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PubMed2007

An integrated approach for the comparative analysis of a multigene family: the nicotianamine synthase genes of barley.

Recent genomic projects reveal that about half of the gene repertoire in plant genomes is made up by multigene families. In this paper, a set of structural and phylogenetic analyses have been applied to compare the differently sized nicotianamine synthase (NAS) gene families in barley and rice. Nicotianamine acts as a chelator of iron and other heavy metals and plays a key role in uptake, phloem transport and cytoplasmic distribution of iron, challenging efforts for the breeding of iron-efficient crop plants. Nine barley NAS genes have been mapped, and co-linearity of flanking genes in barley and rice was determined. The combined analyses reveal that the NAS multigene family members in barley originated through at least one duplication event that occurred before the divergence of rice and barley. Additional duplications appear to have occurred within each of the species. Although we detected no evidence for positive selection of recently duplicated genes within species, codon-based tests revealed evidence for positive selection having contributed to the divergence of some amino acids. The integrated comparative and phylogenetic analysis improved our current view of NAS gene family evolution, might facilitate the functional characterization of individual members and is applicable to other multigene families.

Alkyl and Aryl Transferases↗
PubMed1988

Domain VI of Escherichia coli 23 S ribosomal RNA. Structure, assembly and function.

Domain VI at the 3' end of the 23 S ribosomal RNA from Escherichia coli was prepared using the in vitro T7 RNA polymerase system. Its structure was examined by probing with ribonucleases and chemical reagents, including a psoralen derivative, of various nucleotide specificities, using a reverse transcriptase procedure for analysis. The data provided support for the most recent secondary structure derived from phylogenetic sequence comparisons and for additional structuring that was inferred from earlier experimental data. Moreover, the structure was essentially the same in the free domain, in renatured 23 S RNA and in 50 S subunits. Protein L3 bound to the isolated domain and its binding site was located at a long-range double helix containing a large internal loop. This structure is unusual for a protein-RNA binding site and it may characterize a new (third) class of site. Protein L3 has been implicated, together with L24, in initiating assembly of the 50 S subunit and it shares the exceptional property with L24 that it binds adjacent to the junction of two RNA domains from where it can maximally influence RNA folding. Protein L6 also assembled to domain VI and, in a control experiment, protein L2 bound to isolated domain IV. Domain VI was largely inaccessible in the 50 S subunit and the few accessible RNA sites occurred mainly within conserved sequence regions that constitute potential functional sites. alpha-Sarcin inactivates ribosomes by cutting at one of these sites in 50 S subunits; it also recognized the same site in the free 23 S RNA and in the free domain. Both the EF-Tu ternary complex, and the EF-G ternary complex stabilized by fusidic acid or by a non-hydrolyzable GTP derivative, inhibited alpha-sarcin attack while non-enzymatically bound tRNA did not, thus providing evidence, more direct than before, for the involvement of the RNA region in a common elongation factor binding site.

Autoradiography↗
PubMed1989

Specific sequence deletions in two classes of murine leukemia virus-related proviruses in the mouse genome.

Characteristic long terminal repeats (LTR) of approximately 700 and 750 bp were found, respectively, in the two classes (polytropic and modified polytropic) of murine leukemia virus (MuLV)-related nonecotropic nonxenotropic proviral sequences in eight individual molecular clones of RFM/Un mouse chromosomal DNA fragments. Three proviral clones, two polytropic and one modified polytropic, contained sequence deletions in the viral structural genes. Nucleotide sequence analysis revealed that 7-bp direct repeats occur at both ends of deleted sequences in intact structures and one of the repeats remains in genomes with the deletion. Specifically, the deleted sequences were a 1487-bp gag-pol sequence with ACTGCCC repeat, a 113-bp mid-pol sequence with CAGGCAA repeat, and a 1811-bp env sequence with GGTCCAG repeat. The same specific sequence deletions were found in both classes of MuLV-related proviral structures. Examination of chromosomal DNA from eight inbred laboratory mouse strains and six wild mouse species showed that a minor population of proviruses with these specific deletions were present in Mus musculus and Mus spretus, all of which contain prominent 700-bp LTR polytropic proviral structures. The 750-bp LTR modified polytropic proviral structures were phylogenetically more restricted, being equally predominant in Mus musculus domesticus mice, but minor to undetectable in Mus spretus subspecies, and absent in other wild mouse populations.

Animals↗
PubMedDate not supplied

The functional and phylogenetic significance of dinoflagellate eyespots.

