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 1,099 records · Page 61Linked to original sources
PubMed2000

Genetic diversity among Arthrobacter species collected across a heterogeneous series of terrestrial deep-subsurface sediments as determined on the basis of 16S rRNA and recA gene sequences.

This study was undertaken in an effort to understand how the population structure of bacteria within terrestrial deep-subsurface environments correlates with the physical and chemical structure of their environment. Phylogenetic analysis was performed on strains of Arthrobacter that were collected from various depths, which included a number of different sedimentary units from the Yakima Barricade borehole at the U.S. Department of Energy's Hanford site, Washington, in August 1992. At the same time that bacteria were isolated, detailed information on the physical, chemical, and microbiological characteristics of the sediments was collected. Phylogenetic trees were prepared from the 39 deep-subsurface Arthrobacter isolates (as well as 17 related type strains) based on 16S rRNA and recA gene sequences. Analyses based on each gene independently were in general agreement. These analyses showed that, for all but one of the strata (sedimentary layers characterized by their own unifying lithologic composition), the deep-subsurface isolates from the same stratum are largely monophyletic. Notably, the layers for which this is true were composed of impermeable sediments. This suggests that the populations within each of these strata have remained isolated under constant, uniform conditions, which have selected for a particular dominant genotype in each stratum. Conversely, the few strains isolated from a gravel-rich layer appeared along several lineages. This suggests that the higher-permeability gravel decreases the degree of isolation of this population (through greater groundwater flow), creating fluctuations in environmental conditions or allowing migration, such that a dominant population has not been established. No correlation was seen between the relationship of the strains and any particular chemical or physical characteristics of the sediments. Thus, this work suggests that within sedimentary deep-subsurface environments, permeability of the deposits plays a major role in determining the genetic structure of resident bacterial populations.

Arthrobacter↗
PubMed1988

Partial characterization of immunoglobulin light chains of carcharhine sharks: evidence for phylogenetic conservation of variable region and divergence of constant region structure.

Isolated light chains of IgM-type immunoglobulins of carcharhine sharks were analyzed by serological and biochemical means. When analyzed by isoelectric focusing analysis, light chains of the tiger shark (Galecerdo cuvieri), the galapagos shark (Carcharhinus galapagensis) and the sandbar shark (Carcharhinus plumbeus) showed a broad, but patterned, spectrum of bands ranging from pI 5.0 to 7.7 in which discrete families were observed. Serologically, light chains of the galapagos shark cross-reacted with rabbit antibodies against mouse immunoglobulin and a synthetic peptide corresponding to the J segment of T cell receptor beta chain. The latter cross-reaction is shared among light chains and T cell receptors. Although there was considerable heterogeneity in isoelectric focusing analysis, the light chains were homogeneous on the basis of apparent mass (23 kDa) and those of tiger shark and galapagos shark had relatively homogeneous dominant N-terminal sequences representing the first framework. The N-terminal sequences of these two shark light chains, were strongly homologous to one another and showed 75% identity to certain V kappa sequences of man and dog. Homology was also shown to V lambda sequences, but the degree of identity was approximately 50%. Following cleavage of the tiger shark light chain with o-iodosobenzoic acid which cleaves at tryptophanyl residues, a constant region peptide was isolated by gel filtration. It was possible to identify the homolog of this peptide within the constant regions of mammalian kappa and lambda chain, but the relationship to C kappa chain was stronger. The degree of identity among the corresponding C region peptides of mammalian, avian and elasmobranch species was much less than that observed for the framework 1 sequence of the light chain variable region. These data support the concept that variable and J region sequence have been conserved in the evolution of placoderm-derived vertebrates, but that constant regions show much greater phylogenetic variation.

Amino Acid Sequence↗
PubMed1983

Structure of E. coli 16S RNA elucidated by psoralen crosslinking.

