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 721 records · Page 40Linked to original sources
PubMedDate not supplied

[Tecto-thalamo-telencephalic visual system of the brain in 13-day-old chick embryos].

Light and electron microscopic studies have been made of the nervous tissue in three parts of the tecto-thalamo-telencephalic visual system--i.e. tectum opticum, nucleus rotundus of thalamus and ectostriatum of telencephalon--of 13-day chick embryos. Neuroblasts and neurones at various stages of differentiation were described together with various types of synaptic and nonsynaptic intercellular contacts in the neuropil of these brain structures. Heterochronous maturation of these parts of the visual system in embryogenesis was noted which reflects the level of their phylogenetic maturity. Being phylogenetically more ancient structures, tectum opticum and nucleus rotundus reveal differentiation earlier than ectostriatum which is phylogenetically younger.

Animals↗
PubMed2006

Integrating protein structures and precomputed genealogies in the Magnum database: examples with cellular retinoid binding proteins.

BACKGROUND: When accurate models for the divergent evolution of protein sequences are integrated with complementary biological information, such as folded protein structures, analyses of the combined data often lead to new hypotheses about molecular physiology. This represents an excellent example of how bioinformatics can be used to guide experimental research. However, progress in this direction has been slowed by the lack of a publicly available resource suitable for general use. RESULTS: The precomputed Magnum database offers a solution to this problem for ca. 1,800 full-length protein families with at least one crystal structure. The Magnum deliverables include 1) multiple sequence alignments, 2) mapping of alignment sites to crystal structure sites, 3) phylogenetic trees, 4) inferred ancestral sequences at internal tree nodes, and 5) amino acid replacements along tree branches. Comprehensive evaluations revealed that the automated procedures used to construct Magnum produced accurate models of how proteins divergently evolve, or genealogies, and correctly integrated these with the structural data. To demonstrate Magnum's capabilities, we asked for amino acid replacements requiring three nucleotide substitutions, located at internal protein structure sites, and occurring on short phylogenetic tree branches. In the cellular retinoid binding protein family a site that potentially modulates ligand binding affinity was discovered. Recruitment of cellular retinol binding protein to function as a lens crystallin in the diurnal gecko afforded another opportunity to showcase the predictive value of a browsable database containing branch replacement patterns integrated with protein structures. CONCLUSION: We integrated two areas of protein science, evolution and structure, on a large scale and created a precomputed database, known as Magnum, which is the first freely available resource of its kind. Magnum provides evolutionary and structural bioinformatics resources that are useful for identifying experimentally testable hypotheses about the molecular basis of protein behaviors and functions, as illustrated with the examples from the cellular retinoid binding proteins.

Amino Acid Sequence↗
PubMedDate not supplied

[The dynamics of the electrical activity of the forebrain structures in rats in the waking-sleep cycle after electrostimulations of the emotiogenic zones in the lateral hypothalamic area].

One series of ES (multiple priming) of emotion-positive zone (1) ore the ambivalent zone (2) of lateral hypothalamus (LH) during one hour in Wistar male rats resulted in disorders of the W-S cycle: reduction of deep slow-wave sleep down to about 4.7% (zone 1) and down to 0.9% (zone 2), as well as a considerable reduction of REM sleep down to 0.8% (zone 1). The results of the analysis of bioelectrical brain activity dynamics in the W-S cycle suggest that hyperactivation of emotiogenic zones generated by ES is responsible for the establishment of paroxysmal states corresponding to the second and the third stages of kindling and the disorders of the W-S cycle. Kindling is assumed to form due to emotiogenic zones of the brain involved in to this process. The longer bursts of hypersynchronous bioelectrical activity in the cortex than in the subcortical structures during transient stages of sleep may be in favour of more active participation of phylogenetically younger brain structures in the process of epileptogenesis.

Animals↗
PubMed1990

S71 is a phylogenetically distinct human endogenous retroviral element with structural and sequence homology to simian sarcoma virus (SSV).

