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PubMed2005

Expanded electrochemical capabilities of the electrospray ion source using porous flow-through electrodes as the upstream ground and emitter high-voltage contact.

Use of a porous flow-through electrode at the upstream ground contact or at both the upstream ground contact and the high-voltage emitter contact in an electrospray ion source was shown to provide for new types of electrochemical experiments utilizing only the electrochemistry inherent to electrospray. The normal stainless steel bore-through union serving as the upstream grounding point in a floated electrospray emitter system was replaced with a high surface area porous flow-through electrode assembly to achieve effective electrochemical reduction of analytes at this point in positive ion mode, and effective electrochemical oxidation of analytes in negative ion mode. This was demonstrated by the oxidation of 3,4-dihydroxybenzoic acid and reserpine in negative ion mode and by the reduction of thionine in positive ion mode. In the case of reversible oxidation (3,4-dihydroxybenzoic acid) and reduction (thionine) processes, partial rereduction and reoxidation of the products due to reaction with products generated by cathodic and anodic processes at the emitter were observed, respectively. By implementing two high surface area porous flow-through electrodes in the system, one as the upstream grounding point and the other as the emitter electrode, a multiple-step reaction scheme was achieved that included consecutive electrochemical reduction and oxidation reactions and a following chemical reaction as demonstrated by the hydroquinone tagging of an initially disulfide-linked peptide.

Electrochemistry↗
PubMed2005

Upstream polybasic region in peptides enhances dual specificity for prenylation by both farnesyltransferase and geranylgeranyltransferase type I.

Protein farnesyltransferase (FTase) and protein geranylgeranyltransferase type I (GGTase I) catalyze the attachment of a farnesyl or geranylgeranyl lipid, respectively, near the C-terminus of their protein substrates. FTase and GGTase I differ in both their substrate specificity and magnesium dependence, where the activity of FTase, but not GGTase I, is activated by magnesium. Many protein substrates of these enzymes contain an upstream polybasic region that is proposed to increase the affinity of the substrate and aid in plasma membrane association. Here, we demonstrate that the addition of an upstream polybasic region to a peptide substrate enhances the binding affinity of FTase approximately 4-fold for the peptide but diminishes the catalytic efficiency of the reaction, reflected by decreases in both the prenylation rate constant and kcat/KM. Specifically, the prenylation rate constant decreases 7-fold at 5 mM MgCl2 for the peptide KKKSKTKCVIM (C-terminal sequence of K-Ras4B) in comparison to TKCVIM. This decrease is accompanied by an alteration in the dependence on magnesium, as the K(Mg) increases from 2.2 +/- 0.1 mM for TKCVIM to 11.5 +/- 0.1 mM for KKKSKTKCVIM. The presence of an upstream polybasic region does not significantly affect GGTase I-catalyzed reactions, as only minimal changes are seen in Kd, kcat/KM, and k(chem) values. Thus, the presence of an upstream polybasic region enhances the dual prenylation of these substrates, by decreasing the catalytic efficiency of farnesylation catalyzed by FTase to a level comparable to that of geranylgeranylation catalyzed by GGTase I.

Alkyl and Aryl Transferases↗
PubMed2000

SBP, SECIS binding protein, binds to the RNA fragment upstream of the Sec UGA codon in glutathione peroxidase mRNA.