E. coli 16S RNA in solution was photoreacted with hydroxymethyltrimethylpsoralen and long wave ultraviolet light. Positions of crosslinks were determined to high resolution by partially digesting the RNA with T1 RNase, separating the crosslinked fragments by two-dimensional gel electrophoresis, reversing the crosslink, and sequencing the separated fragments. This method yielded the locations of crosslinks to +/- 15 nucleotides. Even finer placement has been made on the basis of our knowledge of psoralen reactivity. Thirteen unique crosslinks were mapped. Seven crosslinks confirmed regions of secondary structure which had been predicted in published phylogenetic models, three crosslinks discriminated between phylogenetic models, and three proved the existence of new structures. The new structures were all long range interactions which appear to be in dynamic equilibrium with local secondary structure. Because this technique yields direct information about the secondary structure of large RNAs, it should prove invaluable in studying the structure of other RNAs of all sizes.

Base Sequence↗
PubMed1991

Ultrastructure of sperm and spermatogenesis of Lobatostoma manteri (Trematoda, Aspidogastrea).

Mature sperm has two axonemes of the 9 + '1' pattern incorporated in the sperm body, a row of peripheral microtubules interrupted along part of the sperm by the axonemes, some microtubules in the interior of the sperm and a long lateral extension (lobe) of the sperm body, an elongate nucleus and mitochondrion, and many dense rod-like structures. A supporting rod extends underneath a specialized region consisting of alternating thin and thick transverse rows of irregular dense patches, and with surface ridges around (all or) most of the surface of the sperm. Primary spermatocytes in the prophase of the first meiotic division have synaptonemal complex(es), and are rich in mitochondria. In early spermiogenesis, mitochondria are arranged around the surface of the nucleus, a dense layer appears at one pole of the nucleus, close to an apposed dense layer at the cell membrane in which a row of microtubules develops. The intercentriolar (= central) body develops close to the nucleus. The fully developed intercentriolar body has a regular striation and is located perpendicular and close to the surface of the nucleus. Two flagella extend into the space surrounding the outgoing median process, their basal bodies are located perpendicular to the intercentriolar body and their cross-striated rootlets extend along the surface of the rounded nucleus. At a later stage, rootlets and flagella become more parallel with the intercentriolar body, the nucleus and the fused mitochondria migrate into the median process, and the flagella become incorporated into the median process (= sperm body). The outgrowing spermatozoa are connected to the cytoplasm of the cytophore by dense arching membranes. Finally, rootlets of flagella are resorbed and the spermatozoa are pinched off close to the basal bodies. Two species (Lobatostoma and Multicotyle) of the same family differ strongly in the type of spermiogenesis, although their mature sperm is of the same basic type, i.e. spermiogenesis is not necessarily more useful for phylogenetic considerations than sperm structure.

Animals↗
PubMed2002

A structural approach to understanding the iron-binding properties of phylogenetically different frataxins.

Friedreich's ataxia (FRDA), an autosomal recessive cardio- and neurodegenerative disease, is caused by low expression of frataxin, a small mitochondrial protein, encoded in the nucleus. At the biochemical level, the lack of frataxin leads to dysregulation of mitochondrial iron homeostasis and oxidative damage, which eventually causes neuronal death. It is, however, still unclear whether frataxin is directly involved in iron binding, since the yeast orthologue, but not the human protein, has been shown to form large aggregates in the presence of large iron excess. We have compared the properties of three proteins from the frataxin family--the bacterial CyaY from Escherichia coli, the yeast Yfh1 and human frataxin--as representative of organisms of increasing complexity. We show that the three proteins have the same fold but different thermal stabilities and iron-binding properties. While human frataxin has no tendency to bind iron, CyaY forms iron-promoted aggregates with a behaviour similar to that of yeast frataxin. However, aggregation can be competed by chelator agents or by ionic strength. At physiological salt conditions, almost no aggregation is observed. The design of mutants produced to identify the protein surface involved in iron-promoted aggregation allows us to demonstrate that the process is mediated by a negatively charged surface ridge. Mutation of three of these residues is sufficient to convert CyaY in a protein with properties similar to those of human frataxin. On the other hand, mutation of the exposed surface of the beta sheet, which contains most of the conserved residues, does not affect aggregation, suggesting that iron binding is a non-conserved part of a more complex cellular function of frataxins.

