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At least 1,441 records · Page 80Linked to original sources
PubMed1994

Rev-erb beta, a new member of the nuclear receptor superfamily, is expressed in the nervous system during chicken development.

We have identified and characterized a new orphan member of the nuclear hormone receptor superfamily in the chicken. This new gene, called Rev-erb beta, exhibits strong homologies with the Rev-erb alpha/ear-1 orphan receptor gene, which partially overlaps the thyroid hormone receptor alpha gene in opposite orientation. We demonstrate that both Rev-erb alpha and Rev-erb beta genes are conserved in their C and E domains. Rev-erb beta binds to DNA as a monomer and recognizes the same binding motif as the alpha gene product. The Rev-erb beta gene product does not interact with retinoid X receptors, as revealed by gel shift experiments. In situ hybridization experiments show that Rev-erb beta is expressed in the central and peripheric nervous system, spleen, and mandibular and maxillar processes, as well as in blood islands. During embryonic development, we noticed a striking specific distribution of Rev-erb beta transcripts in the notochord at 24 h and later on, in the floor plate of the neural tube. We propose that Rev-erb beta may play an important role in the complex network of inductive signals, which control neuron differentiation.

Amino Acid Sequence↗
PubMed1994

Molecular characterization of an NAD-specific glutamate dehydrogenase gene inducible by L-glutamine. Antisense gene pair arrangement with L-glutamine-inducible heat shock 70-like protein gene.

The gene for an NAD-specific glutamate dehydrogenase (NAD-GDH) that is allosterically activated by NADP+ (non-substrate) was cloned, and its physical structure and nucleotide sequence was determined. The gene consists of 9 introns and 10 exons; the 10th and largest exon, which is 1863 nucleotides long, is at the 3'-end of the gene. The shortest exon of 33 base pairs is the first and is located at the 5'-end of the gene. The large exon is in perfect register along the complementary strand with a heat shock 70 (HSP)-like protein gene. The NAD-GDH gene is inducible with L-glutamine, just as the HSP 70-like protein gene (LéJohn, H.B., Cameron, L.E., Yang, B., MacBeath, G., Barker, D.S., and Williams, S.A. (1994) J. Biol. Chem. 269, 4513-4522). The phenomenon of anti-parallel coupling of two genes is named antisense gene pair. By Northern and Western blotting techniques, we obtained indirect evidence that the gene is expressed in vivo. The gene encodes a protein of M(r) 118,740 which consists of 1063 amino acid residues. The 5' and 3' borders of the gene display typical but unproven promoter motifs of CCAAT, TATAAT, and AAATAAAA polyadenylation signal bounded by a pyrimidine-rich transcription termination-type format. Restriction endonuclease site mapping of all the genomic clones isolated that carry most or all of the gene, and of the genome itself, gave hybridization patterns that are consistent with the interpretation that the organism, Achlya klebsiana, has only one form of the gene. 3'-End-labeling of a 5.2-kb XbaI DNA fragment (carrying the antisense gene pair) that was then asymmetrically cleaved to produce two single 3'-end-labeled pieces that were used as probes on L-glutamine-induced cell poly(A)+ RNA, showed that the end-labeled DNA equivalent to the HSP 70-like protein mRNA hybridized to a 3.4-kb transcript and the end-labeled DNA equivalent to the NAD-GDH mRNA hybridized to a 2.4-kb transcript.

Amino Acid Sequence↗
PubMed1993

[New developments of molecular genetic analysis on human mitochondrial DNA].

The use of magnet beads for the capture and purification of PCR product allows simple preparation of immobilized single-stranded template. This template is ideal for use in DNA direct sequencing. The end labeling of PCR product with biotin is achieved simply by using a biotinylated primer. Capture and purification are then accomplished by incubation with Streptavidin attached magnet beads and magnet separation. Once immobilized, the DNA is converted to a single-stranded template by elution with alkali and another magnetic separation. Immobilized single-stranded template prepared in this manner are suitable for manual and automated solid-phase DNA sequencing by the dideoxynucleotide chain termination method. A 100% single-stranded template is produced, without interference from primers, free nucleotides or the complementary strand. The solid phase approach provides reproducible sequencing results with high yields. The eluted complementary strand can also be sequenced after neutralization.

Bacterial Proteins↗
PubMed1997

p53 represses Sp1 DNA binding and HIV-LTR directed transcription.

