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Results for “RNA Stability”

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At least 595 records · Page 33Linked to original sources

PubMed2005

Molecular basis of florfenicol-induced increase in adherence of Staphylococcus aureus strain Newman.

OBJECTIVES: The aim of this study was to determine the molecular basis of the florfenicol-dependent increased adherence of Staphylococcus aureus strain Newman to HEp-2 cells. METHODS AND RESULTS: Northern slot blot analysis showed that mRNA expression of fnbA, fnbB, coa, emp and eap, coding for adhesins, was increased in the presence of 0.5 x MIC of florfenicol. Under the same conditions expression of cap5, coding for type 5 capsular polysaccharides, was distinctly decreased. Since global regulatory systems can modulate the expression of adhesins, their role in this process was investigated by including three isogenic mutants with functionally inactive global regulator systems, agr, sar or sae. Growth in the presence of 0.5 x MIC of florfenicol significantly increased the adherence to HEp-2 cells, fibronectin and fibrinogen of the Deltaagr and Deltasar mutant strains, but not that of the Deltasae mutant strain. In contrast to components of the agr or sar system, expression of saeRS was increased, suggesting a potential sae-directed decrease in the expression of cap5 and increase in the expression of genes coding for adhesins under the influence of florfenicol. Analysis of RNA stability revealed that the increased amount of transcripts of saeRS and adherence-associated genes was due to a stabilization of the respective mRNAs by florfenicol. CONCLUSIONS: Our data provide evidence that an activation of the global regulator sae and a stabilization of mRNA coding for specific adhesins seem to act synergically in generating a more adherent phenotype in the presence of a high subinhibitory concentration of florfenicol.

Adhesins, Bacterial↗

PubMed1989

S4-16 S ribosomal RNA complex. Binding constant measurements and specific recognition of a 460-nucleotide region.

The region of the Escherichia coli 16 S ribosomal RNA recognized by the ribosomal protein S4 has been defined by assaying a set of 13 16 S rRNA fragments for S4 binding. The fragments were prepared by transcription in vitro, and binding constants were measured in three ways: retention of labeled RNA fragments on nitrocellulose filters by S4; co-sedimentation of labeled S4 with RNA fragments in sucrose gradients; and the distribution of labeled S4 between two RNAs of different sizes in a sucrose gradient. All three methods gave similar relative binding strengths for a variety of 16 S rRNA and non-specific (23 S rRNA) sequences, with the exception of two of the largest 16 S rRNA fragments; these gave smaller association constants in the filter retention assay than in the other methods. We found that specific complexes of S4 with these larger RNAs do not bind well to filters, leaving non-specific complexes to dominate the assay. Specific complexes with RNAs less than or equal to 891 nucleotides were retained efficiently by S4 on filters, and gave reliable binding constants. All 16 S rRNA fragments containing nucleotides 39 to 500 bound S4 with the same affinity as intact 16 S rRNA, while all fragments with endpoints within 39 to 500 bound at least tenfold more weakly. This sequence must be able to fold independently of the rest of the rRNA. Comparison of this minimal 462-nucleotide S4 binding site with S4 footprinting results suggests that S4 binding might alter the conformations of RNA neighboring the 39 to 500 region in the intact 16 S rRNA. Specific S4-rRNA binding is not sensitive to KCl concentration, but a more normal salt dependence is seen in K2SO4 (delta logK/delta log[K+] approximately -3.3). This duplicates the behavior of the specific S4-alpha mRNA translational repression complex, arguing that S4 recognizes both the mRNA and rRNA substrates by the same mechanism. Mg2+ is not required to form the specific rRNA complex, at least under conditions which stabilize RNA structure (0.35 M-KCl, 5 degrees C).

Binding Sites↗

PubMed1984

Recognition of cap structure in splicing in vitro of mRNA precursors.

Substrate RNAs are only efficiently spliced in HeLa whole-cell extract when they possess capped 5' termini. This cap requirement is observed with substrate RNAs prepared by transcription with either mammalian RNA polymerase II or bacterial RNA polymerase. Addition of less than 10 microM of cap analogs such as m7G(5')ppp(5')N or m7GTP strongly inhibits splicing of capped RNAs. This observation, as well as experiments following the fate of substrate RNA, indicates that the dependence of splicing on a cap structure is not due to an effect on RNA stability. More interestingly, cap analogs inhibit splicing when added at the start of the reaction but not at later times of incubation. This suggests that the cap recognition might be an important step in the formation of a specific ribonucleoprotein complex required for splicing.

