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At least 289 records · Page 16Linked to original sources

PubMed2006

Evolution of thermoTRP ion channel homologs in vertebrates.

In mammalian thermosensation, nine temperature-sensitive ion channels that are activated by distinct temperature thresholds have been identified as thermosensors. These ion channels belong to the transient receptor potential (TRP) superfamily and are referred to as "thermoTRPs" (TRPV1, TRPV2, TRPV3, TRPV4, TRPM2, TRPM4, TRPM5, TRPM8, and TRPA1). To elucidate the evolutionary processes of thermoTRPs, we conducted comprehensive searches for mammalian thermoTRP gene homologs in the draft genome sequences of chicken (Gallus gallus), western clawed frog (Xenopus tropicalis), zebrafish (Danio rerio), and pufferfish (Fugu rubripes). Newly identified homologs were compared with known thermoTRPs, and phylogenetic analyses were conducted. Our comparative analyses revealed that most of the mammalian thermo-TRP members already existed in the common ancestor of fishes and tetrapods. Tetrapods shared almost the same repertoire, except that the western clawed frog expanded TRPV4s (six copies) and TRPM8s (two copies), which were diversified considerably. Comparisons of nonsynonymous and synonymous substitution rates among TRPV4s suggested that one copy of the TRPV4 channel in the western clawed frog retained its original function, while the other copies diversified and obtained slightly different properties. In fish lineages, several members of thermo-TRPs have duplicated in the whole genome duplication occurred in the ancestral ray-finned fish; however, some of the copies have subsequently been lost. Furthermore, fishes do not possess the three members of thermoTRPs existed in mammals, e.g., thermoTRPs activated by noxious heat, warm, and cool temperatures. Our results suggest that thermosensation mechanisms have changed through vertebrate evolution with respect to thermosensor repertoires.

Animals↗

PubMed2004

An esterase gene from Lactobacillus casei cotranscribed with genes encoding a phosphoenolpyruvate:sugar phosphotransferase system and regulated by a LevR-like activator and sigma54 factor.

A new esterase-encoding gene was found in the draft genome sequence of Lactobacillus casei BL23 (CECT5275). It is located in an operon together with genes encoding the EIIA, EIIB, EIIC, and EIID proteins of a mannose class phosphoenolpyruvate:sugar phosphotransferase system. After overproduction in Escherichia coli and purification, the esterase could hydrolyze acetyl sugars, hence the operon was named esu for esterase-sugar uptake genes. Upstream of the genes encoding the EII components (esuABCD) and the esterase (esuE), two genes transcribed in the opposite sense were found which encode a Bacillus subtilis LevR-like transcriptional activator (esuR) and a sigma54-like transcriptional factor (rpoN). As compared with the wild-type strain, elevated fructose phosphorylation was detected in L. casei mutants constitutively expressing the esu operon. However, none of the many sugars tested could induce the esu operon. The fact that EsuE exhibits esterase activity on acetyl sugars suggests that this operon could be involved in the uptake and metabolism of esterified sugars. Expression of the esu operon is similar to that of the B. subtilis lev operon: it contains a -12,-24 consensus promoter typical of sigma54-regulated genes, and EsuR and RpoN are essential for its transcription which is negatively regulated by EIIB(Esu). The esuABCDE transcription unit represents the first sigma54-regulated operon in lactobacilli. Furthermore, replacement of His852 in the phosphoenolpyruvate:sugar phosphotransferase system regulation domain II of EsuR with Ala indicated that the transcription activator function of EsuR is inhibited by EIIB(Esu)-mediated phosphorylation at His852.

DNA-Binding Proteins↗

PubMed2005

Human retroelements may introduce intragenic polyadenylation signals.

In the human genome, the insertion of LINE-1 and Alu elements can affect genes by sequence disruption, and by the introduction of elements that modulate the gene's expression. One of the modulating sequences retroelements may contribute is the canonical polyadenylation signal (pA), AATAAA. L1 elements include these within their own sequence and AATAAA sequences are commonly created in the A-rich tails of both SINEs and LINEs. Computational analysis of 34 genes randomly retrieved from the human genome draft sequence reveals an orientation bias, reflected as a lower number of L1s and Alus containing the pA in the same orientation as the gene. Experimental studies of Alu-based pA sequences when placed in pol II or pol III transcripts suggest that the signal is very weak, or often not used at all. Because the pA signal is highly affected by the surrounding sequence, it is likely that the Alu constructs evaluated did not provide the required recognition signals to the polyadenylation machinery. Although the effect of pA signals contributed by Alus is individually weak, the observed reduction of "sense" oriented pA-containing L1 and Alu elements within genes reflects that even a modest influence causes a change in evolutionary pressure, sufficient to create the biased distribution.

