Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “structural phylogenetics”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 1,045 records · Page 58Linked to original sources
PubMedDate not supplied

Phylogenetic relationships of Bacteria based on comparative sequence analysis of elongation factor Tu and ATP-synthase beta-subunit genes.

Comparative sequence analyses were performed on 14 genes encoding bacterial elongation factors EF-Tu and 7 genes encoding the beta-subunit of bacterial F1F0 type ATP-synthases. The corresponding predicted amino acid sequences were compared with published primary structures of homologous molecules. Phylogenetic trees were reconstructed from both data sets of aligned protein sequences and from an equivalent selection of 16S rRNA sequences by applying distance matrix and maximum parsimony methods. The EF-Tu data were in very good agreement with the rRNA data, although the resolution within the EF-Tu tree was reduced at certain phylogenetic levels. The resolution power of the ATPase beta-subunit sequence data were more reduced than those of the EF-Tu data. In comparison with the 16S rRNA tree there are minor differences in the order of adjacent branchings within the ATPase beta-subunit tree.

Amino Acid Sequence↗
PubMed1988

Structural organization, DNA sequence, and expression of the calmodulin gene.

Calmodulin is encoded in Chlamydomonas reinhardtii by a single gene that 1) has multiple intervening sequences, 2) has 5' structural motifs that are phylogenetically conserved, 3) contains 5' sequences that are similar to those found in genes of some transforming, cytoskeletal, and stress-response proteins, and 4) produces at both life cycle stages, a single size class of mRNA and proteins that are identical in amino acid sequence. Based on the amino acid sequence of calmodulin from the vegetative phase of the life cycle, synthetic oligonucleotide probes, containing inosine in order to reduce codon redundancy, were used to detect and isolate cloned cDNAs coding for the gametic phase calmodulin. The complete DNA sequence was elucidated and shown to code for a protein identical to the vegetative phase protein. Analysis of the production of calmodulin mRNA indicates that protein production is under quantitative regulation and possibly coupled with the synthesis of other proteins in the flagellar apparatus. The full length cDNA was used to isolate overlapping genomic clones that include the entire calmodulin transcriptional unit and 5' regulatory sequences. The complete DNA sequence of the gene, including all intron sequences, was elucidated. The DNA sequence of the coding regions shows some phylogenetic conservation. Finally, there are regions of 5' sequence reminiscent of sequence motifs recently identified as binding sites of transcriptional regulatory proteins. Overall, these studies suggest possible molecular genetic relationships between calmodulin, a transducer of intracellular calcium signals, and other proteins involved in eukaryotic cell structure, motility, and homeostasis.

Amino Acid Sequence↗
PubMed1988

Molecular genetics of group I introns: RNA structures and protein factors required for splicing--a review.

In vivo and in vitro genetic techniques have been widely used to investigate the structure-function relationships and requirements for splicing of group-I introns. Analyses of group-I introns from extremely diverse genetic systems, including fungal mitochondria, protozoan nuclei, and bacteriophages, have yielded results which are complementary and highly consistent. In vivo genetic studies of fungal mitochondrial systems have served to identify cis-acting sequences within mitochondrial introns, and trans-acting protein products of mitochondrial and nuclear genes which are important for splicing, and to show that some mitochondrial introns are mobile genetic elements. In vitro genetic studies of the self-splicing intron within the Tetrahymena thermophila nuclear large ribosomal RNA precursor (Tetrahymena LSU intron) have been used to examine essential and nonessential RNA sequences and structures in RNA-catalyzed splicing. In vivo and in vitro genetic analysis of the intron within the bacteriophage T4 td gene has permitted the detailed examination of mutant phenotypes by analyzing splicing in vivo and self-splicing in vitro. The genetic studies combined with phylogenetic analysis of intron structure based on comparative nucleotide sequence data [Cech 73 (1988) 259-271] and with biochemical data obtained from in vitro splicing experiments have resulted in significant advances in understanding the biology and chemistry of group-I introns.

Introns↗
PubMed2003

Crystal complexes of a predicted S-adenosylmethionine-dependent methyltransferase reveal a typical AdoMet binding domain and a substrate recognition domain.