DNA-Directed RNA Polymerases↗

PubMed1988

Mapping of brain areas containing RNA homologous to cDNAs encoding the alpha and beta subunits of the rat GABAA gamma-aminobutyrate receptor.

An in situ hybridization technique was used to determine the distribution in rat brain of RNA homologous to cDNA clones encoding the alpha and beta subunits of the rat brain GABAA gamma-aminobutyrate receptor. The subunit proteins were mapped in adjacent sections autoradiographically and immunohistochemically. Many brain areas containing high densities of GABAA receptors showed strong hybridization signals with both the alpha- and the beta-subunit antisense RNA probe--e.g., cerebral cortex, hippocampus, and cerebellum. On a cellular level, a dense dendritic localization of GABAA receptors was correlated with a strong hybridization in the corresponding somata--e.g., in mitral cells of the olfactory bulb, pyramidal cells of hippocampus, granule cells of the dentate gyrus, and Purkinje and granule cells of the cerebellum. In some brain areas--e.g., substantia nigra--the intensity of the hybridization signal with the beta-subunit probe was much weaker than that with the alpha-subunit probe, whereas the inverse ratio of hybridization intensity was found in others--e.g., in bed nucleus. This regional heterogeneity in the hybridization pattern may reflect regional differences in RNA stability, transcription rate, or subunit composition. The results open the way for studies on the regulation of GABAA-receptor gene expression in normal and pathological brain in situ.

Animals↗

PubMed2026

Amplification of RNA for identification of Zika and HCV in whole blood.

Direct RNA amplification from whole blood is fundamentally limited by rapid enzymatic degradation and inhibitory matrix effects. Here, we present a blood drying protocol that enables sensitive and robust RNA detection without the need for extraction, purification, or cold-chain logistics. Using whole blood, the platform achieves high detection sensitivity, down to 10 copies per microliter for Zika virus and 1 international unit per microliter for hepatitis C virus (HCV). We further demonstrate that the protocol can be scaled to larger blood volumes and achieve single-copy sensitivity without any sample loss. This is accomplished through thermal treatments of the sample combined with a primer-limited reverse transcription step, which together stabilize RNA within a dried blood matrix and permit spatially resolved enzymatic amplification. The system supports multiplexed detection from a single sample, enabling simultaneous identification of multiple targets. Separately, we introduce a concept wherein the very few copies of the preserved RNA within the matrix can be accessed repeatedly for molecular analysis. Furthermore, we demonstrated the detection of Zika and HCV using a portable fluorometer for point-of-care (POC) uses. With lyophilized reagents and minimal instrumentation such as a heater and an inexpensive portable fluorometer, this platform enables robust, reusable, and field-deployable diagnostics, advancing toward truly accessible on-site RNA testing in urgent care or low-resource settings from whole blood.

Humans↗

PubMed1995

Inhibitory effect of 3'-untranslated region (3'-UTR) of human tissue-plasminogen activator (ht-PA) mRNA on its expression.

A series of t-PA cDNA mutants containing different parts of 3'-UTR sequences have been constructed. In vitro translation of t-PA transcripts in rabbit reticulocyte lysates and its expression in COS-7 cells show that the 3'-UTR sequence has a very strong inhibitory effect on t-PA translation. The deletion of 3'-UTR results in 3-8-fold increase of t-PA expression. Further study shows that an AU-rich sequence of some 200 nt at 3' end of 3'-UTR is responsible for the translational inhibition. RNA stability experiment reveals that the AU-rich segment leads to a 3-fold decrease of t-PA mRNA stability. The insertion of this segment into the 3'-UTR of luciferase gene results in an obvious inhibition of Luc expression. A model is proposed for the regulation of t-PA expression.

Animals↗

PubMed1993

Expression cloning of 2-5A-dependent RNAase: a uniquely regulated mediator of interferon action.