Base Sequence↗

PubMed2006

Evolution and origin of vomeronasal-type odorant receptor gene repertoire in fishes.

BACKGROUND: In teleost fishes that lack a vomeronasal organ, both main odorant receptors (ORs) and vomeronasal receptors family 2 (V2Rs) are expressed in the olfactory epithelium, and used for perception of water-soluble chemicals. In zebrafish, it is known that both ORs and V2Rs formed multigene families of about a hundred copies. Whereas the contribution of V2Rs in zebrafish to olfaction has been found to be substantially large, the composition and structure of the V2R gene family in other fishes are poorly known, compared with the OR gene family. RESULTS: To understand the evolutionary dynamics of V2R genes in fishes, V2R sequences in zebrafish, medaka, fugu, and spotted green pufferfish were identified from their draft genome sequences. There were remarkable differences in the number of intact V2R genes in different species. Most V2R genes in these fishes were tightly clustered in one or two specific chromosomal regions. Phylogenetic analysis revealed that the fish V2R family could be subdivided into 16 subfamilies that had diverged before the separation of the four fishes. Genes in two subfamilies in zebrafish and another subfamily in medaka increased in their number independently, suggesting species-specific evolution in olfaction. Interestingly, the arrangements of V2R genes in the gene clusters were highly conserved among species in the subfamily level. A genomic region of tetrapods corresponding to the region in fishes that contains the V2R cluster was found to have no V2R gene in any species. CONCLUSION: Our results have indicated that the evolutionary dynamics of fish V2Rs are characterized by rapid gene turnover and lineage-specific phylogenetic clustering. In addition, the present phylogenetic and comparative genome analyses have shown that the fish V2Rs have expanded after the divergence between teleost and tetrapod lineages. The present identification of the entire V2R repertoire in fishes would provide useful foundation to the future functional and evolutionary studies of fish V2R gene family.

Animals↗

PubMed2002

Molecular diversity of phospholipase D in angiosperms.

BACKGROUND: The phospholipase D (PLD) family has been identified in plants by recent molecular studies, fostered by the emerging importance of plant PLDs in stress physiology and signal transduction. However, the presence of multiple isoforms limits the power of conventional biochemical and pharmacological approaches, and calls for a wider application of genetic methodology. RESULTS: Taking advantage of sequence data available in public databases, we attempted to provide a prerequisite for such an approach. We made a complete inventory of the Arabidopsis thaliana PLD family, which was found to comprise 12 distinct genes. The current nomenclature of Arabidopsis PLDs was refined and expanded to include five newly described genes. To assess the degree of plant PLD diversity beyond Arabidopsis we explored data from rice (including the genome draft by Monsanto) as well as cDNA and EST sequences from several other plants. Our analysis revealed two major PLD subfamilies in plants. The first, designated C2-PLD, is characterised by presence of the C2 domain and comprises previously known plant PLDs as well as new isoforms with possibly unusual features catalytically inactive or independent on Ca2+. The second subfamily (denoted PXPH-PLD) is novel in plants but is related to animal and fungal enzymes possessing the PX and PH domains. CONCLUSIONS: The evolutionary dynamics, and inter-specific diversity, of plant PLDs inferred from our phylogenetic analysis, call for more plant species to be employed in PLD research. This will enable us to obtain generally valid conclusions.

Journal Article↗

PubMed2004

Identification and characterization of a novel nasopharyngeal carcinoma-associated peptide: NAP-1.

Nasopharyngeal carcinoma (NPC) is one of the most commons cancers in Southeast Asia and Southern China. Several NPC-associated genes have been so far described and here we describe the identification and the characterization of a novel nasopharyngeal carcinoma-associated peptide: NAP-1. NAP-1 was identified with the human genome draft searching method combined with nested PCR mapping of the chromosome 4q13 region. NAP-1 encodes an 85 amino acid alkaline peptide with a calculated isoelectric point of 9.3, three phosphorilation sites and a proline-rich region. Northern blot analysis revealed that NAP-1 is expressed as a 0.6 kb transcript in normal lymph nodes and trachea. In addition, reverse transcription (RT)-PCR showed that NAP-1 is expressed not only in NPC but in normal nasopharynx (NP) and various other tumors and tissues of the head and neck including: tonsils, lymph nodes, carcinoma of the tonsil, T cell lymphomas, squamous cell carcinoma of the hard palate, papilloma of the nasopharynx, nasopharyngitis, lymphoma of the tongue root and follicular dendritic cells (FDC). In addition, NAP-1 is not expressed in normal tissues or tumors from other anatomical regions and was not expressed by NPC cell lines. Surprisingly, differential RT-PCR demonstrated decreased expression of NAP-1 in NPC compared with paired NP biopsies in 42.5 % of cases (17 out of 40). In addition, in situ hybridization and immunohistochemistry demonstrated that NAP-1 is expressed by S100+ CD35+ FDCs of the germinal center and not in other normal immune cells infiltrating NP or NPC. Therefore, it is likely that NAP-1 is secreted by FDC in the NP and may play an immune modulatory role in NPC.