Human endogenous retroviral element S71 had previously been shown to contain gag- and pol-related regions and a 3' LTR-like sequence. The nucleotide sequence of S71 was determined and compared with the corresponding regions of SSV and its helper virus SSAV. The 1.48-kb S71 gag region consists of matrix protein p15 (MA)-, capsid protein p30 (CA)-, and nucleocapsid protein p10 (NC)-related sections and the 1.82-kb pol region of tether, RNase H (RH), and endonuclease/integrase (IN) sections. The S71 nucleotide sequence contains a 167 amino acid open reading frame encompassing MA. The boundaries of the S71 element are delimited by direct repeats and the entire element is 5.4 kb long. Similarity between S71 and the v-sis-bearing, defective SSV provirus also covers overall structural organization, including the presence of presumably nonretroviral sequences. Both the gag and the pol regions of S71 contain sequences highly conserved in numerous retroviruses. Phylogenetic analysis with conserved CA, RH, and IN sequences showed that of all other (C-type) human retroviral elements available for comparison, S71 is most closely related to infectious primate and murine retroviruses. This suggests that S71 represents a phylogenetic subgroup of its own. In addition we identified short ranges of conserved amino acid sequences within C-type retroviral gag and pol genes sufficient for phylogenetic analysis. Use of these may facilitate large-scale phylogenetic evaluation of C-type retroviral elements and allow rapid classification of new elements.

Amino Acid Sequence↗
PubMed2006

Comparative fine structure of the epididymal spermatozoa from three Korean shrews with considerations on their phylogenetic relationships.

This study examined the fine structures of epididymal spermatozoa on the lesser white-toothed shrew (Crocidura suaveolens), the Japanese white-toothed shrew (C. dsinezumi) and the big white-toothed shrew (C. lasiura) belonging to the subfamily Crocidurinae living in Korea. In the spermatozoa of C. suaveolens, the head has a large acrosome, a smooth inner acrosomal membrane and a wavy, finger-like, electron-dense apical body. The neck has a solid proximal centriole that is filled with electron-dense material. These results showed the spermatozoa of C. suaveolens possess the characteristics of both Crocidurinae and Soricinae. In C. dsinezumi and C. lasiura, the head has a large acrosome, a serrated inner acrosomal membrane and a common apical body. The neck has a fistulous proximal centriole with slightly dense electron granules. These results showed the typical characteristics of Crocidurinae. Although C. suaveolens belongs to the subfamily Crocidurinae, the spermatozoan morphology is different from C. dsinezumi and C. lasiurai because it has conserved characteristics of the subfamily Soricinae.

Animals↗
PubMed1990

Evolution of large-subunit rRNA structure. The diversification of divergent D3 domain among major phylogenetic groups.

During evolution, the potential for sequence (and length) variation of large-subunit rRNA has been mostly restricted over 12 divergent domains (termed D1-D12) interspersed along the molecule. Here, we have focused our attention onto the D3 divergent domain, through a detailed analysis of its pattern of variation in the phylogeny, both in terms of primary and secondary structures. We have systematically compared all the procaryotic and eucaryotic sequences published so far (i.e. 36 species), together with a series of 10 additional eucaryotic specimens, which were determined by direct RNA sequencing. Secondary structures supported by comparative evidence have been derived for archaebacteria, eubacteria and eucaryotes respectively, which shows that the D3 domain contains a subset of universally conserved structural features interspersed with four variable subdomains. Within the four portions where a structural diversification has taken place, elementary structures specific of large phylogenetic groups can be identified. Remarkably such diversified structures appear to be preserved despite sequence divergence, suggesting they correspond to functionally important structures. Accordingly, the mode of sequence variation of the D3 domain suggests this region of the molecule may encode elementary functions of rRNA which could have significantly diversified during the evolution of the major groups of organisms.

Animals↗
PubMed2000

Intercodon dinucleotides affect codon choice in plant genes.

