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At least 1,531 records · Page 85Linked to original sources
PubMed2000

Complete sequences of two highly divergent european isolates of TT virus.

TT virus is a virus distantly related to the Circoviridae family. We report here the complete genome characterization of two European human isolates (T3PB and TUPB) using a new and simple protocol for sequencing GC-rich genomic regions. Sequence analysis confirmed the existence of two major ORFs, of a CAV-like VP2 motif in ORF2 and of potential stem-loop structures in non-coding regions. Phylogenetic analyses based on complete genomic sequences of human isolates suggested that three different lineages exist at least. The first lineage includes genotypes 1, 2, and 3, and two other lineages include viruses related to the Japanese SANBAN and to the North American TUS01 isolates respectively. Sequence comparison made it possible to assign strain T3PB to genotype 3, and strain TUPB to the TUS01 group. Consequently, this study reports the first full-length sequence of a genotype 3 isolate and demonstrates that viruses belonging to the TUS01 lineage are present in the Old Word.

Circoviridae↗
PubMed1995

Molecular evolution of genes encoding ribonucleases in ruminant species.

Phylogenetic analysis, based on the primary structures of mammalian pancreatic-type ribonucleases, indicated that gene duplication events, which occurred during the evolution of ancestral ruminants, gave rise to the three paralogous enzymes present in the bovine species. Herein we report data that demonstrate the existence of the orthologues of the bovine pancreatic, seminal, and cerebral ribonucleases coding sequences in the genomes of giraffe and sheep. The "seminal" sequence is a pseudogene in both species. We also report an analysis of the transcriptional expression of ribonuclease genes in sheep tissues. The data presented support a model for positive selection acting on the molecular evolution of ruminant ribonuclease genes.

Amino Acid Sequence↗
PubMed1993

Calmodulin mediates melatonin cytoskeletal effects.

In this article, we review the data concerning melatonin interactions with calmodulin. The kinetics of melatonin-calmodulin binding suggest that the hormone modulates cell activity through intracellular binding to the protein at physiological concentration ranges. Melatonin interaction with calmodulin may allow the hormone to modulate rhythmically many cellular functions. Melatonin's effect on tubulin polymerization, and cytoskeletal changes in MDCK and N1E-115 cells cultured with melatonin, suggest that at low concentrations (10(-9) M) cytoskeletal effects are mediated by its antagonism to Ca2+-calmodulin. At higher concentrations (10(-5)M) non-specific binding of melatonin to tubulin occurs thus overcoming the specific melatonin antagonism to Ca2+-calmodulin. Since the structures of melatonin and calmodulin are phylogenetically well preserved, calmodulin-melatonin interaction probably represents a major mechanism for regulation and synchronization of cell physiology.

Animals↗
PubMed2002

Functional and structural adaptations of bacterial communities growing on particulate substrates under stringent nutrient limitation.

Biomass recycle reactors (BRRs) were used as a model system to study the functional and structural adaptations of mixed bacterial communities in response to the imposition of increasingly severe nutrient limitation. BRRs were fed synthetic media containing either spinach homogenate or autoclaved yeast cells to simulate the complex mixtures of particulate carbon sources that are often present in nature. In the BRRs fed spinach homogenate, the biomass (measured as particulate protein) exhibited a physiological response similar to previous studies as detected by 40-80% reductions in respiratory potential and by relatively stable catabolic ectoenzyme activities. Concomitant adaptations in bacterial community structure were detected by PCR-DGGE and RT-PCR-DGGE of 16S rDNA and 16S rRNA fragments, respectively. The microbial community structure was dynamic even after the biomass had reached a quasi-steady state with respect to physiological measurements. In the BRRs fed yeast cells, respiratory potentials increased 2- to 5-fold during the initial portion of the BRR run and alpha-glucosidase and beta-glucosidase activities increased 2- to 4-fold. Substantial bacterial community shifts were also detected in both the rDNA and rRNA profiles, indicating that this community was also structurally dynamic. These experiments suggest that phylogenetically different bacteria sustained the functional activities in these ecosystems in response to increasingly stringent nutrient limitation.