Journal Article↗

PubMed2002

On the importance of being finished.

The publication of an increasing number of draft genome sequences presents problems that will only be resolved by improved search tools and by complete finishing of the sequences - and their deposition in publicly accessible databases.

Computational Biology↗

PubMed2006

Circadian rhythms lit up in Chlamydomonas.

Recent work on the circadian clock of the unicellular green alga Chlamydomonas reinhardtii strengthens its standing as a convenient model system for circadian study. It was shown to be amenable to molecular engineering using a luciferase-based real-time reporter for circadian rhythms. Together with the completed draft genomic sequence, the new system opens the door for genome-scale forward and reverse genetic analysis.

Animals↗

PubMed2002

A second gene for peroxisomal HMG-CoA reductase? A genomic reassessment.

HMG-CoA reductase (HMGCR) catalyzes the conversion of HMG-CoA to mevalonate, the rate-limiting step of eukaryotic isoprenoid biosynthesis, and is the main target of cholesterol-lowering drugs. The classical form of the enzyme is a transmembrane-protein anchored to the endoplasmic reticulum. However, during the last years several lines of evidence pointed to the existence of a second isoform of HMGCR localized in peroxisomes, where mevalonate is converted further to farnesyl diphosphate. This finding is relevant for our understanding of the complex regulation and compartmentalization of the cholesterogenic pathway. Here we review experimental evidence suggesting that the peroxisomal activity might be due to a second HMGCR gene in mammals. We then present a comprehensive analysis of completely sequenced eukaryotic genomes, as well as the human and mouse genome drafts. Our results provide evidence for a large number of independent duplications of HMGCR in all eukaryotic kingdoms, but not for a second gene in mammals. We conclude that the peroxisomal HMGCR activity in mammals is due to alternative targeting of the ER enzyme to peroxisomes by an as yet uncharacterized mechanism.

Animals↗

PubMed2001

[Identification and characterization of histamine H4 receptor].

Recently, we and other groups have identified cDNA encoding the novel histamine H4 receptor. All of the groups have initially found a clue for the H4 receptor-nucleotides sequence in the human draft genomic DNA database. The primary structure of H4 receptor reveals the highest homology with H3 receptor among known G-protein coupled receptors (37.4%). H4 receptor binds to histamine with high affinity, which results in the down-regulation of intracellular cAMP level. H4 receptor is activated not only by histamine, but also R-(alpha)-methylhistamine (H3 receptor agonist), clobenpropit (H3 receptor antagonist), clozapine (neuroleptic) and other histaminergic compounds, while it is antagonized by thioperamide (H3 receptor antagonist). The H4 receptor is localized in the peripheral blood leukocytes, spleen, thymus, small intestine, colon, bone marrow and so on. The tissue distribution of the H4 receptor and known physiological function of histamine tempts us to speculate about its function as an immune modulator. Although there needs much additional work on characterization of the H4 receptor, the discovery of this receptor subtype will unveil a new phase for determining the physiological role of histamine.

Amino Acid Sequence↗

PubMed2004

Ureases of extreme halophiles of the genus Haloarcula with a unique structure of gene cluster.

We searched for urease activities in 71 strains of extreme halophiles by a urea-phenol red-agar plate method. Positive strains were further investigated by measuring the ammonia released from urea in cell-free extracts. Only 4 strains of the genus Haloarcula, Har. aidinensis, Har. hispanica, Har. japonica, and Har. marismortui were finally shown as the urease producers. A partially purified urease from Har. hispanica was a typical halophilic enzyme in that it showed maximum activity at 18-23% NaCl and lost the activity irreversibly in the absence of NaCl. Partial genes (1596 bp) of the urease encoding from upstream of the beta subunit down to the N-terminal 139 amino acids of the alpha subunit, were PCR amplified from the four strains, as well as from five urease-negative Haloarcula strains. Strains of other genera, which were urease-negative, did not yield PCR products. The deduced amino acid sequences of the beta subunit and partial alpha subunit were similar to each other (92-100% similarities) and to those from other organisms. Analysis of the draft genome sequence of Har. marismortui, however, suggested that the order of the genes encoding the three subunits (with the total number of amino acids of 834) and four accessory proteins was beta-alpha-gamma-UreG-UreD-UreE-UreF. This order is quite unique, since in other microorganisms the order is gamma-beta-alpha-UreE-UreF-UreG-UreD in most cases. No open reading frames were detected in the PCR-amplified upstream of the beta subunit, suggesting that all Haloarcula species have the same unique structure of the urease gene cluster.

