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PubMed1978

[Aspects related to the antigenic structure and serological specificity of brucellae phylogenetically related to S- and R-forms and dissociated into R-variants].

The antigenic structures and serological properties of Brucellae S- and R-forms, phylogenetically differentiated, and dissociated R-variants are studied by means of gel-precipitation, immunoelectrophoresis and fixation of the complement. The Brucella suis 1330S, Brucella suis 1330R, Brucella ovis 02 and Brucella abortus 99 are involved in the experiments. Both specific and general antigenic structures are established in all strains studied, but only homologous antibodies from the antigen-antibody complex in the complement-fixation test, induced by the phylogenetically differentiated S- and R-forms (Brucella ovis) or brucellae, diverged into R-variants. Cross complement-fixation tests between the antisera, prepared against S-forms and antigens from natural R-forms (Brucella ovis) or dissociative R-forms (R-variants) have not been observed. Also cross reactions between antisera, induced by R-forms (natural R-forms--Brucella ovis, or dissociative R-variants) and antigens, obtained from S-forms of brucellae are found.

Antigen-Antibody Complex↗
PubMed2003

Molecular evolution of CXC chemokines: extant CXC chemokines originate from the CNS.

The mammalian CXC chemokine system comprises 16 ligands and six receptors, and its actions stretch well beyond the immune system. Recent elucidation of the pufferfish genome, a representative of an evolutionary ancient vertebrate class, has enabled analysis of the mammalian CXC chemokine system in a phylogenetic context. Comparison of the phylogenies of vertebrate CXC chemokines revealed that fish and mammals have found different solutions to similar problems, grafted on the same basic structural motif. Phylogenetic analyses showed that the large, highly redundant CXC chemokine family is a very recent phenomenon that is exclusive to higher vertebrates. Moreover, its ancestral role is found within the central nervous system and not within the immune system.

Algorithms↗
PubMed1995

Phylogenetic relationships between Toxoplasma and Sarcocystis deduced from a comparison of 18S rDNA sequences.

The current taxonomy of parasites in the genus Sarcocystis is largely based on morphological characteristics as well as on host specificity and life-cycle structure. Recently, phylogenetic analyses of partial ribosomal RNA (rRNA) sequences provided support for paraphyly of Sarcocystis. We have tested the validity of this hypothesis by sequencing the complete 18S rRNA genes of Sarcocystis arieticanis, Sarcocystis gigantea and Sarcocystis tenella and comparing them with gene sequences derived from other taxa of the phylum Apicomplexa. The results obtained from this study do not reject the hypothesis of monophyly of Sarcocystis species, although the bootstrap data were inconclusive for some species.

Animals↗
PubMed1996

Structure, function, and evolution of adenovirus-associated RNA: a phylogenetic approach.

To explore the structure and function of a small regulatory RNA, we examined the virus-associated (VA) RNA species of all 47 known human adenovirus serotypes and of one simian virus, SA7. The VA RNA gene regions of 43 human adenoviruses were amplified and sequenced, and the structures of 10 representative VA RNAs were probed by nuclease sensitivity analysis. Most human viruses have two VA RNA species, VA RNA, and VA RNAII, but nine viruses (19%) have a single VA RNA gene. Sequence alignments classified the RNAs into eight families, corresponding broadly to the known virus groups, and three superfamilies. One superfamily contains the single VA RNAs of groups A and F and the VA RNAI species of group C; the second contains the VA RNAI species of groups B1, D, and E and the unclassified viruses (adenovirus types 42 to 47), as well as the single VA RNAs of group B2; and the third contains all VA RNAII species. Fourteen regions of homology occur throughout the molecule. The longest of these correspond to transcription signals; most of the others participate in RNA secondary structure. The previously identified tetranucleotide pair, GGGU:ACCC, is nearly invariant, diverging slightly (to GGGU:ACCU) only in the two group F viruses and forming a stem in the central domain that is critical for VA RNA structure and function. Secondary structure models which accommodate the nuclease sensitivity data and sequence variations within each family were generated. The major structural features-the terminal stem, apical stem-loop, and central domain-are conserved in all VA RNAs, but differences exist in the apical stem and central domains, especially of the VA RNAII species. Sequence analysis suggests that an ancestral VA RNA gene underwent duplication during the evolution of viruses containing two VA RNA genes. Although the VA RNAII gene seems to have been lost or inactivated by secondary deletion events in some viruses, the high degree of homology among the VA RNAII species implies that this RNA may play an undiscovered role in virus survival. We speculate that the VA RNA genes originated from cellular sequences containing multiple tRNA genes.