S-adenosyl-L-methionine-dependent methyltransferases (MTs) are abundant, and highly conserved across phylogeny. These enzymes use the cofactor AdoMet to methylate a wide variety of molecular targets, thereby modulating important cellular and metabolic activities. Thermotoga maritima protein 0872 (TM0872) belongs to a large sequence family of predicted MTs, ranging phylogenetically from relatively simple bacteria to humans. The genes for many of the bacterial homologs are located within operons involved in cell wall synthesis and cell division. Despite preliminary biochemical studies in E. coli and B. subtilis, the substrate specificity of this group of more than 150 proteins is unknown. As part of the Midwest Center for Structural Genomics initiative (www.mcsg.anl.gov), we have determined the structure of TM0872 in complexes with AdoMet and with S-adenosyl-L-homocysteine (AdoHcy). As predicted, TM0872 has a typical MT domain, and binds endogenous AdoMet, or co-crystallized AdoHcy, in a manner consistent with other known MT structures. In addition, TM0872 has a second domain that is novel among MTs in both its location in the sequence and its structure. The second domain likely acts in substrate recognition and binding, and there is a potential substrate-binding cleft spanning the two domains. This long and narrow cleft is lined with positively charged residues which are located opposite the S(+)-CH(3) bond, suggesting that a negatively charged molecule might be targeted for catalysis. However, AdoMet and AdoHcy are both buried, and access to the methyl group would presumably require structural rearrangement. These TM0872 crystal structures offer the first structural glimpses at this phylogenetically conserved sequence family.

Amino Acid Sequence↗
PubMed2005

libcov: a C++ bioinformatic library to manipulate protein structures, sequence alignments and phylogeny.

BACKGROUND: An increasing number of bioinformatics methods are considering the phylogenetic relationships between biological sequences. Implementing new methodologies using the maximum likelihood phylogenetic framework can be a time consuming task. RESULTS: The bioinformatics library libcov is a collection of C++ classes that provides a high and low-level interface to maximum likelihood phylogenetics, sequence analysis and a data structure for structural biological methods. libcov can be used to compute likelihoods, search tree topologies, estimate site rates, cluster sequences, manipulate tree structures and compare phylogenies for a broad selection of applications. CONCLUSION: Using this library, it is possible to rapidly prototype applications that use the sophistication of phylogenetic likelihoods without getting involved in a major software engineering project. libcov is thus a potentially valuable building block to develop in-house methodologies in the field of protein phylogenetics.

Algorithms↗
PubMed2005

Morphological characterisation of Andrya Railliet, 1893, Neandrya n. g. and Paranoplocephala Lühe, 1910 (Cestoda: Anoplocephalidae) in rodents and lagomorphs.

The taxonomic significance of the main morphological features of the 25 species allocated to Andrya Railliet, 1893 and Paranoplocephala Lühe, 1910 is re-evaluated in the light of the recent molecular phylogenetic hypotheses for anoplocephaline cestodes. The present analysis and the existing phylogenetic data suggest that the structure and complexity of the early uterus are not, as previously assumed, the main phylogenetic or systematic determinants for anoplocephaline cestodes. Instead, the position of the early uterus with respect to other organs, combined with the morphology of the female genitalia, appear to allow a fairly straightforward discrimination of the three genera recognised here, without contradicting current phylogenetic hypotheses. A new genus, Neandrya n. g., is proposed for N. cuniculi (Blanchard, 1891) n. comb. (previously in Andrya), amended diagnoses are provided for Andrya and Paranoplocephala and a diagnostic key to these three genera is presented.

Animals↗
PubMed2000

Template boundary in a yeast telomerase specified by RNA structure.

The telomerase ribonucleoprotein has a phylogenetically divergent RNA subunit, which contains a short template for telomeric DNA synthesis. To understand how telomerase RNA participates in mechanistic aspects of telomere synthesis, we studied a conserved secondary structure adjacent to the template. Disruption of this structure caused DNA synthesis to proceed beyond the normal template boundary, resulting in altered telomere sequences, telomere shortening, and cellular growth defects. Compensatory mutations restored normal telomerase function. Thus, the RNA structure, rather than its sequence, specifies the template boundary. This study reveals a specific function for an RNA structure in the enzymatic action of telomerase.

