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PubMedDate not supplied

Antigenic variation in vector-borne pathogens.

Several pathogens of humans and domestic animals depend on hematophagous arthropods to transmit them from one vertebrate reservoir host to another and maintain them in an environment. These pathogens use antigenic variation to prolong their circulation in the blood and thus increase the likelihood of transmission. By convergent evolution, bacterial and protozoal vector-borne pathogens have acquired similar genetic mechanisms for successful antigenic variation. Borrelia spp. and Anaplasma marginale (among bacteria) and African trypanosomes, Plasmodium falciparum, and Babesia bovis (among parasites) are examples of pathogens using these mechanisms. Antigenic variation poses a challenge in the development of vaccines against vector-borne pathogens.

Anaplasma↗
PubMed2006

A SINE in the genome of the cephalochordate amphioxus is an Alu element.

Transposable elements of about 300 bp, termed "short interspersed nucleotide elements or SINEs are common in eukaryotes. However, Alu elements, SINEs containing restriction sites for the AluI enzyme, have been known only from primates. Here I report the first SINE found in the genome of the cephalochordate, amphioxus. It is an Alu element of 375 bp that does not share substantial identity with any genomic sequences in vertebrates. It was identified because it was located in the FoxD regulatory region in a cosmid derived from one individual, but absent from the two FoxD alleles of BACs from a second individual. However, searches of sequences of BACs and genomic traces from this second individual gave an estimate of 50-100 copies in the amphioxus genome. The finding of an Alu element in amphioxus raises the question of whether Alu elements in amphioxus and primates arose by convergent evolution or by inheritance from a common ancestor. Genome-wide analyses of transposable elements in amphioxus and other chordates such as tunicates, agnathans and cartilaginous fishes could well provide the answer.

Alu Elements↗
PubMed1999

Identification of homologous core structures.

Using a large database of protein structure-structure alignments, we test a new method for distinguishing homologous and "analogous" structural neighbors. The homologous neighbors included in the test set show no detectable sequence similarity, but they may be well superimposed and show functional similarity or other evidence of evolutionary relationship. Analogous neighbors also show no sequence similarity and may be well superimposed, but they have different functions and their structural similarity may be the result of convergent evolution. Confirming results of other analyses, we find that remote homologs and analogs are not well distinguished by measures of pairwise structural similarity, including the percentage of identical residues and root-mean-square (RMS) superposition residual. We show, however, that with structure-structure alignments of analogous neighbors rarely superimpose the particular substructure that is shared among homologous neighbors. We call this characteristic substructure the homologous core structure (HCS), and we show that a cross-validated test for presence of the HCS correctly identifies 75% of remote homologs with a false-positive rate of 16% analogs, significantly better than discrimination by RMS or other measures of pairwise similarity. The HCS describes conservation of spatial structure within a protein family in much the way that a sequence motif describes sequence conservation. We suggest that it may be used in the same way, to identify homologous neighbors at greater evolutionary distance than is possible by pairwise comparison.

Amino Acid Sequence↗
PubMedDate not supplied

Provenance of SET-domain histone methyltransferases through duplication of a simple structural unit.

SET domains are protein lysine methyltransferases that methylate diverse proteins, such as, histones, Rubisco and cytochrome C. In particular, they play an important role in the dynamics of the eukaryotic chromatin and are present in several chromatin-associated proteins. Recently, structures of several SET domains have been solved, and they contain a conserved fold that is unrelated to previously characterized methyltransferases, which possess either Rossmann fold or SPOUT domains. Phylogenetic and phyletic-profile analysis of the SET domain suggests that it was an evolutionary "invention" of the eukaryotic lineage, with secondary lateral transfers to bacteria. We show that the conserved N- and C- terminal regions, which comprise the core barrel-like module of the SET domain, are symmetric repeats of a simple 3-stranded unit. Furthermore, the two symmetrically arranged repeats contribute to the binding sites for the two substrates of the SET domain. This suggests the SET domain arose from an ancestral dimer of this 3-stranded unit, with each unit probably functioning as generic-ligand binding structure. The divergence between the two repeat units appears to have arisen as a result of their interactions with the central module of the SET domain, which was inserted between the two repeats. One of the repeats appears to have acquired adaptations, which helped it to specialize in AdoMet binding, whereas the second repeat contributed to histone-interaction, and in orienting a crucial active site residue. The central module of the SET domain supplies a critical asparagine to the active site, and its structural features suggest that it may have also arisen from a further duplication of one of the repeats comprising the core barrel. However, it appears to have structurally diverged from the two canonical repeats due to the lack of an obligate dimerization partner. The spatial position of the two repeats in the ancestral dimer appears to have favored the formation of the structural knot typical of the SET domain. A comparable knot is seen in the SPOUT-domain methyltransferases, and this represents a case of convergent evolution of an active-site-associated configuration in two otherwise unrelated classes of methylases. Thus, the SET domain provides a model for the innovation of a complex enzymatic fold through the duplications of a structurally simple non-enzymatic unit.