The HIV-LTR region contains binding sites for, and is regulated by, a number of transcription factors including Sp1 and NF-kB. The wild-type p53 tumor suppressor protein represses transcription from the HIV-LTR promoter while oncogenic mutant forms of p53 stimulate expression from the HIV-LTR. We have shown previously that wild-type p53 is a site specific DNA binding protein that binds to a region of the SV40 virus which contains GC-box DNA binding sites for the ubiquitously expressed transcription factor Sp1. In this study using DNase I footprinting, we have shown that purified p53 is able to protect the Sp1 binding sites and the adjacent NF-kB site of the HIV-LTR. Furthermore we have demonstrated that when p53 and Sp1 are mixed together both proteins change each other's interaction with DNA. Interestingly, we noted that oncogenic mutant p53 is also able to change the interaction of Sp1 with DNA. We confirmed p53 dependent repression of HIV-LTR driven transcription by comparing the expression from an HIV-LTR reporter construct in the presence and absence of p53. EMSA of an oligonucleotide sequence derived from the HIV-LTR sequence demonstrated a slight decrease in Sp1 DNA binding activity with nuclear extract derived from the cell line expressing a high level of wild-type p53. These data suggest that the influence of p53 on the transcription of promoters with Sp1 binding sites may be partially due to a change in the DNA binding ability of Sp1.

Animals↗
PubMed1995

Calcitonin, calcitonin gene-related peptide, adrenomedullin and amylin: homologous peptides, separate receptors and overlapping biological actions.

Calcitonin, calcitonin gene-related peptide, adrenomedullin and amylin are structurally related peptides with N-terminal 6-7 amino acid ring structures linked by a disulfide bridge and with amidated C-termini. Among the related bioactive peptides, the structures of the calcitonin receptor and subtypes thereof have been identified so far through molecular cloning. Cross-reaction between receptors of calcitonin, calcitonin gene-related peptide, adrenomedullin and amylin, as well as overlapping biological actions, anticipate that the respective receptors belong to a family of G-protein-coupled receptors that include those of parathyroid hormone, secretin and vasointestinal peptide.

Adrenomedullin↗
PubMed1999

A novel imprinted gene, encoding a RING zinc-finger protein, and overlapping antisense transcript in the Prader-Willi syndrome critical region.

We describe a complex imprinted locus in chromosome 15q11-q13 that encodes two genes, ZNF127 and ZNF127AS. The ZNF127 gene encodes a protein with a RING (C3HC4) zinc-finger and multiple C3H zinc-finger motifs, the former being closely related to a protein from variola major virus, the smallpox etiological agent. These motifs allow prediction of ZNF127 function as a ribonucleoprotein. The intronless ZNF127 gene is expressed ubiquitously, but the entire coding sequence and 5' CpG island overlaps a second gene, ZNF127AS, that is transcribed from the antisense strand with a different transcript size and pattern of expression. Allele-specific analysis shows that ZNF127 is expressed only from the paternal allele. Consistent with this expression pattern, in the brain the ZNF127 5' CpG island is completely unmethylated on the paternal allele but methylated on the maternal allele. Analyses of adult testis, sperm and fetal oocytes demonstrates a gametic methylation imprint with unmethylated paternal germ cells. Recent findings indicate that ZNF127 is part of the coordinately regulated imprinted domain affected in Prader-Willi syndrome patients with imprinting mutations. Therefore, ZNF127 and ZNF127AS are novel imprinted genes that may be associated with some of the clinical features of the polygenic Prader-Willi syndrome.

Adolescent↗
PubMed1985

Promoter selectivity of E. coli RNA polymerase: analysis of the promoter system of convergently-transcribed dnaQ-rnh genes.

Promoter properties were analyzed for the convergently-overlapped E. coli genes coding for the DNA polymerase III epsilon subunit (dnaQ) and the ribonuclease H (rnh). The rates of open complex formation for a single promoter of the rnh gene and two tandem promoters of the dnaQ gene were constant whether they are located on a single DNA fragment or separated into individual fragments. The relative expression levels of these three promoters, as measured using an in vitro mixed transcription system, varied differentially depending on the concentration of RNA polymerase. At low enzyme concentrations, the downstream promoter (P2) of the dnaQ gene was utilized preferentially, but the upstream promoter (P1) was utilized as well when the enzyme concentration was increased. This indicates different physiological roles between the two dnaQ promoters. The level of rnh transcription was as low as that of dnaQ-1 RNA synthesis but the rnh promoter was utilized as well as the dnaQ P2 promoter when it was separated from the dnaQ promoters. This implies a promoter interference between the convergently transcribed genes.

Base Sequence↗
PubMed1983

Two RNA polymerase sigma factors from Bacillus subtilis discriminate between overlapping promoters for a developmentally regulated gene.

A developmentally regulated gene (spoVG) from the spore-forming bacterium Bacillus subtilis is expressed from two overlapping promoters, which direct transcription initiating from sites separated by 10 base pairs. Utilization of the upstream promoter is determined by an RNA polymerase sigma factor of molecular weight 37,000 (sigma 37). We report the isolation of a 32,000-molecular weight species of sigma factor (sigma 32), which exclusively dictates transcription initiation from the downstream promoter, and suggest a model for the way in which sigma-specific recognition sequences are intermeshed within the spoVG transcription initiation region.

Bacillus subtilis↗
PubMed1999

Human molybdopterin synthase gene: identification of a bicistronic transcript with overlapping reading frames.

