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PubMed1996

Population dynamics of flaviviruses revealed by molecular phylogenies.

The phylogeny of 123 complete envelope gene sequences was reconstructed in order to understand the evolution of tick- and mosquito-borne flaviviruses. An analysis of phylogenetic tree structure reveals a continual and asymmetric branching process in the tick-borne flaviviruses, compared with an explosive radiation in the last 200 years in viruses transmitted by mosquitoes. The distinction between these two viral groups probably reflects differences in modes of dispersal, propagation, and changes in the size of host populations. The most serious implication of this work is that growing human populations are being exposed to an expanding range of increasingly diverse viral strains.

Animals↗
PubMed2000

Zinedin, SG2NA, and striatin are calmodulin-binding, WD repeat proteins principally expressed in the brain.

Striatin is an intracellular protein characterized by four protein-protein interaction domains, a caveolin-binding motif, a coiled-coil structure, a calmodulin-binding domain, and a WD repeat domain, suggesting that it is a signaling or a scaffold protein. Down-regulation of striatin, which is expressed in a few subsets of neurons, impairs the growth of dendrites as well as rat locomotor activity (Bartoli, M., Ternaux, J. P., Forni, C., Portalier, P., Salin, P., Amalric, M., and Monneron, A. (1999) J. Neurobiol. 40, 234-243). Zinedin, a "novel" protein described here, and SG2NA share with striatin identical protein-protein interaction domains and the same overall domain structure. A phylogenetic analysis supports the hypothesis that they constitute a multigenic family deriving from an ancestral gene. DNA probes and antibodies raised against specific domains of each protein showed that zinedin is mainly expressed in the central nervous system, whereas SG2NA, of more widespread occurrence, is mainly expressed in the brain and muscle. All three proteins are both cytosolic and membrane-bound. All three bind calmodulin in the presence of Ca(2+). In rat brain, SG2NA and striatin are generally not found in the same neurons. Both localize to the soma and dendrites, suggesting that they share a similar type of addressing and closely related functions.

Amino Acid Sequence↗
PubMed2004

Lactose: the milk sugar from a biotechnological perspective.

Lactose is a very important sugar because of its abundance in the milk of humans and domestic animals. Lactose is a valuable asset as a basic nutrient and the main substrate in fermentative processes that led to the production of fermented milk products, such as yogurt and kefir. In some instances, lactose also can be a problem as the causative agent of some diseases, such as lactose intolerance and galactosemia, or for being a by-product generated in huge amounts by the cheese industry. The study of the biochemical reactions leading to the synthesis and assimilation of lactose has provided valuable models for the understanding of biosynthetic and catabolic processes. Lactose-hydrolyzing enzymes are structurally and phylogenetically related to different types of beta-galactosidases and bacterial cellobiases involved in the enzymatic degradation of cellulose. Biotransformation of lactose, by either enzymatic or fermentative procedures, is important for different types of industrial applications in dairy and pharmaceutical industries.

Animals↗
PubMed1998

Genetic distances and ordination: the land snail Helix aspersa in north Africa as a test case.

We examined the efficiencies of ordination methods in the treatment of gene frequency data at intraspecific level, using metric and nonmetric distance measures (Nei's and Rogers' genetic distances, chi 2 distance). We assessed initial processes responsible for the geographical distribution of the Mediterranean land snail Helix aspersa. Seventeen enzyme loci from 30 North African snail populations were considered in the present analysis. Five combinations of distance/multivariate analysis were compared: correspondence analysis (CA), nonmetric multidimensional scaling (NMDS) on Nei's, Rogers', and chi 2 distances, and principal coordinates analysis on Rogers' distances. Configuration of the objects resulting from ordination was projected onto three-dimensional graphics with the minimum spanning tree or the relative neighborhood graph superimposed. Pre- and postordination or clustering distance matrices were compared by means of correlation methods. As expected, all combinations led to a clear west versus east pattern of variation. However, the intraregional relationships and degree of connectivity between pairs of operational taxonomic units were not necessarily constant from one method to another. Ordination methods when applied with Nei's and Rogers' distances provided the best fit, with original distances (r = 0.98) compared with UPGMA clustering (r approximately 0.75). The Nei/NMDS combination seems to be a good compromise (distortion index dt = 10%) between Rogers/NMDS, which produces a more confusing pattern of differentiation (dt = 24%), and chi 2/CA, which tends to distort large distances (dt = 31%). NMDS obviously provides a powerful method to summarize relationships between populations, when neither hierarchical structure nor phylogenetic inference are required. These findings led the discussion on the good performance of NMDS, the appropriate distances to be used, and the potential application of this method to other types of allelic data (such as microsatellite loci) or data on nucleotide sequences of genes.