Amino Acid Sequence↗
PubMed1992

Structure, expression, and regulation of the major noncollagenous matrix proteins of bone.

The noncollagenous proteins (NCPs) that predominate the bone matrix have recently been the focus of intense investigation because of their potential influence on cell attachment, Ca2+ and hydroxyapatite binding, and the mineralization of bone tissue. With the advent of molecular biology, all of the major NCPs of bone have been cloned and their amino acid sequences completely determined. While each of the proteins has distinct structural properties, some proteins appear to be part of gene families. Examples include the small proteoglycans, decorin and biglycan, as well as the gamma carboxyglutamic acid proteins, such as matrix gla protein and osteocalcin (bone gla protein). Some of the NCPs that are clearly not members of any known gene family still share several common characteristics. One such example of this "convergent evolution" is bone sialoprotein and osteopontin. Both are highly posttranslationally modified glycoproteins that share the cell attachment amino acid sequence RGD (arginine-glycine-aspartic acid), which facilitates the attachment of bone cells in vitro, yet they are clearly not related genetically. Using cDNAs and antisera as probes, the precise temporal localization of NCP expression has been determined, and it has been shown that NCPs are produced in skeletal, and in most cases, nonskeletal tissue as well. This observation implies that the functions of the NCPs are not necessarily limited to bone tissue. Many of the promoters for these genes have been isolated and functional domains determined by a combination of chloramphenicol acetyltransferase assay, gel shift, and footprint analyses. The most extensively studied promoter in the NCP category is osteocalcin, whose sensitivity to 1,25-dihydroxycholecalciferol has been delineated in detail. Future studies on the individual and cooperative activities of the NCPs in bone are likely to involve site-directed mutagenesis of cloned DNA and a combination of in vitro and in vivo functional analyses.

Biglycan↗
PubMed2005

Venezuelan equine encephalitis virus in the guinea pig model: evidence for epizootic virulence determinants outside the E2 envelope glycoprotein gene.

Epizootic strains of Venezuelan equine encephalitis virus (VEEV) cause epidemics by exploiting equines as highly efficient amplification hosts for mosquito transmission. Although phylogenetic studies indicate that epizootic VEEV strains emerge via mutation from enzootic progenitors that are incapable of efficient equine amplification, the molecular mechanism(s) involved remain enigmatic. The convergent evolution of E2 envelope glycoprotein mutations suggests that they are critical to VEEV emergence, but little is known about the role of non-envelope genes. We used the guinea pig, the small animal model that best predicts the ability to generate equine viremia, to assess the role of envelope versus other mutations in the epizootic phenotype. Using reciprocal chimeric viruses generated by swapping the envelope genes of closely related epizootic IC and enzootic ID strains, infections of guinea pigs demonstrated that envelope and non-envelope genes and sequences both contributed to virulence. However, early replication in lymphoid tissues appeared to be primarily envelope dependent.

Animals↗
PubMed1991

Covalent structure of the diheme cytochrome subunit and amino-terminal sequence of the flavoprotein subunit of flavocytochrome c from Chromatium vinosum.