2-5A-dependent RNAase, an interferon-induced enzyme that is activated by 5'-phosphorylated, 2',5'-linked oligoadenylates (2-5A), is implicated in both the molecular mechanisms of interferon action and the fundamental control of RNA stability in mammalian cells. Here we report the expression cloning and analysis of murine and human 2-5A-dependent RNAases. The 2-5A binding properties and RNAse activities of recombinant and naturally occurring forms of 2-5A-dependent RNAase were identical. Interferon induction of 2-5A-dependent RNAse expression was demonstrated by measuring the mRNA levels in cells treated with interferon and cycloheximide. Analysis of aligned murine and human 2-5A-dependent RNAse sequences revealed several intriguing features, including similarity to RNAase E, which is implicated in the control of mRNA stability in E. coli. Interestingly, a duplicated phosphate-binding loop motif was determined by deletion analysis and site-directed mutagenesis to function in the binding of 2-5A.

Amino Acid Sequence↗

PubMed1992

Growth-regulated expression of rhoG, a new member of the ras homolog gene family.

Cellular transition from the resting state to DNA synthesis involves master switches genes encoding transcriptional factors (e.g., fos, jun, and egr genes), whose targets remain to be fully characterized. To isolate coding sequences specifically accumulated in late G1, a differential screening was performed on a cDNA library prepared from hamster lung fibroblasts stimulated for 5 h with serum. One of the positive clones which displayed a sevenfold induction, turned out to code for a protein sharing homology to Ras-like products. Cloning and sequence analysis of the human homolog revealed that this putative new small GTPase, referred to as rhoG, is more closely related to the rac, CDC42, and TC10 members of the rho (ras homolog) gene family and might have diverged very early during evolution. rhoG mRNA accumulates in proportion to the mitogenic strength of various purified growth factors used for the stimulation, as a consequence of transcriptional activation. G1-specific RNA accumulation is impaired upon addition of antimitogenic cyclic AMP and is enhanced when protein synthesis is inhibited, mainly as a result of RNA stabilization. rhoG mRNA expression is observed in a wide variety of human organs but reaches a particularly high level in lung and placental tissues.

Amino Acid Sequence↗

PubMed2004

Chloroplast RNA-binding and pentatricopeptide repeat proteins.

Chloroplast gene expression is mainly regulated at the post-transcriptional level by numerous nuclear-encoded RNA-binding protein factors. In the present study, we focus on two RNA-binding proteins: cpRNP (chloroplast ribonucleoprotein) and PPR (pentatricopeptide repeat) protein. These are suggested to be major contributors to chloroplast RNA metabolism. Tobacco cpRNPs are composed of five different proteins containing two RNA-recognition motifs and an acidic N-terminal domain. The cpRNPs are abundant proteins and form heterogeneous complexes with most ribosome-free mRNAs and the precursors of tRNAs in the stroma. The complexes could function as platforms for various RNA-processing events in chloroplasts. It has been demonstrated that cpRNPs contribute to RNA stabilization, 3'-end formation and editing. The PPR proteins occur as a superfamily only in the higher plant species. They are predicted to be involved in RNA/DNA metabolism in chloroplasts or mitochondria. Nuclear-encoded HCF152 is a chloroplast-localized protein that usually has 12 PPR motifs. The null mutant of Arabidopsis, hcf152, is impaired in the 5'-end processing and splicing of petB transcripts. HCF152 binds the petB exon-intron junctions with high affinity. The number of PPR motifs controls its affinity and specificity for RNA. It has been suggested that each of the highly variable PPR proteins is a gene-specific regulator of plant organellar RNA metabolism.

Arabidopsis Proteins↗

PubMed1991

Localization of beta 2-adrenoceptor messenger RNA in human and rat lung using in situ hybridization: correlation with receptor autoradiography.