Africa, Northern↗
PubMed2026

Functional characterization of SHC-like triterpene cyclase genes in azole response and virulence-related traits of Aspergillus fumigatus.

Aspergillus fumigatus is a major opportunistic fungal pathogen, and increasing azole resistance poses a challenge for aspergillosis treatment. Squalene is an upstream precursor of ergosterol biosynthesis and may also be utilized by SHC-like triterpene cyclases, suggesting a potential link between squalene-associated metabolism, membrane adaptation, and azole response. However, the roles of SHC-like triterpene cyclase genes in A. fumigatus remain unclear. Here, we characterized three candidates, shc1, shc2, and shc3, using comparative bioinformatic analysis, gene deletion, phenotypic assays, azole susceptibility testing, transcriptomics, and host-interaction models. Sequence, genomic-context, phylogenetic, and structural analyses suggested divergence among the three candidates. Individual shc deletion caused limited effects on vegetative growth, whereas loss of shc1 mildly reduced susceptibility to voriconazole and posaconazole, as reflected by twofold MIC increases and lower inhibition rates. Transcriptomic analysis revealed distinct remodeling patterns, with Δshc3 showing the broadest transcriptional changes despite no detectable MIC shift. Targeted metabolite profiling and PI uptake analysis further supported an association between shc deletion, sterol/hopane-type triterpenoid balance, and membrane-associated properties. shc deletion also altered epithelial cell interaction phenotypes, while Δshc1 showed reduced lethality in Galleria mellonella. In clinical isolates, elevated shc transcription was associated with azole-resistant backgrounds. These findings suggest functional diversification among SHC-like triterpene cyclase genes and indicate that shc1 may contribute to azole-associated adaptation and virulence-related traits in A. fumigatus.

Aspergillus fumigatus↗
PubMed2001

On the parallelisation of bioinformatics applications.

This paper surveys the computational strategies followed to parallelise the most used software in the bioinformatics arena. The studied algorithms are computationally expensive and their computational patterns range from regular, such as database-searching applications, to very irregularly structured patterns (phylogenetic trees). Fine- and coarse-grained parallel strategies are discussed for these very diverse sets of applications. This overview outlines computational issues related to parallelism, physical machine models, parallel programming approaches and scheduling strategies for a broad range of computer architectures. In particular, it deals with shared, distributed and shared/distributed memory architectures.

Algorithms↗
PubMed1996

Constraints on allele size at microsatellite loci: implications for genetic differentiation.

Microsatellites are promising genetic markers for studying the demographic structure and phylogenetic history of populations. We present theoretical arguments indicating that the usefulness of microsatellite data for these purposes may be limited to a short time perspective and to relatively small populations. The evolution of selectively neutral markers is governed by the interaction of mutation and random genetic drift. Mutation pressure has the inherent tendency to shift different populations to the same distribution of alleles. Hence, mutation pressure is a homogenizing force, and population divergence is caused by random genetic drift. In case of allozymes or sequence data, the diversifying effect of drift is typically orders of magnitude larger than the homogenizing effect of mutation pressure. By a simple model, we demonstrate that the situation may be different for microsatellites where mutation rates are high and the range of alleles is limited. With the help of computer simulations, we investigate to what extent genetic distance measures applied to microsatellite data can nevertheless yield useful estimators for phylogenetic relationships or demographic parameters. We show that predictions based on microsatellite data are quite reliable in small populations, but that already in moderately sized populations the danger of misinterpretation is substantial.

Alleles↗
PubMed1997

Genetic analysis of the Chlamydomonas reinhardtii I-CreI mobile intron homing system in Escherichia coli.