The complete sequence of the 21-kDa cytochrome subunit of the flavocytochrome c (FC) from the purple phototrophic bacterium Chromatium vinosum has been determined to be as follows: EPTAEMLTNNCAGCHG THGNSVGPASPSIAQMDPMVFVEVMEGFKSGEIAS TIMGRIAKGYSTADFEKMAGYFKQQTYQPAKQSF DTALADTGAKLHDKYCEKCHVEGGKPLADEEDY HILAGQWTPYLQYAMSDFREERRPMEKKMASKL RELLKAEGDAGLDALFAFYASQQ. The sequence is the first example of a diheme cytochrome in a flavocytochrome complex. Although the locations of the heme binding sites and the heme ligands suggest that the cytochrome subunit is the result of gene doubling of a type I cytochrome c, as found with Azotobacter cytochrome c4, the extremely low similarity of only 7% between the two halves of the Chromatium FC heme subunit rather suggests that gene fusion is at the evolutionary origin of this cytochrome. The two halves also require a single residue internal deletion for alignment. The first half of the Chromatium FC heme subunit is 39% similar to the monoheme subunit of the FC from the green phototrophic bacterium Chlorobium thiosulfatophilum, but the second half is only 9% similar to the Chlorobium subunit. The N-terminal sequence of the Chromatium FC flavin subunit was determined up to residue 41 as AGRKVVVVGGGTGGATAAKYIKLADPSIEVTLIEP NTKYYT. It shows more similarity to the Chlorobium FC flavin subunit (60%) than do the two heme subunits. The N terminus of the flavin subunit is homologous to a number of flavoproteins, including succinate dehydrogenase, glutathione reductase, and monamine oxidase. There is no obvious homology to the Pseudomonas putida FC flavin subunit, which suggests that the two types of flavocytochrome c arose by convergent evolution. This is consistent with the dissimilar enzyme activities of FC as sulfide dehydrogenase in the phototrophic bacteria and as p-cresol methylhydroxylase in Pseudomonas. We also present a sequence "fingerprint" pattern for the recognition of FAD-binding proteins which is an extended version of the consensus sequence previously presented (Wierenga, R. K., Terpstra, P., and Hol, W. G. J. (1986) J. Mol. Biol. 187, 101-107) for nucleotide binding sites.

Amino Acid Sequence↗
PubMed1991

Crystallins of the octopus lens. Recruitment from detoxification enzymes.

The eye lens crystallins of the octopus Octopus dofleini were identified by sequencing abundant proteins and cDNAs. As in squid, the octopus crystallins have subunit molecular masses of 25-30 kDa, are related to mammalian glutathione S-transferases (GST), and are encoded in at least six genes. The coding regions and deduced amino acid sequences of four octopus lens cDNAs are 75-80% identical, while their non-coding regions are entirely different. Deduced amino acid sequences show 52-57% similarity with squid GST-like crystallins, but only 20-25% similarity with mammalian GST. These data suggest that the octopus and squid lens GST-like crystallin gene families expanded after divergence of these species. Northern blot hybridization indicated that the four octopus GST-like crystallin genes examined are lens-specific. Lens extracts showed about 40 times less GST activity using 1-chloro-2,4-dinitrobenzene as substrate than liver extracts of the octopus, indicating that the major GST-like crystallins are specialized for a lens structural role. A prominent 59-kDa crystallin polypeptide, previously observed in octopus but not squid and called omega-crystallin (Chiou, S.-H. (1988) FEBS Lett. 241, 261-264), has been identified as an aldehyde dehydrogenase. Since cytoplasmic aldehyde dehydrogenase is a major protein in elephant shrew lenses (eta-crystallin; Wistow, G., and Kim, H. (1991) J. Mol. Evol. 32, 262-269) the octopus aldehyde dehydrogenase crystallin provides the first example of a similar enzyme-crystallin in vertebrates and invertebrates. The use of detoxification stress proteins (GST and aldehyde dehydrogenase) as cephalopod crystallins indicates a common strategy for recruitment of enzyme-crystallins during the convergent evolution of vertebrate and invertebrate lenses. For historical reasons we propose that the octopus GST-like crystallins, like those of the squid, are called S-crystallins.

Aldehyde Dehydrogenase↗
PubMed1990

Purification, characterization, and cDNA cloning of a novel metallothionein-like, cadmium-binding protein from Caenorhabditis elegans.