In mammals, most of the selenium contained in the body is present as an unusual amino acid, selenocysteine (Sec), whose codon is UGA. Because the UGA codon is typically recognized as a translation stop signal, it is intriguing how a cell recognizes and distinguishes a UGA Sec codon from a UGA stop codon. For eukaryotic selenoprotein mRNAs, it has been proposed that a conserved stem-loop structure designated the Sec insertion sequence (SECIS) in the 3'-untranslated (3'-UTR) region is required for recognition of UGA as a Sec codon. Some proteins which bind to SECIS (SBP) have been reported. However, it is not clear how the SECIS element in the 3'-UTR can mediate Sec insertion far at the in-frame UGA Sec codons. The idea that there must be a signal near the UGA Sec codon is still considered. Therefore, we searched for a protein which binds to an RNA sequence surrounding the UGA Sec codon on human glutathione peroxidase (GPx) mRNA. We found a protein which strongly bound to the RNA fragment upstream of the UGA Sec codon. However, this protein did not bind to the RNA sequence downstream of the UGA codon. This protein also bound to the SECIS sequence in the 3'-UTR of human GPx, and this binding to SECIS was competed with the RNA fragment upstream of the UGA Sec codon. Comparison of the RNA fragment with the SECIS fragment identified the conserved regions, which appeared in the region upstream of the in-frame UGA Sec codon of Se-protein mRNAs. Thus, this study proposes a novel model to understand the mechanisms of Sec incorporation at the UGA Sec codon, especially the regions upstream of the UGA codon of mRNAs of mammalian selenoproteins. This model explains that the stem-loop structure covering the UGA codon is recognized by SBP and how the UGA Sec codon escapes from attack by eRF of the peptide releasing factor.

3' Untranslated Regions↗
PubMed1985

Upstream activation of ribosomal RNA biosynthesis in Saccharomyces cerevisiae.

Yeast was transformed with eight recombinants that contained an rRNA minigene and upstream elements of rDNA in different orientations in the multi-copy yeast-Escherichia coli shuttle vector, pJDB207. The effect of these elements of upstream rDNA on the initiation of transcription of the minigene at the site for rRNA biosynthesis was determined by using an S1 nuclease mapping procedure to measure the abundance of the minigene transcript in RNA from the yeast transformants. Transcription of the minigene was enhanced 3-fold by DNA within a 2.2 kb element more than 1.5 kb upstream from the initiation site. Inversion of the 2.2 kb element decreased expression of the minigene by 40%. This 2.2 kb element contained approx. 500 bp from the 25S rRNA coding region at the 3' end of the preceding rRNA gene and 1 kb of adjacent nontranscribed spacer rDNA. The enhancing activity was independent of interference from readthrough that might have contributed to the 7-fold decrease in minigene expression caused by removing all rDNA upstream from -209 bp.

DNA, Ribosomal↗
PubMed1998

Functional characterization of transcriptional regulatory elements in the upstream region and intron 1 of the human S6 ribosomal protein gene.

Expression of housekeeping genes involves regulation at comparable levels in a wide spectrum of cells. To define the cis-regulatory elements in the human S6 ribosomal protein (rpS6) gene, we made a series of deletions of the upstream non-transcribed region, including or excluding exon 1 or intron 1 sequences. The mutated rpS6 gene regulatory regions were fused to the chloramphenicol acetyltransferase reporter gene and transfected into HeLa and COS-1 cells. The results have identified three parts of the rpS6 gene that are required for efficient and specific transcription. The core promoter includes only a 40 bp region upstream of the transcription start site and initiation region. Both upstream and intronic elements enhance transcription from the core promoter. Furthermore, mutation of the splice donor site of intron 1 almost completely abolished the enhancing activity of the intronic transcriptional modulator. We used gel retardation assays to identify sequence-specific binding sites in the upstream region and in the proximal half of intron 1. Both common and different nuclear factors that bind the rpS6 gene promoter were identified in extracts from HeLa and COS-1 cells, suggesting that different transcription factors may bind specifically to the same binding region and might be interchangeable in their function to ensure high-level expression of housekeeping genes independently of the cell type.

Animals↗
PubMed1998

Regulation of human erythropoietin gene induction by upstream flanking sequences in transgenic mice.