Base Pairing↗
PubMed2000

Left-right asymmetric expression of BbPtx, a Ptx-related gene, in a lancelet species and the developmental left-sidedness in deuterostomes.

The long-standing question of how asymmetric development or asymmetric body structures in lancelets (amphioxus) are phylogenetically related to the body plan of other animals is still untouched. Three anterior structures, the preoral pit, club-shaped gland and mouth, are remarkable asymmetric features in developing lancelets that all open on the left side of the body. A Ptx-related gene, BbPtx is the first identified transcription factor gene with an asymmetrical expression pattern in lancelets similar to that in vertebrates, and thus it may provide a clue for the above question. Expression of the BbPtx gene is first detected at the dorsal margin of the blastopore in early mid-gastrulae and then becomes restricted to the left anterodorsal wall of the primitive gut and to the developing left somitocoelomic system. Expression continues on the left side in the developing preoral pit, club-shaped gland and mouth as well as in the mesoderm at the caudal end. Unlike D-Ptx1 in Drosophila, BbPtx is not coexpressed with a fork head gene in lancelets; instead the two genes are expressed in a complementary fashion on the left side of the embryo. The expression pattern of BbPtx is not compatible with the calcichordate hypothesis of Jefferies, in which the proposed ancestor of chordates rotated its tail 90 degrees counterclockwise in relation to the head/trunk. The expression of both BbPtx and vertebrate Pitx2 in tissues derived from the coelom implies that the left-right asymmetric development has a common origin between cephalochordates and vertebrates. Considering the development of the coelom in deuterostomes, however, left-right asymmetric development involving Pitx2-related genes is rather likely to be a primitive character shared among deuterostomes.

Amino Acid Sequence↗
PubMed1999

Secondary structure model for the ITS-2 precursor rRNA of strongyloid nematodes of equids: implications for phylogenetic inference.

In order to maximise the positional homology in the primary sequence alignment of the second internal transcribed spacer for 30 species of equine strongyloid nematodes, the secondary structures of the precursor ribosomal RNA were predicted using an approach combining an energy minimisation method and comparative sequence analysis. The results indicated that a common secondary structure model of the second internal transcribed spacer of these nematodes was maintained despite significant interspecific differences (2-56%) in primary sequences. The secondary structure model was then used to refine the primary second internal transcribed spacer sequence alignment. The 'manual' and 'structure' alignments were both subjected to phylogenetic analysis to compare the effect of using different sequence alignments on phylogenetic inference. The topologies of the phylogenetic trees inferred from the manual second internal transcribed spacer alignment were usually different to those derived from the structure second internal transcribed spacer alignment. The results suggested that the positional homology in the second internal transcribed spacer primary sequence alignment was maximised when the secondary structure model was taken into consideration.

Animals↗
PubMed1998

Variation of the ribosomal operon 16S-23S gene spacer region in representatives of Salmonella enterica subspecies.

The 16S-23S spacer regions of two ribosomal operons (rrnA and rrnE) have been sequenced in seven representatives of the Salmonella enterica subspecies. Isolated nucleotide substitutions were found at the same sites as in Escherichia coli but the number of polymorphic sites was much larger, as could be expected for a more heterogeneous species. Still, as in E. coli, most of the variation found was due to insertions and/or deletions affecting blocks of nucleotides generally located at equivalent regions of the putative secondary structure for both species. Isolated polymorphic sites generated phylogenetic trees generally consistent with the subspecies structure and the accepted relationships among the subspecies. However, the sequences of rrnE put subspecies I closer to E. coli K-12 than to the other S. enterica subspecies. The distribution of polymorphisms affecting blocks of nucleotides was much more random, and the presence of equivalent sequences in distantly related subspecies, and even in E. coli, could reflect relatively frequent horizontal transfer. The smallest 16S-23S spacers in other genera of the family Enterobacteriaceae were also sequenced. As expected, the level of variation was much larger. Still, the phylogenetic tree inferred is consistent with those of 16S rRNA or housekeeping genes.

Base Sequence↗
PubMedDate not supplied

[A comparative phylogenetic analysis of the coding portion of the genes for structural protein E1 in the Shi-Min' strain and in other strains of the classic hog cholera virus].