Adenoviridae↗
PubMed1997

Remarks on the phylogeny and structure of fatty acid binding proteins from parasitic platyhelminths.

Four fatty acid binding proteins (FABPs) have been described in 4 parasitic platyhelminths: Schistosoma mansoni, Schistosoma japonicum, Fasciola hepatica and Echinococcus granulosus. FABPs form a multigenic family of cytosolic proteins widely distributed in metazoan tissues, the function of which is still poorly understood. These helminth proteins have recently received attention, since there are reports to indicate that S. mansoni and F. hepatica FABPs may be protective antigens. In addition, these proteins could play a major role in the parasites' life-cycles because platyhelminths are unable to synthesize de novo most of their lipids. We have undertaken phylogenetic and structural analyses of platyhelminth FABPs in an attempt to characterize features of biological relevance. Phylogenetically, these FABPs appear to be more closely related to those of vertebrate heart, mammary gland, muscle, retina, skin, brain and myelin, although no clear functional relationships were established between them. We describe several conserved motifs characteristic of specific groups of FABPs. Hydrophilicity, flexibility and accessibility analyses revealed several major putative epitopes for the E. granulosus FABP, EgDf1, that appear to be centred in loops of the EgDf1 3-dimensional structure modelled by molecular replacement.

Amino Acid Sequence↗
PubMed2002

Dynamic conformational model for the role of ITS2 in pre-rRNA processing in yeast.

Maturation of the large subunit rRNAs includes a series of cleavages that result in removal of the internal transcribed spacer (ITS2) that separates mature 5.8S and 25/28S rRNAs. Previous work demonstrated that formation of higher order secondary structure within the assembling pre-ribosomal particle is a prerequisite for accurate and efficient pre-rRNA processing. To date, it is not clear which specific sequences or secondary structures are required for processing. Two alternative secondary structure models exist for Saccharomyces cerevisiae ITS2. Chemical and enzymatic structure probing and phylogenetic comparisons resulted in one structure (Yeh & Lee, J Mol Biol, 1990, 211:699-712) referred to here as the "hairpin model." More recently, an alternate folded structure was proposed (Joseph et al., Nucleic Acids Res, 1999, 27:4533-4540), called here the "ring model." We have used a functional genetic assay to examine the potential significance of these predicted structures in processing. Our data indicate that elements of both structural models are important in efficient processing. Mutations that prevent formation of ring-specific structures completely blocked production of mature 25S rRNA, whereas those that primarily disrupt hairpin elements resulted in reduced levels of mature product. Based on these results, we propose a dynamic conformational model for the role of ITS2 in processing: Initial formation of the ring structure may be required for essential, early events in processing complex assembly and may be followed by an induced transition to the hairpin structure that facilitates subsequent processing events. In this model, yeast ITS2 elements may provide in cis certain of the functions proposed for vertebrate U8 snoRNA acting in trans.

Base Sequence↗
PubMedDate not supplied

[Morphological analysis of the reaction of the animal brain to short-term hyperoxia].

Reactions of various structures of the central nervous system of animals to short-term hyperoxia were investigated, using morphological methods available. Reactive, destructive and compensatory-adaptive changes in the structures taken under study were identified. These changes were nonspecific and similar in sign in rats and dogs. In most cases they were reversible but their polymorphism was different in phylogenetically dissimilar structures.

Animals↗
PubMed2006

Simultaneous effects of phylogenetic niche conservatism and competition on avian community structure.

