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At least 397 records · Page 22Linked to original sources
PubMed2005

Identification and characterization of RHEBL1, a novel member of Ras family, which activates transcriptional activities of NF-kappa B.

The Ras family of small GTPases regulates a wide variety of cellular functions that include cell growth, differentiation, and transformation. In this study, we identified and characterized a novel member of Ras family named RHEBL1, belonging to the Rheb branch of small GTPase proteins. The cDNA sequence contains an open reading frame of 551 bp, encoding a putative protein of 183 amino acid residues. The expression pattern of RHEBL1 showed that it was ubiquitously expressed in 17 tissues. RHEBL1 gene encodes a 20.69 kDa protein, localized in cytoplasm when overexpressed in COS7 cells. Reporter gene assays showed that overexpression of RHEBL1 in HEK 293T cells strongly activated the transcriptional activities of NF-kappa B, while the mutant (D60K) only weakly activates NF-kappa B-mediated transcription. Our findings suggest that RHEBL1 is a positive regulator of NF-kappa B-mediated gene transcription.

Amino Acid Sequence↗
PubMed2005

Isolation and characterization of ubiquitin-activating enzyme E1-domain containing 1, UBE1DC1.

Ubiquitin and other ubiquitin-like proteins play important roles in post-translational modification. They are phylogenetically well-conserved in eukaryotes. Activated by other proteins, ubiquitin and ubiquitin-like proteins can covalently modify target proteins. The enzymes responsible for the activation of this modification have been known to include UBA1, SAE2, UBA3, SAE1 and ULA1. Here we report a new ubiquitin activating enzyme like cDNA, named ubiquitin activating enzyme E1-domain containing 1 (UBE1DC1), whose cDNA is 2654 base pairs in length and contains an open reading frame encoding 404 amino acids. The UBE1DC1 gene consists of 12 exons and is located at human chromosome 3q22. The result of RT-PCR showed that UBE1DC1 is expressed in most of human tissues.

Amino Acid Sequence↗
PubMed2005

Highly unsaturated fatty acid synthesis in vertebrates: new insights with the cloning and characterization of a delta6 desaturase of Atlantic salmon.

Fish are an important source of the n-3 highly unsaturated fatty acids (HUFA), eicosapentaenoic (EPA) and docosahexaenoic (DHA) acids that are crucial to the health of higher vertebrates. The synthesis of HUFA involves enzyme-mediated desaturation, and a delta5 fatty acyl desaturase cDNA has been cloned from Atlantic salmon (Salmo salar) and functionally characterized previously. Here we report cloning and functional characterization of a delta6 fatty acyl desaturase of Atlantic salmon and describe its genomic structure, tissue expression, and nutritional regulation. A salmon genomic library was screened with a salmon delta5 desaturase cDNA and positive recombinant phage isolated and subcloned. The full-length cDNA for the putative fatty acyl desaturase was shown to comprise 2106 bp containing an open reading frame of 1365 bp specifying a protein of 454 amino acids (GenBank accession no. AY458652). The protein sequence included three histidine boxes, two transmembrane regions, and an N-terminal cytochrome b5 domain containing the heme-binding motif HPGG, all of which are characteristic of microsomal fatty acid desaturases. Functional expression showed that this gene possessed predominantly delta6 desaturase activity. Screening and sequence analysis of the genomic DNA of a single fish revealed that the delta6 desaturase gene constituted 13 exons in 7965 bp of genomic DNA. Quantitative real-time PCR assay of gene expression in Atlantic salmon showed that both delta6 and delta5 fatty acyl desaturase genes, and a fatty acyl elongase gene, were highly expressed in intestine, liver, and brain, and less so in kidney, heart, gill, adipose tissue, muscle, and spleen. Furthermore, expression of both delta6 and delta5 fatty acyl desaturase genes in intestine, liver, red muscle, and adipose tissue was higher in salmon fed a diet containing vegetable oil than in fish fed a diet containing fish oil.

Animals↗
PubMed1989

Molecular analysis and rescue of a vitelline membrane mutant in Drosophila.