We have developed and used a genetic selection system in Escherichia coli to study functional requirements for homing site recognition and cleavage by a representative eukaryotic mobile intron endonuclease. The homing endonuclease, I-CreI, was originally isolated from the chloroplast of the unicellular green alga Chlamydomonas reinhardtii. I-CreI homing site mutants contained base pair substitutions or single base deletions that altered the rate of homing site cleavage and/or product release. I-CreI endonuclease mutants fell into six phenotypic classes that differed in in vivo activity, toxicity or genetic dominance. Inactivating mutations clustered in the N-terminal 60% of the I-CreI amino acid sequence, and two frameshift mutations were isolated that resulted in premature translation termination though retained partial activity. These mutations indicate that the N-terminal two-thirds of the I-CreI endonuclease is sufficient for homing site recognition and cleavage. Substitution mutations altered in four potential active site residues were examined: D20N, Q47H or R70A substitutions inactivated endonuclease activity, whereas S22A did not. The genetic approach we have taken complements phylogenetic and structural studies of mobile intron endonucleases and has provided new information on the mechanistic basis of I-CreI homing site recognition and cleavage.

Animals↗
PubMed2003

Identification of Nogo-66 receptor (NgR) and homologous genes in fish.

The Nogo-66 receptor NgR has been implicated in the mediation of inhibitory effects of central nervous system (CNS) myelin on axon growth in the adult mammalian CNS. NgR binds to several myelin-associated ligands (Nogo-66, myelin associated glycoprotein, and oligodendrocyte-myelin glycoprotein), which, among other inhibitory proteins, impair axonal regeneration in the CNS of adult mammals. In contrast to mammals, severed axons readily regenerate in the fish CNS. Nevertheless, fish axons are repelled by mammalian oligodendrocytes in vitro. Therefore, the identification of fish NgR homologs is a crucial step towards understanding NgR functions in vertebrate systems competent of CNS regeneration. Here, we report the discovery of four zebrafish (Danio rerio) and five fugu (Takifugu rubripes) NgR homologs. Synteny between fish and human, comparable intron-exon structures, and phylogenetic analyses provide convincing evidence that the true fish orthologs were identified. The topology of the phylogenetic trees shows that the extra fish genes were produced by duplication events that occurred in ray-finned fishes before the divergence of the zebrafish and pufferfish lineages. Expression of zebrafish NgR homologs was detected relatively early in development and prominently in the adult brain, suggesting functions in axon growth, guidance, or plasticity.

Animals↗
PubMed2004

A potentially functional mariner transposable element in the protist Trichomonas vaginalis.

Mariner transposable elements encoding a D,D34D motif-bearing transposase are characterized by their pervasiveness among, and exclusivity to, animal phyla. To date, several hundred sequences have been obtained from taxa ranging from cnidarians to humans, only two of which are known to be functional. Related transposons have been identified in plants and fungi, but their absence among protists is noticeable. Here, we identify and characterize Tvmar1, the first representative of the mariner family to be found in a species of protist, the human parasite Trichomonas vaginalis. This is the first D,D34D element to be found outside the animal kingdom, and its inclusion in the mariner family is supported by both structural and phylogenetic analyses. Remarkably, Tvmar1 has all the hallmarks of a functional element and has recently expanded to several hundred copies in the genome of T. vaginalis. Our results show that a new potentially active mariner has been found that belongs to a distinct mariner lineage and has successfully invaded a nonanimal, single-celled organism. The considerable genetic distance between Tvmar1 and other mariners may have valuable implications for the design of new, high-efficiency vectors to be used in transfection studies in protists.

Amino Acid Sequence↗
PubMed1986

Site-directed mutagenesis of the binding site for ribosomal protein S8 within 16S ribosomal RNA from Escherichia coli.

Twelve specific alterations have been introduced into the binding site for ribosomal protein S8 in Escherichia coli 16S rRNA. Appropriate rDNA segments were first cloned into bacteriophage M13 vectors and subjected to bisulfite and oligonucleotide-directed mutagenesis in vitro. Subsequently, the mutagenized sequences were placed within the rrnB operon of plasmid pNO1301 and the mutant plasmids were used to transform E. coli recipients. The growth rates of cells containing the mutant plasmids were determined and compared with that of cells containing the wild-type plasmid. Only those mutations which occurred at highly conserved positions, or were expected to disrupt the secondary structure of the binding site, increased the doubling time appreciably. The most striking changes in growth rate resulted from mutations that altered a small internal loop within the S8 binding site. This structure is phylogenetically conserved in prokaryotic 16S rRNAs and may play a direct role in S8-16S rRNA recognition and interaction.