The eyespots or stigmas from five species of dinoflagellates fall into three distinct categories: independent eyespot which is not membrane bound; independent eyespot which is surrounded by three membranes; eyespot situated at the periphery of a chloroplast. In all cases the eyespot is situated behind the longitudinal groove or sulcus and there is a strand of microtubules between the eyespot and the cell covering or theca. In two cases the strand has been clearly shown to originate near the base of the longitudinal flagellum, which is the one passing over the eyespot and is also responsible for directional movement of the cell. The microtubular strand is presumed to play a part in the transmission of directional stimulation from eyespot to flagellum and a hypothesis is advanced to explain how this may be brought about. Phylogenetically, the structure of the various types of eyespots would link these dinoflagellates with euglenids and chrysophytes , and the diversity found in the dinoflagellates is probably a reflection of the diverse origin of chloroplasts in this group.

Animals↗
PubMed1992

Ontogeny and distribution of GABAA receptors in rat brainstem and rostral brain regions.

Previous studies from our laboratory and others have shown that there are major age-related differences in brainstem neuronal function. Since GABAA receptors are major targets for GABA-mediated inhibitory modulation and play a key role in regulating cardiorespiratory function, especially during O2 deprivation, we examined differences in GABAA receptor density and distribution during postnatal development. Using quantitative receptor autoradiography, the present study was performed to examine the postnatal expression of GABAA receptors in the rat brainstem and rostral brain areas at five ages, i.e. postnatal day 1 (P1), P5, P10, P21 and P120. Ten-micrometer brain sections at different brain levels were labelled with [3H]muscimol in Tris-citrate buffer. We found that (i) GABAA receptors appeared very early in almost all the brainstem as well as rostral areas; (ii) at P1, the brainstem had a higher GABAA receptor binding density than rostral areas and its density peaked at P5 or P10; and (iii) receptor densities of the cerebellum and rostral brain areas such as cortex, thalamus and dentate gyrus increased with age, especially between P10 and P21, but most other subcortical areas like caudate-putamen and hippocampal CA1 area did not increase remarkably after birth. We conclude that: (i) GABAA receptors exist in most brain areas at birth; (ii) there are several patterns of postnatal development of GABAA receptors in the CNS with dramatic differences between the brainstem and cortex; (iii) brainstem functions rely more on GABAA receptors in early postnatal life than at more mature stages. We speculate that GABAA receptors develop earlier in phylogenetically older structures (such as brainstem) than in newer brain regions (such as cortex).

Aging↗
PubMed2026

Evolutionary characterization and expression profiling of ACC and FASN genes in Chinese mitten crab Eriocheir sinensis.

Acetyl-CoA carboxylase (ACC) and fatty acid synthase (FASN) are rate-limiting enzymes in the fatty acid biosynthetic pathway, yet their evolutionary relationships, sequence features, and expression profiles remain poorly understood in crustaceans, particularly in the economically important Chinese mitten crab (Eriocheir sinensis). Here, we identified and systematically analyzed ACC and FASN genes in E. sinensis using comparative genomic analyses across 43 species. ACC was highly conserved as a single-copy gene in invertebrates, in contrast to the multiple paralogs observed in vertebrates. Similarly, FASN was generally maintained as a single-copy gene across most taxa but exhibited lineage-specific expansion in certain insect groups. Phylogenetic and structural analysis revealed strong conservation of both genes within crustaceans, supported by multiple conserved motifs and canonical functional domains. Expression profiling showed predominant expression in the hepatopancreas and midgut, suggesting their potential involvement in crustacean lipid metabolism. During the molting cycle, ACC and FASN exhibited higher expression levels during stages C and D, suggesting an increased capacity for fatty acid biosynthesis before molting. In addition, dietary lipid levels experiment revealed that ACC and FASN expression responded dynamically to dietary lipid availability, with increased expression at moderate lipid levels but reduced expression under excessive lipid supplementation, indicating a possible adaptive transcriptional response to lipid status. Collectively, this study provides insights into the evolutionary conservation and expression dynamics of ACC and FASN and improves our understanding of lipid metabolic adaptation in crustaceans.

Animals↗
PubMed2006

Molecular characterization and classification of a clip domain containing peptidase from the ectoparasite Lepeophtheirus salmonis (Copepoda, Crustacea).