We have used in situ hybridization to study the localization of mRNA encoding the beta 2-adrenoceptor in tissue sections of the human and rat lung and compared this with the distribution of beta 2-receptor binding sites using receptor autoradiography. To localize beta 2-receptor mRNA, a [32P]labeled antisense RNA probe (riboprobe) was generated from human or rat beta 2-receptor cDNA. A similar distribution of beta 2-receptor mRNA was identified in both species. The highest intensity of beta 2-receptor mRNA was detected in smooth muscle of small airways, airway epithelium and pulmonary blood vessels. Lower intensity of beta 2-receptor mRNA was identified in smooth muscle of large airways, and alveolar epithelium (presumably type I and type II pneumocytes). No significant hybridization signal was detected in interstitial tissue. The specificity of the hybridization signal was confirmed with a sense probe (having identical sequence to the mRNA) and preincubation with RNase A, and by Northern blot analysis which revealed a single band of mRNA of 2.2 kb. There was a correspondence between mRNA localization and the distribution of beta 2-receptors visualized by [125I]iodocyanopindolol autoradiographically in the presence of CGP 20712 (a beta 1-selective antagonist). However, alveolar walls that showed a high beta 2-receptor density had relatively low levels of mRNA. This cellular heterogeneity may reflect differences in RNA stability or transcription rate in different lung cells. This approach opens up new options in the investigation of the regulation of pulmonary beta 2-receptor gene expression in health and disease.

Animals↗

PubMed1997

HNF4beta, a new gene of the HNF4 family with distinct activation and expression profiles in oogenesis and embryogenesis of Xenopus laevis.

The transcription factor hepatocyte nuclear factor 4 (HNF4) is an orphan member of the nuclear receptor superfamily expressed in mammals in liver, kidney, and the digestive tract. Recently, we isolated the Xenopus homolog of mammalian HNF4 and revealed that it is not only a tissue-specific transcription factor but also a maternal component of the Xenopus egg and distributed within an animal-to-vegetal gradient. We speculate that this gradient cooperates with the vegetally localized embryonic induction factor activin A to activate expression of HNF1alpha, a tissue-specific transcription factor with an expression pattern overlapping that of HNF4. We have now identified a second Xenopus HNF4 gene, which is more distantly related to mammalian HNF4 than the previously isolated gene. This new gene was named HNF4beta to distinguish it from the known HNF4 gene, which is now called HNF4alpha. By reverse transcription-PCR, we detected within the 5' untranslated region of HNF4beta two splice variants (HNF4beta2 and HNF4beta3) with additional exons, which seem to affect RNA stability. HNF4beta is a functional transcription factor acting sequence specifically on HNF4 binding sites known for HNF4alpha, but it seems to have a lower DNA binding activity and is a weaker transactivator than the alpha isoform. Furthermore, the two factors differ with respect to tissue distribution in adult frogs: whereas HNF4alpha is expressed in liver and kidney, HNF4beta is expressed in addition in stomach, intestine, lung, ovary, and testis. Both factors are maternal proteins and present at constant levels throughout embryogenesis. However, using reverse transcription-PCR, we found the RNA levels to change substantially: whereas HNF4alpha is expressed early during oogenesis and is absent in the egg, HNF4beta is first detected in the latest stage of oogenesis, and transcripts are present in the egg and early cleavage stages. Furthermore, zygotic HNF4alpha transcripts appear in early gastrula and accumulate during further embryogenesis, whereas HNF4beta mRNA transiently appears during gastrulation before it accumulates again at the tail bud stage. All of these distinct characteristics of the newly identified HNF4 protein imply that the alpha and beta isoform have different functions in development and in adult tissues.

Amino Acid Sequence↗

PubMed1996

Regulation of beta-adrenoceptor density and mRNA levels in the rat heart cell-line H9c2.

The regulation of the expression of beta-adrenoceptor (beta-ARs) is not thoroughly understood. We demonstrate that the rat heart cell-line H9c2 expresses both beta 1- and beta 2-ARs. In radioligand-binding experiments, the maximal binding capacity of (-)-[125I]-iodocyanopindolol was determined as 18 +/- 0.6 fmol/mg of protein with a KD of 35.4 +/- 4.1 pM. Competitive radioligand-binding experiments with subtype-specific beta-antagonists reveal a subtype ratio of beta 1- to beta 2-ARs of 29%: 71%. With competitive reverse-transcriptase PCR we found beta 2-mRNA to be up to 1600 times more frequent than beta 1-mRNA. Treatment of the H9c2 cell-line with the beta-adrenergic agonist (-)-isoproterenol (10(-6) M), the antagonist (-)-propranolol (10(-6) M) and the glucocorticoid dexamethasone (500 nM) induces regulatory effects on both the beta-AR protein and mRNA level. Isoproterenol treatment leads to down-regulation of the total receptor number by 56 +/- 4%, due to a decrease in beta 2-ARs, while maintaining the beta 1-AR number constant. On the transcription level, both beta 1-and beta 2-mRNAs are decreased by 30% and 42% respectively. mRNA stability measurements reveal a reduced half-life of beta 2-mRNA from 9.3 h to 6.5 h after isoproterenol treatment. Incubation of cells with (-)-propranolol does not affect the amounts of beta-ARs and their mRNAs. Dexamethasone induces a 1.8 +/- 0.2-fold increase in beta-AR number over the basal level as well as a 1.9 +/- 0.2-fold increase in the amount of beta 2-mRNA. Because the half-life of beta 2-mRNA was unaffected by dexamethasone, the increased beta 2-mRNA level must be due to an enhanced transcription rate. The beta 1-mRNA levels are unchanged during dexamethasone-incubation of the cells. Our data clearly demonstrate that treatment of H9c2 rat heart cells with isoproterenol and dexamethasone induces alterations in the level of RNA stability as well as gene transcription, leading to altered receptor numbers.