Bacteria↗
PubMed1999

Cloning and characterization of iron-containing superoxide dismutase from the human malaria species Plasmodium ovale, P. malariae and P. vivax.

The iron-containing superoxide dismutase (FeSOD) gene from three human malaria species, namely Plasmodium ovale, P. malariae and P. vivax, was amplified by polymerase chain reaction, cloned and then sequenced. Comparisons of their deduced amino acid sequences with that of the FeSOD from P. falciparum revealed a very low polymorphism at the FeSOD locus in human malaria species. One P. ovale and the P. vivax FeSOD genes presented the same nucleotide sequence as that of the P. falciparum strain HB3 whereas the second P. ovale and the P. malariae genes exhibited two punctual mutations. These mutations did not affect the function and structure of the enzyme. The FeSOD polymorphism was so low that no phylogenetic relationship among human malaria species could be proposed, but this conservative structure strengthened the potentiality of this enzyme as a possible target for antimalarial drugs.

Amino Acid Sequence↗
PubMed2005

Chromosomal organization, evolutionary relationship, and expression of zebrafish GnRH family members.

Multiple forms of gonadotropin-releasing hormone (GnRH) are found in different vertebrates. In this study, we have cloned cDNA encoding the full-length gnrh3 and gnrh2 from zebrafish brain and characterized their structure and expression patterns. We performed phylogenetic analysis and compared conserved syntenies in the region surrounding the GnRH genes from human, chicken, pufferfish, and zebrafish genores. The gnrh3 and gnrh2 genes were mapped to LG17 and LG21, respectively. The zebrafish genome appears to lack an ortholog to human GNRH1, and the human genome appears to lack an ortholog of gnrh3. Expression of gnrh3 began in the olfactory pit at 24-26 h postfertilization and expanded to the olfactory bulb during early larval stage. Expression of gnrh2 is always in the midbrain. In addition, GnRH is also expressed in boundary cells surrounding seminiferous cysts of the testis. Thus, this detailed phylogenetic, chromosomal comparison, and expression study defines the identity and the evolutionary relationship of two zebrafish gnrh genes. We propose a model describing the evolution of gnrh genes involving ancestral duplication of the genes followed by selective loss of one gene in some teleosts.

Animals↗
PubMed1978

The amino acid sequence of the alpha chain of badger (Meles meles) haemoglobin.

The complete amino acid sequence of the alpha chain from the badger (Meles meles) haemoglobin was elucidated using conventional methods chiefly performed on tryptic peptides separated by peptide "mapping" and comparison with human alpha chain. Sixteen differences were noted between the alpha chain of badger and man. Phylogenetic aspects and three-dimensional structure requirements are discussed.

Amino Acid Sequence↗
PubMed1993

Holobionts, hybrids, and cladistic classification.

David P. Mindell assumes that incorporation of the holobionts (evolutionarily stable symbiotic complexes) and hybrids into phylogenetic trees necessarily distorts the hierarchical structure of cladistic classification, and must lead to reformulation of some basic cladistic concepts (BioSystems, 27, 53-62, 1992). He does not regard the Eukarya and Eubacteria as monophyletic taxa, the former being 'polyphyletic', the latter 'paraphyletic'. We attempt to show that the existence of holobionts/hybrids is not a cladistic problem. Cladistics is a systematic methodology, not a system of evolutionary hypotheses; cladograms are statements about distribution of shared characters (synapomorphies) and, consequently, the cladograms are always branching and hierarchically structured. A taxon is monophyletic if it has a single root in the cladogram, not a single ancestor 'in reality'. Cladistic methodology does not provide a clue for distinguishing whether a conflicting distribution of the potential synapomorphies is due to reticulation (e.g., symbiogenesis) or convergent evolution. Consequently, both Eubacteria and Eukarya either are or are not monophyletic taxa if they are or are not determined to be so during cladistic analysis.

Biological Evolution↗
PubMed1983

Nucleotide sequence of the Streptococcus faecalis plasmid gene encoding the 3'5"-aminoglycoside phosphotransferase type III.