In this work, 710 CDSs corresponding to over 290 000 codons equally distributed between Brassica napus, Arabidopsis thaliana, Lycopersicon esculentum, Nicotiana tabacum, Pisum sativum, Glycine max, Oryza sativa, Triticum aestivum, Hordeum vulgare and Zea mays were considered. For each amino acid, synonymous codon choice was determined in the presence of A, G, C or T as the initial nucleotide of the subsequent triplet; data were statistically analysed under the hypothesis of an independent assortment of codons. In 33.4% of cases, a frequency significantly (P: = 0.01) different from that expected was recorded. This was mainly due to a pervasive intercodon TpA and CpG deficiency. As a general rule, intercodon TpAs and CpGs were preferably replaced by CpAs and TpGs, respectively. In several instances, codon frequencies were also modified to avoid homotetramer and homotrimer formation, to reduce intercodon ApCs downstream (1,2) GG or AG dinucleotides, as well as to increase GpA or ApG intercodons under certain contexts. Since TpA, CpG and homotetra(tri)mer deficiency directly or indirectly accounted for 77% of significant variation in the codon frequency, it can be concluded that codon usage mirrors precise needs at the DNA structure level. Plant species exhibited a phylogenetically-related adaptation to structural constraints. Codon usage flexibility was reflected in strikingly different arrays of optimum codons for probe design.

Base Composition↗
PubMed1996

[Morphological changes in the vestibular analyzer in the dynamics of an experimental disorder of the cerebral circulation].

The alterations of microcirculatory structures and of neurons as a result of chronic cerebrovascular disturbances induced by ligation of the left common carotid artery were studied on 56 noninbred white male rats. The objects of investigation were central links of vestibular analyser such as anterior vestibular nucleus, posterior ventro-lateral part of hypothalamus, sensomotor brain cortex. It was established that one-sided ligation of common carotid artery resulted in alterations in vessels of microcirculatory bed, in neurons' bodies, in synapses. These disorders were similar to oxygen-deficient damages, described in literature which confirm the model's adequacy. These alterations appeared in different time and had various degree of expression in different structures. The latter observation may reflect different phylogenetic age of the structures studied. The reaction of the neuronal population as the functional system was observed as the process of alterations of the correlation of neurons with different functional activity. This process had periodic pattern.

Animals↗
PubMed1999

Modular assembly of voltage-gated channel proteins: a sequence analysis and phylogenetic study.

Voltage-sensitive cation-selective ion channels of the voltage-gated ion channel (VGC) superfamily were examined by a combination of sequence alignment and phylogenetic tree construction procedures. Segments of the alpha-subunits of K+-selective channels homologous to the structurally elucidated KcsA channel of Streptomyces lividans were multiply aligned, and this alignment provided the database for computer-assisted structural analyses and phylogenetic tree construction. Similar analyses were conducted with the four homologous repeats of the alpha-subunits from representative Ca2+- and Na+-selective channels, as well as with the ensemble of K+, Ca2+ and Na+ channels. In both the single subunit of the K+ channels and the individual repeats of the Ca2+ and Na+ channels, the analyses suggest the occurrence of at least two tandemly arranged modules corresponding to the predicted voltage-sensor domain and the pore domain. The phylogenetic analyses reveal strict clustering of segments according to cation-selectivity and repeat unit. We surmise that the pore module of the prokaryotic K+ channel was the primordial polypeptide upon which other modules were superimposed during evolution in order to generate phenotypic diversity. These observations may prove applicable to all members of the VGC family yet to be discovered throughout the prokaryotic and eukaryotic kingdoms.

Amino Acid Sequence↗
PubMed2000

A functional-phylogenetic classification system for transmembrane solute transporters.