Amino Acid Sequence↗

PubMed2002

Chromosome localization analysis of genes strongly expressed in human visceral adipose tissue.

To understand fully the physiologic functions of visceral adipose tissue and to provide a basis for the identification of novel genes related to obesity and insulin resistance, the gene expression profiling of human visceral adipose tissue was established by using cDNA array. The characterization and chromosome localization of 400 expressed sequence tags (ESTs) strongly expressed in visceral adipose tissue were analyzed by searching PubMed, UniGene, the Human Genome Draft Database, and Location Data Base. Two hundred eighty-nine clones were classified into known genes among the 400 ESTs strongly expressed in the tissue. Among them, <20% have been previously reported to be expressed in adipose tissue. The chromosome localization of 389 ESTs strongly expressed in visceral adipose tissue showed that their relative abundance was significantly increased on chromosomes 1, 16, 19, 20, and 22 compared with the expected distribution of the same number of random genes. The intrachromosome distribution of the genes strongly expressed in visceral adipose tissue was concentrated in certain regions, such as 1p36.2-1p36.3, 6p21.3-6p22.1, 19p13.3 and 19q13.1. Among them, the region of 1p36.2-1p36.3 appeared to be specific for visceral adipose tissue. Interestingly, some genes playing an important role in the pathogenesis of insulin signal transduction and adipocyte differentiation, such as tumor necrosis factor-alpha and its receptors; CCAAT/enhancer-binding proteina; and phosphoinositide-3-kinase, regulatory subunit, polypeptide 2 (p85beta), were also localized in the concentrated regions, which may provide clues to identifying novel genes closely related to adipocyte function with potential pathophysiologic implications.

Adipocytes↗

PubMed2003

Construction of a cDNA microarray derived from the ascidian Ciona intestinalis.

A cDNA microarray was constructed from a basal chordate, the ascidian Ciona intestinalis. The draft genome of Ciona has been read and inferred to contain approximately 16,000 protein-coding genes, and cDNAs for transcripts of 13,464 genes have been characterized and compiled as the "Ciona intestinalis Gene Collection Release I". In the present study, we constructed a cDNA microarray of these 13,464 Ciona genes. A preliminary experiment with Cy3- and Cy5-labeled probes showed extensive differential gene expression between fertilized eggs and larvae. In addition, there was a good correlation between results obtained by the present microarray analysis and those from previous EST analyses. This first microarray of a large collection of Ciona intestinalis cDNA clones should facilitate the analysis of global gene expression and gene networks during the embryogenesis of basal chordates.

Animals↗

PubMed2004

Fluorescent in situ hybridization to ascidian chromosomes.

The draft genome of the ascidian Ciona intestinalis has been sequenced. Mapping of the genome sequence to the Ciona 14 haploid chromosomes is essential for future studies of the genome-wide control of gene expression in this basal chordate. Here we describe an efficient protocol for fluorescent in situ hybridization for mapping genes to the Ciona chromosomes. We demonstrate how the locations of two BAC clones can be mapped relative to each other. We also show that this method is efficient for coupling two so-far independent scaffolds into one longer scaffold when two BAC clones represent sequences located at either end of the two scaffolds.

Animals↗

PubMed2004

Development of Ciona intestinalis juveniles (through 2nd ascidian stage).

Following the reading of its draft genome sequence and the collection of a large quantity of cDNA information, Ciona intestinalis is now becoming a model organism for whole-genome analyses of the expression and function of developmentally relevant genes. Although most studies have focused on larval structures, the development of the adult form is also very interesting in relation to tissues and organs of vertebrate body. Here we conducted detailed observations of the development of tissues and organs in Ciona intestinalis larva and juveniles until so-called the 2nd ascidian stage. These observations included examination of the oral siphon, tentacle, oral pigments and atrial pigments, atrial siphon, ganglion and neural gland, longitudinal muscle, stigmata, transverse bar and languet, longitudinal bar and papilla, heart, digestive organ, gonad, endostyle, and stalk and villi. The findings from these observations make a new staging system for juvenile development possible. Based on the development of the internal organs, we propose here nine stages (stage 0-stage 8) starting with swimming larvae and proceeding through juveniles until the 2nd ascidian stage. These descriptions and staging system provide a basis for studying cellular and molecular mechanisms underlying the development of adult organs and tissues of this basal chordate.