We have cloned in Escherichia coli and sequenced a 1489-bp DNA fragment conferring resistance to kanamycin and originating from the streptococcal plasmid pJH1. The resistance gene was located by analysis of the initiation and termination codons in an open reading frame (ORF) of 792 bp. The deduced gene product, a 3'5''-aminoglycoside phosphotransferase of type III, has an Mr of 29,200. Comparison of its amino acid sequence with those of type I (Oka et al., 1981) and type II (Beck et al., 1982) 3' phosphotransferase, from transposable elements Tn903 and Tn5, respectively, indicated a statistically significant structural relationship between these enzymes from phylogenetically remote bacterial genera. The degree of homology observed indicate that phosphotransferase type III and type I genes have diverged from a common ancestor and that the phosphotransferase type II gene has emerged more recently from the type I evolutionary pathway.

Amino Acid Sequence↗
PubMed2004

The complete amino acid sequences of four globins from the land leech Haemadipsa zeylanica var. japonica.

The amino acid sequences of four globins from the land leech, Haemadipsa zeylanica var. japonica, were determined using nucleotide sequencing and protein sequencing. The mature globin-molecules were composed of 146 amino acid residues for M-1 globin, 156 for M-2 globin, 143 for D-1 globin, and 149 for D-2 globin. Alignment of the four kinds of globins by Clustal X revealed 22 invariant amino acids. The four globins were 26-33% identical. A striking feature of amino acid alteration was: the replacement of the E7 distal-His of D-1 globin by phenylalanine because histidine is conserved among the rest of the globins of H. zeylanica, those of other representative species (Lumbricus and Tylorrhynchus) of Annelida and most other hemoglobins. A phylogenetic tree constructed of 18 globin structures including two species of leeches, H. zeylanica (a land leech) and Macrobdella decora (a freshwater leech), T. heterochaetus (a representative species of polychaetes), L. terrestris (a representative species of oligochaetes), and human alpha and beta globins strongly indicated that the leech globins first separated from globin lineage of annelids.

Amino Acid Sequence↗
PubMed2006

Interval timing by an invertebrate, the bumble bee Bombus impatiens.

Sensitivity to temporal information and the ability to adjust behavior to the temporal structure of the environment should be phylogenetically widespread. Some timing abilities, such as sensitivity to circadian cycles, appear in a wide range of invertebrate and vertebrate taxa [1,2]. Interval timing--sensitivity to the duration of time intervals--has, however, only been shown to occur in vertebrates [3,4]. Insect pollinators make a variety of decisions that would appear to require the ability to estimate elapsed durations. We exposed bumble bees to conditions in which proboscis extension was reinforced after a fixed duration had elapsed or after either of two fixed durations had elapsed. Two groups of bees were trained with a short duration (either 6 s or 12 s) and a long duration (36 s) in separate experimental phases (independent timing groups), whereas two other groups were trained with a short duration (either 6 s or 12 s) and long duration (36 s) always intermixed unpredictably (multiple timing groups). On long intervals, independent timing groups waited longer than mixed timing groups to generate the first response and responded maximally near the end of the interval. Multiple timing groups waited the same amount of time on average before generating the first response on both long and short intervals. On individual trials, multiple timing groups appeared to time either the long duration only or both the short and long durations: most trials were characterized by a single burst of responding that began between the short and long duration values or by two bursts of responding with the first burst bracketing the short value and the second burst beginning in anticipation of the long value. These results show that bumble bees learn to time interval durations and can flexibly time multiple durations simultaneously. The results indicate no phylogenetic divide between vertebrates and invertebrates in interval timing ability.

Animals↗
PubMed2026

Bioprospecting microbial genomes to expand the biocatalytic toolbox of rubber oxygenases.

