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At least 703 records · Page 39Linked to original sources
PubMed1991

Phylogenetic study of serotonin-immunoreactive structures in the pancreas of various vertebrates.

The distribution pattern of serotonin (5HT) in the pancreas was studied immunohistochemically by using a 5HT monoclonal antibody in various vertebrates including the eel, bullfrog, South African clawed toad, turtle, chicken, mouse, rat, guinea-pig, cat, dog and human. In all species examined, except the bullfrog, 5HT-like immunoreactivity was observed in nerve fibers, in endocrine cells, or in both. Positive nerve fibers were found in the eel, turtle, mouse, rat and guinea-pig. These fibers ran mainly along the blood vessels and partly through the gap between the exocrine glands. In the eel and guinea-pig, positive fibers invaded the pancreatic islet. Occasionally, these positive fibers were found adjacent to the surface of both exocrine and endocrine cells, suggesting a regulatory role of 5HT in pancreatic function. 5HT-positive endocrine cells were observed in the pancreas of all species except for the bullfrog and rat. In the eel and in mammals such as the mouse, guinea-pig, cat, dog and human, 5HT-positive cells were mainly observed within the pancreatic islet. In the South African clawed toad, turtle and chicken, the positive cells were mainly in the exocrine region. The present study indicates that the distribution patterns of 5HT in the pancreas varies considerably among different species.

Amphibians↗
PubMed2003

Key metabolic enzymes and muscle structure in triplefin fishes (Tripterygiidae): a phylogenetic comparison.

Metabolic potential and muscle development were investigated relative to habitat and phylogeny in seven species of New Zealand triplefin fishes. Activity was measured in three principal glycolytic enzymes (lactate dehydrogenase, pyruvate kinase and phosphofructokinase) and two oxidative enzymes (citrate synthase and L3-hydroxyacyl CoA:NAD(+) oxidoreductase). The non-bicarbonate buffering capacity of caudal muscle was also estimated. Phylogenetic independent contrast analyses were used to reduce the effects of phylogenetic history in analyses. A positive relationship between metabolic potential and the effective water velocity at respective habitat depths was found only after the exclusion from analyses of the semi-pelagic species Obliquichthys maryannae. O. maryannae showed high glycolytic enzyme activities, and displayed double the activity of both oxidative enzymes relative to the six benthic species. Histochemically stained sections taken immediately posterior to the vent showed that adult O. maryannae and larval Forsterygion lapillum had significantly more red muscle, and smaller cross-sectional areas of white and red muscle fibres, than adults of benthic species. The distribution of red muscle in adult O. maryannae resembled that of larval F. lapillum, and differed from the typical teleost pattern seen in adults of the six benthic species. Both adult O. maryannae and larval F. lapillum have an expansive lateralis superficialis muscle, typical of larval fish, which encompasses much of the caudal trunk. Results suggest that anaerobic potential in New Zealand triplefins: (a) increases with the locomotory requirements of different habitats, and (b) displays a negative relationship with depth-dependent water velocities in benthic species. O. maryannae appears to have increased aerobic potential for sustained swimming by paedomorphic retention of larval muscle architecture.

Animals↗
PubMed2006

Structure of zebra fish HIUase: insights into evolution of an enzyme to a hormone transporter.

During early vertebrate evolution, a duplication event in the gene encoding 5-hydroxyisourate hydrolase (HIUase), a widely distributed enzyme of purine metabolism, gave rise to transthyretin (TTR), a thyroid hormone transporter. We report here on the crystal structure of zebra fish HIUase in two different crystal forms. Despite the phylogenetic distance, this structure compares well with those of newly characterized bacterial HIUases, especially with regard to catalytic regions, which are highly preserved. Comparison with TTR structure reveals a highly conserved scaffold, harbouring distinct functional sites located in the same regions of the two vertebrate proteins. Residues that are differentially conserved in HIUases compared to TTR map in putative catalytic regions occupying significant portions of the two halves of a central channel that transverses the whole TTR protein. The evolution of TTR has been accompanied by remarkable changes of the HIUase active sites that gave rise to a channel open at both ends, thus allowing free access to hormone molecules.

Amidohydrolases↗
PubMed1985

Immunoglobulin VH gene structure and diversity in Heterodontus, a phylogenetically primitive shark.