Clip domain containing serine peptidases (CSPs) include one or more N-terminal clip domain(s) and a C-terminal serine peptidase domain that shares traits with both chymotrypsin and trypsin. CSPs are found in arthropods and are involved in embryonic patterning, immune responses and blood clotting. Among crustaceans only one CSP, which activates prophenoloxidase in crayfish, have previously been reported. We here present LsCSP1, the first CSP found in copepods. LsCSP1 is expressed in the subcuticular tissue and the transcription appears to be upregulated during development. In conjunction with previous studies of CSPs, this study suggests that LsCSP1 may play a role in the immune responses of L. salmonis. Phylogenetic and structural analyses indicate that the CSPs and catalytically inactive CSP homologs (CSPHs) constitute a monophyletic lineage.

Amino Acid Sequence↗
PubMed2026

Zhiling Jiangya decoction treats hypertension in rats: An integrative study of network pharmacology, immune infiltration, molecular simulation, and 16S rDNA sequencing.

OBJECTIVE: This study integrated network pharmacology, immune infiltration analysis, molecular docking, molecular dynamics simulation, ADMET prediction, 16S rDNA sequencing, and rat experiments to elucidate the potential mechanisms underlying the antihypertensive effects of Zhiling Jiangya Decoction (ZLJYD). METHODS: Active compounds and their potential targets were screened from the PubChem, TCMSP, NovoPro, and SwissTargetPrediction databases. Hypertension-related targets were retrieved from the OMIM and GeneCards databases, and overlapping targets were identified. The STRING database and Cytoscape 3.10.1 software were used to construct a protein-protein interaction network and a herb-component-target-disease network. Gene Ontology functional enrichment analysis and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis were performed to identify the key biological processes and signaling pathways involved. Using the CIBERSORT algorithm combined with correlation analysis, we investigated the association between key targets and immune cell infiltration. Molecular docking, molecular dynamics simulations, and ADMET predictions were performed to assess the binding stability and pharmacokinetic properties of the main compounds with their corresponding targets. Finally, the antihypertensive efficacy of ZLJYD was validated using a spontaneously hypertensive rat model, and alterations in gut microbiota were analyzed using 16S rDNA sequencing. RESULTS: A total of 123 active compounds and 267 hypertension-related targets of ZLJYD were identified. Enrichment analysis revealed that these targets were primarily associated with the PI3K-Akt signaling pathway and lipid and atherosclerosis pathways. Immune infiltration analysis suggested that the therapeutic effects of ZLJYD may involve the regulation of follicular helper T cells, naïve B cells, and naïve CD4⁺ T cells. Molecular docking and dynamics simulations supported the stable binding of key compounds to their target proteins, while ADMET predictions indicated favorable pharmacokinetic properties and safety profiles. Rat experiments demonstrated that ZLJYD significantly reduced blood pressure in spontaneously hypertensive rats, partially alleviated gut microbiota dysbiosis, and altered microbial community structure and phylogenetic diversity. CONCLUSION: This study systematically elucidates the potential mechanisms underlying the antihypertensive effects of ZLJYD through multiple components, targets, and pathways, particularly immune regulation and gut microbiota remodeling. These findings provide mechanistic insights into its potential therapeutic application.

16S rDNA sequencing↗
PubMed2005

Differential expression of three Paralichthys olivaceus Hsp40 genes in responses to virus infection and heat shock.

Heat shock proteins (Hsps) are a family of highly conserved cellular proteins present in all organisms, mediating a range of essential housekeeping and cytoprotective functions as well-known molecular chaperones and recently as regulators of the immune response. By subtractive suppression hybridization, three Hsp40 homologues have been identified in the flounder (Paralichthys olivaceus) embryonic cells (FEC) after treatment with UV-inactivated turbot (Scophthalmus maximus L.) rhabdovirus (SMRV), termed PoHsp40A4, PoHsp40B6 and PoHsp40B11, whose encoded proteins all possess the conserved DnaJ domain, a signature motif of the Hsp40 family. Based on different protein structure and phylogenetic analysis, they can be categorized into two subfamilies, PoHsp40A4 for Type I Hsp40, PoHsp40B6 and PoHsp40B11 for Type II Hsp40. Further expression analysis revealed two very different types of kinetics in response either to heat shock or to virus infection, with a marked induction for PoHsp40A4 and a weak one for both PoHsp40B6 and PoHsp40B11. A very distinct tissue distribution of mRNA was also revealed among the three genes, even between PoHsp40B6 and PoHsp40B11. This is the first report on the transcriptional induction of Hsp40 in virally stimulated fish cells, and the differential expressions might reflect their different roles in unstressed and stressed cells.

Amino Acid Sequence↗
PubMed2004

Genomic organization and developmental expression of globin genes in the teleost Oryzias latipes.

