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At least 1,135 records · Page 63Linked to original sources
PubMed2000

The KLK7 (PRSS6) gene, encoding for the stratum corneum chymotryptic enzyme is a new member of the human kallikrein gene family - genomic characterization, mapping, tissue expression and hormonal regulation.

The human stratum corneum chymotryptic enzyme (HSCCE; PRSS6, KLK7 gene) has been purified from human stratum corneum and is known to participate in the cell shedding process. The cDNA of the gene has previously been reported. Here, we describe the identification of 5' and 3' extensions of the published mRNA, and the complete genomic organization of the gene. KLK7 is composed of five coding exons which have similar lengths to exons of other kallikrein-like genes. The intron phases are completely conserved between this gene and other members of the kallikrein-like gene family. Precise mapping of KLK7 has indicated that it is located at chromosomal locus 19q13. 3-q13.4 between the already known genes zyme (KLK6) (centromere) and neuropsin (KLK8) (telomere). Until recently, it was thought that this gene is expressed only in the skin. We here provide evidence that KLK7 is also expressed at relatively high levels in the central nervous system, kidney, mammary and salivary glands. Its expression is up-regulated by estrogens and glucocorticoids in the breast carcinoma cell line BT-474. The cDNA and protein of this gene are homologous to sequences of other kallikrein-like genes. The gene encodes for a secreted protein. Phylogenetic analysis, the close structural similarities, and its co-localization in the same chromosomal region, suggest that the gene encoding for the stratum corneum chymotryptic enzyme is a new member of the expanded human kallikrein gene family.

Amino Acid Sequence↗
PubMed2004

Phylogeny of holoparasitic Orobanche (Orobanchaceae) inferred from nuclear ITS sequences.

Orobanche is the largest genus among the holoparasitic members of Orobanchaceae. We present the first molecular phylogenetic analysis (using nuclear ITS sequences) that includes members of all sections of Orobanche, Gymnocaulis, Myzorrhiza, Trionychon, and Orobanche. Orobanche is not monophyletic, but falls into two lineages: (1) the Orobanche group comprises Orobanche sect. Orobanche and the small Near Asian genus Diphelypaea and is characterized by a chromosome base number of x=19 and (2) the Phelipanche group contains Orobanche sects. Gymnocaulis, Myzorrhiza, and Trionychon and possesses a chromosome base number of x=12. The relationships between these two groups and to other genera such as Boschniakia or Cistanche remain unresolved. Within the Orobanche group, Orobanche macrolepis and Orobanche anatolica (including Orobanche colorata) constitute two phylogenetically distinct lineages. Intrasectional structurings proposed by some authors for O. sect. Orobanche are not confirmed by the molecular data. In most cases, intraspecific sequence divergence between accessions, if present, is negligible and not correlated with morphological or ecological traits. In a few cases, however, there is evidence for the presence of cryptic taxa.

Biological Evolution↗
PubMed2001

Fish gonadotropin and thyrotropin receptors: the evolution of glycoprotein hormone receptors in vertebrates.

We have cloned and characterized, for the first time in fish, two different gonadotropin receptors (GTHR) and a single thyrotropin receptor (TSHR) from amago salmon (Oncorhynchus rhodurus) and Nile tilapia (Oreochromis niloticus). Phylogenetic analyses and intron/exon structure suggest that the two GTHRs in fish are comparable to tetrapod follicle stimulating hormone and luteinizing hormone receptors. Temporal and spatial expression patterns, examined by Northern blot analysis and in situ hybridization, paralleled those seen in mammals and birds. Consequently, genetic and functional divergence of two GTHRs and TSHR probably occurred before the teleost and tetrapod split.

Animals↗
PubMed2001

Genetic variability and molecular identification of Brazilian Biomphalaria species (Mollusca: Planorbidae).

