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PubMed2004

Functional divergence caused by ancient positive selection of a Drosophila hybrid incompatibility locus.

Interspecific hybrid lethality and sterility are a consequence of divergent evolution between species and serve to maintain the discrete identities of species. The evolution of hybrid incompatibilities has been described in widely accepted models by Dobzhansky and Muller where lineage-specific functional divergence is the essential characteristic of hybrid incompatibility genes. Experimentally tractable models are required to identify and test candidate hybrid incompatibility genes. Several Drosophila melanogaster genes involved in hybrid incompatibility have been identified but none has yet been shown to have functionally diverged in accordance with the Dobzhansky-Muller model. By introducing transgenic copies of the X-linked Hybrid male rescue (Hmr) gene into D. melanogaster from its sibling species D. simulans and D. mauritiana, we demonstrate that Hmr has functionally diverged to cause F1 hybrid incompatibility between these species. Consistent with the Dobzhansky-Muller model, we find that Hmr has diverged extensively in the D. melanogaster lineage, but we also find extensive divergence in the sibling-species lineage. Together, these findings implicate over 13% of the amino acids encoded by Hmr as candidates for causing hybrid incompatibility. The exceptional level of divergence at Hmr cannot be explained by neutral processes because we use phylogenetic methods and population genetic analyses to show that the elevated amino-acid divergence in both lineages is due to positive selection in the distant past-at least one million generations ago. Our findings suggest that multiple substitutions driven by natural selection may be a general phenomenon required to generate hybrid incompatibility alleles.

Amino Acid Sequence↗

PubMedDate not supplied

[Comparative molecular biologic characterization of Dictyocaulus viviparus and Dictyocaulus eckerti].

For a comparative characterization of the lungworm species D. viviparus and D. eckerti which is not generally accepted as a separate species, the restriction fragment length polymorphism (RFLP) of the PCR amplified ribosomal second internal transcribed spacer (ITS2) and their sequences of both species have been examined. Ribosomal ITS2 DNA was amplified from genomic DNA of individual worms using primer that correspond to the conserved 3' and 5' ends of the ITS2 flanking 5.8S and 28S regions of Caenorhabditis elegans. PCR products were digested with restriction endonucleases AluI, NspI, SspI, BclI and MseI and separated electrophoretically on a 1% agarose gel. Each restriction enzyme produced a species specific fragment length pattern. PCR products were cloned into pCRII and sequenced. The length of the ITS2 varied between 403 (D. viviparus) and 481 bases (D. eckerti) with a GC content ranged from 25 to 33%. Intraspecific variations were low (0-1.5%). Interspecific differences occur at 112 bases. The sequence homology between D. viviparus and D. eckerti was found with 76.7%. ITS2 sequence differences between D. viviparus and D. eckerti by far exceeded intraspecific variations. Therefore both methods showed distinct differences between the lungworm species examined, thus proving that D. eckerti is correctly described as a separate species. Both species occur in deer and specific primers have been designed for both species that will be used in prevalence studies to investigate the actual role of deer in the transmission of D. viviparus to cattle.

Animals↗

PubMed2000

Evidence for two distinct subgroups of alfalfa mosaic virus (AMV) from france and italy and their relationships with other AMV strains Brief report.

The nucleotide sequence of the putative coat protein open reading frame of seven previously uncharacterized AMV strains from Italy and France was determined and aligned with comparable sequences of other AMV strains (425 L, 425 M, YSMV, S, VRU, 15/64 and Da). The data set of AMV sequences was used to determine phylogenetic relationships by both a stochastic (stationary Markov model) and a deterministic method (maximum-parsimony) of analysis. The topology of the trees obtained with the two methods was essentially the same showing that all AMV strains clustered in two monophyletic groups. Close clustering of Italian strains in subgroup I and of French strains in subgroup II seems to suggests the effect of geographic distinctiveness of evolutionary dynamics of these AMV strains. This separation did not correlate with differences in host range or symptoms (necrotic or non necrotic) induced in tomato but rather it reflected variations in the amino acid sequence of their CP, which might be related to structural properties of virus particles. A simple and rapid procedure based on the reverse transcriptase-polymerase chain reaction (RT-PCR) followed by ezymatic digestion (RFLP) was developed to identify and classify AMV isolates into the two subgroups. The method applied to a number of other AMV isolates from Italy and France supported their division in two distinct subgroups. This RT-PCR RFLP method may be useful way to investigate the dynamics of AMV populations in nature.

Alfalfa mosaic virus↗

PubMed1999

Sequence comparisons of medium RNA segment among 15 California serogroup viruses.