Human erythropoietin (Epo) gene expression is inducible by hypoxia or anaemia in the kidney and liver. Previous transgenic mouse experiments have demonstrated that sequences required for Epo gene induction in the kidney reside in a 7 8 kb Barn HI fragment located 6 kb upstream of the gene. To sublocalize these sequences, we performed Desoxyribonuclease I (DNAse I) mapping studies using transgenic mice which carried this DNA fragment. These studies revealed a DNAse I hypersensitive site (DNAse I HS) located 4 6 kb from the upstream end of the 7.8 kb fragment in anaemic kidney and liver samples. Sequence analysis of the region encompassing the DNAse I HS revealed an element with remarkable homology to the 3' Epo gene hypoxia-inducible enhancer. This suggested the presence of an additional regulatory element that contributes to the control of hypoxia-inducible Epo gene expression in kidney and liver. We constructed transgenic mice containing the human Epo gene linked to either the 5 kb upstream or 2.5 kb downstream portion of the 7.8kb fragment. Inducible expression was limited to the liver. Thus, neither fragment was alone sufficient to confer kidney inducible expression. These findings indicate that sequences more than 8.5 kb upstream of the Epo gene are required for kidney-specific induction. They suggest that either those sequences reside in an 0.3 kb Hind III fragment located between the 5 kb and the 2.5 kb fragments or that sequences in the 5 kb or 0.3 kb fragments must interact with sequences in the 2.5 kb fragment to allow Epo gene induction in the kidney.

Anemia↗
PubMed1998

Hierarchical and co-operative binding of OmpR to a fusion construct containing the ompC and ompF upstream regulatory sequences of Escherichia coli.

BACKGROUND: OmpR is a transcription factor that regulates the expression of the porin genes ompF and ompC in Escherichia coli. The phosphorylation state of OmpR, directed by the osmosensor EnvZ, determines its ability to bind to the upstream regulatory regions of these genes, a total of 14 phospho-OmpR binding sites. While it has been possible to study the stoichiometry and hierarchy of the OmpR-DNA interaction in the upstream regions of ompF and ompC, their disunited location on the bacterial chromosome has made it difficult to compare the individual binding affinities of respective sites. RESULTS: Using 1,10-phenanthroline-Cu+ footprinting on a fused construct containing both the ompF and ompC upstream regulatory sequences, and gel shift experiments on oligomers corresponding to individual sites, we have established a comparative hierarchy for OmpR binding, as F1, C1 > F2, F3 > C2 > C3. In addition, the binding patterns reveal an apparent co-operative relationship between OmpR molecules bound at several upstream motifs. Densitometric analyses of the footprinted regions provide support for these observations. Mutational analysis of this construct reveals that the alteration of a conserved cytidine in the F1 motif (-86) causes a loss of OmpR affinity and disrupts hierarchical OmpR-binding in the entire ompF region. CONCLUSIONS: The present results provide a unique view of the OmpR interaction with the two respective promoters, ompF and ompC, and an insight into the question of how the expression of ompF and ompC are reciprocally regulated by medium osmolarity.

Bacterial Proteins↗
PubMed1996

Tissue-specific expression of the vasoactive intestinal peptide gene requires both an upstream tissue specifier element and the 5' proximal cyclic AMP-responsive element.

An upstream enhancer element [tissue specifier element (TSE)] located between 4.66 and 4.02 kb from the transcription start site is important for cell type-specific expression and phorbol ester induction of the vasoactive intestinal peptide (VIP) gene. An element located within 100 bases of the VIP promoter [the VIP cyclic AMP-responsive element (VIP-CRE)] confers cyclic AMP and phorbol ester responsiveness to heterologous promoters. The possibility that these two regions of the VIP gene function cooperatively to determine tissue-specific and second messenger-dependent expression of the VIP gene was addressed by assaying transcription from a VIP-luciferase reporter gene with progressive deletions from the 5' flanking sequence of the gene, with or without inactivation of the proximal VIP-CRE. Basal expression of the reporter gene in both SH-EP and SK-N-SH human neuroblastoma cells, which express endogenous VIP mRNA, was absolutely dependent on the presence of the upstream TSE. Full constitutive expression was also dependent on the intact VIP-CRE. Forskolin-mediated induction of the reporter gene in SH-EP and SK-N-SH cells was completely abolished by mutations in the VIP-CRE but not by deletion of the upstream sequence, indicating that the VIP-CRE alone determines cyclic AMP responsiveness. In contrast to reports that the VIP-CRE imparts 12-O-tetradecanoylphorbol 13-acetate (phorbol 12-myristate 13-acetate; PMA) responsiveness to heterologous promoters, PMA stimulation in SK-N-SH cells was independent of an intact VIP-CRE but dependent on a region between -2.5 kb and the VIP-CRE. Sequencing of the entire 5.2-kb VIP 5' flank revealed a consensus PMA-responsive element (TGACTCA) 2.25 kb upstream of the transcription start site that may represent the site imparting PMA responsiveness to the VIP gene.