A mouse VH probe has been used to identify and isolate VH homologs in a DNA library of Heterodontus francisci (horned shark). The complete nucleotide sequence of one VH gene, HXIA, has been determined and found to exhibit striking organizational homology and nucleotide identity with mammalian prototype VH genes. Metric analysis of the complete sequence is consistent with the early phylogenetic diversification of framework and complementarity-determining regions (CDR). Both the predicted amino acid sequence and the specific hybridization of the CDR2-specific, synthetic oligodeoxynucleotide probe in spleen mRNA suggest that HXIA is functionally expressed. A probe consisting of the entire coding region of this gene hybridizes with multiple components in Southern blot analysis of Heterodontus genomic DNA and together with the identification of additional unique VH+-lambda clones indicates that considerable complexity is associated with the germline VH gene family in a contemporary species that represents an early stage in the phylogenetic development of the vertebrates.

Amino Acid Sequence↗
PubMed1992

Characterization of the Bacillus subtilis rpsD regulatory target site.

The Bacillus subtilis rpsD gene, which encodes ribosomal protein S4, is subject to autogenous regulation. Repression of rpsD expression by excess S4 protein was previously shown to be affected by mutations in the leader region of the gene. A large number of deletion and point mutations in the leader region were generated, and their effect on repression by S4 in vivo was tested. These studies indicated that the required region was within positions +30 to +190 relative to the transcription start point. Replacement of the rpsD promoter with a lac promoter derivative which is expressed in B. subtilis had no effect, indicating that repression by S4 occurs at a level subsequent to transcription initiation. The rpsD leader region was isolated from several Bacillus species. Members of the B. subtilis group, as defined by analysis of 16S rRNA sequence, contained a leader region target site very closely related in structure to that of B. subtilis, despite considerable primary sequence variation; the B. brevis rpsD leader contained some but not all of the structural features found in the regulatory target sites of the other Bacillus species. Very little similarity to the Escherichia coli alpha operon S4 target site was found at either the primary-sequence or the secondary-structure level. Mutagenic and phylogenetic data indicate that the secondary structure of the leader region regulatory target site contains two large stem-loop domains. The first of these helices has a side loop which is essential for autoregulation, is highly conserved among Bacillus rpsD genes, and is similar to a region of 16S rRNA important in S4 binding.

Bacillus subtilis↗
PubMed2004

Secondary structure and function of the 5'-proximal region of the equine arteritis virus RNA genome.

Nidoviruses produce an extensive 3'-coterminal nested set of subgenomic mRNAs, which are used to express their structural proteins. In addition, arterivirus and coronavirus mRNAs contain a common 5' leader sequence, derived from the genomic 5' end. The joining of this leader sequence to different segments (mRNA bodies) from the genomic 3'-proximal region presumably involves a unique mechanism of discontinuous minus-strand RNA synthesis. Key elements in this process are the so-called transcription-regulating sequences (TRSs), which determine a base-pairing interaction between sense and antisense viral RNA that is essential for leader-to-body joining. To identify RNA structures in the 5'-proximal region of the equine arteritis virus genome that may be involved in subgenomic mRNA synthesis, a detailed secondary RNA structure model was established using bioinformatics, phylogenetic analysis, and RNA structure probing. According to this structure model, the leader TRS is located in the loop of a prominent hairpin (leader TRS hairpin; LTH). The importance of the LTH was supported by the results of a mutagenesis study using an EAV molecular clone. Besides evidence for a direct role of the LTH in subgenomic RNA synthesis, indications for a role of the LTH region in genome replication and/or translation were obtained. Similar LTH structures could be predicted for the 5'-proximal region of all arterivirus genomes and, interestingly, also for most coronaviruses. Thus, we postulate that the LTH is a key structural element in the discontinuous subgenomic RNA synthesis and is likely critical for leader TRS function.

Animals↗
PubMed1983

Phylogenetic and ecological features of the structural organization of the forebrain cortical plate in Chelonia: 1. Neuronal composition and dendrite spines of the cortical zones in land and aquatic Chelonia.

A comparative study was made of cytoarchitectonics, neuronal composition and ultrastructural organization of the three basic cortical zones (hippocampal, dorsal and pyriform) of the forebrain of four members of Chelonia (two aquatic and two land species). The features under study fall into three major groups as follows: (1) common to all the Chelonia under investigation and possibly of the entire order; (2) ecologically specific, i.e. common to animals with similar ecology and different in animals with different ecology; (3) species-specific, i.e. differing in individual species. The common structural features of the forebrain cortical plate in Chelonia underlie the morphological substrate responsible for specific functions in different cortical zones. It is precisely with respect to the common features that the dorsomedial dorsal cortex exhibits a more complex neuronal and synaptic organization as compared with other cortical zones. This part of Chelonia cortex is assumed to be homologous to mammalian neocortex. The more plastic ecologically specific and species specific features appear to provide adaptive specializations within a particular level of the nervous system organization.