The complete nucleotide sequences have been determined for the M segment of 12 California (CAL) serogroup bunyaviruses. A method is described here of long reverse transcription-polymerase chain reaction (RT-PCR) that yields the full-length medium (M) RNA genomic segment. A phylogenetic tree was constructed by comparison of the open reading frames (ORFs) in the M RNA segment of 15 CAL serogroup viruses. Three distinct branches were identified and they are represented by the California encephalitis (CE), Melao (MEL), and Trivittatus (TVT) complexes. These groups correspond to those previously established by small (S) RNA genomic sequences. In addition, except for Inkoo virus, the predicted relationship among these viruses agreed with those found by serology.

Encephalitis Virus, California↗

PubMed2002

Inhibition of hemostasis by a high affinity biogenic amine-binding protein from the saliva of a blood-feeding insect.

The saliva of the blood-feeding insect Rhodnius prolixus contains numerous pharmacologically active substances. Included among these are a number of lipocalin proteins that bind various ligands important in hemostasis and inflammation. One such protein is a biogenic amine-binding protein (ABP) that binds serotonin, epinephrine, and norepinephrine. Based on amino acid alignments, it is most similar to the nitrophorin group of lipocalins found in the same insect species. Physiologically, this protein appears to act as both a vasodilator and platelet aggregation inhibitor. This protein inhibits smooth muscle contraction of the rat uterus in response to serotonin and of the rabbit aorta in response to norepinephrine. Platelet aggregation induced by a combination of low concentrations of ADP and either serotonin or epinephrine is inhibited because of the binding of serotonin and epinephrine. Potentiation of aggregation induced by low concentrations of collagen along with serotonin or epinephrine is also inhibited. Dissociation constants for biogenic amines were measured using isothermal titration calorimetry and the Hummel-Dreyer method of equilibrium gel filtration. In this manner, K(d) values of 102, 24, and 345 nm were found for serotonin, norepinephrine, and epinephrine, respectively. Molecular modeling of ABP suggests that ligand binding is mediated by interaction with the side chains of aromatic amino acids and charged residues that line the binding pocket.

Amino Acid Sequence↗

PubMed1997

[Cloning and sequencing of cDNA of E2/NS1 gene of hepatitis C virus].

Hepatitis C virus (HCV) RNA extracted from serum of a patient infected with HCV in Beijing was converted to cDNA by reverse transcription. HCV E2/NS1 gene (approximately 930 bp) was amplified by nested polymerase chain reaction and was inserted into pGEM-T plasmid vector. The 431 bp nucleotide sequence at 5' terminus of this gene was determined by dideoxy-mediated chain termination method. The result of comparison of this sequence and sequences of another 9 HCV isolates suggested that the isolate we obtained was highly homologous to HCV genotype II. There are two hypervariable regions (HVR) at the N terminus of envelope protein encoded by HCV E2/NS1 gene. Several relatively conserved amino acid residues and areas located in and out of HVR were also observed. They are concerned in maintenance of spatial conformation of HCV envelope protein, but their immune function remains to be further studied.

Amino Acid Sequence↗

PubMed2006

(Z)-9-nonacosene-major component of the contact sex pheromone of the beetle Megacyllene caryae.

Male Megacyllene caryae (Gahan) (Coleoptera: Cerambycidae) respond to females only after touching them with their antennae, indicating that mate recognition is mediated by a contact sex pheromone. Gas chromatography-mass spectrometry analyses of whole-body solvent extracts of male and female M. caryae revealed substantial differences in hydrocarbon profiles, with nearly half of the compounds in the extracts from females being absent from those of males. Biological activities of fractions of crude extracts of females, and reconstructed blends of the most abundant straight-chain (nC(27), nC(28), nC(29)), methyl-branched (2Me-C(26), 9Me-C(29), 11, 13, 15Me-C(29)), and unsaturated (Z9:C(29), Z13:C(29), Z14:C(29), Z13:C(31), Z14:C(31), Z15:C(31)) compounds in extracts of females were tested in arena bioassays, assessing four steps in the mating behavior sequence of males (orientation, arrestment, body alignment, mounting and attempting to couple the genitalia). Males showed limited response to dead females treated with fractions of the crude extract or blends of synthetic straight-chain and methyl-branched alkanes, but responded strongly to the blend of synthetic monoenes. Further trials determined that the complete sequence of mating behaviors, up to and including coupling the genitalia, was elicited by Z9:C(29) alone. Z9:C(29) is a homolog of the contact pheromone (Z9:C(25)) of the congener M. robiniae (Förster). Previous work with M. robiniae suggested that wipe sampling of cuticular hydrocarbons of females by solid phase microextraction yielded a more representative profile of components actually encountered by a male's antennae, and so provided a more readily interpretable profile of potential semiochemicals present in the wax layer than does solvent extraction. We tested this hypothesis by comparing hydrocarbon profiles of female M. caryae by the two sampling methods. Z9:C(29) was the only compound among the dominant hydrocarbons that was present in higher abundance in SPME than in solvent extracts ( approximately 12% vs. approximately 8%, respectively), supporting this hypothesis.