Caenorhabditis elegans adapted for survival in high concentrations of Cd(II) express a heavy metal binding protein designated C. elegans metallothionein-like protein or MT-Ce. This protein was purified to homogeneity and characterized. MT-Ce binds 6 mol of Cd(II)/mol protein. The sequence of 39 amino-terminal residues in MT-Ce was determined. A radiolabeled 41-mer oligonucleotide, designed from the partial MT-Ce sequence, was used in conjunction with sucrose gradient centrifugation to obtain size-fractionated poly(A+) RNA enriched in MT-Ce sequences. Subsequently, cloned cDNAs, corresponding to MT-Ce mRNA sequences, were isolated from a lambda ZapII cDNA library prepared from the enriched template mRNA. cDNA and protein sequence analysis revealed that MT-Ce comprises 62 amino acid residues and has a predicted Mr of 6462. Seventeen of the 18 Cys residues in the nematode cadmium-binding protein are included in Cys-X-Cys and X-Cys-Cys-X motifs that are characteristic of mammalian metallothioneins (MTs). However, the resemblance of MT-Ce to mammalian MTs is superficial. The amino acid sequence of MT-Ce is unique, and neither its putative alpha and beta domains nor its Cys residues can be readily aligned with the corresponding regions of other eukaryotic MTs. This suggests that MT-Ce is an example of convergent evolution. The MT-Ce mRNA level in nematodes that were selected and grown with Cd(II) concentrations that are lethal for wild-type worms, was 55-fold higher than the level of MT-Ce mRNA in wild-type C. elegans. Comparison of the sequences of MT-Ce cDNAs revealed the occurrence of two types of MT-Ce mRNA. Each contains an identical coding region, but the cDNAs diverge markedly in their 5'-untranslated regions. This suggests the possibilities of regulation by alternative splicing and/or the presence of multiple MT-Ce genes encoding a single protein, but controlled by different regulatory elements.

Amino Acid Sequence↗
PubMed1987

Primary structure and comparative sequence analysis of an insect apolipoprotein. Apolipophorin-III from Manduca sexta.

The amino acid sequence of an insect apolipoprotein, apolipophorin-III from Manduca sexta, was determined by a combination of cDNA and protein sequencing. The mature hemolymph protein consists of 166 amino acids. The cDNA also encodes for an amino-terminal extension of 23 amino acids which is not represented in the mature hemolymph protein. The existence of a precursor protein was confirmed by in vitro translation of fat body mRNA. Computer-assisted comparative sequence analysis revealed the following points: 1) the protein is composed of tandemly repeating tetradecapeptide units with a high potential for forming amphiphilic helical structures. Compared to mammalian apolipoproteins the repeat units in the insect apolipoprotein show considerable length variability; 2) the sequence has a striking resemblance to several human apolipoproteins including apoE, AIV, AI, and CI. However, the homology seems to be entirely functional since, although the insect and mammalian apoproteins contain very similar types of amino acid residues, the actual degree of sequence identity is quite low. Whether the mammalian and insect apoproteins are derived from a common ancestral amphiphilic helix forming, lipid-binding protein, or arose by convergent evolution can not be determined at present. This represents the first complete amino acid sequence for an insect apolipoprotein.

Algorithms↗
PubMed1987

The phylogeny of the fine structure of blood vessels and lymphatics: similarities and differences.

As animals increased in size, various modifications had to come into being to carry nutrients and waste around the body. Different phyla solved the various problems differently; sometimes there was convergent evolution. In invertebrates the endothelial cells are often widely separated from each other; permeability is limited by the pericyte layer; the reverse occurs in vertebrates. In primitive chordates small peripheral vessels often consist only of the basement membrane, and even this may be partly missing; the more centrally one looks, the more the endothelial cells become continuous. Fenestrae appeared first in the agnatha, but only become common in the elasmobranchs. Increased size and activity necessitated still larger blood hydrostatic pressure and increased blood colloidal osmotic pressures to balance this. Since the permeability of the vessels could not be reduced, much more protein (and fluid) had to leak to the tissues. So the lymphatic system had to evolve. This is first seen in the torpedoes and fully evolved in the bony fishes. However, the small venous vessels of the elasmobranchs have openable inter-endothelial junctions and other structures very similar to those of the initial lymphatics. Apart from the absence of fenestrae in lymphatics, or when this system is injected with a tracer, it is not always possible to tell them apart with the electron microscope. There are, however, various differences between them which will help to differentiate them.

Animals↗
PubMed1984

Cobra venom factor: structural homology with the third component of human complement.