The primary nucleotide sequence of the fragment of E1 (gp51-55) gene (772 bp in length) of virulent strain Shi-Min' of classical swine fever virus (CSFV) has been determined. Multiple alignments of the E1 gene fragments of various strains and isolates of CSFV, which are homologues to the cloned fragment, has been carried out; the phylogenetic tree has been plotted and the consensus sequence has been determined. The strain Shi-Min', which was used as a control CSFV strain in former Soviet republics, and the referent strain Alfort were shown to be located on the opposite sides of the dendrogram, while Shi-Min' was more close to the western European group of CSFVs. We suggest that Shi-Min' strain as a positive viral antigen for vaccine testing represents a selective factor for the formation of virus population in Ukraine. The data obtained are the first results in molecular epizootic study of hog cholera in Ukraine.

Antigens, Viral↗
PubMedDate not supplied

Mycoplasma evolution: a review of the use of ribosomal and transfer RNA nucleotide sequences in the determination of phylogenetic relationships.

Comparison of the nucleotide sequences of "structural" RNAs (ribosomal and transfer RNA) has enabled the construction of phylogenetic trees to be achieved. Data from 16S rRNA, 5S rRNA, and tRNA from a total of eight Mollicutes (excluding T. acidophilum) including representatives of the families Mycoplasmataceae, Spiroplasmataceae, and Acholeplasmataceae, show that these families share a close relationship and a common ancestor with the gram-positive eubacteria. Thermoplasma acidophilum is a member of the kingdom Archaebacteriae and has no relationship to the other Mollicutes.

Base Sequence↗
PubMed1993

VH gene organization in a relict species, the coelacanth Latimeria chalumnae: evolutionary implications.

The living coelacanth Latimeria chalumnae is a relict species whose higher-level phylogenetic relationships have not been resolved clearly by traditional systematic approaches. Previous studies show that major differences in immunoglobulin gene structure and organization typify different phylogenetic lineages. To date, mammalian-, avian-, and elasmobranch-type gene organizations have been identified in representatives of these different phylads. A fourth form or organization is found in Latimeria, which possesses immunoglobulin heavy-chain variable region (VH) elements separated by approximately 190 nucleotides from diversity (D) elements. Adjacency of VH and D elements is characteristic of the elasmobranch "clustered" arrangement, although many other features of coelacanth VH gene organization and structure are more similar to those of bony fishes and tetrapods. These observations strongly support a phylogenetic hypothesis in which Latimeria occupies a sister-group relationship with teleosts and tetrapods.

Amino Acid Sequence↗
PubMed1998

Structural organization and chromosomal localization of the human hepatocyte growth factor activator gene--phylogenetic and functional relationship with blood coagulation factor XII, urokinase, and tissue-type plasminogen activator.

The organization and structure of the gene coding for hepatocyte growth factor activator (HGFA) have been determined by isolation of unique clones from a human genomic library. These clones were characterized by restriction mapping, Southern blotting and DNA sequencing. The complete sequence of the gene was determined and found to span about 7.5 kilobases of DNA and consist of 14 exons separated by 13 introns. The coding region of HGFA consists of multiple putative domains that are homologous to those observed in blood coagulation factor XII (FXII). These regions were found as separate exons in the gene, and the exon/intron arrangement was similar to that of FXII, suggesting that the genes for HGFA and FXII have arisen through gene duplication events from a common ancestral gene. The major transcription initiation site is located 75 bp upstream of the translational start codon. The gene was mapped to chromosome 4p16, using spot-blot hybridization on sorted chromosomes and fluorescence in situ hybridization on metaphase chromosome spreads. The phylogenetic and functional relationships between HGFA and FXII as well as urokinase and tissue-type plasminogen activator are discussed.

Base Sequence↗
PubMed1996

The Ribosomal Database Project (RDP).

The Ribosomal Database Project (RDP) is a curated database that offers ribosome-related data, analysis services and associated computer programs. The offerings include phylogenetically ordered alignments of ribosomal RNA (rRNA) sequences, derived phylogenetic trees, rRNA secondary structure diagrams and various software for handling, analyzing and displaying alignments and trees. The data are available via anonymous ftp (rdp.life.uiuc.edu), electronic mail (server@rdp.life.uiuc.edu), gopher (rdpgopher.life.uiuc.edu) and World Wide Web (WWW)(http://rdpwww.life.uiuc.edu/). The electronic mail and WWW servers provide ribosomal probe checking, screening for possible chimeric rRNA sequences, automated alignment and approximate phylogenetic placement of user-submitted sequences on an existing phylogenetic tree.