Animals↗

PubMed1994

Sensitive methods for determining the relatedness of proteins with limited sequence homology.

Recently, considerable advances have been made in attempts to determine the relatedness of protein sequences distant in evolution, when little or no knowledge is available concerning the corresponding tertiary architectures. Several improvements have been made to existing techniques, and these include better amino acid substitution weights contained in scoring matrices, better understanding of the effect of different gap penalty values in delineating the optimal alignment of two sequences, improved assessment of the significance of suggested sequence similarities, consideration of high scoring alternative alignments, and advances in searching entire sequence databases with the profile technique utilizing multiple-sequence information. New approaches that search for similarity a query sequence against large data banks rely on highly conserved segmental motifs defined from an aligned family of sequences. A sensitive algorithm to find distant repeats within one primary structure has also been developed recently. Solution of the inverse protein-folding problem, which involves an estimation of the ability of a sequence to take on a known main-chain tertiary topology (despite little homology with the known sequence), is being facilitated by the recent explosion in the number of new algorithms.

Amino Acid Sequence↗

PubMed1998

Fold assembly of small proteins using monte carlo simulations driven by restraints derived from multiple sequence alignments.

The feasibility of predicting the global fold of small proteins by incorporating predicted secondary and tertiary restraints into ab initio folding simulations has been demonstrated on a test set comprised of 20 non-homologous proteins, of which one was a blind prediction of target 42 in the recent CASP2 contest. These proteins contain from 37 to 100 residues and represent all secondary structural classes and a representative variety of global topologies. Secondary structure restraints are provided by the PHD secondary structure prediction algorithm that incorporates multiple sequence information. Predicted tertiary restraints are derived from multiple sequence alignments via a two-step process. First, seed side-chain contacts are identified from correlated mutation analysis, and then a threading-based algorithm is used to expand the number of these seed contacts. A lattice-based reduced protein model and a folding algorithm designed to incorporate these predicted restraints is described. Depending upon fold complexity, it is possible to assemble native-like topologies whose coordinate root-mean-square deviation from native is between 3.0 A and 6.5 A. The requisite level of accuracy in side-chain contact map prediction can be roughly 25% on average, provided that about 60% of the contact predictions are correct within +/-1 residue and 95% of the predictions are correct within +/-4 residues. Precision in tertiary contact prediction is more critical than absolute accuracy. Furthermore, only a subset of the tertiary contacts, on the order of 25% of the total, is sufficient for successful topology assembly. Overall, this study suggests that the use of restraints derived from multiple sequence alignments combined with a fold assembly algorithm holds considerable promise for the prediction of the global topology of small proteins.

Amino Acid Sequence↗

PubMed2006

Cloning, sequencing and analysis of the 16S-23S rDNA intergenic spacers (IGSs) of two strains of Vibrio vulnificus.

According to the conserved sequences flanking the 3' end of the 16S and the 5' end of the 23S rDNAs, PCR primers were designed, and the 16S-23S rDNA intergenic spacers (IGSs) of two strains of Vibrio vulnificus were amplified by PCR and cloned into pGEM-T vector. Different clones were selected to be sequenced and the sequences were analyzed with BLAST and the software DNAstar. Analyses of the IGS sequences suggested that the strain ZSU006 contains five types of polymorphic 16S-23S rDNA intergenic spacers, namely, IGSGLAV, IGSGLV, IGSIA, IGSG and IGSA; while the strain CG021 has the same types of IGSs except lacking IGSA. Among these five IGS types, IGSGLAV is the biggest type, including the gene cluster of tRNAGlu-tRNALys-tRNAAla-tRNAVal; IGSGLV includes that of tRNAGlu-tRNALys-tRNAVal; IGSAG, tRNAAla-tRNAGlu; IGSIA, tRNAIle-tRNAAla; IGSG, tRNAGlu and IGSA, tRNAAla. Intraspecies multiple alignment of all the IGS sequences of these two strains with those of V. vulnificus ATCC27562 available at GenBank revealed several highly conserved sequence blocks in the non- coding regions flanking the tRNA genes within all of strains, most notably the first 40 and last 200 nucleotides, which can be targeted to design species-specific PCR primers or detection probes. The structural variations of the 16S-23S rDNA intergenic spacers lay a foundation for developing diagnostic methods for V. vulnificus.