The eggshell in Drosophila is produced by ovarian follicle cells during the later stages of oogenesis. Eggshell formation involves the ordered synthesis and assembly of several protein components. Genes encoding the most abundant eggshell proteins have been identified by molecular cloning studies. Morphological examination of eggs produced by females carrying female sterile mutations on the X and third chromosomes have revealed additional loci involved in chorion formation. In this study we screened a collection of female sterile mutants carrying EMS-induced mutations on the second chromosome for eggshell mutants. A class of six mutants with potential vitelline membrane defects was identified on the basis of the response of mutant eggs to hypochlorite solutions. Biochemical analysis showed that one mutant, fs(2)QJ42, failed to produce a major vitelline membrane protein, sV23. The mutation was mapped cytogenetically to 26A, a region previously implicated in vitelline membrane formation by molecular cloning studies. Northern blot analysis using a cloned copy of the sV23 gene as probe showed a 10- to 15-fold reduction of sV23 RNA levels in the mutant. sV23 synthesis and fertility were restored when a normal copy of the sV23 gene was introduced into the mutant via germ line transformation. Transposons carrying the sV23 gene with as little as 147 bp of 5' flanking DNA were capable of restoring fertility and sV23 protein to wild type levels.

Animals↗
PubMed2004

Mass spectrometric analysis of expression of ATPase subunits encoded by duplicated genes in the 19S regulatory particle of rice 26S proteasome.

The 26S proteasome consisting of a 20S proteasome and a pair of 19S regulatory particles (RP) plays important roles in degradation of the ubiquitinated protein in eukaryotic cells. The RP consists of six different ATPase subunits and, at least, 11 non-ATPase subunits. In rice, we previously identified duplicated genes encoding four ATPase subunits, OsRpt1, OsRpt2, OsRpt4, and OsRpt5. In this study, the genomic sequences of all rice ATPase subunits were identified from the rice genome database and the genomic structure of ATPase subunit genes was determined. The rice RP was purified, and the ATPase subunit isoforms encoded by three pairs of duplicated genes, OsRpt2a/OsRpt2b, OsRpt4a/OsRpt4b, and OsRpt5a/OsRpt5b, were identified in RP by using electrospray ionization quadrupole time-of-flight mass spectrometry. The relative amounts and the expression patterns of these ATPase subunit isoforms in the bran were found to be different from those of the callus, suggesting the presence of multiform 19S regulatory particles engaged in the tissue-specific protein metabolism.

Adenosine Triphosphatases↗
PubMed2004

The rat enhancer of split- and hairy-related protein-2 gene: hepatic expression, genomic structure, and promoter analysis.

The rat enhancer of split- and hairy-related protein-2 (SHARP-2) is a basic helix-loop-helix transcription factor. The hepatic expression of SHARP-2 mRNA was investigated under various conditions. The level was decreased in the regenerating rat liver and malignant hepatoma cells. In contrast, the expression of SHARP-2 mRNA was induced in rat livers by feeding a high-carbohydrate diet. To analyze the molecular mechanism involved in the regulation of the rat SHARP-2 gene expression, the gene was cloned. It was approximately 6-kb in length and consists of five exons and four introns. To investigate the transcriptional regulatory region of this gene, SHARP-2/firefly luciferase reporter plasmids were transfected into hepatoma cells. A functional analysis of 5(')-deletion constructs revealed that two E box sequences between -160 and -144 are mainly responsible for promoter activity. Although upstream stimulatory factors (USFs) bound to the element in vitro, USF2 failed to stimulate promoter activity from the element using the co-transfection experiment. Therefore, other E box-binding transcription factors differing from USF proteins or USF-associated proteins are necessary for transcriptional stimulation of the rat SHARP-2 gene.

Animals↗
PubMed2004

Cloning and characterization of metallothionein gene in ayu Plecoglossus altivelis.