Freshwater snails belonging to the genus Biomphalaria are intermediate hosts of the trematode Schistosoma mansoni in the Neotropical region and Africa. In Brazil, one subspecies and ten species of Biomphalaria have been identified: B. glabrata, B. tenagophila, B. straminea, B. occidentalis, B. peregrina, B. kuhniana, B. schrammi, B. amazonica, B. oligoza, B. intermedia and B.t. guaibensis. However, only the first three species are found naturally infected with S. mansoni. The classical identification of these planorbids is based on comparison of morphological characteristics of the shell and male and female reproductive organs, which is greatly complicated by the extensive intra-specific variation. Several molecular techniques have been used in studies on the identification, genetic structure as well as phylogenetic relationships between these groups of organisms. Using the randomly amplified polymorphic DNAs (RAPD) analysis we demonstrated that B. glabrata exhibits a remarkable degree of intra-specific polymorphism. Thus, the genetics of the snail host may be more important to the epidemiology of schistosomiasis than those of the parasite itself. Using the simple sequence repeat anchored polymerase chain reaction (SSR-PCR) in intra-populational and intra-specific studies we have demonstrated that snails belonging to the B. straminea complex (B. straminea, B. kuhniana and B. intermedia) clearly presented higher heterogeneity. Using the low stringency polymerase chain reaction (LS-PCR) technique we were able to separate B. glabrata from B. tenagophila and B. tenagophila from B. occidentalis. To separate all Brazilian Biomphalaria species we used the restriction fragment length polymorphism (PCR-RFLP) of the internal transcribed spacer region (ITS) of the DNA gene. The method also proved to be efficient for the specific identification of DNA extracted from snail eggs. Recently we have sequenced the ITS2 region for phylogenetic studies of all Biomphalaria snails from Brazil.

Animals↗
PubMed2000

Mutations in helix 27 of the yeast Saccharomyces cerevisiae 18S rRNA affect the function of the decoding center of the ribosome.

A dynamic structural rearrangement in the phylogenetically conserved helix 27 of Escherichia coli 16S rRNA has been proposed to directly affect the accuracy of translational decoding by switching between "accurate" and "error-prone" conformations. To examine the function of helix 27 in eukaryotes, random and site-specific mutations in helix 27 of the yeast Saccharomyces cerevisiae 18S rRNA have been characterized. Mutations at positions of yeast 18S rRNA corresponding to E. coli 886 (rdn8), 888 (rdn6), and 912 (rdn4) increased translational accuracy in vivo and in vitro, and caused a reduction in tRNA binding to the A-site of mutant ribosomes. The double rdn4rdn6 mutation separated the killing and stop-codon readthrough effects of the aminoglycoside antibiotic, paromomycin, implicating a direct involvement of yeast helix 27 in accurate recognition of codons by tRNA or release factor eRF1. Although our data in yeast does not support a conformational switch model analogous to that proposed for helix 27 of E. coli 16S rRNA, it strongly suggests a functional conservation of this region in tRNA selection.

Aldehydes↗
PubMed1999

Structure of the most conserved internal loop in SRP RNA.

The signal recognition particle (SRP) directs translating ribosomes to the protein translocation apparatus of endoplasmic reticulum (ER) membrane or the bacterial plasma membrane. The SRP is universally conserved, and in prokaryotes consists of two essential subunits, SRP RNA and SRP54, the latter of which binds to signal sequences on the nascent protein chains. Here we describe the solution NMR structure of a 28-mer RNA composing the most conserved part of SRP RNA to which SRP54 binds. Central to this function is a six-nucleotide internal loop that assumes a novel Mg2+-dependent structure with unusual cross-strand interactions; besides a cross-strand A/A stack, two guanines form hydrogen bonds with opposite-strand phosphates. The structure completely explains the phylogenetic conservation of the loop bases, underlining its importance for SRP54 binding and SRP function.

Base Sequence↗
PubMed2026

Chromosome-scale genomes and population resequencing resolve subgenome diversity and halophyte adaptation in Salicornia.