A comprehensive classification system for transmembrane molecular transporters has been developed and recently approved by the transport panel of the nomenclature committee of the International Union of Biochemistry and Molecular Biology. This system is based on (i) transporter class and subclass (mode of transport and energy coupling mechanism), (ii) protein phylogenetic family and subfamily, and (iii) substrate specificity. Almost all of the more than 250 identified families of transporters include members that function exclusively in transport. Channels (115 families), secondary active transporters (uniporters, symporters, and antiporters) (78 families), primary active transporters (23 families), group translocators (6 families), and transport proteins of ill-defined function or of unknown mechanism (51 families) constitute distinct categories. Transport mode and energy coupling prove to be relatively immutable characteristics and therefore provide primary bases for classification. Phylogenetic grouping reflects structure, function, mechanism, and often substrate specificity and therefore provides a reliable secondary basis for classification. Substrate specificity and polarity of transport prove to be more readily altered during evolutionary history and therefore provide a tertiary basis for classification. With very few exceptions, a phylogenetic family of transporters includes members that function by a single transport mode and energy coupling mechanism, although a variety of substrates may be transported, sometimes with either inwardly or outwardly directed polarity. In this review, I provide cross-referencing of well-characterized constituent transporters according to (i) transport mode, (ii) energy coupling mechanism, (iii) phylogenetic grouping, and (iv) substrates transported. The structural features and distribution of recognized family members throughout the living world are also evaluated. The tabulations should facilitate familial and functional assignments of newly sequenced transport proteins that will result from future genome sequencing projects.

Animals↗
PubMedDate not supplied

[The role of conserved sequences in the regulatory elements of the Antp-like homeobox-containing genes of vertebrates].

By the present time the homeobox genes have been found in the representatives of the main invertebrate and vertebrate taxa. It has been demonstrated that these genes play the key role in the space and time genome expression orchestration in ontogenesis. The autoregulatory and cross-regulatory functional interactions integrate the homeobox genes into the gene networks. We found a correlation in variability of the coding and regulatory regions for vertebrate homeobox genes. The phylogenetic relations of structure and regulatory elements involved into the cross- and autoregulatory connections have been investigated in detail. The comprehensive phylogenetic analysis of the promoter region for these genes compared to results of such analysis of their homeoboxes has revealed two opposed tendencies in evolution of the regulatory elements of genes. The first trend is conservation of many regulatory elements in evolution of vertebrate homeobox genes and the second one is high variability of other non-coding gene regions.

Amino Acid Sequence↗
PubMed1994

The mitochondrial ribosomal RNA genes of the nematodes Caenorhabditis elegans and Ascaris suum: consensus secondary-structure models and conserved nucleotide sets for phylogenetic analysis.

The small- and large-subunit mitochondrial ribosomal RNA genes (mt-s-rRNA and mt-l-rRNA) of the nematode worms Caenorhabditis elegans and Ascaris suum encode the smallest rRNAs so far reported for metazoa. These size reductions correlate with the previously described, smaller, structurally anomalous mt-tRNAs of C. elegans and A. suum. Using primer extension analysis, the 5' end nucleotides of the mt-s-rRNA and mt-l-rRNA genes were determined to be adjacent to the 3' end nucleotides of the tRNA(Glu) and tRNA(His) genes, respectively. Detailed, consensus secondary-structure models were constructed for the mt-s-rRNA genes and the 3' 64% of mt-l-rRNA genes of the two nematodes. The mt-s-rRNA secondary-structure model bears a remarkable resemblance to the previously defined universal core structure of E. coli 16S rRNA: most of the nucleotides that have been classified as variable or semiconserved in the E. coli model appear to have been eliminated from the C. elegans and A. suum sequences. Also, the secondary structure model constructed for the 3' 64% of the mt-l-rRNA is similar to the corresponding portion of the previously defined E. coli 23S rRNA core secondary structure. The proposed C. elegans/A. suum mt-s-rRNA and mt-l-rRNA models include all of the secondary-structure element-forming sequences that in E. coli rRNAs contain nucleotides important for A-site and P-site (but not E-site) interactions with tRNAs. Sets of apparently homologous sequences within the mt-s-rRNA and mt-l-rRNA core structures, derived by alignment of the C. elegans and A. suum mt-rRNAs to the corresponding mt-rRNAs of other eukaryotes, and E. coli rRNAs were used in maximum-likelihood analyses. The patterns of divergence of metazoan phyla obtained show considerable agreement with the most prevalent metazoan divergence patterns derived from more classical, morphological, and developmental data.

Animals↗
PubMed1994

Bases defining an ammonium and magnesium ion-dependent tertiary structure within the large subunit ribosomal RNA.