Metallothionein (MT) has been used widely as a potential molecular marker to detect the deleterious effects of heavy metals in aquatic ecosystem. Here we exposed ayu, Plecoglossus altivelis, to zinc (Zn) and tested the distribution as well as the induction of MT in various tissues such as liver, kidney, intestine and stomach. MT induction was significant in liver tissue, followed by kidney and intestine, whereas no induction was detected in stomach. The gene encoding ayu MT was successfully cloned and characterized. Complete nucleotide sequencing and analysis of the 4.5 kb DNA fragment containing the ayu MT gene revealed that the gene has three exons interrupted by two introns, a 5'-flanking region of about 2.5 kb and about 1.6 kb of 3'-flanking region. In grouper heart and kidney cells, the 2.5 kb promoter containing eight metal responsive elements (MREs), two hepatic nuclear factor 5 responsive elements (HNF5REs) and one cAMP responsive element (CRE) had the highest reporter activity.

Amino Acid Sequence↗
PubMed2004

Unprecedented genomic diversity of AhR1 and AhR2 genes in Atlantic salmon (Salmo salar L.).

Aryl hydrocarbon receptor (AhR) genes encode proteins involved in mediating the toxic responses induced by several environmental pollutants. Here, we describe the identification of the first two AhR1 (alpha and beta) genes and two additional AhR2 (alpha and beta) genes in the tetraploid species Atlantic salmon (Salmo salar L.) from a cosmid library screening. Cosmid clones containing genomic salmon AhR sequences were isolated using a cDNA clone containing the coding region of the Atlantic salmon AhR2gamma as a probe. Screening revealed 14 positive clones, from which four were chosen for further analyses. One of the cosmids contained genomic AhR sequences that were highly similar to the rainbow trout (Oncorhynchus mykiss) AhR2alpha and beta genes. SMART RACE amplified two complete, highly similar but not identical AhR type 2 sequences from salmon cDNA, which from phylogenetic analyses were determined as the rainbow trout AhR2alpha and beta orthologs. The salmon AhR2alpha and beta encode proteins of 1071 and 1058 residues, respectively, and encompass characteristic AhR sequence elements like a basic-helix-loop-helix (bHLH) and two PER-ARNT-SIM (PAS) domains. Both genes are transcribed in liver, spleen and muscle tissues of adult salmon. A second cosmid contained partial sequences, which were identical to the previously characterized AhR2gamma gene. The last two cosmids contained partial genomic AhR sequences, which were more similar to other AhR type 1 fish genes than the four characterized salmon AhR2 genes. However, attempts to amplify the corresponding complete cDNA sequences of the inserts proved very difficult, suggesting that these genes are non-functional or very weakly transcribed in the examined tissues. Phylogenetic analyses of the conserved regions did, however, clearly indicate that these two AhRs belong to the AhR type 1 clade and have been assigned as the Atlantic salmon AhR1alpha and AhR1beta genes. Taken together, these findings demonstrate that multiple AhR genes are present in Atlantic salmon genome, which likely is a consequence of previous genome duplications in the evolutionary past of salmonids. Plausible explanations for the high incidence of AhR genes in fish and more specifically in salmonids, like rapid divergences in specialized functions, are discussed.

Amino Acid Sequence↗
PubMed2004

Characterization of the zebrafish vascular endothelial growth factor A gene: comparison with vegf-A genes in mammals and Fugu.

Vascular endothelial growth factor (VEGF-A) is a key angiogenic growth factor which regulates vertebrate embryonic vascularization, adult physiology such as wound healing and reproduction as well as many human diseases. To understand the evolution and regulation of this gene in vertebrates, we have isolated and characterized the zebrafish vegf-A gene and compared it with VEGF-A genes of human, mouse as well as an in silico isolated VEGF-A homologue from pufferfish. Our results indicate that the zebrafish vegf-A gene is organized similarly to mammalian and Fugu VEGF-A genes, with eight exons interrupted by seven introns. However, zebrafish vegf-A introns are generally larger than mammalian introns while Fugu VEGF-A introns are much smaller. Furthermore, zebrafish exon 6 (z6) has a unique sequence while Fugu's exon 6 is highly homologous to the mammalian counterparts. Alternative splicing generates multiple vegf-A mRNA isoforms in zebrafish with Vegf(121) as the dominant isoform in adult and Vegf(165) as the dominant isoform in early embryos. The exon z6 containing isoform Vegf(12345z678) is only detected in heart, muscle, and early embryos while another isoform Vegf-A(1234577)(a)(8) is only detected in heart. Furthermore, no conserved 5' flanking sequences between zebrafish and Fugu were observed while numerous conserved regions exist between human and mouse in this area. These results suggest both conserved and diverged functions of VEGF-A from fish to mammals since the separation of these two groups from their common ancestor about 450 million years ago and a diverged regulation of this gene since the separation of zebrafish from Fugu. These data will be valuable for future studies of VEGF-A gene regulation and function in different vertebrates.