Amid escalating water scarcity and groundwater depletion, halophytes such as Salicornia (Amaranthaceae) represent valuable models for extreme salt tolerance and hold promise for saltwater-based agriculture. Here, we show chromosome-scale genome assemblies for six Salicornia species, revealing four distinct subgenomes, reconciling our assemblies with two existing reference genomes (S. ramosissima UK and S. europaea China), correcting chromosome numbering and orientation. Comparative analyses across ploidy levels demonstrate genome expansion in North American lineages driven by Gypsy retrotransposons, and lineage-specific expansions of two gene families implicated in stress metabolism. Phylogenetic and population-structure analyses of a global resequencing panel of 318 accessions resolve interspecific relationships and establish curated germplasm collections for future crop breeding. Genetic analyses uncover a contrasting population-genetic signal on chromosome 6A between two species, highlighting an OSCA calcium-permeable channel gene as a candidate locus for osmotic adaptation. Together, these resources establish a genomic framework for Salicornia that supports evolutionary studies of halophyte adaptation and crop development.

Chenopodiaceae↗
PubMed2025

Integrated genomics and morphological approach reveals interspecific gene flow cases and decodes the origin of selected feathergrasses (Poaceae, Stipa).

Central Asia is a diversity hotspot of arid-adapted grasses from the genus Stipa, with approximately 100 taxa found in the region. Recent studies in the steppe areas of Kazakhstan revealed specimens displaying intermediate morphology, distinguishing them from other taxa that grow sympatrically. Using integrative taxonomy, we investigated whether these individuals resulted from natural speciation or hybridisation, and if so, we would like to know which species were involved in this process feathergrasses. Research conducted in steppes of central Kazakhstan (Kyzylorda region), revealed the existence of individuals morphologically intermediate between S. arabica and S. richteriana, suggesting that these are probably of hybrid origin. Morphology and SNP markers validated the specimens as F1 hybrid between the aforementioned species by cladding separately based on neighbor-joining phylogenetic tree. Moreover, genetic structure displayed a separate cluster and showed almost equal genetic admixture between S. arabica and S. richteriana. Additionally, fastStructure analysis detected two geographically separated cryptic genotypes within S. richteriana population and their involvement in the hybridisation resulted in occurrence of S. × heptapotamica, S. × czerepanovii and S. × korshinskyi which recently were suggested as hybrids. Based on these evidences, we described a new nothospecies S. × kyzylordensis, as F1 hybrid. Furthermore, morphologically, the nothospecies delimited with other hybrids in Kazakh steppe area, marking the first report of hybridisation between S. arabica and S. richteriana, along with molecular evidence for the origin of further species supposed to be hybrids. This finding is crucial to understanding species diversity and hybridisation process in morphologically and genetically distant Stipa species.

Poaceae↗
PubMed2003

DOK4 and DOK5: new Dok-related genes expressed in human T cells.

Dok proteins are adapter proteins involved in signal transduction. Several intracellular proteins expressed in lymphocytes meet the criteria of membrane-associated adapter proteins such as members of the Dok family. To understand the role and the formation of multiprotein networks involving Dok proteins in T lymphocytes, we search for potential additional members of this family. Here, we describe the two new human dok-related genes DOK4 and DOK5 and present data showing the expression of DOK4 and DOK5 genes in T cells. These genes are the orthologues of mouse Dok4 and Dok5 genes. Based on analysis of phylogenetic trees and exon/intron structure of Dok family members, DOK4 and DOK5 define a subfamily within dok genes distinct from DOK1, DOK2 and DOK3. So, Dok-4 and Dok-5 molecules constitute a new group of adapter proteins in T cells, requiring further functional analysis.

Adaptor Proteins, Signal Transducing↗
PubMed1998

Structure of the Shigella dysenteriae haem transport locus and its phylogenetic distribution in enteric bacteria.