Cloning, Molecular↗

PubMed1995

Detection and analysis of hepatitis C virus by a combined RT-PCR method: variation in the 5' non-coding region of the viral genome.

A combined reverse transcription-polymerase chain reaction (RT-PCR) method was employed for the detection of hepatitis C virus (HCV) RNA in serum from patients with chronic active hepatitis, with primers corresponding to the 5' non-coding region. The diagnosis was based on serological and biochemical methods and on liver biopsy. HCV-RNA was detected in 27 (90%) of 30 sera examined. The nucleotide sequence of PCR-amplified HCV cDNAs (256 bp) was determined from five specimens and heterogeneity varying between 0.58% and 2.89% among the clinical samples and the prototype HCV-1 was found.

Base Sequence↗

PubMed2004

Phylogenetic analysis of methyl coenzyme-M reductase detected from the bovine rumen.

AIMS: The object of the present study is isolation of methyl coenzyme-M reductase (MCR) genes (mcrA) from the bovine rumen fluid and determination of phylogenetical placements of the genes to investigate mechanisms of methanogenesis in the rumen from a point of view of mcrA genes. METHODS: Genes for methanogen-specific MCR were isolated from the bovine rumen by PCR amplification. The deduced amino acid sequences were fitted to the alignments of mcrA gene products from the referred sequences. SIGNIFICANCE AND IMPACT OF THE STUDY: Although the deduced amino acid sequences of mcrA genes, isolated from the bovine rumen in the present study, were close to that of Methanobrevibacter ruminantium, these amino acid sequences did not fall into known clusters of MCR. The findings suggest that methanogenesis in the rumen would be partially carried out by unknown methanogens.

Animals↗

PubMed1998

Characterization of cytoplasmic dynein light-intermediate chain isoforms in rat testis.

We obtained three kinds of novel cytoplasmic dynein light-intermediate chain (LIC) isoforms from rat testis and brain by reverse transcription polymerase chain reaction (RT-PCR). The primers for RT-PCR were designed according to LIC-2 (LIC 53/55) (15). In one novel isoform, the 42 bp specific sequence named TDL was inserted between 1,106 and 1,107 nucleotides (nts) of LIC-2, whereas the 57 bp sequence corresponding to LIC-2 1,339-1,395 nts (BDL) was absent. The TDL and BDL regions were specifically digested with restriction enzymatic treatment and followed by subcloning of non-digested cDNA band in testis and brain, producing an isoform without TDL and BDL regions. BDL specific RT-PCR of testis cDNA followed by sequencing produced an isoform with two specific regions. By Northern blot hybridization using TDL and BDL specific antisense oligo DNA probe, 4.4, 3.5, and 2.0 kb of signals were detected. With both TDL and BDL probes, the 2.0 kb signal was intensely detected in testis, while the 4.4 kb was defected in brain. This indicates that TDL and BDL are derived from the same size of mRNAs. In situ hybridization method using these probes showed that all seminiferous epithelial cells, especially late pachytene spermatocytes, were positive, indicating that LIC 53/55 isoforms were coexpressed in these cells. These findings indicate that LIC 53/55 isoforms provide a variety of dynein subunits, and thus may regulate the dynein-dependent intracellular transport system.

Alternative Splicing↗

PubMed2000

Structure and site-directed mutagenesis of a flavoprotein from Escherichia coli that reduces nitrocompounds: alteration of pyridine nucleotide binding by a single amino acid substitution.

The crystal structure of a major oxygen-insensitive nitroreductase (NfsA) from Escherichia coli has been solved by the molecular replacement method at 1.7-A resolution. This enzyme is a homodimeric flavoprotein with one FMN cofactor per monomer and catalyzes reduction of nitrocompounds using NADPH. The structure exhibits an alpha + beta-fold, and is comprised of a central domain and an excursion domain. The overall structure of NfsA is similar to the NADPH-dependent flavin reductase of Vibrio harveyi, despite definite difference in the spatial arrangement of residues around the putative substrate-binding site. On the basis of the crystal structure of NfsA and its alignment with the V. harveyi flavin reductase and the NADPH-dependent nitro/flavin reductase of Bacillus subtilis, residues Arg(203) and Arg(208) of the loop region between helices I and J in the vicinity of the catalytic center FMN is predicted as a determinant for NADPH binding. The R203A mutant results in a 33-fold increase in the K(m) value for NADPH indicating that the side chain of Arg(203) plays a key role in binding NADPH possibly to interact with the 2'-phosphate group.