Adrenergic beta-Agonists↗

PubMed2004

Impact of pre-analytical handling on bone marrow mRNA gene expression.

Large clinical trials on leukaemia, require the transport of bone marrow (BM) from participating clinics to central diagnostic laboratories. We have investigated the impact of RNA extraction protocols and time delays between sample aspiration and RNA extraction on RNA quality and gene expression profiles. Intact RNA can be extracted from BM samples stored at room temperature for up to 48 h. Gene expression analyses using Affymetrix U95Av2 GeneChips and a custom-designed cDNA array in parallel showed that even short-term storage of BM has dramatic effects on mRNA expression of individual transcripts. Many probe sets/genes showed either reproducible deregulation (18.8%, analysis of variance <0.05), or inconsistent expression that differed from patient to patient (38.4%). Moderate alterations were observed in 42.8% genes, with a maximum fold change <2.0 in all experiments and at all time points. These profound effects complicate the use of unstabilized, shipped BM samples for gene expression analyses. The comparison of a variety of RNA stabilization reagents (e.g. PAXgene) resulted in partial conservation of the mRNA expression patterns. Immediate density centrifugation or erythrocyte lysis and freezing at -80 degrees C represent simple procedures that reliably preserved mRNA gene expression patterns in BM.

Bone Marrow↗

PubMed1989

Glucocorticoid regulation of parathyroid hormone-related peptide gene transcription in a human neuroendocrine cell line.

A PTH-related peptide (PTHRP) has been identified and its cDNA cloned from tumors associated with the syndrome of humoral hypercalcemia of malignancy. The PTHRP and PTH genes appear to represent members of a gene family. Whereas the PTH gene is expressed exclusively in the parathyroids, the PTHRP gene appears to be widely expressed, but little is known concerning the regulation of its expression in any site. We studied the regulation of PTHRP gene expression in a human carcinoid cell line (NCI-H727) which has neuroendocrine features and also produces calcitonin, calcitonin gene-related peptide, and chromogranin-A. We found that the synthetic glucocorticoid triamcinolone produced time- and dose-dependent decreases in steady state PTHRP and calcitonin mRNA levels in NCI-H727 cells. This effect was blocked by the competitive glucocorticoid inhibitor RU-486. Messenger RNA stability and transcription run-off experiments revealed that triamcinolone decreased PTHRP and calcitonin expression by repressing the transcription rates of both genes.

Calcitonin↗

PubMedDate not supplied

Analysis of the c-myc and N-ras genes in acute myelogenous leukemia cells which manifest the constitutive expression of the c-myc gene.

The "constitutive" expression of the c-myc gene was detected in leukemia cells obtained from 4 patients with an acute myeloid leukemia, 3 with chronic myeloid leukemia and 1 with a myelodysplastic syndrome. Studies were undertaken to determine whether or not the myc gene was rearranged or mutated in exon I within a 3'Pvu II region, a transcriptional attenuation site. Studies to explore the possibility of a point mutation in the N-ras gene were also conducted. No abnormalities were detected in either gene. Studies should be undertaken evaluating the possibility of a post-transcriptional mechanism, such as alteration of RNA stability, which could be responsible for the constitutive expression of c-myc gene.

Acute Disease↗

PubMed2000

Physiological and regulatory effects of controlled overproduction of five cold shock proteins of Lactococcus lactis MG1363.