The functional analogy between cobra venom factor (CVF), the complement-activating protein in cobra venom, and C3b, the activated form of the third complement component, prompted us to conduct a comparative analysis of structural properties of the two proteins derived from two phylogenetically distant species. We subjected CVF and human C3 and its physiologic cleavage products, C3b and C3c, to a variety of biochemical analyses. We report here structural similarities of these proteins, which include similarities in amino acid composition, far and near UV circular dichroism spectra, secondary structure, band patterns and pI values from isoelectric focusing, immunochemical cross-reactivity, ultrastructural morphology, and amino-terminal amino acid sequences. Analysis of these data reveals that, structurally, CVF resembles C3c more than C3b. We conclude that CVF is not the product of a convergent evolution, but is, in all likelihood, derived from a common C3 ancestor protein.

Amino Acid Sequence↗
PubMedDate not supplied

[The evolutionary kinship of the crystallins of cephalopods and vertebrates with heat-shock proteins and stress-induced proteins].

The lenses of cephalopods and vertebrates are a classical example of convergent evolution. In the course of evolution vertebrates and cephalopods used the same strategy of recruitment of ancestral proteins (primarily enzymes, whose activity is related with stress and detoxification) for structural functions in the lens. Crystallins are defined as water soluble proteins, that form the lenses of cephalopods and vertebrates. In vertebrates, only the beta/gamma-crystallin genes are lens-specific. The other crystallin classes (alpha-, beta-, etc) are overexpressed in the lens, having the various noticeable expression levels in the other tissues as well. Almost all the crystallins, forming squid lens are referred to a single class, namely S-crystallins. The latters are encoded by a family of genes, consisting of at least 10 members S-crystallins of the squid and the octopus are related, but not identical to glutathione S-transferases. S-crystallins show no enzymatic activity, though they have 42-44% homology with a squid glutathione-S-transferase (GST), which we have structurally characterized. Genes of GST and S-crystallins have similar exon-intron structures (5-6 exons), whereas their 5' flanking regions are different. Promoters of both of S-crystallin genes and of some vertebrate crystallin genes bear the similar regulatory element (AP1-site), that must take part in regulation of their lens-specific expression. Besides S-crystallins, octopus lens contains a major polypeptide, omega-crystallin, that was characterized in detail. Though omega-crystallin is related to aldehyde dehydrogenase (ALDG), it has no enzymatic activity. Genes coding for omega- and S-crystallins were shown to be expressed only in the lens cells of squid and octopus. In some mammals ALDG is known to serve as a crystallin (eta-crystallin of elephant shrew). Thus, octopus omega-crystallin and eta-crystallin of elephant shrew--are the first example of similarity between vertebrate and cephalopod crystallins.

Amino Acid Sequence↗
PubMed1994

Localization and characterization of an alpha-thrombin-binding site on platelet glycoprotein Ib alpha.

Glycoprotein (GP) Ib alpha is required for expression of the highest affinity alpha-thrombin-binding site on platelets, possibly contributing to platelet activation through a pathway involving cleavage of a specific receptor. This function may be important for the initiation of hemostasis and may also play a role in the development of pathological vascular occlusion. We have now identified a discrete sequence in the extracytoplasmic domain of GP Ib alpha, including residues 271-284 of the mature protein, which appears to be part of the high affinity alpha-thrombin-binding site. Synthetic peptidyl mimetics of this sequence inhibit alpha-thrombin binding to GP Ib as well as platelet activation and aggregation induced by subnanomolar concentrations of the agonist; they also inhibit alpha-thrombin binding to purified glycocalicin, the isolated extracytoplasmic portion of GP Ib alpha. The inhibitory peptides interfere with the clotting of fibrinogen by alpha-thrombin but not with the amidolytic activity of the enzyme on a small synthetic substrate, a finding compatible with the concept that the identified GP Ib alpha sequence interacts with the anion-binding exosite of alpha-thrombin but not with its active proteolytic site. The crucial structural elements of this sequence necessary for thrombin binding appear to be a cluster of negatively charged residues as well as three tyrosine residues that, in the native protein, may be sulfated. GP Ib alpha has no significant overall sequence homology with the thrombin inhibitor, hirudin, nor with the specific thrombin receptor on platelets; all three molecules, however, possess a distinct region rich in negatively charged residues that appear to be involved in thrombin binding. This may represent a case of convergent evolution of unrelated proteins for high affinity interaction with the same ligand.