Amino Acid Sequence↗
PubMed1991

Phylogenetic analysis and evolution of RNase P RNA in proteobacteria.

The secondary structures of the eubacterial RNase P RNAs are being elucidated by a phylogenetic comparative approach. Sequences of genes encoding RNase P RNA from each of the recognized subgroups (alpha, beta, gamma, and delta) of the proteobacteria have now been determined. These sequences allow the refinement, to nearly the base pair level, of the phylogenetic model for RNase P RNA secondary structure. Evolutionary change among the RNase P RNAs was found to occur primarily in four discrete structural domains that are peripheral to a highly conserved core structure. The new sequences were used to examine critically the proposed similarity (C. Guerrier-Takada, N. Lumelsky, and S. Altman, Science 246:1578-1584, 1989) between a portion of RNase P RNA and the "exit site" of the 23S rRNA of Escherichia coli. Phylogenetic comparisons indicate that these sequences are not homologous and that any similarity in the structures is, at best, tenuous.

Alcaligenes↗
PubMed1998

The subcommissural organ.

The subcommissural organ (SCO) is a phylogenetically ancient and conserved structure. During ontogeny, it is one of the first brain structures to differentiate. In many species, including the human, it reaches its full development during embryonic life. The SCO is a glandular structure formed by ependymal and hypendymal cells highly specialized in the secretion of proteins. It is located at the entrance of the aqueduct of Sylvius. The ependymal cells secrete into the ventricle core-glycosylated proteins of high molecular mass. The bulk of this secretion is formed by glycoproteins that would derive from two different precursors of 540 and 320 kDa and that, upon release into the ventricle aggregate, form a threadlike structure known as Reissner's fiber (RF). By addition of newly released glycoproteins to its proximal end, RF grows caudally and extends along the aqueduct, fourth ventricle, and the whole length of the central canal of the spinal cord. RF material continuously arrives at the dilated caudal end of the central canal, known as the terminal ventricle or ampulla. When reaching the ampulla, the RF material undergoes chemical modifications, disaggregates, and then escapes through openings in the dorsal wall of the ampulla to finally reach local blood vessels. The SCO also appears to secrete a cerebrospinal fluid (CSF)-soluble material that is different from the RF material that circulates in the ventricular and subarachnoidal CSF. Cell processes of the ependymal and hypendymal cells, containing a secretory material, terminate at the subarachnoidal space and on the very special blood capillaries supplying the SCO. The SCO is sequestered within a double-barrier system, a blood-brain barrier, and a CSF-SCO barrier. The function of the SCO is unknown. Some evidence suggests that the SCO may participate in different processes such as the clearance of certain compounds from the CSF, the circulation of CSF, and morphogenetic mechanisms.

Animals↗
PubMed1985

Insensitivity of archaebacterial ribosomes to protein synthesis inhibitors. Evolutionary implications.

The effect on Sulfolobus solfataricus (an extremely thermoacidophilic archaebacterium) of selected inhibitors affecting reactions of the polypeptide elongation cycle has been tested by using poly(U) and poly(UG) directed cell-free systems. The results reveal a unique pattern of antibiotic sensitivity of Sulfolobus ribosomes with an inhibitory effect observed for only three of 60 compounds tested. Through comparison with suitable eubacterial and eukaryotic cell-free systems the insensitivity of Sulfolobus ribosomes to most inhibitors of protein synthesis appears to reflect a phylogenetic distinction of ribosome structure, rather than the high temperature conditions of the Sulfolobus assay system. In this respect ribosomes of thermoacidophilic archaebacteria differ not only from their eubacterial and eukaryotic counterparts, but also from ribosomes of archaebacteria belonging to the methanogenic-halophilic branch of the 'third' kingdom. The evolutionary implications of these findings are discussed.

Anti-Bacterial Agents↗
PubMed1991

Identification of a novel iron-responsive element in murine and human erythroid delta-aminolevulinic acid synthase mRNA.