Animals↗
PubMed1983

Phylogenetic and ecological properties of the structural organization of the cortical plate in the forebrain of Chelonia. 2. Axo-spinal synaptic complexes of the plexiform layer of the cortical zones in aquatic and land Chelonia.

An ultrastructural study is performed with a quantitative analysis of some parameters of the synaptic organization of the superficial plexiform layer of the three basic cortical zones (hippocampal, dorsal and pyriform) of the forebrain in two aquatic and two land Chelonia species. On the basis of our own and literature data it is inferred that all the basic elements of the axo-spino synaptic complexes (dendritic spines--active synaptic zones--nerve endings) exhibit both stability, ensuring the structural durability and reliability of the contacts' functioning, on the one hand, and plasticity responsible for homeostasis and adequate transformations, on the other. Normally, functional shifts in the fine structure of synaptic apparatus are presumably too slight to conceal the specific features of the nerve centres' synaptic organization. This made feasible a comparative study of the structure of the axo-spinal complexes in functionally dissimilar zones, which revealed the following three categories of characters: (1) stable, common of all the Chelonia species under study and characterizing a particular level of the integration of nervous processes, and (2) variable, ecologically-specific and (3) species-specific, ensuring adaptation changes within a given level of interneuronal organization. It has been revealed that ecological differences in the synaptic organization of the cortical zones in the aquatic and land Chelonia are most pronounced in the pyriform and hippocampal cortices, i.e. zones of exclusively and predominantly olfactory projections respectively, and are considerably less pronounced in the dorsal cortex, the zone of predominantly visual afferentation.

Animals↗
PubMed1996

Structural organization, chromosomal localization, expression and phylogenetic evaluation of mouse glutathione peroxidase encoding genes.

We have reported earlier the cloning and the chromosomal localization of 2 GPX-encoding sequences expressed differentially within the mouse epididymis, gpx5 and gpx3. Here, we have mapped on the mouse chromosomes the third known murine GPX-encoding gene, the cytosolic GPX or gpx1. We have compared the degree of identity of the 3 GPX proteins, the respective organization of the 3 corresponding single copy genes and, using degenerated oligonucleotides designed in highly conserved domains of the proteins, we have analyzed the expression of GPX-encoding genes in the mouse epididymis as well as in control tissues known to express GPX proteins (the liver for GPX1 and the kidney for GPX3). The 3 genes characterized to date were found expressed in each of the tissues tested but in a highly tissue-restricted manner. Nucleotidic sequences comparisons were carried out on GPX-encoding sequences from various species and were used to draw a dendrogram. Phylogenetic evaluation of the sequence information, as well as the chromosomal localizations, suggest that the GPX genes have evolved by duplication events followed by random insertions from a single ancestral gene.

Amino Acid Sequence↗
PubMed1999

Primary and secondary structure of the small-subunit ribosomal RNA of the naked, marine amoeba Vannella anglica: phylogenetic implications.

The primary and secondary structure of the small-subunit ribosomal RNA (ssrRNA) gene from the naked, marine amoeba, Vannella anglica (subclass Gymnamoebia), was determined. The ssrRNA is 1962 nucleotides in length, with a low G+C content of 37.1%. The ssrRNA is composed of several uncommon secondary structure features including helix E8-1, which may be a useful target for rRNA probes for the direct identification of isolates in mixed culture. Phylogenetic analysis of sequence data showed that V. anglica branched prior to the rapid diversification of the eukaryotes. It did not associate with the other naked, lobose amoebae represented by Acanthamoeba and Hartmannella, indicating that Vannella represents a separate amoeboid lineage and the subclass Gymnamoebia is polyphyletic.

Amino Acid Sequence↗
PubMed1992

Structural features in TAR RNA of human and simian immunodeficiency viruses: a phylogenetic analysis.