We isolated globin genes from a genomic DNA library of the drR strain of medaka Oryzias latipes, and walked on chromosome. The present study is the first demonstration of the full-length structure of globin gene locus in the teleosts. Two gene clusters were found. One cluster of 36 kbp consisted of nine globin genes and two pseudogenes. Based on structural and phylogenetic similarity of amino acid sequences, the cluster was named embryonic globin gene cluster (E1). The orientation of the genes was in (5')alpha0(3')-(3')beta1(5')-(5')alpha1(3')-(5')beta2(3')-(5')alpha2(3')-(3')alpha3(5')-(5')beta3(3')-(3')beta4(5')-(5')alpha4(3')-(3')psialpha(5')-(5')psibeta(3'). The other cluster of 20 kbp contained three globin genes ((3')ad.alpha1(5')-(5')ad.beta1(3')-(3')ad.alpha2(5')), and was named adult globin gene cluster (A1). Genetic linkage analysis clarified that E1 and A1 were mapped on linkage groups 8 and 19, respectively. The E1 cluster included other genes homologous to human EST clone KIAA0172, Sushi-1 retrotransposon, and protein 14 gene-like gene, while the A1 cluster linked to aquaporin-8 gene-like gene. The expression patterns of the genes were classified into four types: embryo-specific expression (alpha3, beta3, alpha4 and beta4), expression in embryo to young fish (alpha0, beta1, alpha1 and ad.alpha2), expression in young to adult fish (alpha2 and ad.alpha1) and successive expression in embryo to adult (ad.beta1).

5' Flanking Region↗
PubMed2004

Secreted subtilisin gene family in Trichophyton rubrum.

Secreted proteases constitute potential virulence factors of dermatophytes. A total of seven genes encoding putative serine proteases of the subtilisin family (SUB) were isolated in Trichophyton rubrum. Based on sequence data and intron-exon structure, a phylogenetic analysis of subtilisins from T. rubrum and other fungi revealed a presumed ancestral lineage comprising T. rubrum SUB2 and Aspergillus SUBs. All other SUBs (SUB1, SUB3-7) are dermatophyte-specific and have apparently emerged more recently, through successive gene duplication events. We showed that two subtilisins, Sub3 and Sub4, were detected in culture supernatants of T. rubrum grown in a medium containing soy protein as a sole nitrogen source. Both recombinant enzymes produced in Pichia pastoris are highly active on keratin azure suggesting that these proteases play an important role in invasion of keratinised tissues by the fungus. The set of deduced amino acid sequences of T. rubrum SUB ORFs allowed the identification of orthologous Subs secreted by other dermatophyte species using proteolysis and mass spectrometry.

Cloning, Molecular↗
PubMed2005

Catarrhine primate divergence dates estimated from complete mitochondrial genomes: concordance with fossil and nuclear DNA evidence.

Accurate divergence date estimates improve scenarios of primate evolutionary history and aid in interpretation of the natural history of disease-causing agents. While molecule-based estimates of divergence dates of taxa within the superfamily Hominoidea (apes and humans) are common in the literature, few such estimates are available for the Cercopithecoidea (Old World monkeys), the sister taxon of the hominoids in the primate infraorder Catarrhini. To help fill this gap, we have sequenced the entire mitochondrial DNA (mtDNA) genomes from a representative of three cercopithecoid tribes, Cercopithecini (Chlorocebus aethiops), Colobini (Colobus guereza), and Presbytini (Trachypithecus obscurus), and analyzed these new data together with other catarrhine mtDNA genomes available in public databases. Molecular divergence date estimates are dependent on calibration points gleaned from the paleontological record. We defined criteria for the selection of good calibration points and identified three points meeting these criteria: Homo-Pan, 6.0 Ma; Pongo-hominines, 14.0 Ma; hominoid/cercopithecoid, 23.0 Ma. Because a uniform molecular clock does not fit the catarrhine mtDNA data, we estimated divergence dates using a penalized likelihood and a Bayesian method, both of which take into account the effects of rate differences on lineages, phylogenetic tree structure, and multiple calibration points. The penalized likelihood method applied to the coding regions of the mtDNA genome yielded the following divergence date estimates, with approximate 95% confidence intervals: cercopithecine-colobine, 16.2 (14.4-17.9) Ma; colobin-presbytin, 10.9 (9.6-12.3) Ma; cercopithecin-papionin, 11.6 (10.3-12.9) Ma; and Macaca-Papio, 9.8 (8.6-10.9) Ma. Within the hominoids, the following dates were inferred: hylobatid-hominid, 16.8 (15.0-18.5) Ma; Gorilla-Homo+Pan, 8.1 (7.1-9.0) Ma; Pongo pygmaeus pygmaeus-P. p. abelii, 4.1 (3.5-4.7) Ma; and Pan troglodytes-P. paniscus, 2.4 (2.0-2.7) Ma. These dates were similar to those found using penalized likelihood on other subsets of the data, but slightly younger than several of the Bayesian estimates.