Iron-responsive elements (IREs) are regulatory RNA elements which are characterized by a phylogenetically defined sequence-structure motif. Their biological function is to provide a specific binding site for the IRE-binding protein (IRE-BP). Iron starvation of cells induces high affinity binding of the cytoplasmic IRE-BP to an IRE which has at least two different known biological consequences, repression of ferritin mRNA translation and stabilization of the transferrin receptor transcript. We report the identification of a novel, evolutionarily conserved IRE motif in the 5' UTR of murine and human erythroid-specific delta-aminolevulinic acid synthase (eALAS) mRNA which encodes the first, and possibly rate limiting, enzyme of the heme biosynthetic pathway. We demonstrate the function of the eALAS IRE as a specific binding site for the IRE-BP by gel retardation analyses and by in vitro translation experiments. In addition, we show that the 5' UTR of eALAS mRNA is sufficient to mediate iron-dependent translational regulation in vivo. These findings strongly suggest involvement of the IRE-IRE-BP system in the control of heme biosynthesis during erythroid differentiation.

5-Aminolevulinate Synthetase↗
PubMed1994

Architecture of telomerase RNA.

Telomerase, an essential ribonucleoprotein reverse transcriptase, adds telomeric DNA to the ends of eukaryotic chromosomes. We examined the conformational properties of the naked RNA moiety of telomerase from two related ciliates, Tetrahymena thermophila and Glaucoma chattoni. As well as finding evidence for features proposed previously on the basis of phylogenetic comparisons, novel conserved structural properties were revealed. Specifically, although the region around helix III was previously proposed to form a pseudoknot, our results indicate that in the naked RNA this region maintains a level of 'plasticity', probably in an equilibrium favoring one of two helices. In addition, these studies reveal that the templating domain is not entirely single-stranded as previously proposed, but is ordered due to constraints imposed by other parts of the RNA. Finally, our results suggest that the GA bulge in helix IV may introduce a structurally conserved kink. We now propose a 'two-domain' structure for the telomerase RNA based on function: one conformationally flexible domain, which includes the template and the region around helix III, involved with enzymatic function, and a second largely helical domain, including helices I and IV and the proposed kink, which may serve as a scaffold for protein binding.

Animals↗
PubMed2000

Early evolution of cytochrome bc complexes.

Primary structures, functional characteristics and phylogenetic relationships of subunits of cytochrome bc complexes from phylogenetically diverse bacterial and archaeal species were analysed. A single case of lateral gene transfer, i.e. the import of an epsilon-proteobacterial cytochrome bc(1) complex into Aquificales, was identified. For the enzyme in the remainder of the species studied, the obtained phylogenies were globally in line with small subunit rRNA trees. The distribution of a few key phylogenetic markers, such as contiguousness of cytochrome b, nature of the c-type subunit or spacing between b-heme ligands, are discussed. A localised modification of previous tree topologies is proposed on the basis of the obtained data. The comparison of extant enzymes furthermore allowed us to define the minimal functional and evolutionary core of the enzyme. The data furthermore suggest that the ancestral enzyme was put together from subunits that previously had played a role in other electron transfer chains.

Amino Acid Sequence↗
PubMed1996

Expression in human endothelial cells of ADP-ribosylation factors, 20-kDa guanine nucleotide-binding proteins involved in the initiation of vesicular transport.