Animals↗
PubMed2001

Structural and functional characterization of the 5' upstream promoter of the human Phox2a gene: possible direct transactivation by transcription factor Phox2b.

The specification of neurotransmitter identity is a critical step in neural development. Recent progresses have indicated that the closely related homeodomain factors Phox2a and 2b are essential for development of noradrenergic (NA) neuron differentiation, and may directly determine the neurotransmitter identity. With a long-term goal of understanding the regulatory cascade of NA phenotype determination, we isolated and characterized a hPhox2a genomic clone encompassing approximately 7.5 kb of the 5' upstream promoter region, the entire exon-intron structure, and approximately 4 kb of the 3' flanking region. Using mRNAs isolated from the Phox2a-expressing human cell line, both primer extension and 5'-rapid amplification of cDNA ends analyses identified a single transcription start site that resides 172 nucleotides upstream of the start codon. The transcription start site was preceded by a TATA-like sequence motif and transcripts from this site contained an additional G residue at the 5' position, supporting the authenticity of this site as the transcriptional start site of hPhox2a. We assembled hPhox2a-luciferase reporter constructs containing different lengths of the 5' upstream sequences. Transient transfection assays of these reporter constructs in both hPhox2a-positive and -negative cell lines show that 1.3-kb or longer upstream sequences of the hPhox2a gene may confer NA cell-specific reporter gene expression. Furthermore, cotransfection assays in the Phox2a-negative HeLa cell line show that forced expression of Phox2b, but not that of Phox2a or MASH1, significantly transactivates the transcriptional activity of hPhox2a. This study will provide a frame to further delineate the regulatory cascade of NA neuron differentiation.

Amino Acid Sequence↗
PubMed2003

Far-upstream elements are dispensable for tissue-specific proenkephalin expression using a Cre-mediated knock-in strategy.

Several cis-regulatory DNA elements are present in the 5' upstream regulatory region of the enkephalin gene (ENK) promoter. To determine their role in conferring organ-specificity of ENK expression in mice and to circumvent the position effects from random gene insertion that are known to often frustrate such analysis in transgenic mice, we used a Cre-mediated gene knock-in strategy to target reporter constructs to a "safe haven" loxP-tagged locus in the hypoxanthine phosphoribosyltransferase (HPRT) gene. Here we report reliable and reproducible reporter gene expression under the control of the 5' upstream regulatory region of the mouse ENK gene in gene-modified mice using this Cre-mediated knock-in strategy. Comparison of two 5'ENK regulatory regions (one with and the other without known cis-regulatory DNA elements) in the resulting adult mice showed that conserved far-upstream cis-regulatory DNA elements are dispensable for correct organ-specific gene expression. Thus the proximal 1.4 kb of the murine ENK promoter region is sufficient for organ-specificity of ENK gene expression when targeted to a safe-haven genomic locus. These results suggest that conservation of the far-upstream DNA elements serves more subtle roles, such as the developmental or cell-specific expression of the ENK gene.

5' Flanking Region↗
PubMed2003

Identification and functional validation of a 5' upstream regulatory sequence in the human tyrosinase gene homologous to the locus control region of the mouse tyrosinase gene.

Comparison analysis of the sequences of the mouse and human genomes has proven a powerful approach in identifying functional regulatory elements within the non-coding regions that are conserved through evolution between homologous mammalian loci. Here, we applied computational analysis to identify regions of homology in the 5' upstream sequences of the human tyrosinase gene, similar to the locus control region (LCR) of the mouse tyrosinase gene, located at -15 kb. We detected several stretches of homology within the first 30 kb 5' tyrosinase gene upstream sequences of both species that include the proximal promoter sequences, the genomic region surrounding the mouse LCR, and further upstream segments. We cloned and sequenced a 5' upstream regulatory sequence found between -8 and -10 kb of the human tyrosinase locus (termed h5'URS) homologous to the mouse LCR sequences, and confirmed the presence of putative binding sites at -9 kb, homologous to those described in the mouse tyrosinase LCR core. Finally, we functionally validated the presence of a tissue-specific enhancer in the h5'URS by transient transfection analysis in human and mouse cells, as compared with homologous DNA sequences from the mouse tyrosinase locus. Future experiments in cells and transgenic animals will help us to understand the in vivo relevance of this newly described h5'URS sequence as a potentially important regulatory element for the correct expression of the human tyrosinase gene.