We currently have only a partial understanding of how phylogenetic relationships relate to patterns of community structure, in part because, for most groups of organisms, we do not know the extent to which ecological similarity results from common ancestry. Associations between phylogenetic relatedness and local community structure are particularly interesting for groups in which many species that span a gradient of phylogenetic divergence occur in potential sympatry. We explored the relationship between evolutionary relatedness and current species co-occurrence among the North American wood-warblers (Aves: Parulidae), a group of songbirds known both for its species diversity and for exhibiting high levels of sympatry at breeding sites. Species co-occurrences were derived from North American Breeding Bird Survey transects comprising 160,000 census points distributed across North America. The nested point-within-transect structure of this survey provides an unusual opportunity to remove larger-scale geographical effects on local community composition and thereby consider patterns of co-occurrence only among regionally sympatric pairs of species. We indexed evolutionary relatedness among all pairs of taxa by genetic distances based on long mitochondrial DNA protein-coding sequences. Most regionally sympatric taxon pairs rarely co-occur at local sites, and the most closely related never exhibit high local co-occurrences, as predicted if past or present competitive effects are strongest for these recently separated lineages. Quantile regression shows that, for a subset of taxa, local co-occurrence does increase with time since common ancestry, and that this apparent relaxation of competitive exclusion is strongest for distantly related species that have differentiated in fundamental ecological and behavioral traits, such as terrestrial vs. arboreal foraging. Comparisons against a null model of species co-occurrence further demonstrate that these patterns occur against a background of phylogenetic niche conservatism: across all phylogenetic distances, sympatric species co-occurred at higher rates than expected by chance, a pattern that might stem from a tendency by these species to show conservatism in their selection of similar general habitat types. Considered in concert, these analyses suggest the simultaneous mediation of local community structure by the ecological similarity of closely related species and by trait divergence among a subset of more distant lineages.

Animals↗
PubMed2004

Analysis of near full-length genome sequences of HIV type 1 BF intersubtype recombinant viruses from Brazil reveals their independent origins and their lack of relationship to CRF12_BF.

We analyze the recombinant structures and phylogenetic relationships of nine near full-length genome sequences of HIV-1 BF intersubtype recombinant viruses from Brazil, eight of them newly derived. These were obtained by PCR amplification from peripheral blood mononuclear cells (PBMCs) DNA or PBMCs culture supernantant RNA. The recombinants exhibited unique mosaic structures, except two viruses with a single near coincident breakpoint. Comparison with CRF12_BF revealed only two coincident breakpoints in two recombinants. Phylogenetic analyses failed to support a common ancestry of Brazilian recombinants or their relationship to CRF12_BF, which widely circulates in Argentina. Intersubtype breakpoint distribution along the genome was uneven, with the highest mean frequency in the polymerase domain of reverse transcriptase, and the lowest in env. These results indicate that HIV-1 BF recombinants from Brazil have independent origins and are unrelated to CRF12_BF, and that intersubtype breakpoints are frequent in pol segments analyzed for drug resistance detection.

Brazil↗
PubMed1995

Structural characterization, chromosomal localization and phylogenetic evaluation of two pairs of AGAMOUS-like MADS-box genes from maize.

In order to gain a better understanding of the development and evolution of cereal flowers, we have cloned and sequenced two MADS-box genes from maize and the partial cDNA of a third one. One of the genomic clones was identified as ZAG2 (Zea AGAMOUS 2), while the other has a very similar structure and the potential to encode a protein which shares 94% sequence identity with the putative ZAG2 gene product. The cDNA reveals considerable similarity to ZAG1. Phylogenetic evaluation of the sequence information, as well as chromosomal localization, both suggest that we have identified two pairs of AGAMOUS-like MADS-box genes which were created during duplication of chromosomal segments or complete chromosomes.

AGAMOUS Protein, Arabidopsis↗
PubMed1999

Structural comparison of cephalopod hemocyanins: phylogenetic significance.