ADP-ribosylation factors (ARFs) are approximately 20-kDa, guanine nucleotide-binding proteins, initially discovered as stimulators of cholera toxin ADP-ribosyltransferase activity and subsequently shown to participate in vesicular trafficking. Five of the six mammalian ARFs have been identified in human tissues by molecular cloning. They fall into three classes (class I: ARFs 1-3; class II: ARFs 4, 5; class III: ARF 6) based on deduced amino acid sequence, size, phylogenetic analysis, and gene structure. Similar to the rab family of approximately 20 kDa guanine nucleotide-binding proteins, the ARFs appear to function in specific trafficking pathways. The presence of a specific ARF might serve as a marker for that pathway. To verify expression of ARF mRNA and protein in human umbilical vein endothelial cells, immunoreactivity using antibodies specific for each ARF class, quantitative polymerase chain reaction (PCR) using ARF-specific, internal cRNA standards containing unique restriction enzyme cleavage sites introduced by point mutations, and Northern analysis with probes specific for ARFs 1, and 3-6, were utilized. PCR and Northern analysis were in agreement in showing that amounts of mRNA for ARF 1 and ARF 4 were similar and higher than those of ARF 3 and ARF 5 which were greater than ARF 6. Primarily, Class 1 ARF proteins were detected by immunoreactivity, with the majority in the supernatant fraction. The relative expression of ARFs in endothelial cells thus differs from that in neuronal tissues where it had been found that ARF3 is the predominant species.

ADP-Ribosylation Factor 6↗
PubMed1999

Origin of the unisexual lizard Gymnophthalmus underwoodi (Gymnophthalmidae) inferred from mitochondrial DNA nucleotide sequences.

Analysis of variation in nucleotide sequences in mitochondrial DNA genes among species of Gymnophthalmus supports three major conclusions. First, samples of G. underwoodi, a unisexual species of hybrid origin, have identical nucleotide sequences, supporting the hypothesis that all individuals from localities in the Guianan Region of South America and the Lesser Antilles descended from a single hybridization event. Second, G. underwoodi and G. cryptus share derived similarities in nucleotide sequences of the maternally inherited mitochondrial DNA, suggesting that the female participant in the hybridization event that produced the hybrid species was either G. cryptus or most closely related to it. Last, phylogenetic analyses recovered historical structure among population samples of G. speciosus supporting previous claims that there is unrecognized diversity under that binomial, and some analyses suggest that G. speciosus does not comprise a natural group.

Animals↗
PubMed1994

ADP-ribosylation factors: a family of approximately 20-kDa guanine nucleotide-binding proteins that activate cholera toxin.

ADP-ribosylation factors (ARFs) comprise a family of approximately 20 kDa guanine nucleotide-binding proteins that were discovered as one of several cofactors required in cholera toxin-catalyzed ADP-ribosylation of Gs alpha, the guanine nucleotide-binding protein responsible for stimulation of adenylyl cyclase, and was subsequently found to enhance all cholera toxin-catalyzed reactions and to directly interact with, and activate the toxin. ARF is dependent on GTP or its analogues for activity, binds GTP with high affinity in the presence of dimyristoylphosphatidylcholine/cholate and contains consensus sequences for GTP-binding and hydrolysis. Six mammalian family members have been identified which have been classified into three groups (Class I, II, and III) based on size, deduced amino acid sequence identity, phylogenetic analysis and gene structure. ARFs are ubiquitous among eukaryotes, with a deduced amino acid sequence that is highly conserved across diverse species. They have recently been shown to associate with phospholipid and Golgi membranes in a GTP-dependent manner and are involved in regulating vesicular transport.

ADP-Ribosylation Factors↗
PubMed1990

Carnivora: the primary structure of hemoglobin from adult coati (Nasua nasua rufa, Procyonidae).

The complete primary structure of the hemoglobin from the adult coati (Nasua nasua rufa) is presented. The erythrocytes contain one hemoglobin component and two globin chains. The isolation of globin chains was achieved by reversed-phase HPLC on a column of Nucleosil-C4. The primary structures of globin chains and tryptic peptides was determined in liquid- and gas-phase sequenators. The sequence of the alpha and beta-chains of coati compared with those of other Carnivora species. Results are discussed with respect to structural variations and the phylogenetic relationship.

Amino Acid Sequence↗
PubMed1993

Regulated expression of the rat medium chain hydrolase gene in transgenic rape seed.