Albinism, Oculocutaneous↗
PubMed2004

Highly conserved upstream sequences for transcription factor genes and implications for the regulatory network.

Identifying evolutionarily conserved blocks in orthologous genomic sequences is an effective way to detect regulatory elements. In this study, with the aim of elucidating the architecture of the regulatory network, we systematically estimated the degree of conservation of the upstream sequences of 3,750 human-mouse orthologue pairs along 8-kb stretches. We found that the genes with high upstream conservation are predominantly transcription factor (TF) genes. In particular, developmental process-related TF genes showed significantly higher conservation of the upstream sequences than other TF genes. Such extreme upstream conservation of the developmental process-related TF genes suggests that the regulatory networks involved with developmental processes have been evolutionarily well conserved in both human and mouse lineages.

Animals↗
PubMed2003

Activation of yeast Snf1 and mammalian AMP-activated protein kinase by upstream kinases.

The Snf1/AMP-activated protein kinase (AMPK) family plays fundamental roles in cellular responses to metabolic stress in eukaryotes. In humans, AMPK regulates lipid and glucose metabolism and has been implicated in such metabolic disorders as diabetes and obesity and in cardiac abnormalities. Snf1 and AMPK are the downstream components of kinase cascades, but the upstream kinase(s) have remained elusive. We have here identified three yeast kinases, Pak1p, Tos3p, and Elm1p, that activate Snf1 kinase in vivo. Triple deletion of the cognate genes causes a Snf- mutant phenotype and abolishes Snf1 catalytic activity. All three kinases phosphorylate recombinant Snf1p on the activation-loop threonine. Moreover, Tos3p phosphorylates mammalian AMPK on the equivalent residue and activates the enzyme, suggesting functional conservation of the upstream kinases between yeast and mammals. We further show that the closely related mammalian LKB1 kinase, which is associated with Peutz-Jeghers cancer-susceptibility syndrome, phosphorylates and activates AMPK in vitro. Thus, the identification of the yeast upstream kinases should facilitate identification of the corresponding, physiologically important mammalian upstream kinases.

AMP-Activated Protein Kinase Kinases↗
PubMed1982

Sequences upstream from the T-A-T-A box are required in vivo and in vitro for efficient transcription from the adenovirus serotype 2 major late promoter.

We show that sequences located upstream from the T-A-T-A box, between positions -97 and -34, are necessary for efficient in vivo transcription from the adenovirus serotype 2 major late promoter. The effect of these upstream sequences was also investigated in vitro using a whole cell or an S100 extract and circular or linear templates. With the whole cell extract, the in vivo effect of the upstream sequences was reproduced in vitro. With the S100 extract, some effect of the upstream sequences was observed with circular, but not with linear, templates.

Adenoviruses, Human↗
PubMed1982

A GAL10-CYC1 hybrid yeast promoter identifies the GAL4 regulatory region as an upstream site.

We have identified the promoter region of the GAL10 gene (whose product is UDP-galactose epimerase) of Saccharomyces cerevisiae; this promoter mediates galactose induction of transcription in conjunction with the product of the GAL4 regulatory gene. This identification was achieved by excising a 365-base-pair fragment of GAL10 leader DNA with a GAL10 proximal endpoint greater than 100 base pairs upstream of the transcriptional start site and substituting it in place of the upstream activation site of the CYC1 (iso-1-cytochrome c) promoter [Guarente, L. & Ptashne, M. (1981) Proc. Natl. Acad. Sci. USA 78, 2199-2203]. The hybrid promoter is composed of DNA encoding CYC1 mRNA start sites and the GAL segment upstream of these sites. This promoter is regulated in a manner analogous to GAL10; i.e., it is induced by galactose and responds to mutations in the GAL4 and GAL80 regulatory loci. The activity of the hybrid promoter requires sequences in the region of the CYC1 mRNA start sites but does not require a precise spacing between these sequences and the GAL segment. The transposed GAL segment appears not to contain sequences that mediate glucose repression. Thus, the picture of the GAL10 promoter that emerges is one of an upstream activation site that responds to the GAL4 product plus galactose, and a region of transcription initiation that may contain sequences that mediate glucose repression. Experiments employing strains inducible (GAL80) or constitutive (gal80) for GAL10 expression indicate that an additional component of glucose repression is inducer exclusion.