The ability to transport and use haemin as an iron source is frequently observed in clinical isolates of Shigella spp. and pathogenic Escherichia coli. We found that many of these haem-utilizing E. coli strains contain a gene that hybridizes at high stringency to the S. dysenteriae type 1 haem receptor gene, shuA. These shuA-positive strains belong to multiple phylogenetic groups and include clinical isolates from enteric, urinary tract and systemic infections. The distribution of shuA in these strains suggests horizontal transfer of the haem transport locus. Some haem-utilizing pathogenic E. coli strains did not hybridize with shuA, so at least one other haem transport system is present in this group. We also characterized the chromosomal region containing shuA in S. dysenteriae. The shuA gene is present in a discrete locus, designated the haem transport locus, containing eight open reading frames. Several of the proteins encoded in this locus participate with ShuA in haem transport, as a Salmonella typhimurium strain containing the entire haem transport locus used haem much more efficiently than the same strain containing only shuA. The haem transport locus is not present in E. coli K-12 strains, but the sequences flanking the haem transport locus in S. dysenteriae matched those at the 78.7 minute region of E. coli K-12. The junctions and flanking sequences in the shuA-positive pathogenic E. coli strains tested were nearly identical to those in S. dysenteriae, indicating that, in these strains, the haem transport locus has an organization similar to that in S. dysenteriae, and it is located in the same relative position on the chromosome.

Bacterial Outer Membrane Proteins↗
PubMedDate not supplied

Gene expression and larval evolution: changing roles of distal-less and orthodenticle in echinoderm larvae.

We describe the expression of the homeobox genes orthodenticle (Otx) and distal-less (Dlx) during the larval development of seven species representing three classes of echinoderms: Holothuroidea, Asteroidea, and Echinoidea. Several expression domains are conserved between species within a single class, including Dlx expression within the brachiolar arms of asteroid larvae and Otx expression within the ciliated bands of holothuroid larvae. Some expression domains are apparently conserved between classes, such as the expression of Dlx within the hydrocoel (left mesocoel) in all three classes. However, several substantial differences in expression domains among taxa were also evident for both genes. Some autapomorphic (unique derived) features of gene expression are phylogenetically associated with autapomorphic structures, such as Dlx expression within the invaginating rudiment of euechinoids. Other autapomorphic gene expression domains are associated with evolutionary shifts in life history from feeding to nonfeeding larval development, such as Otx expression within the ciliated bands of a nonfeeding holothuroid larva. Similar associations between evolutionary changes in morphology and life history mode with changes in regulatory gene expression have also been observed in arthropods, urochordates, and chordates. We predict that recruitment of regulatory genes to a new developmental role is commonly associated with evolutionary changes in morphology and may be particularly common in clades with complex life cycles and diversity of life history modes. Caution should be used when making generalizations about gene expression and function based on a single species, which may not accurately reflect developmental processes and life histories of the phyla to which it belongs.

Animals↗
PubMed1989

[Disorders of learning and memory in focal cerebral tissue lesions].

Memory and learning in man depend on complex cognitive systems, and thus on efficient associative information stores in different neocortical areas of our brain. In addition, phylogenetically older, "limbic" brain structures are needed, in order to manage these huge accociative stores in our telencephalon. This "operating system" manages memory and learning capabilities considering the "milieu interne", and especially biological and individual priorities. Our contribution attempts to sketch the anatomical outlines of this limbic operating system. Two interdependent neuronal networks may be of pivotal importance: 1. a medial limbic loop with Papez circuit as the main structure, and 2. a basolateral limbic loop including the amygdala, the subcallosal area (and the septum verum?) as well as the mediodorsal thalamic nucleus. Based on the anatomical evidence of (largely) selective, i.e. focal brain lesions the likelihood for all these relay stations as memory-related structures is discussed. Our working hypothesis assumes that combined, bilateral lesions of both limbic neuronal networks make severe, global and lasting deficits in memory and learning performance fairly likely. The lesion of only one of these limbic loops seems to cause modality-specific deficits. Unilateral lesions of the retrocommissural hippocampal formation may also account for lasting amnesia.

Brain Damage, Chronic↗
PubMed2005

Small RNA genes expressed from Staphylococcus aureus genomic and pathogenicity islands with specific expression among pathogenic strains.