A universal molybdenum-containing cofactor (MoCo) is essential for the activity of all human molybdoenzymes, including sulphite oxidase. The free cofactor is highly unstable, and all organisms share a similar biosynthetic pathway. The involved enzymes exhibit homologies, even between bacteria and humans. We have exploited these homologies to isolate a cDNA for the heterodimeric molybdopterin (MPT)-synthase. This enzyme is necessary for the conversion of an unstable precursor into molybdopterin, the organic moiety of MoCo. The corresponding transcript shows a bicistronic structure, encoding the small and large subunits of the MPT-synthase in two different open reading frames (ORFs) that overlap by 77 nucleotides. In various human tissues, only one size of mRNA coinciding with the bicistronic transcript was detected. In vitro translation and mutagenesis experiments demonstrated that each ORF is translated independently, leading to the synthesis of a 10-kDa protein and a 21-kDa protein for the small and large subunits, respectively, and indicated that the 3'-proximal ORF of the bicistronic transcript is translated by leaky scanning.

Amino Acid Sequence↗
PubMed1987

Structure and sequence of the Drosophila melanogaster calmodulin gene.

A series of phage clones overlapping the single calmodulin gene locus of Drosophila melanogaster has been isolated and the exons of the gene positioned and sequenced within these clones. A calmodulin cDNA clone of the electric eel was used to identify these clones and to position the two major protein-coding exons of the gene. cDNA clones for D. melanogaster calmodulin were then isolated, characterized and used to identify the remaining exons. The gene consists of four exons separated by three introns of 3400 to 4300 bases in length. Exon 1 consists of the 5' untranslated region and the initiator ATG; exon 2 encodes amino acid residues 1 to 58.3; exon 3 encodes residues 58.3 to 139.3; and exon 4 encodes residues 139.3 to 148 and the 3' untranslated region. From the sequence of the 3' untranslated region and the lengths of the cDNA clones, two or three polyadenylation sites are indicated. Sequences potentially involved in the control of transcription of the gene and splicing of the mRNA product have been identified. Comparison of the intron-exon structures of the D. melanogaster calmodulin gene, the chick calmodulin gene, and other genes of the troponin C superfamily reinforces previous hypotheses that these genes arose from a common progenitor and permits identification of four introns that were probably present in the progenitor gene structure. The D. melanogaster calmodulin gene contains three of these introns, and the chick gene contains all four. These gene comparisons also indicate that the region of these genes encoding Ca2+-binding loop 3 is highly variable in structure. The chick and D. melanogaster calmodulin genes differ in this region, the chick gene containing a fifth intron here that is absent from the D. melanogaster gene.

Animals↗
PubMed2004

The bacterial signal molecule, ppGpp, regulates Salmonella virulence gene expression.

Numerous, overlapping global regulatory systems mediate the environmental signalling controlling the virulence of Salmonella typhimurium. With both extra- and intracellular lifestyles, unravelling the mechanisms involved in regulating Salmonella pathogenesis has been complex. Here, we report a factor co-ordinating environmental signals with global regulators involved in pathogenesis. An S. typhimuriumDeltarelADeltaspoT strain deficient in guanosine tetraphosphate (ppGpp) synthesis was found to be highly attenuated in vivo and non-invasive in vitro. The DeltarelADeltaspoT strain exhibited severely reduced expression of hilA and invF, encoding major transcriptional activators required for Salmonella pathogenicity island 1 (SPI-1) gene expression and at least two other pathogenicity islands. None of the growth conditions intended to mimic the intestinal milieu was capable of inducing hilA expression in the absence of ppGpp. However, the expression of global regulators of Salmonella virulence, RpoS and PhoP/Q, and RpoS- and PhoP/Q-dependent, non-virulence-related genes was not significantly different from the wild-type strain. The results indicate that ppGpp plays a central role as a regulator of virulence gene expression in S. typhimurium and implicates ppGpp as a major factor in the environmental and host-dependent regulation of Salmonella pathogenesis.

Animals↗
PubMed1989

Nucleotide sequence of the plasminogen activator gene of Yersinia pestis: relationship to ompT of Escherichia coli and gene E of Salmonella typhimurium.

We have determined the nucleotide sequence of the 1.4-kilobase DNA fragment containing the plasminogen activator gene (pla) of Yersinia pestis, which determines both plasminogen activator and coagulase activities of the species. The sequence revealed the presence of a 936-base-pair open reading frame that constitutes the pla gene. This reading frame encodes a 312-amino-acid protein of 34.6 kilodaltons and containing a putative 20-amino-acid signal sequence. The presence of a single large open reading frame is consistent with our previous conclusion that the two Pla proteins which appear in the outer membrane of pla+ Y. pestis are derived from a common precursor. The deduced amino acid sequence of Pla revealed that it possesses a high degree of homology to the products of gene E of Salmonella typhimurium and ompT of Escherichia coli but does not possess significant homology to other plasminogen activators of known sequence. We also identified a transcription unit that resides on the complimentary strand and overlaps the pla gene.

Amino Acid Sequence↗