The physiological and regulatory effects of overproduction of five cold shock proteins (CSPs) of Lactococcus lactis were studied. CspB, CspD, and CspE could be overproduced at high levels (up to 19% of the total protein), whereas for CspA and CspC limited overproduction (0.3 to 0.5% of the total protein) was obtained. Northern blot analysis revealed low abundance of the cspC transcript, indicating that the stability of cspC mRNA is low. The limited overproduction of CspA is likely to be caused by low stability of CspA since when there was an Arg-Pro mutation at position 58, the level of CspA production increased. Using two-dimensional gel electrophoresis, it was found that upon overproduction of the CSPs several proteins, including a number of cold-induced proteins of L. lactis, were induced. Strikingly, upon overproduction of CspC induction of CspB, putative CspF, and putative CspG was also observed. Overproduction of CspB and overproduction of CspE result in increased survival when L. lactis is frozen (maximum increases, 10- and 5-fold, respectively, after 4 freeze-thaw cycles). It is concluded that in L. lactis CSPs play a regulatory role in the cascade of events that are initiated by cold shock treatment and that they either have a direct protective effect during freezing (e.g., RNA stabilization) or induce other factors involved in the freeze-adaptive response or both.

Adaptation, Physiological↗

PubMed2004

PPR motifs of the nucleus-encoded factor, PGR3, function in the selective and distinct steps of chloroplast gene expression in Arabidopsis.

Plastid gene expression is regulated by a variety of nuclear genes. We have isolated Arabidopsis thaliana proton gradient regulation 3 (pgr3) mutants, which display aberrant chlorophyll fluorescence because of defects in chloroplast gene expression. High chlorophyll fluorescence (HCF) because of a reduced level of the cytochrome b6/f complex was observed in two alleles, pgr3-1 and pgr3-2 but not in pgr3-3. In contrast, a transient increase in fluorescence after turning off the actinic light, which was ascribed to chloroplast NADPH dehydrogenase (NDH) activity, was impaired in pgr3-1 and pgr3-3 but not in pgr3-2. Both phenotypes were complemented by the introduction of a single gene, PGR3, encoding a protein containing 27 pentatrico-peptide repeat (PPR) motifs. PPR motifs are present in proteins functioning in the post-transcriptional regulation of organellar gene expression. The conserved threonine in the motif was substituted by isoleucine in the 15th and 12th PPR motifs in pgr3-1 and pgr3-2, respectively, and the conserved leucine by phenylalanine in the final incomplete motif of pgr3-3. We consider that the different domains of the PPR repeats in PGR3 might have different functions in conferring RNA stability and probably allowing translation as well as recognizing at least two distinct target RNAs.

Amino Acid Motifs↗

PubMed1990

Transforming growth factor beta alters the expression of heparan sulfate proteoglycan in human colon carcinoma cells.

Transforming growth factor beta (TGF-beta) stimulated the synthesis of heparan sulfate proteoglycan in cultured human colon carcinoma cells without affecting its rates of intracellular degradation or secretion. The overall hydrodynamic size, electrophoretic mobility, and degree of sulfation of the TGF-beta-induced proteoglycan was indistinguishable from that of untreated cells. The synthesis of the protein core was significantly stimulated by TGF-beta, although total cellular protein was unaltered. The stimulatory effects of TGF-beta were prevented by the inhibitors of protein synthesis and DNA transcription, cycloheximide, or actinomycin D, respectively. Analysis of protein core mRNA levels using a murine cDNA encoding a basement membrane protein core, revealed a marked elevation of the steady state levels of mRNA for this gene product. In contrast, the mRNA levels for glyceraldehyde-3-phosphate dehydrogenase or beta-actin genes were not significantly affected by TGF-beta. Finally, nuclear run-off experiments showed increases in neither protein core-specific transcription nor in general transcriptional activity. Taken together, these results indicate that TGF-beta is a potent modulator of heparan sulfate proteoglycan expression in human colon carcinoma cells and that its effect is mediated primarily through an increase in mRNA levels encoding the protein core, perhaps a result of enhanced RNA stability. The TGF-beta-induced elevation of heparan sulfate proteoglycan may contribute to the control of stromal cell proliferation and matrix production by human colon carcinoma cells.

Cell Line↗