We demonstrate that TIO is tightly localized to the midline of the nascent phragmoplast and remains associated with the expanding phragmoplast ring. These data reveal the evolution of a divergent role for the Fu kinase family as an essential phragmoplast-associated protein that functions in different cell type-specific modes of cytokinesis in plants.

Arabidopsis↗
PubMed1986

Human inhibitor of the first component of complement, C1: characterization of cDNA clones and localization of the gene to chromosome 11.

C1 inhibitor is a heavily glycosylated plasma protein that regulates the activity of the first component of complement (C1) by inactivation of the serine protease subcomponents, C1r and C1s. C1 inhibitor cDNA clones have been isolated, and one of these (pC1INH1, 950 base pairs) has been partially sequenced. Sequence analysis demonstrates that the C1 inhibitor is a member of the serpin "superfamily" of protease inhibitors. In the region sequenced, C1 inhibitor has 22% identity with antithrombin III, 26% with alpha 1-antitrypsin and alpha 1-antichymotrypsin, and 18% with human angiotensinogen. C1 inhibitor has a larger amino-terminal extension than do the other plasma protease inhibitors. In addition, inspection of residues that are invariant among the other protease inhibitors shows that C1 inhibitor differs at 14 of 41 of these positions. Thus, it appears that C1 inhibitor diverged from the group relatively early in evolution, although probably after the divergence of angiotensinogen. Southern blot analysis of BamHI-digested DNA from normal individuals and from rodent-human somatic cell hybrid cell lines (that contain a limited but varied human chromosome complement) was used to localize the human C1 inhibitor gene to chromosome 11.

Amino Acid Sequence↗
PubMed2004

Polymorphism and transcription at the p44-1/p44-18 genomic locus in Anaplasma phagocytophilum strains from diverse geographic regions.

A polymorphic multigene family (p44) of Anaplasma phagocytophilum encodes the immunodominant 44-kDa major outer membrane proteins. With p44-specific PCR and gene-specific probes, p44-1 was found in all human isolates from New York State but not in isolates from Minnesota, whereas p44-18 and two other p44 species were found in isolates from both regions. We therefore sequenced the genomic locus corresponding to the p44-1/p44-18 tandem locus of A. phagocytophilum HZ in 14 other geographically divergent strains from various hosts. The locus was found in all 14 strains, and p44-18 was conserved among all 13 United States isolates studied. In all nine northeastern strains, p44-1 was conserved. However, in three of the Minnesota strains and in one California strain, p44-1 was replaced at this genomic locus by the novel gene p44-61 (p44-61/18), whose hypervariable region (hv) was a chimera of p44-20hv and p44-23hv. The conserved base sequence within the hv region linked the two segments. In contrast, in the Old Sourhope strain isolated from sheep in the United Kingdom, only a single and distinct p44, p44-OS, was found in this locus. This suggests different rates of evolution of p44-1 and p44-18 at this locus and conservation of the locus within strains isolated from the same geographic region. Locus-specific reverse transcription-PCR revealed expression of p44-1 by New York and p44-61 by Minnesota strains at this locus. These p44 loci provide insight into the molecular evolution and functional divergence of p44 paralogs and may serve as markers for typing strains from different geographic regions.

Anaplasma phagocytophilum↗
PubMed2006

Rates and patterns of chromosomal evolution in Drosophila pseudoobscura and D. miranda.

Comparisons of gene orders between species permit estimation of the rate of chromosomal evolution since their divergence from a common ancestor. We have compared gene orders on three chromosomes of Drosophila pseudoobscura with its close relative, D. miranda, and the distant outgroup species, D. melanogaster, by using the public genome sequences of D. pseudoobscura and D. melanogaster and approximately 50 in situ hybridizations of gene probes in D. miranda. We find no evidence for extensive transfer of genes among chromosomes in D. miranda. The rates of chromosomal rearrangements between D. miranda and D. pseudoobscura are far higher than those found before in Drosophila and approach those for nematodes, the fastest rates among higher eukaryotes. In addition, we find that the D. pseudoobscura chromosome with the highest level of inversion polymorphism (Muller's element C) does not show an unusually fast rate of evolution with respect to chromosome structure, suggesting that this classic case of inversion polymorphism reflects selection rather than mutational processes. On the basis of our results, we propose possible ancestral arrangements for the D. pseudoobscura C chromosome, which are different from those in the current literature. We also describe a new method for correcting for rearrangements that are not detected with a limited set of markers.

Animals↗
PubMed2002

Complete cDNA sequence of SAP-like pentraxin from Limulus polyphemus: implications for pentraxin evolution.

The serum amyloid P component (SAP)-like pentraxin Limulus polyphemus SAP is a recently discovered, distinct pentraxin species, of known structure, which does not bind phosphocholine and whose N-terminal sequence has been shown to differ markedly from the highly conserved N terminus of all other known horseshoe crab pentraxins. The complete cDNA sequence of Limulus SAP, and the derived amino acid sequence, the first invertebrate SAP-like pentraxin sequence, have been determined. Two sequences were identified that differed only in the length of the 3' untranslated region. Limulus SAP is synthesised as a precursor protein of 234 amino acid residues, the first 17 residues encoding a signal peptide that is absent from the mature protein. Phylogenetic analysis clusters Limulus SAP pentraxin with the horseshoe crab C-reactive proteins (CRPs) rather than the mammalian SAPs, which are clustered with mammalian CRPs. The deduced amino acid sequence shares 22% identity with both human SAP and CRP, which are 51% identical, and 31-35% with horseshoe crab CRPs. These analyses indicate that gene duplication of CRP (or SAP), followed by sequence divergence and the evolution of CRP and/or SAP function, occurred independently along the chordate and arthropod evolutionary lines rather than in a common ancestor. They further indicate that the CRP/SAP gene duplication event in Limulus occurred before both the emergence of the Limulus CRP variants and the mammalian CRP/SAP gene duplication. Limulus SAP, which does not exhibit the CRP characteristic of calcium-dependent binding to phosphocholine, is established as a pentraxin species distinct from all other known horseshoe crab pentraxins that exist in many variant forms sharing a high level of sequence homology.

Amino Acid Sequence↗