Small RNA (sRNA) genes are expressed in all organisms, primarily as regulators of translation and message stability. We have developed comparative genomic approaches to identify sRNAs that are expressed by Staphylococcus aureus, the most common cause of hospital-acquired infections. This study represents an in-depth analysis of the RNome of a Gram-positive bacterium. A set of sRNAs candidates were identified in silico within intergenic regions, and their expression levels were monitored by using microarrays and confirmed by Northern blot hybridizations. Two sRNAs were also detected directly from purification and RNA sequence determination. In total, at least 12 sRNAs are expressed from the S. aureus genome, five from the core genome and seven from pathogenicity islands that confer virulence and antibiotic resistance. Three sRNAs are present in multiple (two to five) copies. For the sRNAs that are conserved throughout the bacterial phylogeny, their secondary structures were inferred by phylogenetic comparative methods. In vitro binding assays indicate that one sRNA encoded within a pathogenicity island is a trans-encoded antisense RNA regulating the expression of target genes at the posttranscriptional level. Some of these RNAs show large variations of expression among pathogenic strains, suggesting that they are involved in the regulation of staphylococcal virulence.

Base Pairing↗
PubMed1999

RNase P RNAs from some Archaea are catalytically active.

The RNA subunits of RNase Ps of Archaea and eukaryotes have been thought to depend fundamentally on protein for activity, unlike those of Bacteria that are capable of efficient catalysis in the absence of protein. Although the eukaryotic RNase P RNAs are quite different than those of Bacteria in both sequence and structure, the archaeal RNAs generally contain the sequences and structures of the bacterial, phylogenetically conserved catalytic core. A spectrum of archaeal RNase P RNAs were therefore tested for activity in a wide range of conditions. Many remain inactive in ionically extreme conditions, but catalytic activity could be detected from those of the methanobacteria, thermococci, and halobacteria. Chimeric holoenzymes, reconstituted from the Methanobacterium RNase P RNA and the Bacillus subtilis RNase P protein subunits, were functional at low ionic strength. The properties of the archaeal RNase P RNAs (high ionic-strength requirement, low affinity for substrate, and catalytic reconstitution by bacterial RNase P protein) are similar to synthetic RNase P RNAs that contain all of the catalytic core of the bacterial RNA but lack phylogenetically variable, stabilizing elements.

Archaea↗
PubMed2001

The dimer initiation site hairpin mediates dimerization of the human immunodeficiency virus, type 2 RNA genome.

The untranslated leader of retroviral RNA genomes encodes multiple structural signals that are critical for virus replication. In the human immunodeficiency virus, type 1 (HIV-1) leader, a hairpin structure with a palindrome-containing loop is termed the dimer initiation site (DIS), because it triggers in vitro RNA dimerization through base pairing of the loop-exposed palindromes (kissing loops). Controversy remains regarding the region responsible for HIV-2 RNA dimerization. Different studies have suggested the involvement of the transactivation region, the primer binding site, and a hairpin structure that is the equivalent of the HIV-1 DIS hairpin. We have performed a detailed mutational analysis of the HIV-2 leader RNA, and we also used antisense oligonucleotides to probe the regions involved in dimerization. Our results unequivocally demonstrate that the DIS hairpin is the main determinant for HIV-2 RNA dimerization. The 6-mer palindrome sequence in the DIS loop is essential for dimer formation. Although the sequence can be replaced by other 6-mer palindromes, motifs that form more than two A/U base pairs do not dimerize efficiently. The inability to form stable kissing-loop complexes precludes formation of dimers with more extended base pairing. Structure probing of the DIS hairpin in the context of the complete HIV-2 leader RNA suggests a 5-base pair elongation of the DIS stem as it is proposed in current RNA secondary structure models. This structure is supported by phylogenetic analysis of leader RNA sequences from different viral isolates, indicating that RNA genome dimerization occurs by a similar mechanism for all members of the human and simian immunodeficiency viruses.

Base Sequence↗
PubMed2003

Bifunctional phosphoglucose/phosphomannose isomerases from the Archaea Aeropyrum pernix and Thermoplasma acidophilum constitute a novel enzyme family within the phosphoglucose isomerase superfamily.