A set of rubber oxygenases was discovered through phylogenetic analysis and AI-based structural modeling of complexes of the putative enzymes with a substrate mimicking cis-1,4-polyisoprene. Sixteen candidate proteins were selected from thermophilic microorganisms, all sequence-related to the Latex clearing protein from Streptomyces sp. K30 (LcpK30). Sequence truncation and solubility tags were then evaluated to enhance protein expression, with the SUMO tag proving to be the most effective. Including LcpK30, nine heme-containing oxygenases were successfully expressed in E. coli NEB 10-beta cells, purified (35-157 mg L-1 yield) and characterized. Steady-state kinetics revealed significant rubber latex-degrading properties for six of them, with the truncated SUMO-fused LcpK30 (SUMO-LcpK30T) showing activity in agreement with literature. Notably, the catalytic efficiencies of all the expressed homologs lay within one order of magnitude and the oxygenase from Thermomonospora echinospora was found to be particularly promising in terms of activity, especially at high latex concentrations (more than 1% w/v). The analysis of reaction mixtures by both HPLC and HPLC-MS confirmed the oxidation of cis-1,4-polyisoprene to form the expected isoprenoid oligomers (n = 2-12), whose distribution was consistent with the usual endo-type cleavage pattern in all but one case. This bioprospecting effort afforded a platform of new rubber-degrading enzymes with diverse efficiencies and product profiles, capable of adapting to targeted applications.

Oxygenases↗
PubMed2005

Rapid expansion of killer cell immunoglobulin-like receptor genes in primates and their coevolution with MHC Class I genes.

The gene family of killer cell immunoglobulin-like receptors (KIRs) in primates provides the first line of defense against virus infection and tumor transformation. Interacting with MHC class I molecules, KIRs can regulate the cytotoxic activity of natural killer (NK) cells and distinguish the tumor and virus infected cells from normal body cells. Phylogenetic analysis and comparison of domain structures identified three major groups of KIR genes (group I, II, and III genes). These groups of KIR genes, generated by a series of gene duplications, have acquired different MHC-binding specificity. Inference of ancestral KIR sequences suggested that the functional divergence of group I genes from group II genes occurred by positive selection at the MHC-binding sites after duplication. Our evolutionary study has shown that group I genes diverged from group II genes about 17 million years ago (Mya) apparently after separation of hominoids from Old World (OW) monkeys. Around the same time, gene duplication generating the class I MHC-C locus appears to have occurred. These findings suggest that KIR and MHC class I genes have coevolved as an interacting system. The KIR gene family has experienced a rapid expansion in primate species. The rate of expansion of this gene family seems to be one of the highest among all hominoid gene families. The KIR gene family is also subject to birth-and-death evolution.

Amino Acid Sequence↗
PubMed2005

[To live or to die, an embryonic dilemma].

The development and formation of an organ needs both cell proliferation and cell death. It is commonly possible to decipher three types of basic cell death: 1) the so-called morphogenetic cell death (an example is the formation of the digits); 2) the histogenetic cell death like the apoptotic processes taking place in the spinal cord and allowing to regulate the number of motoneurons according to their targets; and 3) the phylogenetic cell death in which vestigial structures are selectively removed (e.g. destruction of the pronephros or removal of the tail in the anuran larva).

Animals↗
PubMed2005

An unexpected discovery of two interferon gamma-like genes along with interleukin (IL)-22 and -26 from teleost: IL-22 and -26 genes have been described for the first time outside mammals.

By comparative genomics based on chromosome synteny between human and fish, IL-22, IL-26 and two IFN-gamma-like genes have been isolated in fish. Interleukin-22 and -26 have been identified for the first time outside of mammals and their organization and synteny demonstrates that this cluster of cytokines is well conserved during evolution. The cloned zebrafish IL-22 and -26 homologs are 161 and 169-aa long, respectively. Both the genes harbor a well-conserved IL-10-family signature in their respective C-terminus. The coding regions of these genes are spread in five exons and at the same position as in human homologs. Furthermore, surprisingly two IFN-gamma-like genes are present in tandem, 7.0 kb apart from each other, along this locus. IFN-gamma1 and 2 genes are composed of 170- and 185-aa and share a low amino acid identity of 17.0%. The genomic structures of the isolated fish IFN-gamma genes were similar to its mammalian homologs, sharing a four exon and three phase 0 introns. The presence two IFN-gamma genes in both zebra and pufferfishes demonstrate that the duplication of IFN-gamma might have occurred prior to the teleostean split. The structural homology is further validated by phylogenetic analysis showing that the isolated cytokine genes are homologous to mammalian counterparts. Expression analysis of IL-22, IL-26 and two IFN-gamma genes suggests an active role of these genes in immune responses in fish.