Amino Acid Sequence↗
PubMed2004

R-spondin, a novel gene with thrombospondin type 1 domain, was expressed in the dorsal neural tube and affected in Wnts mutants.

We identified a novel gene, which encodes a 265-amino-acid sequence with a thrombospondin (TSP) type 1 motif. Unlike the other secretory proteins of the TSP family, this gene encodes no apparent secretion cleavage site, but has a putative nuclear localization signal. Northern blot analysis showed transient expression in the central nervous system (CNS) during development. In situ hybridization showed its expression in the dorsal part of the neural tube on 10 and 12 dpc, especially in the boundary region between roof plate and neuroepithelium. This expression was enhanced in the rostral part. The signals were observed in other tissues such as truncal region neighboring forelimbs and mesenchymal tissues around the nasal cavity. We named this gene R-spondin (roof plate-specific spondin). Transfection of an epitope-tagged R-spondin into COS7 and 293 cells showed its localization in nuclei and medium, suggesting that R-spondin may become secretory or nuclear protein by some processing, while most of other proteins with TSP type 1 domain are secretory proteins. The expression of R-spondin was reduced in Wnt-1/3a double knockout mouse. R-spondin might be a novel marker of the boundary between the roof plate and neuroepithelium and may contribute to the development of dorsal neural tube under the regulation of Wnts.

Amino Acid Sequence↗
PubMed2005

Structural characterization and transcriptional regulation of the gene encoding diapause hormone and pheromone biosynthesis activating neuropeptide in the cotton bollworm, Helicoverpa armigera.

We have cloned the gene encoding the diapause hormone and the pheromone biosynthesis activating neuropeptide in Helicoverpa armigera (Har-DH-PBAN). The Har-DH-PBAN gene contains six exons and five introns that fall in the same positions as in the Bombyx mori DH-PBAN gene (Bom-DH-PBAN). The transcription initiation site lays 29 bp upstream of the translation initiation site. Southern blot analysis suggests that a single copy of this gene is present per haploid genome. A structural comparison of DH-PBAN promoters between H. armigera and B. mori show similarities in the TATA box and in a potential binding site for a POU family transcription factor, POU-M2. However, testing of these DNA regions for factor binding in vitro and transcription assays in cell culture highlight significant differences in their regulation particularly in reference to the POU-M2 sites. Our results uncover common and different regulatory mechanisms at work in the control of DH-PBAN gene expression in H. armigera and B. mori.

Amino Acid Sequence↗
PubMed2005

T-helper type 2 cell-specific expression of the ST2 gene is regulated by transcription factor GATA-3.

ST2 is a member of the interleukin-1 receptor family and is expressed in type-2 T helper (Th2) cells. Here, we have studied the molecular mechanism responsible for the transcriptional regulation of the ST2 gene in Th2 cells using a mouse thymoma cell line, EL-4. The ST2 gene has distal and proximal promoters. ST2 mRNA was produced from the distal promoter in EL-4 cells stimulated with both phorbol 12-myristate 13-acetate (PMA) and dibutyryl cAMP (Bt2cAMP). The region of approximately 100 bp upstream of transcription start site, containing two GATA consensus sites, was indispensable for the activation of the distal promoter in reporter gene analysis. An electrophoretic mobility shift assay showed that transcription factor GATA-3 bound one of the GATA consensus sites (from -84 to -79) with nuclear extracts from PMA plus Bt2cAMP-stimulated EL-4 cells. The overexpression of GATA-3 enhanced the activity of the distal promoter. On the other hand, mutations of the GATA consensus site canceled out the enhancement by GATA-3. These data suggest that GATA-3 is an important transcription factor for the expression of the ST2 gene in Th2 cells.