Base Sequence↗
PubMed1985

Naturally occurring poly(dA-dT) sequences are upstream promoter elements for constitutive transcription in yeast.

pet56, his3, and ded1 are adjacent but unrelated genes located on chromosome XV of the yeast Saccharomyces cerevisiae. his3 and pet56 are transcribed in opposite directions from initiation sites separated by approximately equal to 200 base pairs. Under normal growth conditions, both genes are transcribed at a similar basal level. Deletion analysis of the his3 gene indicates that the upstream promoter element for constitutive expression is defined by a 17-base-pair region that contains 15 thymidine residues in the coding strand. Sequential deletions of the pet56 gene indicate that this same region is required for wild-type transcription levels. Thus, this poly(dA-dT) sequence acts bidirectionally to activate transcription of two unrelated genes. Transcription of the ded1 gene is initiated approximately equal to 300 base pairs downstream from the his3 gene, and it occurs at a 5-fold higher level. This gene contains a 34-base-pair region containing 28 thymidine residues in the coding strand located upstream from the ded1 TATA box. Deletion of this dA-dT stretch significantly reduces transcription below the wild-type level. Thus, for at least three different yeast genes, naturally occurring stretches of poly(dA-dT) serve as upstream promoter elements for constitutive expression. In addition, it appears that longer stretches of poly(dA-dT) are more effective upstream promoter elements. These transcriptional effects may be due to exclusion of nucleosomes from poly(dA-dT) regions.

Base Sequence↗
PubMed1987

The upstream activation site of a Ty2 element of yeast is necessary but not sufficient to promote maximal transcription of the element.

The Ty elements of yeast are a family of retrovirus-like transposons that are highly transcribed, accounting for about 10% of total mRNA. We have mapped two sites to the nontranscribed region of the element upstream of the transcription start site that are required for maximal gene expression and are similar to sites previously defined in other genes. One, the TATA site, is located 74 base pairs upstream of the transcription start site and has the canonical sequence TATAAAA. This site is required for normal rates of initiation; deletion of the site greatly reduces the amount of Ty917 mRNA without changing its 5' end. A second site is located in a region from 140 to 110 base pairs upstream of the start site. Unlike other upstream activation site (UAS) elements previously defined, the Ty917 UAS is not sufficient to promote any transcription in the absence of downstream transcription regulatory sites. Thus the UAS is necessary but not sufficient for maximal transcription. Comparison of constructs lacking either the UAS or the downstream enhancer or both shows evidence of synergistic interaction between the sites since the effect of the sites on the rate of transcription initiation is more than additive.

DNA Transposable Elements↗
PubMed1988

Structure of the octopine synthase upstream activator sequence.

We have identified a transcriptional activating element within the 5' flanking sequence of the Agrobacterium tumefaciens octopine synthase (ocs) gene that is necessary for ocs expression in transformed tobacco calli. This element is located between 333 and 116 base pairs upstream from the transcription initiation site and functions independent of orientation when placed upstream of the ocs gene. It does not function in either orientation when placed downstream of the gene, nor can it activate its promoter when separated by a distance of 608 base pairs. Deletion analysis indicates that sequences essential for activator function are localized between 222 and 177 base pairs upstream of the transcription initiation site. Another region, located between 333 and 249 base pairs upstream of the transcription initiation site, does not as a monomer activate the ocs promoter, but it can as a dimer.

Amino Acid Oxidoreductases↗