Medium chain hydrolase (MCH) is an enzyme which regulates the chain length of fatty acid synthesis specifically in the mammary gland of the rat. During lactation, MCH interacts with fatty acid synthase (FAS) to cause premature release of acyl chains, thus providing medium chain fatty acids for synthesis of milk fat. In this study we have investigated the ability of rat MCH to interact with the phylogenetically more distant FAS structure present in plant systems and to cause a perturbation of fatty acid synthesis. In in vitro experiments, addition of purified MCH to rapeseed homogenates was found to cause a significant perturbation of fatty acid synthesis towards medium chain length products. The rat MCH gene was expressed in transgenic oilseed rape using a seed specific rape acyl carrier protein (ACP) promoter and a rape ACP plastid targeting sequence. Western analysis showed MCH protein to be present in transgenic seed and for its expression to be developmentally regulated in concert with storage lipid synthesis. The chimaeric preprotein was correctly processed and immunogold labelling studies confirmed MCH to be localized within plastid organelles. However, fatty acid analysis of oil from MCH-expressing rape seed showed no significant differences to that from control seed.

Animals↗
PubMed1996

Ebb and flow of the chloroplast inverted repeat.

The endpoints of the large inverted repeat (IR) of chloroplast DNA in flowering plants differ by small amounts between species. To quantify the extent of this movement and define a possible mechanism for IR expansion, DNA sequences across the IR-large single-copy (IR-LSC) junctions were compared among 13 Nicotiana species and other dicots. In most Nicotiana species the IR terminates just upstream of, or somewhere within, the 5' portion of the rps19 gene. The truncated copy of this gene, rps19', varies in length even between closely related species but is of constant size within a single species. In Nicotiana, six different rps19' structures were found. A phylogenetic tree of Nicotiana species based on restriction site data shows that the IR has both expanded and contracted during the evolution of this genus. Gene conversion is proposed to account for these small and apparently random IR expansions. A large IR expansion of over 12 kb has occurred in Nicotiana acuminata. The new IR-LSC junction in this species lies within intron 1 of the clpP gene. This rearrangement occurred via a double-strand DNA break and recombination between poly (A) tracts in clpP intron 1 and upstream of rps19. Nicotiana acuminata chloroplast DNA contains a "molecular fossil' of the IR-LSC junction that existed prior to this dramatic rearrangement.

Arabidopsis Proteins↗
PubMed2006

Testing introgressive hybridization hypotheses using statistical network analysis of nuclear and cytoplasmic haplotypes in the leaf beetle Timarcha goettingensis species complex.

Previous studies of leaf beetles (Chrysomelidae) in the Timarcha goettingensis species complex using mitochondrial (cox2) and nuclear (ITS-2 rRNA) markers revealed two main clades confined to the Iberian Peninsula and the rest of Europe but showing incongruent distributions indicative of gene exchange between both groups. Because of the anastomosing nature of hybridization, which disrupts the cladistic structure of character variation, phylogenetic trees might be inappropriate to represent and study this process. Here we test for evidence of hybridization in the T. goettingensis complex by analyzing the extra homoplasy arising in hybrid genomes from the simultaneous analysis of genetically independent markers. Haplotype networks obtained by Templeton's statistical parsimony analysis were generated for combined (concatenated) cox2 and ITS-2 sequences from 167 individuals of the T. goettingensis complex. Networks were used to detect runs of homoplasious characters physically clustered along a nucleotide sequence, as evidence for recombination between both gene partitions. A hypergeometric tail probability for the chance occurrence of physically clustered character changes on the connections linking networks of genotypes was applied. The test recognized two instances of statistically significant clustering, indicating the presence of cox2-ITS-2 mosaic genotypes and reticulation of both main T. goettingensis clades, supporting the reticulate origin of samples of T. maritima in southwestern France and T. sinuatocollis/T. monserratensis in the eastern Pyrenees. Although the assessment of reticulation in DNA sequences does not provide direct proof for hybridization, the geographical distribution of mosaic genotypes in the vicinity of "pure" genotypes supports the effect of gene flow between the two divergent lineages. The study demonstrates the utility of statistical parsimony networks for the detection of hybrids in the growing number of phylogeographic studies based on multiple gene markers.

Adaptor Proteins, Vesicular Transport↗