Animals↗
PubMed2005

Positive and negative regulatory elements in the late lactation protein-A gene promoter from the tammar wallaby (Macropus eugenii).

Little is known about the regulation of the marsupial-specific late lactation protein-A (LLP-A) gene, first expressed at mid-lactation in the mammary gland of the tammar wallaby. A genomic clone of LLP-A was sequenced and shown to include seven exons. The LLP-A promoter region of 1969 bp ligated to a secreted alkaline phosphatase (SEAP) gene reporter was co-transfected into CHO-K1 cells with prolactin (PRL) receptor cDNA. Transfected cells cultured with insulin, cortisol and PRL did not secrete SEAP into media. Similarly, this construct was not expressed in the mammary gland of eight lines of transgenic mice. In contrast, when the LLP-A promoter region was reduced to 850 bp, the expression of the SEAP reporter in CHO-K1 cells was constitutive and PRL-independent, despite the presence of two low affinity Stat5 binding sites. The 1969 bp promoter was analyzed using nine serial deletions ligated to the SEAP gene. The expression of these constructs was PRL-independent. Five putative inhibitory elements were identified between -1969 and -1796, -1404 and -1184, -1184 and -992, -992 and -757, and -591 and -425, and a putative enhancer or core transcription element between -425 and-239. These studies indicate that the complex temporal regulation of the LLP-A gene involves elements in its 5'-regulatory region.

5' Flanking Region↗
PubMed2005

A PPAR response element regulates transcription of the gene for human adipose differentiation-related protein.

Lipid droplets are cytoplasmic organelles which serve as storage sites for neutral lipids. Adipose differentiation-related protein (ADRP) is intrinsically associated with the surface of lipid droplets and is believed to play a major role in the maintenance of lipid stores in non-adipocytes. ADRP abundance is intimately linked to the amount of lipid found within cells and agents which increase the levels of intracellular lipid, such as certain agonists of the peroxisome proliferator-activated receptors (PPARs), also are capable of modulating ADRP gene transcription. However, little is known about the molecular mechanisms and promoter control elements, which regulate the transcription of the human gene. Using a reporter system to investigate ADRP transcription, we have identified a PPAR response element (PPRE) with the sequence 5'-AGGTGA A AGGGCG-3' within its promoter region. Mutational analysis revealed that the ADRP PPRE specifically mediated the upregulation of transcription in response to activation by agonists of PPAR subtypes alpha and delta in both rat and human hepatocyte-derived cell lines. These findings offer insight into the mechanisms which serve to regulate ADRP transcription and intracellular lipid storage.

Animals↗
PubMed2005

Translational effects of differential codon usage among intragenic domains of new genes in Drosophila.

Evolved codon usages often pose a technical challenge over the expressing of eukaryotic genes in microbial systems because of changed translational machinery. In the present study, we investigated the translational effects of intragenic differential codon usage on the expression of the new Drosophila gene, jingwei (jgw), a chimera derived from two unrelated parental genes: Ymp and Adh. We found that jgw possesses a strong intragenic differential usage of synonymous codons, i.e. the Adh-derived C-domain has a significantly higher codon bias than that of the Ymp-derived N-domain (P=0.0023 by t-test). Additional evolutionary analysis revealed the heterogeneous distribution of rare codons, implicating its role in gene regulation and protein translation. The in vitro expression of jgw further demonstrated that the heterogeneous distribution of rare codons has played a role in regulating gene expression, particularly, affecting the quality of protein translation.

Alcohol Dehydrogenase↗
PubMed2005

Isolation, sequencing, and functional analysis of the TATA-less human ATPase II promoter.