Africa↗
PubMed2005

Strong expression of NETRIN-G2 in the monkey claustrum.

The claustrum is a phylogenetically conserved structure, with extensive reciprocal connections with cortical regions, and has thus been considered important for sensory, motor, emotional, and mnemonic coordination or integration. Here, we show by in situ hybridization that the adult monkey claustrum is strongly positive for NETRIN-G2, a gene encoding a glycosyl phosphatidyl-inositol-linked membrane protein, which constitutes a subfamily with NETRIN-G1 within the netrin/UNC6 family. There is a conspicuous dorsal/ventral differentiation, where the label is stronger in the ventral claustrum. NETRIN-G2 positive neurons are not GABAergic, but rather correspond to claustrocortical projection neurons, as demonstrated by retrograde transport of Fast Blue from cortical injections and by double in situ hybridization for NETRIN-G2 and GAD67. Since NETRIN-G2 is known to be preferentially expressed in cortex, in contrast with the thalamically expressed NETRIN-G1, these results raise the possibility of some functional similarity in regulation of excitatory neural transmission in the claustrum and cortex.

Acetylcholinesterase↗
PubMed2004

Molecular cloning and sequence analysis of cDNAs encoding for Boophilus microplus, Haemaphysalis longicornis and Rhipicephalus appendiculatus actins.

The nucleotide and deduced amino acid sequences of the actins from ticks, Boophilus microplus, Haemaphysalis longicornis and Rhipicephalus appendiculatus, have been determined. Nucleotide sequence analysis showed open reading frames of 1128-nucleotide-long encoding proteins of 376 amino acids with a predicted molecular weight of 41.82 kDa each. Comparison between the nucleic acid and deduced amino acid sequences as well as structural and phylogenetic analyses of these genes confirmed the high similarity among actins from ticks in comparison to other species.

Actins↗
PubMed2004

Diversity of DNA 1: a satellite-like molecule associated with monopartite begomovirus-DNA beta complexes.

DNA 1 components are satellite-like, single-stranded DNA molecules associated with begomoviruses (family Geminiviridae) that require the satellite molecule DNA beta to induce authentic disease symptoms in some hosts. They have been shown to be present in the begomovirus-DNA beta complexes causing cotton leaf curl disease (CLCuD) and okra leaf curl disease (OLCD) in Pakistan as well as Ageratum yellow vein disease (AYVD) in Singapore. We have cloned and sequenced a further 17 DNA 1 molecules from a diverse range of plant species and geographical origins. The analysis shows that DNA 1 components are associated with the majority of begomovirus-DNA beta complexes, being absent from only two of the complexes examined, both of which have their origins in Far East Asia. The sequences showed a high level of conservation as well as a common organization consisting of a single open reading frame (ORF) in the virion sense, a region of sequence rich in adenine and a predicted hairpin structure. In phylogenetic analyses, there was some evidence of grouping of DNA 1 molecules according to geographic origin, but less evidence for grouping according to host plant origin. The possible origin and function of DNA 1 components are discussed in light of these findings.

Amino Acid Sequence↗
PubMed2003

Parasite manipulation of the proximate mechanisms that mediate social behavior in vertebrates.

Paul MacLean was instrumental in establishing the brain regions that mediate the expression of social behaviors in vertebrates. Pathogens can exploit these central mechanisms to alter host social behaviors, including aggressive, reproductive, and parental behaviors. Although some behavioral changes after infection are mediated by the host (e.g., sickness behaviors), other behavioral modifications are mediated by the pathogen to facilitate transmission. The goal of this review is to provide examples of parasite-mediated changes in social behavior and to illustrate that parasites affect host behavior by infecting neurons, causing central nervous system (CNS) inflammation, and altering neurotransmitter and hormonal communication. Secondarily, a comparative approach will be used to demonstrate that the effects of parasites on social behavior are retained across several classes of vertebrates possibly because parasites affect the phylogenetically primitive structures of the limbic system and related neurochemical systems.

Animals↗