Adenosine Triphosphate↗
PubMed1996

Crystal structure of the human adenovirus proteinase with its 11 amino acid cofactor.

The three-dimensional structure of the human adenovirus-2 proteinase complexed with its 11 amino acid cofactor, pVIc, was determined at 2.6 A resolution by X-ray crystallographic analysis. The fold of this protein has not been seen before. However, it represents an example of either subtly divergent or powerfully convergent evolution, because the active site contains a Cys-His-Glu triplet and oxyanion hole in an arrangement similar to that in papain. Thus, the adenovirus proteinase represents a new, fifth group of enzymes that contain catalytic triads. pVIc, which extends a beta-sheet in the main chain, is distant from the active site, yet its binding increases the catalytic rate constant 300-fold for substrate hydrolysis. The structure reveals several potential targets for antiviral therapy.

Adenoviruses, Human↗
PubMed1996

A left-hand beta-helix revealed by the crystal structure of a carbonic anhydrase from the archaeon Methanosarcina thermophila.

A carbonic anhydrase from the thermophilic archaeon Methanosarcina thermophila that exhibits no significant sequence similarity to known carbonic anhydrases has recently been characterized. Here we present the structure of this enzyme, which adopts a left-handed parallel beta-helix fold. This fold is of particular interest since it contains only left-handed crossover connections between the parallel beta-strands, which so far have been observed very infrequently. The active form of the enzyme is a trimer with three zinc-containing active sites, each located at the interface between two monomers. While the arrangement of active site groups differs between this enzyme and the carbonic anhydrases from higher vertebrates, there are structural similarities in the zinc coordination environment, suggestive of convergent evolution dictated by the chemical requirements for catalysis of the same reaction. Based on sequence similarities, the structure of this enzyme is the prototype of a new class of carbonic anhydrases with representatives in all three phylogenetic domains of life.

Amino Acid Sequence↗
PubMed1996

Proteocephalus brooksi n. sp. (Cestoda:Proteocephalidae) in the neotropical freshwater fish Rhamdia guatemalensis (Siluriformes: Pimelodidae) from Lake Catemaco, Veracruz, Mexico.

Proteocephalus brooksi n. sp. is described from the neotropical pimelodid fish Rhamdia guatemalensis from Lake Catemaco, Veracruz, México. The new species is characterized by the "paramuscular" position of vitellaria, the cortical origin of uterine stem with development of medullar lateral branches, the alternated position of vagina (anteriorly and posteriorly to cirrus sac), and the absence of apical organ and vaginal sphincter. Proteocephalus brooksi most closely resembles Nomimoscolex matogrossensis from which it differs in a series of characters. The probable paraphyletic nature of both Proteocephalus and Nomimoscolex and the convergent evolution of the "paramuscular" location of vitellaria among proteocephalideans are suggested, and the need for a phylogenetic analysis of the group is emphasized. The new species is assigned to Proteocephalus pending such an analysis.

Animals↗
PubMed1996

Crystal structure of the protein serine/threonine phosphatase 2C at 2.0 A resolution.

Protein phosphatase 2C (PP2C) is a Mn2+- or Mg2+-dependent protein Ser/Thr phosphatase that is essential for regulating cellular stress responses in eukaryotes. The crystal structure of human PP2C reveals a novel protein fold with a catalytic domain composed of a central beta-sandwich that binds two manganese ions, which is surrounded by alpha-helices. Mn2+-bound water molecules at the binuclear metal centre coordinate the phosphate group of the substrate and provide a nucleophile and general acid in the dephosphorylation reaction. Our model presents a framework for understanding not only the classical Mn2+/Mg2+-dependent protein phosphatases but also the sequence-related domains of mitochondrial pyruvate dehydrogenase phosphatase, the Bacillus subtilus phosphatase SpoIIE and a 300-residue domain within yeast adenyl cyclase. The protein architecture and deduced catalytic mechanism are strikingly similar to the PP1, PP2A, PP2B family of protein Ser/Thr phosphatases, with which PP2C shares no sequence similarity, suggestive of convergent evolution of protein Ser/Thr phosphatases.

Adenylyl Cyclases↗