Multiple lines of evidence indicate that the P-type Mg(2+)-ATPase, termed ATPase II, could play an important role in apoptosis. With the long-term objective of studying the regulation of this protein during apoptosis, we delineated the exon-intron organization of the human ATPase II gene (within chromosome 4). Subsequently, we used RNA ligase-mediated rapid amplification of cDNA ends to identify a major transcription start site at position -143 with respect to the translation start site. Luciferase reporter analysis of a 1.2-kb 5'-flanking sequence (-1222 to +94 with respect to the transcription start site) revealed strong promoter activity in three human cell lines, human oligodendroglioma (HOG), SHSY5Y (hybrid neuroblastoma), and EA.hy926 (endothelial cell line). Serial deletions from the 5' end of this sequence up to nucleotide -291 yielded some decrease in activity only in the EA.hy926 cells. Further deletion to -217 caused a drastic decrease in activity in all three cell lines, but a -148 fragment showed preferential reduction in activity in the EA.hy926 cells. The promoter activity was nearly equal in two sequence variants of the promoter, one of which (designated as Variant 2) contained a 15-bp direct repeat within a GC-rich region. Additionally, there were several single base-pair changes from the sequence reported by the human genome project. Despite the presence of enhancer/repressor elements, such as Sp1 and NFkappaB, relatively small differences in promoter activity were observed in the three cell lines. However, it is likely that such sequence elements could cause major regulation of promoter activity in cells subjected to conditions that trigger apoptosis. The ATPase II promoter sequence will provide valuable clues to the regulation and role of the ATPase II protein.

Base Sequence↗
PubMed2005

Genomic organisation and tissue specific expression of ABLIM2 gene in human, mouse and rat.

The exon-intron structures of the human, rat and mouse ABLIM2 gene were determined in silico. The experimental verification resulted in the revealing of two mRNA isoforms of the ABLIM2 gene. The isoforms a and b contained 20 exons and 18 exons, respectively. The highest expression of both isoforms was observed in rat brain and eye and in mouse embryos. The 5'-UTR region of the ABLIM2 gene was 127 bp in rat and mouse, but in human, it was 65 bp. The site of polyadenylation was shown to be present at a distance of 682 bp from the stop-codon in human and rat and 684 bp in mouse. The in silico analysis of the gene 5'-region was performed. The high density of brain and CNS specific transcription factors' binding sites in the promoter region was shown for all three organisms. The comparison of the amino acid sequences of the human ABLIM2 and ABLIM1 proteins showed that the number and arrangement of domains (four LIM-domains in the N-end region and the C-end VHP-domain) were similar. The structure of the ABLIM2 proteins was similar in all three organisms. On the basis of our data, it was assumed that the ABLIM2 protein was necessary for the normal functioning of neurons.

Amino Acid Sequence↗
PubMed2005

A novel Rel protein and shortened isoform that differentially regulate antibacterial peptide genes in the silkworm Bombyx mori.

Two cDNAs encoding novel Rel proteins were cloned from the silkworm, Bombyx mori. These cDNA clones (BmRelA and BmRelB) showed identical nucleotide sequences except for the 5'-region. BmRelB cDNA derived probably from an alternatively spliced mRNA lacked 241 bp nucleotides at the 5'-region of the BmRelA cDNA, resulting in a loss of the first 52 amino acids. Expression of antibacterial peptide genes was strongly inhibited upon infection with Micrococcus luteus in transgenic silkworms in which BmRel gene expression was knocked down, suggesting that these two Rel proteins are involved in activation of antibacterial peptide genes. Co-transfection experiments indicated that BmRelB activated the Attacin gene strongly and other genes to a lesser extent, whereas BmRelA activated Lebocin 4 gene strongly and Attacin and Lebocin 3 genes very weakly. The Rel homology domain of BmRelA and BmRelB was shown to bind specifically to kappaB sites of antibacterial peptide genes. Proline-rich domains of the BmRels were necessary for activation of antibacterial peptide genes. These results illustrate that a minor structural change in Rel proteins can provoke a dramatic differential activation of antibacterial peptide genes, suggesting a novel regulatory mechanism for insect antibacterial peptide gene expression.

Amino Acid Sequence↗