A 58 nucleotide RNA derived from a highly conserved domain of the large subunit ribosomal RNA (Escherichia coli 1051 to 1108) has a set of tertiary interactions that is stabilized by NH4+ and Mg2+ in preference to other ions. We have mapped the nucleotides contributing to this structure by examining the thermal denaturation of 25 sequence variants. Where necessary compensatory mutations were made to preserve the phylogenetically conserved secondary structure. Substitutions of bases or base-pairs at eight positions specifically eliminate the ion-dependent tertiary structure without affecting the secondary structure stability; most of these positions are conserved among all large subunit RNA sequences. At two positions, substitutions of bases found in other organisms stabilize the E. coli tertiary structure by substantial amounts (delta G 37 degrees becomes more favorable by -1.8 to -4.5 kcal/mol). One of these variants disrupts a potential A.U base-pair within a helix, suggesting that the tertiary structure competes with alternative structures. The results show that this rRNA domain contains an extensive, highly conserved, and very stable set of tertiary interactions. The sequence in E. coli, and probably most other organisms, has not evolved to maximum stability. It is possible that natural selection has "tuned" the tertiary structure to an optimum stability, perhaps because the structure must open and close during the ribosome cycle.

Base Composition↗
PubMed2006

Sequential and structural analysis of [NiFe]-hydrogenase-maturation proteins from Desulfovibrio vulgaris Miyazaki F.

The complete primary structure of the hyn-region in the genome of Desulfovibrio vulgaris Miyazaki F (DvMF), encoding the [NiFe]-hydrogenase and two maturation proteins has been identified. Besides the formerly reported genes for the large and small subunits, this region comprises genes encoding an endopeptidase (HynC) and a putative chaperone (HynD). The complete genomic region covers 4086 nucleotides including the previously published upstream located promoter region and the sequences of the structural genes. A phylogenetic tree for both maturation proteins shows strongest sequential relationship to the orthologous proteins of Desulfovibrio vulgaris Hildenborough (DvH). Secondary structure prediction for HynC (168 aa, corresponding to a molecular weight of 17.9 kDa) revealed a practically identical arrangement of alpha-helical and beta-strand elements between the orthologous protein HybD from E. coli and allowed a three-dimensional modelling of HynC on the basis of the formerly published structure of HybD. The putative chaperone HynD consists of 83 aa (molecular weight of 9 kDa) and shows 76% homology to DvH HynD. Preliminary experiments demonstrate that the operon is expressed under the control of its own promoter in Escherichia coli, although no further processing could be observed, providing evidence that additional proteins have to be involved in the maturation process. Accession numbers: DQ072852, HynC protein ID AAY90127, HynD protein ID AAY90128.

Amino Acid Sequence↗
PubMed2003

Sequence determinants of quaternary structure in lumazine synthase.

Riboflavin, an essential cofactor for all organisms, is biosynthesized in plants, fungi and microorganisms. The penultimate step in the pathway is catalyzed by the enzyme lumazine synthase. One of the most distinctive characteristics of this enzyme is that it is found in different species in two different quaternary structures, pentameric and icosahedral, built from practically the same structural monomeric unit. In fact, the icosahedral structure is best described as a capsid of twelve pentamers. Despite this noticeable difference, the active sites are virtually identical in all structurally studied members. Furthermore, the main regions involved in the catalysis are located at the interface between adjacent subunits in the pentamer. Thus, the two quaternary forms of the enzyme must meet similar structural requirements to achieve their function, but, at the same time, they should differ in the sequence traits responsible for the different quaternary structures observed. Here, we present a combined analysis that includes sequence-structure and evolutionary studies to find the sequence determinants of the different quaternary assemblies of this enzyme. A data set containing 86 sequences of the lumazine synthase family was recovered by sequence similarity searches. Seven of them had resolved three-dimensional structures. A subsequent phylogenetic reconstruction by maximum parsimony (MP) allowed division of the total set into two clusters in accord with their quaternary structure. The comparison between the patterns of three-dimensional contacts derived from the known three-dimensional structures and variation in sequence conservation revealed a significant shift in structural constraints of certain positions. Also, to explore the changes in functional constraints between the two groups, site-specific evolutionary rate shifts were analyzed. We found that the positions involved in icosahedral contacts suffer a larger increase in constraints than the rest. We found eight sequence sites that would be the most important icosahedral sequence determinants. We discuss our results and compare them with previous work. These findings should contribute to refinement of the current structural data, to the design of assays that explore the role of these positions, to the structural characterization of new sequences, and to initiation of a study of the underlying evolutionary mechanisms.