Animals↗

PubMed2001

Molecular cloning and characterization of LZIC, a novel gene encoding ICAT homologous protein with leucine zipper domain.

ICAT inhibits the interaction between beta-catenin and TCF transcription factors. As ICAT might be a tumor suppressor gene with the potential to negatively regulate the WNT - beta-catenin - TCF signaling pathway, ICAT related gene in the human genome draft sequence was searched for. Here, the LZIC gene, a novel gene encoding a 190-amino-acid polypeptide with leucine zipper domain and ICAT homologous domain, was cloned and characterized. Amino-acid identity between LZIC and ICAT in the ICAT homologous domain was 38%. The LZIC gene, consisting of at least 8 exons, was located in the human chromosome 1p36.32-pter region. The major 5.2-kb LZIC mRNA and minor 2.1-, 1.6-, and 1.0-kb LZIC mRNAs were expressed almost ubiquitously in normal human tissues. LZIC was expressed in all cancer cell lines examined in this study, and was significantly up-regulated in a gastric cancer cell line MKN74 and 5 cases of primary gastric cancer. As LZIC contains ICAT homologous domain, LZIC might inhibit the interaction between beta-catenin and TCF transcription factors, just like ICAT, and, up-regulation of LZIC in gastric cancer might be due to a negative feed-back mechanism to inhibit the WNT - beta-catenin - TCF signaling pathway.

Amino Acid Sequence↗

PubMed2001

Molecular cloning and characterization of human WNT11.

WNT signaling pathway is implicated in carcinogenesis. Here, we cloned and characterized human WNT11, which showed three amino-acid substitutions (Ala121Thr, Gly156Arg, and Ser271Trp) compared with human WNT11 cDNA previously isolated by another group. WNT11 encoded a 354 amino-acid polypeptide with five N-glycosylation sites. Gly156 of human WNT11 was conserved in other members of the human WNT family, such as WNT2B1, WNT2B2, WNT3, WNT3A, WNT5B, WNT6, WNT7B, WNT8A, WNT10A, and WNT14. The Ala121-Gly156-Ser271 WNT11 allele isolated in this study was also identified in human genome draft sequence AC069055. Expression profile of WNT11 was next investigated. The 4.3-kb WNT11 mRNA was expressed in fetal lung, kidney, adult heart, liver, skeletal muscle, and pancreas. WNT11 mRNA was significantly up-regulated in a gastric cancer cell line MKN45 and a cervical cancer cell line SKG-IIIa. Among various types of human primary tumors, WNT11 mRNA was up-regulated in four cases of colorectal adenocarcinoma, and a case of renal cell carcinoma. Up-regulation of WNT11 mRNA might play an important role in human carcinogenesis through activation of the WNT signaling pathway.

Amino Acid Sequence↗

PubMed2001

FRAT1 and FRAT2, clustered in human chromosome 10q24.1 region, are up-regulated in gastric cancer.

FRAT1 and FRAT2 are cancer-associated genes encoding GSK-3beta-binding proteins. Over-expression of FRAT1 or FRAT2 lead to carcinogenesis through activation of WNT--beta-catenin--TCF signaling pathway. We have previously cloned and characterized FRAT2. Here, we found that FRAT1 and FRAT2 genes were clustered in the human chromosome 10q24.1 region. Blast search revealed that FRAT1 and FRAT2 genes, consisting of a single exon, were located together on human genome draft sequences AC006098.1 and AL355490.7, corresponding to the human chromosome 10q24.1 region. FRAT1 and FRAT2 genes were clustered in a tail to tail manner with an interval of about 10.7 kb. The 2.7-kb FRAT1 mRNA was relatively highly expressed in fetal brain, adult spleen, pancreas, HeLa S3 (cervical cancer), and K-562 (chronic myelogenous leukemia). FRAT1 and FRAT2 were co-expressed in 7 gastric cancer cell lines and 10 cases of primary gastric cancer, and were up-regulated together in gastric cancer cell line TMK1 and 2 cases of primary gastric cancer. These results indicated that FRAT1 and FRAT2 genes were up-regulated together in several cases of human gastric cancer. Up-regulation of FRAT1 and FRAT2 in gastric cancer might lead to carcinogenesis through activation of WNT--beta-catenin--TCF signaling pathway.

Adaptor Proteins, Signal Transducing↗