Hemocyanins, the respiratory molecules of cephalopod mollusks, are hollow cylinders with five internal arches. Three hemocyanins representative of three orders of cephalopods (Benthoctopus species, Octopoda; Vampyroteuthis infernalis, Vampyromorpha; Sepia officinalis, Sepioidea) were subjected to cryoelectron microscopy and three-dimensional (3D) reconstruction. The structure of Benthoctopus hemocyanin, solved at 26.4-A resolution, possesses arches comprising two identical functional units. The similarity between these functional units and the structure recently observed in X-ray crystallography for Octopus by Cuff et al. (J. Mol. Biol., 1998, 232, 522-529) allows the identification of their N- and C-terminal domains in the 3D reconstruction volume. Conversely, arches present in the 3D reconstruction volume of Sepia hemocyanin (21.8 A resolution) contain four functional units that are disposed differently. The strong resemblance between the reconstruction volumes of Vampyroteuthis (21.4-A resolution) and Benthoctopus hemocyanins suggests that Sepioidea diverged from a group containing Octopoda and Vampyromorpha.

Animals↗
PubMed2006

Molecular analyses of the metallothionein gene family in rice (Oryza sativa L.).

Metallothioneins are a group of low molecular mass and cysteine-rich metal-binding proteins, ubiquitously found in most living organisms. They play an important role in maintaining intracellular metal homeostasis, eliminating metal toxification and protecting against intracellular oxidative damages. Analysis of complete rice genome sequences revealed eleven genes encoding putative metallothionein (OsMT), indicating that OsMTs constitute a small gene family in rice. Expression profiling revealed that each member of the OsMT gene family differs not only in sequence but also in their tissue expression patterns, suggesting that these isoforms may have different functions they perform in specific tissues. On the basis of OsMT structural and phylogenetic analysis, the OsMT family was classified as two classes and class I was subdivided into four types. Additionally, in this paper we also present a complete overview of this family, describing the gene structure, genome localization, upstream regulatory element, and exon/intron organization of each member in order to provide valuable insight into this OsMT gene family.

Amino Acid Sequence↗
PubMed1996

Structure of 4.5S RNA in the signal recognition particle of Escherichia coli as studied by enzymatic and chemical probing.

The structure of 4.5S RNA, the Escherichia coli homologue of the signal recognition particle (SRP) RNA, alone and in the SRP complex with protein P48 (Ffh) was probed both enzymatically and chemically. The molecule is largely resistant against single strand-specific nucleases, indicating a highly base paired structure. Reactivity appears mainly in the apical tetraloop and in one of the conserved internal loops. Although some residues are found reactive toward dimethylsulphate and kethoxal in regions predicted to be unpaired by the phylogenetic secondary structure model of 4.5S RNA, generally the reactivity is low, and some residues in internal loops are not reactive at all. RNase V1 cleaves the RNA at multiple sites that coincide with predicted helices, although the cleavages show a pronounced asymmetry. The binding of protein P48 to 4.5S RNA results in a protection of residues in the apical part of the molecule homologous to eukaryotic SRP RNA (domain IV), whereas the cleavages in the conserved apical tetraloop are not protected. Hydroxyl radical treatment reveals an asymmetric pattern of backbone reactivity; in particular, the region encompassing nucleotides 60-82, i.e., the 3' part of the conserved domain IV, is protected. The data suggest that a bend in the domain IV region, most likely at the central asymmetric internal loop, is an important element of the tertiary structure of 4.5S RNA. Hyperchromicity and lead cleavage data are consistent with the model as they reveal the unfolding of a higher-order structure between 30 and 40 degrees C. Protection by protein P48 occurs in this region of the RNA and, more strongly, in the 5' part of domain IV (nt 26-50, most strongly from 35 to 49). It is likely that P48 binds to the outside of the bent form of 4.5S RNA.

Bacterial Proteins↗
PubMed2004

Genome-wide identification of NBS genes in japonica rice reveals significant expansion of divergent non-TIR NBS-LRR genes.