Amino Acid Sequence↗
PubMed2026

Contrasting redox-related physiological responses associated with HaGATA23 and HaGATA36 during Orobanche cumana parasitism in sunflower (Helianthus annuus L.).

Helianthus annuus is an economically important Asteraceae species used for seed oil production and ornamental purposes, but its production is seriously affected by the root-parasitic plant Orobanche cumana. GATA transcription factors are zinc-finger DNA-binding regulators involved in plant development and stress adaptation. However, the molecular characteristics of GATA transcription factors in Helianthus annuus and their contribution to Helianthus annuus -Orobanche cumana interaction remain poorly understood. Here, 36 HaGATA members were retrieved from the Helianthus annuus genome and classified into four phylogenetic clades. Chromosomal placement, collinearity, gene structure, motif composition, and promoter elements varied among the 36 HaGATA members, indicating evolutionary conservation coupled with functional diversification. Expression analysis and RT-qPCR analyses revealed differential expression patterns among HaGATA genes under O. cumana stress, with HaGATA23 markedly downregulated and HaGATA36 strongly upregulated. Overexpression of HaGATA23 was associated with increased malondialdehyde (MDA) accumulation and unfavorable changes in antioxidant enzyme activities, whereas its silencing showed the opposite physiological tendency. In contrast, overexpression of HaGATA36 reduced malondialdehyde accumulation, increased peroxidase (POD), catalase (CAT), and superoxide dismutase (SOD) activities, while its silencing showed the reverse tendency. These results indicate that HaGATA23 and HaGATA36 are candidate genes associated with contrasting redox-related physiological responses during O. cumana stress. This work provides evidence that GATA transcription factors are associated with redox-related physiological responses in sunflower under O. cumana treatment and identifies HaGATA23 and HaGATA36 as functionally divergent candidate genes for further validation.

Helianthus↗
PubMed2026

Genome-wide identification of the carotenoid cleavage dioxygenase gene family in wheat and analysis of the TaDREB-7A-TaNCED9a regulatory module conferring drought tolerance.

Carotenoid cleavage dioxygenases (CCDs) play critical roles in plant growth, development, and abiotic stress responses, yet their genome-wide identification and drought response mechanisms remain unexplored in wheat. In this study, 34 TaCCD genes were identified in wheat, distributed across 15 chromosomes and phylogenetically classified into five subfamilies. Gene structure analysis indicated that members within each subfamily shared conserved motifs and similar intron-exon arrangements. Cis-regulatory element analysis suggested the potential roles of these genes in stress adaptation, developmental processes, and hormone signaling. Moreover, prediction of tertiary structures and protein-protein interactions revealed unique structural features and potential interacting partners of the TaCCD proteins. In addition, TaNCED9a, a member of the TaCCD family, showed the highest transcript level in wheat roots among all detected TaCCD genes and was significantly induced by drought stress. Subcellular localization assay indicated that TaNCED9a was located in chloroplasts. Downregulation of TaNCED9a expression led to reduced drought resistance in wheat, accompanied by an accumulation of reactive oxygen species and a decrease in endogenous abscisic acid levels. Using yeast one-hybrid, dual-luciferase, and tobacco transient co-expression assays, the upstream regulatory factor TaDREB-7A was identified, which can regulate the expression of TaNCED9a. Additionally, a KASP molecular marker was developed to identify the superior haplotype TaNCED9a-HapI, which exhibited a significantly higher germination rate compared to TaNCED9a-HapII under drought conditions, and was predominant in wheat. These results offer valuable insights into the TaCCD gene family's response mechanisms to drought stress in wheat, simultaneously identifying promising genetic resources for enhancing drought tolerance through molecular breeding.

CCD↗