A comparative analysis of TAR RNA structures in human and simian immunodeficiency viruses reveals the conservation of certain structural features despite the divergence in sequence. Both the TAR elements of HIV-1 and SIV-chimpanzee can be folded into relatively simple one-stem hairpin structures. Chemical and RNAase probes were used to analyze the more complex structure of HIV-2 TAR RNA, which folds into a branched hairpin structure. A surprisingly similar RNA conformation can be proposed for SIV-mandrill, despite considerable divergence in nucleotide sequence. A third structural presentation of TAR sequences is seen for SIV-african green monkey. These results are generally consistent with the classification of HIV-SIV viruses in four subgroups based on sequence analyses (both nucleotide- and amino acid-sequences). However, some conserved TAR structures were detected for members of different virus subgroups. It is therefore proposed that RNA structure analysis might provide an additional tool for determining phylogenetic relationships among the HIV-SIV viruses.

Base Composition↗
PubMed2000

Conservation of substructures in proteins: interfaces of secondary structural elements in proteasomal subunits.

It is observed that during divergent evolution of two proteins with a common phylogenetic origin, the structural similarity of their backbones is often preserved even when the sequence similarity between them decreases to a virtually undetectable level. Here we analyzed, whether the conservation of structure along evolution involves also the local atomic structures in the interfaces between secondary structural elements. We have used as study case one protein family, the proteasomal subunits, for which 17 crystal structures are known. These include 14 different subunits of Saccharomyces cerevisiae, 2 subunits of Thermoplasma acidophilum and one subunit of Escherichia coli. The structural core of the 17 proteasomal subunits has 23 secondary structural elements. Any two adjacent secondary structural elements form a molecular interface consisting of two molecular patches. We found 61 interfaces that occurred in all 17 subunits. The 3D shape of equivalent molecular patches from different proteasomal subunits were compared by superposition. Our results demonstrate that pairs of equivalent molecular patches show an RMSD which is lower than that of randomly chosen patches from unrelated proteins. This is true even when patch comparisons with identical residues were excluded from the analysis. Furthermore it is known that the sequential dissimilarity is correlated to the RMSD between the backbones of the members of protein families. The question arises whether this is also true for local atomic structures. The results show that the correlation of individual patch RMSD values and local sequence dissimilarities is low and has a wide range from 0 to 0.41, however, it is surprising that there is a good correlation between the average RMSD of all corresponding patches and the global sequence dissimilarity. This average patch RMSD correlates slightly stronger than the C(alpha)-trace RMSD to the global sequence dissimilarity.

Algorithms↗
PubMed1999

Using protein structural information in evolutionary inference: transmembrane proteins.

We present a model of amino acid sequence evolution based on a hidden Markov model that extends to transmembrane proteins previous methods that incorporate protein structural information into phylogenetics. Our model aims to give a better understanding of processes of molecular evolution and to extract structural information from multiple alignments of transmembrane sequences and use such information to improve phylogenetic analyses. This should be of value in phylogenetic studies of transmembrane proteins: for example, mitochondrial proteins have acquired a special importance in phylogenetics and are mostly transmembrane proteins. The improvement in fit to example data sets of our new model relative to less complex models of amino acid sequence evolution is statistically tested. To further illustrate the potential utility of our method, phylogeny estimation is performed on primate CCR5 receptor sequences, sequences of l and m subunits of the light reaction center in purple bacteria, guinea pig sequences with respect to lagomorph and rodent sequences of calcitonin receptor and K-substance receptor, and cetacean sequences of cytochrome b.

Animals↗
PubMed2005

Structural and functional studies of vertebrate metallothioneins: cross-talk between domains in the absence of physical contact.

In previous studies, we showed that the chemical and dynamic properties of fish and mouse MTs (metallothioneins) present a number of distinctive differences linked to their primary structures, and that phylogenetic relationships of mammal and fish MTs correlate with their three-dimensional structures. The different behaviours of MTs may also be linked to the interaction between their two domains. In the present study, we have compared the physicochemical properties of the isolated recombinant domains constituting Notothenia coriiceps and mouse MTs, and compared them with those of the corresponding whole MTs. NMR spectra of the separated domains of N. coriiceps are almost superimposable on those of the parent MT, suggesting an apparent lack of interaction between the two domains in the protein. However, certain dynamic and physicochemical features of the isolated domains are unlike those of the whole protein. In particular, the temperature-induced changes in the chiroptical properties, thiol reactivity of the Zn-MT domains and the Zn2+/Cd2+ rate of exchange are different for the two domains and with respect to the whole protein. Taken together, these results provide a strong argument in favour of the interaction of the two domains in the MT molecule, in spite of the elusive evidence provided by the structural analyses.

Animals↗