Computer Communication Networks↗
PubMed2002

The latex-fruit syndrome.

Approximately 30-50% of individuals who are allergic to natural rubber latex (NRL) show an associated hypersensitivity to some plant-derived foods, especially freshly consumed fruits. This association of latex allergy and allergy to plant-derived foods is called latex-fruit syndrome. An increasing number of plant sources, such as avocado, banana, chestnut, kiwi, peach, tomato, potato and bell pepper, have been associated with this syndrome. The prevailing hypothesis is that allergen cross-reactivity is due to IgE antibodies that recognize structurally similar epitopes on different proteins that are phylogenetically closely related or represent evolutionarily conserved structures. Several types of proteins have been identified to be involved in the latex-fruit syndrome. Two of these are plant defence proteins. Class I chitinases containing an N-terminal hevein-like domain cross-react with hevein (Hev b 6.02), a major IgE-binding allergen for patients allergic to NRL. A beta-1,3-glucanase was identified as an important latex allergen which shows cross-reactivity with proteins of bell pepper. Another important NRL allergen, Hev b 7, is a patatin-like protein that shows cross-reactivity with its analogous protein in potato. Furthermore, patients with allergy to plant-derived foods and associated pollinosis show a high frequency of IgE reactivity to the pan-allergen profilin, which may cause positive serum IgE determinations to NRL. Although there is much information about the plant-derived foods and some data about the allergens involved in the latex-fruit syndrome, it is not always clear whether latex sensitization precedes or follows the onset of food allergy.

Antimicrobial Cationic Peptides↗
PubMed1999

Molecular characterization of human group C rotavirus genes 6, 7 and 9.

Genes 6, 7 and 9 of human group C rotavirus 'Bristol' strain, encoding non-structural proteins (NSP) 3, 1 and 2, respectively, were cloned and sequenced. Human group C rotavirus genome segment 6 is 1350 bp and contains a single ORF of 1231 nucleotides (encoding 402 amino acids). Genome segment 7 is 1270 bp and encodes a protein of 394 amino acids and genome segment 9 is 1037 bp and encodes a 312 amino acid protein. The human group C rotavirus genes 6, 7 and 9 showed 78, 67 and 88% sequence identity, respectively, to the corresponding porcine group C rotavirus genes. The derived protein sequences were compared with those of the porcine 'Cowden' group C and mammalian group A rotavirus strains. The human group C rotavirus NSP1 protein sequence is one amino acid longer than the porcine group C equivalent. In common with group A and porcine group C rotaviruses, the human group C rotavirus NSP1 protein has a zinc finger motif. Human group C rotavirus NSP2 has two hydrophobic heptad repeat regions, a basic, RNA-binding domain and a basic, proline-rich region. Human group C rotavirus NSP3 has both single- and double-stranded RNA-binding domains and several hydrophobic heptad repeat regions, one of which forms a leucine zipper. This work completes the molecular characterization of the non-structural proteins of a human group C rotavirus. Phylogenetic analysis of all the non-structural genes of group A, B and C rotaviruses suggests that these viruses have diverged at a constant rate from a common ancestor.

Amino Acid Sequence↗
PubMed1999

Peptidoglycan fine structure of the radiotolerant bacterium Deinococcus radiodurans Sark.

Peptidoglycan from Deinococcus radiodurans was analyzed by high-performance liquid chromatography and mass spectrometry. The monomeric subunit was: N-acetylglucosamine-N-acetylmuramic acid-L-Ala-D-Glu-(gamma)-L-Orn-[(delta)Gly-Gly]-D-Ala-D-Ala. Cross-linkage was mediated by (Gly)2 bridges, and glycan strands were terminated in (1-->6)anhydro-muramic acid residues. Structural relations with the phylogenetically close Thermus thermophilus are discussed.

Amino Acid Sequence↗