Base Sequence↗
PubMed2001

tmRDB (tmRNA database).

The tmRNA database (tmRDB) is maintained at the University of Texas Health Science Center at Tyler, Texas, and accessible on the World Wide Web at the URL http://psyche.uthct.edu/dbs/tmRDB/tmRDB.++ +html. Mirror sites are located at Auburn University, Auburn, Alabama (http://www.ag.auburn.edu/mirror/tmRDB/) and the Institute of Biological Sciences, Aarhus, Denmark (http://www.bioinf.au. dk/tmRDB/). The tmRDB provides information and citation links about tmRNA, a molecule that combines functions of tRNA and mRNA in trans-translation. tmRNA is likely to be present in all bacteria and has been found in algae chloroplasts, the cyanelle of Cyanophora paradoxa and the mitochondrion of the flagellate Reclinomonas americana. This release adds 26 new sequences and corresponding predicted tmRNA-encoded tag peptides for a total of 86 tmRNAs, ordered alphabetically and phylogenetically. Secondary structures and three-dimensional models in PDB format for representative molecules are being made available. tmRNA alignments prove individual base pairs and are generated manually assisted by computational tools. The alignments with their corresponding structural annotation can be obtained in various formats, including a new column format designed to improve and simplify computational usability of the data.

Databases, Factual↗
PubMed2001

Tracing the origin of the compensasome: evolutionary history of DEAH helicase and MYST acetyltransferase gene families.

Dosage compensation in Drosophila is mediated by a complex of proteins and RNAs called the "compensasome." Two of the genes that encode proteins of the complex, maleless (mle) and males-absent-on-the-first (mof), respectively, belong to the DEAH helicase and MYST acetyltransferase gene families. We performed comprehensive phylogenetic and structural analyses to determine the evolutionary histories of these two gene families and thus to better understand the origin of the compensasome. All of the members of the DEAH and MYST families of the completely sequenced Saccharomyces cerevisiae and Caenorhabditis elegans genomes, as well as those so far (June 2000) found in Drosophila melanogaster (for which the euchromatic part of the genome has also been fully sequenced) and Homo sapiens, were analyzed. We describe a total of 39 DEAH helicases in these four species. Almost all of them can be grouped in just three main branches. The first branch includes the yeast PRP2, PRP16, PRP22, and PRP43 splicing factors and their orthologs in animal species. Each PRP gene has a single ortholog in metazoans. The second branch includes just four genes, found in yeast (Ecm16) and Drosophila (kurz) and their orthologs in humans and Caenorhabditis. The third branch includes (1) a single yeast gene (YLR419w); (2) six Drosophila genes, including maleless and spindle-E/homeless; (3) four human genes, among them the ortholog of maleless, which encodes RNA helicase A; and (4) three C. elegans genes, including orthologs of maleless and spindle-E. Thus, this branch has largely expanded in metazoans. We also show that, for the whole DEAH family, only MLE and its metazoan orthologs have acquired new protein domains since the fungi/animals split. We found a total of 17 MYST family proteins in the four analyzed species. We determined putative orthologs of mof in both C. elegans and H. sapiens, and we show that the most likely ortholog in yeast is the Sas2 gene. Moreover, a paralog of mof exists in Drosophila. All of these results, together with those found for a third member of the compensasome, msl-3, suggest that this complex emerged after the fungi/animals split and that it may be present in mammalian species. Both gene duplication and the acquisition of new protein modules may have played important roles in the origin of the compensasome.

Acetyltransferases↗
PubMed2002

Comparative genomics of the RBR family, including the Parkinson's disease-related gene parkin and the genes of the ariadne subfamily.

Genes of the RBR family are characterized by the RBR signature (two RING finger domains separated by an IBR/DRIL domain). The RBR family is widespread in eukaryotes, with numerous members in animals (mammals, Drosophila, Caenorhabditis) and plants (Arabidopsis). But yeasts, such as Saccharomyces cerevisiae or Schizosaccharomyces pombe, contain only two RBR genes. We determined the phylogenetic relationships and the most likely orthologs in different species of several family members for which functional data are available. These include: (1) parkin, whose mutations are involved in forms of familial Parkinson's disease; (2) the ariadne genes, recently characterized in Drosophila and mammals; (3) XYbp and Dorfin, two mammalian genes whose products interact with the centrosome; (4) XAP3, RBCK1, and UIP28, mammalian genes encoding Protein Kinase-C-binding proteins; and (5) ARA54, an androgen receptor coactivator. Because several of these genes are involved in ubiquitination, we used phylogenetic and structural analyses to explore the hypothesis that all RBR proteins might play a role in ubiquitination. We show that the involvement of RBR proteins in ubiquitination predates the animals-plants-fungi divergence. On the basis of the evidence provided by cases of gene fusion, we suggest that Ariadne proteins interact with cullin domain-containing proteins to form complexes with ubiquitin-ligase activity.