Amino Acid Sequence↗

PubMed2002

Occurrence, conformational features and amino acid propensities for the pi-helix.

The most abundant helix type in proteins is the alpha-helix, accounting for about 31% of amino acid secondary structure states, while the 3(10)-helix accounts for about 4%. The pi-helix appears to be extremely rare and is considered to be unstable. Existing secondary structure definition methods find very few within the Protein Data Bank. Using an improved pi-helix definition algorithm to search a non-redundant subset of high-resolution and well-refined protein structures, we found that almost every tenth protein contained a pi-helix. This enabled us to show for the first time that the pi-helix has structural parameters that are different from the hypothesized model values. It also has distinctive amino acid preferences and it is conserved within functionally related proteins. Features that may contribute to the stability of the pi-helical structure have also been identified. In addition to hydrogen bonds, several other factors contribute to the stability of pi-helices. The pi-helix may have some functional advantages over other helical structures. Thus, we describe cases where the side chains of functionally important residues at every fourth position within a pi-helix could be aligned and brought close together in a way that would not be allowed by any other helix type.

Algorithms↗

PubMed2005

Characterization of zebrafish Rad52 and replication protein A for oligonucleotide-mediated mutagenesis.

Zebrafish has become a favorite model organism not only in genetics and developmental biology, but also for the study of cancer, neuroscience and metabolism. However, strategies for reverse genetics in zebrafish are mostly limited to the use of antisense oligonucleotides, and therefore the development of other targeting methods is highly desirable. Here, we report an approach to gene targeting in this system in which single-stranded oligonucleotides and zebrafish Rad52 protein are employed. It has been proposed that a single-stranded oligonucleotide containing a mutation can be incorporated into the genome by annealing to the single-stranded region of the lagging strand of the replication fork. Rad52 is expected to accelerate the annealing step. In vitro experiments using purified truncated Rad52 proteins and replication protein A (RPA) showed that annealing of oligonucleotides is accelerated by Rad52 in the presence of RPA. We developed a simple and sensitive PCR-based method to detect point mutations in the genome. In exploratory experiments, we found that microinjection of single-stranded oligonucleotide targeted to a specific gene together with truncated Rad52 into zebrafish embryos resulted in a low level of recombinant copies in 3 of the 80 embryos tested under these conditions.

Amino Acid Sequence↗

PubMed1993

An evaluation of the performance of an automated procedure for comparative modelling of protein tertiary structure.

A 3-D model of a protein can be constructed from its amino acid sequence and the 3-D structures of one or more homologues by annealing three sets of fragments: the structurally conserved regions, structurally variable regions and the side chains. The method encoded in the computer program COMPOSER was assessed by generating 3-D models of eight proteins whose crystal structures are already known and for which 3-D structures of homologues are available. In the structurally conserved regions, differences between modelled and X-ray structures are smaller than the differences between the X-ray structures of the modelled protein and the homologues used to build the model. When several homologues are used, the contributions of the known structures are weighted, preferably by the square of sequence similarity; this is especially important when the similarities of the homologues to the modelled structure differ greatly. The 'collar' extension approach, in which a similar region of different length in a homologue is used to extend the framework, can result in a more accurate model. If known homologues comprise more than one related group of proteins and they are both distantly related to the unknown, then alignment of the sequence to be modelled with each group of homologues facilitates identification of structurally conserved regions of the unknown and leads to an improved model. Models have root mean square differences (r.m.s.d.s) with the structures defined by X-ray analysis of between 0.73 and 1.56 A for all C alpha atoms, for seven the eight models. For the model of mucor pepsin, where the closest homologue has 33% sequence identity and 20% of the residues are in structurally variable regions, the r.m.s.d. for the framework region is 1.71 A and the r.m.s.d. for all C alpha atoms is 3.47 A.

Amino Acid Sequence↗

PubMedDate not supplied

Molecular diagnostics of clinical strains of filamentous Basidiomycetes.

Eleven clinical and veterinary strains of filamentous Basidiomycetes were compared with 15 reference strains representing the orders Aphyllophorales and Agaricales. The methods used were restriction analysis of small subunit (18S) (SSU) rDNA and internal transcribed spacers (ITS) 1 and 2 and variable domain 9 (V9)-ITS1 sequencing. Six strains were found to belong to the teleomorph genera Schizophyllum or Coprinus, whereas five could not be identified unequivocally. A rapid diagnostic overview is obtained with HaeIII and HinfI digestion of the ITS region.

Agaricales↗