The hyperthermophilic crenarchaeon Aeropyrum pernix contains phosphoglucose isomerase (PGI) activity. However, obvious homologs with significant identity to known PGIs could not be identified in the sequenced genome of this organism. The PGI activity from A. pernix was purified and characterized. Kinetic analysis revealed that, unlike all known PGIs, the enzyme catalyzed reversible isomerization not only of glucose 6-phosphate but also of epimeric mannose 6-phosphate at similar catalytic efficiency, thus defining the protein as bifunctional phosphoglucose/phosphomannose isomerase (PGI/PMI). The gene pgi/pmi encoding PGI/PMI (open reading frame APE0768) was identified by matrix-assisted laser desorption ionization time-of-flight analyses; the gene was overexpressed in Escherichia coli as functional PGI/PMI. Putative PGI/PMI homologs were identified in several (hyper)thermophilic archaea and two bacteria. The homolog from Thermoplasma acidophilum (Ta1419) was overexpressed in E. coli, and the recombinant enzyme was characterized as bifunctional PGI/PMI. PGI/PMIs showed low sequence identity to the PGI superfamily and formed a distinct phylogenetic cluster. However, secondary structure predictions and the presence of several conserved amino acids potentially involved in catalysis indicate some structural and functional similarity to the PGI superfamily. Thus, we propose that bifunctional PGI/PMI constitutes a novel protein family within the PGI superfamily.

Aeropyrum↗
PubMedDate not supplied

The bestrophin family of anion channels: identification of prokaryotic homologues.

The human disease protein, Bestrophin-1, associated with vitelliform macular dystrophy, has recently been shown to be an integral membrane anion channel-forming protein. In this study we have recovered all bestrophin homologues from the NCBI database and analyzed their sequences using bioinformatic approaches. Eukaryotic homologues were found in animals and fungi but not in plants or protozoans, and prokaryotic homologues distantly related to the eukaryotic proteins, were identified in certain Gram-negative bacterial kingdoms but not in Gram-positive bacteria or archaea. Our analyses suggest a uniform 4 TMS topology for most of these homologues with regions of conservation overlapping and preceding the odd numbered TMSs and overlapping and following the even numbered TMSs. Well-conserved motifs were identified in both the eukaryotic and the prokaryotic homologues, and these proved to overlap, suggesting common structural and functional properties. Phylogenetic analyses revealed that the eukaryotic proteins cluster according to organismal type, and that the prokaryotic proteins sometimes (but not always) do so. This suggests that eukaryotic paralogues arose exclusively by recent gene duplication events although both early and late gene duplication events occurred in prokaryotes.

Animals↗
PubMed2000

Developmental variation, homology, and the pharyngula stage.

Understanding how development varies both inter- and intraspecifically can be important for systematic and evolutionary studies. This review will explore three different ways such understanding can be applied to evolutionary analyses. First, developmental data can be useful for homology determination. Interspecific variation in development has been thought to make developmental data poor candidates for determining homology. However, an updated developmental criterion that is more broadly comparative and mechanistic augments the available criteria used in homology determination. Second, modern cell and molecular biology are providing a better understanding of the many developmental processes involved in a structure's formation and will augment the number of characters available for phylogenetic analyses. Recent work has revealed that what had been thought to be a highly conserved developmental stage, the pharyngula (the phylotypic and zootypic stage of craniates) is highly variable. This variation can be seen in the development of such tissues as neural crest and placodes. These tissues are particularly interesting from a phylogenetic standpoint because they and the structures they form contribute to key synapomorphies of craniates. Finally, understanding developmental processes and how they form the variety of morphologies seen in nature will help in constructing the transformations that occurred during evolution. One such example involves descriptions of how lateral line development is affected in different mutant lines of zebrafish. The many species of teleost fishes express great variation in the patterns of their lateral lines, and this is often an important systematic character. Understanding the genetic basis of lateral line development would help not only in hypothesizing possible transformational series but also in determining how many genes may have been required for these transformations.

Animals↗