Animals↗
PubMed1983

Structure and evolution of human and African ape rDNA pseudogenes.

We discuss the evolutionary significance of four aberrant 18S rDNA clones that were obtained from human, chimpanzee, and gorilla DNA libraries. We show that these clones carry representatives of a small 18S rDNA pseudogene family that arose in a common ancestor of these species. Aspects of their structure and phylogenetic distribution suggest that the 18S pseudogenes no longer interact genetically with normal ribosomal genes and therefore may not be linked to nucleolus organizer regions.

Animals↗
PubMed1995

Context dependence of phenotype prediction and diversity in combinatorial mutagenesis.

Two different combinatorial mutagenesis experiments on the light-harvesting II (LH2) protein of Rhodobacter capsulatus indicate that heuristic rules relating sequence directly to phenotype are dependent on which sets or groups of residues are mutated simultaneously. Previously reported combinatorial mutagenesis of this chromogenic protein (based on both phylogenetic and structural models) showed that substituting amino acids with large molar volumes at Gly beta 31 caused the mutated protein to have a spectrum characteristic of light-harvesting I (LH1). The six residues that underwent combinatorial mutagenesis were modeled to lie on one side of a transmembrane alpha-helix that binds bacteriochlorophyll. In a second experiment described here, we have not used structural models or phylogeny in choosing mutagenesis sites. Instead, a set of six contiguous residues was selected for combinatorial mutagenesis. In this latter experiment, the residue substituted at Gly beta 31 was not a determining factor in whether LH2 or LH1 spectra were obtained; therefore, we conclude that the heuristic rules for phenotype prediction are context dependent. While phenotype prediction is context dependent, the ability to identify elements of primary structure causing phenotype diversity appears not to be. This strengthens the argument for performing combinatorial mutagenesis with an arbitrary grouping of residues if structural models are unavailable.

Amino Acid Sequence↗
PubMed2003

Evolution and genetic structure of the great tit (Parus major) complex.

The great tit complex is divided into four groups, each containing several subspecies. Even though the groups are known to differ markedly on morphological, vocal and behavioural characters, some hybridization occurs in the regions where they meet. The great tit has often been referred to as an example of a ring species, although this has later been questioned. Here, we have studied the genetic structure and phylogenetic relationships of the subspecies groups to clarify the evolutionary history of the complex using control region sequences of the mitochondrial DNA. The subspecies groups were found to be monophyletic and clearly distinct in mitochondrial haplotypes, and therefore must have had long-independent evolutionary histories. This conflicts with the ring species assignment and supports the formation of secondary contact zones of previously temporarily isolated groups. According to the phylogenetic species concept, all the subspecies groups could be considered as separate species, but if the definition of the biological species concept is followed, none of the subspecies groups is a true species because hybridization still occurs.

Animals↗
PubMed1990

Partial 16S rRNA primary structure of five Actinomyces species: phylogenetic implications and development of an Actinomyces israelii-specific oligonucleotide probe.

The intra- and intergeneric relationships of the genus Actinomyces were determined by comparing long 16S rRNA sequences, generated by reverse transcriptase. All species formed a phylogenetically coherent cluster in which Actinomyces bovis, A. viscosus, A. naeslundii, A. odontolyticus and A. israelii constituted genetically well defined species. A. israelii DSM 43322 (serotype 2) was not closely related to three other strains of this species (serotype 1) and, as judged from phylogenetic distances, could be accommodated within A. naeslundii, or represent a new species. In contrast to previous findings, members of the genus Actinomyces appear to be related to Bifidobacterium bifidum. Sequence information was used to develop an oligonucleotide probe for the A. israelii serotype 1 strains, which did not react with the serotype 2 strain or with rRNA from strains of eight Actinomyces species.

Actinomyces↗