Base Sequence↗
PubMed1999

Ribonuclease P: the diversity of a ubiquitous RNA processing enzyme.

Ribonuclease P is the endonuclease required for generating the mature tRNA 5'-end. The ribonucleoprotein character of this enzyme has now been proven in most organisms and organelles. Exceptions, however, are still the chloroplasts, plant nuclei and animal mitochondria where no associated RNAs have been detected to date. In contrast to the known RNA subunits, which are fairly well-conserved in size and structure among diverse phylogenetic groups, the protein contribution to the holoenzyme is highly variable in size and number of the individual components. The structure of the bacterial protein component has recently been solved. In contrast, the spatial arrangement of the multiple subunits in eukaryotic enzymes is still enigmatic. Substrate requirements of the enzymes or their catalytic RNA subunits are equally diverse, ranging from simple single domain mimics to an almost intact three-dimensional structure of the pre-tRNA substrate. As an example for an intermediate in the enzyme evolution, ribonuclease P from the Cyanophora paradoxa cyanelle will be discussed in more detail. This enzyme is unique, as it combines cyanobacterial and eukaryotic features in its function, subunit composition and holoenzyme topology.

Animals↗
PubMed2006

Phylogenetic relationship within the Erythrobasidium clade: molecular phylogenies, secondary structure, and intron positions inferred from partial sequences of ribosomal RNA and elongation factor-1alpha genes.

Phylogenetic relationships within the Erythrobasidium clade as a lineage of the urediniomycetous yeasts were examined using partial regions of 18S rDNA, 5.8S rDNA, 26S rDNA, internal transcribed spacers (ITSs), and elongation factor (EF)-1alpha. Combined data analysis of all segments successfully yielded a reliable phylogeny and confirmed the cohesion of species characterized by Q-10(H2) as a major ubiquinone. Differences in secondary structure predicted for a variable region in 26S rDNA corresponded to major divergences in the phylogenetic tree based on the primary sequence. The common presence of a shortened helix in this region was considered to be evidence of monophyly for species with Q-10(H2), Sakaguchia dacryoides, Rhodotorula lactosa, and Rhodotorula lamellibrachiae, although it was not as strongly supported by the combined data tree. The information on intron positions in the EF-1alpha gene had potential usefulness in the phylogenetic inference between closely related species.

Basidiomycota↗
PubMed2002

maT--a clade of transposons intermediate between mariner and Tc1.

A group of transposons, named maT, with characteristics intermediate between mariner and Tc1 transposons, is described. Two defective genomic copies of MdmaT from the housefly Musca domestica, with 85% identity, were found flanking and imbedded in the MdalphaE7 esterase gene involved in organophosphate insecticide resistance. Two cDNA clones, with 99% identity to each other and 72%-89% identity to the genomic copies were also obtained, but both represented truncated versions of the putative open reading frame. A third incomplete genomic copy of MdmaT was also identified upstream of the putative M. domestica period gene. The MdmaT sequences showed high identity to the transposable element Bmmar1 from the silkworm moth, Bombyx mori, and to previously unidentified sequences in the genome of Caenorhabditis elegans. A total of 16 copies of full-length maT sequences were identified in the C. elegans genome, representing three variants of the transposon, with 34%-100% identity amongst them. Twelve of the copies, named CemaT1, were virtually identical, with eight of them encoding a putative full length, intact transposase. Secondary structure predictions and phylogenetic analyses confirm that maT elements belong to the mariner-Tc1 superfamily of transposons, but their intermediate sequence and predicted structural characteristics suggest that they belong to a unique clade, distinct from either mariner-like or Tc1-like elements.

Animals↗