A complete set of candidate disease resistance ( R) genes encoding nucleotide-binding sites (NBSs) was identified in the genome sequence of japonica rice ( Oryza sativaL. var. Nipponbare). These putative R genes were characterized with respect to structural diversity, phylogenetic relationships and chromosomal distribution, and compared with those in Arabidopsis thaliana. We found 535 NBS-coding sequences, including 480 non-TIR (Toll/IL-1 receptor) NBS-LRR (Leucine Rich Repeat) genes. TIR NBS-LRR genes, which are common in A. thaliana, have not been identified in the rice genome. The number of non-TIR NBS-LRR genes in rice is 8.7 times higher than that in A. thaliana, and they account for about 1% of all of predicted ORFs in the rice genome. Some 76% of the NBS genes were located in 44 gene clusters or in 57 tandem arrays, and 16 apparent gene duplications were detected in these regions. Phylogenetic analyses based both NBS and N-terminal regions classified the genes into about 200 groups, but no deep clades were detected, in contrast to the two distinct clusters found in A. thaliana. The structural and genetic diversity that exists among NBS-LRR proteins in rice is remarkable, and suggests that diversifying selection has played an important role in the evolution of R genes in this agronomically important species. (Supplemental material is available online at http://gattaca.nju.edu.cn.)

Amino Acid Sequence↗
PubMed2001

Myosins in protists.

This review focuses on selected papers that illustrate an historical perspective and the current knowledge of myosin structure and function in protists. The review contains a general description of myosin structure, a phylogenetic tree of the myosin classes, and descriptions of myosin isoforms identified in protists. Each myosin is discussed within the context of the taxonomic group of the organism in which the myosin has been identified. Domain structure, cellular location, function, and regulation are described for each myosin.

Adenosine Triphosphate↗
PubMed1984

Biochemical and electrophysiological characteristics of toxins isolated from the venom of the scorpion Centruroides sculpturatus.

Recent progress in biochemical, structural and physiological studies has revealed several interesting properties of the toxins from the American scorpion, Centruroides sculpturatus. These toxins, together with similar toxins from other species of scorpions, comprise a unique family of homologous proteins with phylogenetically related structural differences. There is now evidence from both binding and electrophysiological studies that two distinct classes of toxins are present in the venom of C. sculpturatus. One class of toxins markedly slows inactivation of the sodium permeability but has no demonstrable effect on activation, whereas the second class induces a transient shift in the voltage-dependence of activation. Both groups make inactivation incomplete.

Amino Acid Sequence↗
PubMed1990

Structural analysis of a group II intron by chemical modifications and minimal energy calculations.

Folding of the yeast mitochondrial group II intron aI5c has been analysed by chemical modification of the in vitro synthesised RNA with dimethylsulfate and diethylpyrocarbonate. Computer calculations of the intron secondary structure through minimization of free energy were also performed in order to study thermodynamic properties of the intron and to relate these to data obtained from chemical modification. Comparison of the two sets of data with the current phylogenetic model structure of the intron aI5 reveals close agreement, thus lending strong support for the existence of a typical group II intron core structure comprising six neighbouring stem-loop domains. Local discrepancies between the experimental data and the model structures have been analyzed by reference to thermodynamic properties of the structure. This shows that use of the latest refined set of free energy values improves the structure calculation significantly.

Base Sequence↗
PubMed1993

Rates and patterns of base change in the small subunit ribosomal RNA gene.

The small subunit ribosomal RNA gene (srDNA) has been used extensively for phylogenetic analyses. One common assumption in these analyses is that substitution rates are biased toward transitions. We have developed a simple method for estimating relative rates of base change that does not assume rate constancy and takes into account base composition biases in different structures and taxa. We have applied this method to srDNA sequences from taxa with a noncontroversial phylogeny to measure relative rates of evolution in various structural regions of srRNA and relative rates of the different transitions and transversions. We find that: (1) the long single-stranded regions of the RNA molecule evolve slowest, (2) biases in base composition associated with structure and phylogenetic position exist, and (3) the srDNAs studied lack a consistent transition/transversion bias. We have made suggestions based on these findings for refinement of phylogenetic analyses using srDNA data.

Animals↗