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At least 883 records · Page 49Linked to original sources
PubMed2006

Involvement of the Escherichia coli folate-binding protein YgfZ in RNA modification and regulation of chromosomal replication initiation.

The Escherichia coli hda gene codes for a DnaA-related protein that is essential for the regulatory inactivation of DnaA (RIDA), a system that controls the initiation of chromosomal replication. We have identified the ygfZ gene, which encodes a folate-binding protein, as a suppressor of hda mutations. The ygfZ null mutation suppresses an hda null mutation. The over-initiation and abortive elongation phenotypes conferred by the hda mutations are partially suppressed in an hda ygfZ background. The accumulation of the active form of DnaA, ATP-DnaA, in the hda mutant is suppressed by the disruption of the ygfZ gene, indicating that YgfZ is involved in regulating the level of ATP-DnaA. Although ygfZ is not an essential gene, the ygfZ disruptant grows slowly, especially at low temperature, demonstrating that this gene is important for cellular proliferation. We have identified mnmE (trmE) as a suppressor of the ygfZ disruption. This gene encodes a GTPase involved in tRNA modification. Examination of RNA modification in the ygfZ mutant reveals reduced levels of 2-methylthio N(6)-isopentenyladenosine [corrected] indicating that YgfZ participates in the methylthio-group formation of this modified nucleoside in some tRNAs. These results suggest that YgfZ is a key factor in regulatory networks that act via tRNA modification.

Bacterial Proteins↗
PubMed2002

Photo-regulation of transcription by RNA polymerase with azobenzene-tethered promoter.

Photo-regulation of transcription reaction by T7-RNA polymerase was investigated by introducing an azobenzene residue into the non-template strand of T7-promoter. It was found that transcription was strongly interfered under dark or visible light irradiation, whereas it efficiently proceeded after UV irradiation. With this photo-responsive promoter, on-off switching of transcription by light irradiation was achieved. This strategy was also effective for the photo-regulation of SP6-RNA polymerase.

Base Sequence↗
PubMed1992

In-vivo regulation of messenger RNA encoding insulin-like growth factor-I (IGF-I) and its receptor by diabetes, insulin and IGF-I in rat muscle.

The effects of continuous or acute administration of insulin or insulin-like growth factor-I (IGF-I) on IGF-I mRNA and IGF-I receptor mRNA were studied in the skeletal muscle (gastrocnemius), heart muscle and vascular smooth muscle (aorta) of non-diabetic and diabetic rats using a solution hybridization assay. The levels of IGF-I mRNA in the different types of muscle markedly decreased by diabetes, whereas changes in IGF-I receptor mRNA were less consistent. Continuous infusion of diabetic rats with insulin (28 or 35 nmol/day) for 4 days normalized the altered levels of IGF-I mRNA and IGF-1 receptor mRNA. Infusion of equimolar concentrations of IGF-I did not affect IGF-I mRNA, but decreased the level of IGF-I receptor mRNA in skeletal muscle. In acute experiments, rats were injected with equipotent blood glucose-lowering doses of insulin (14 nmol) or IGF-I (107 nmol). Insulin did not significantly affect levels of IGF-I mRNA, but decreased levels of IGF-I receptor mRNA in skeletal muscle and aorta. IGF-I increased levels of IGF-I mRNA in heart muscle, and markedly decreased levels of IGF-I receptor mRNA in skeletal muscle and heart muscle from non-diabetic and diabetic rats. In conclusion, exogenous IGF-I and insulin can increase IGF-I mRNA and decrease IGF-I receptor mRNA, indicating that both insulin and IGF-I can act as regulators of the IGF-I system in muscle in vivo.

Animals↗
PubMed1995

Thyroid hormones rapidly and stringently regulate the messenger RNA levels of the thyrotropin-releasing hormone (TRH) receptor and the TRH-degrading ectoenzyme.

The responsiveness of adenohypophyseal target cells for the hypothalamic neuropeptide TRH is known to change depending on the hormonal and physiological conditions of the organism. We describe here the effects of thyroid hormones on the transcript levels of the TRH receptor, the TRH-degrading ectoenzyme, and TSH in rat pituitary, as revealed by Northern blot analysis. After a single injection of T3 (30 micrograms/100 g BW), the transcript levels of the TRH receptor decreased transiently, reaching 35% of control values 4 h after injection, and returned to basal levels within 24 h. In contrast, the messenger RNA (mRNA) levels of the TRH-degrading ectoenzyme increased more dramatically in response to the same hormonal stimulus. Maximal levels (> 10 times above the control value) were present from 6-24 h after the injection, returning to basal values within 96 h. For both transcripts, the observed effects changed in a dose-dependent manner, but the mRNA levels of the TRH-degrading ectoenzyme were more tightly regulated. Under the experimental conditions used, the mRNA levels of PRL and GH were not affected by the application of T3, and those of alpha-subunit exhibited only minor reductions. The TSH beta transcripts however, decreased rapidly in length and slowly in concentration, finally reaching almost undetectable levels 48 h after the injection. Subsequently, newly synthesized TSH beta mRNA, the same size as the transcripts from euthyroid rats, could be detected 96 h after treatment with T3. Upon treatment of the animals with the mild goitrogenic agent n-propylthiouracil (200 mg/liter drinking water), a fast reduction in the transcript levels of the TRH-degrading ectoenzyme became evident. Within 1 day, mRNA levels decreased to less than 50% of control values. At this stage, no effects were observed on the transcript levels of either the TRH receptor or TSH beta. After 4 days of n-propylthiouracil treatment, the mRNA levels of the enzyme decreased further to 15% of control values, whereas the transcript concentrations of the TRH receptor and TSH beta rose by factors of 2 and 3.3, respectively. The extremely stringent regulation of the TRH-degrading ectoenzyme, a mirror image of that of the TRH receptor, strongly suggests that this enzyme represents an important regulatory element, controlling the stimulation of TRH target cells and, thus, adenohypophyseal hormone secretion.

Aminopeptidases↗
PubMed1992

A possible role for c-Myc oncoproteins in post-transcriptional regulation of ribosomal RNA.

Overexpression of members of the myc family of oncogenes contributes to the development of many vertebrate malignancies. Although several functions for myc gene products have been proposed, the targets for Myc activity during oncogenesis or normal development remain to be identified. Oocytes of Xenopus laevis, which are non-dividing cells that accumulate abundant c-Myc protein, provide an unusual opportunity to examine c-Myc function. We have investigated whether the accumulation of massive amounts of ribosomal RNA (rRNA) by Xenopus laevis oocytes may be related to their elevated expression of myc proto-oncogenes. Our data show that anti-Myc antibodies and some (but not all) c-Myc peptides from conserved regions of the c-Myc protein enhance the turnover of rRNA synthesized in homogenates of oocyte nuclei. These results suggest that one or more members of the Myc protein family may be involved in post-transcriptional regulation of rRNA metabolism. The regulation by c-Myc of rRNA could account, in part, for the generalized stimulation of cells during tumorigenesis.

Animals↗
PubMed2002

Vascular endothelial growth factor in the human oviduct: localization and regulation of messenger RNA expression in vivo.

In this study, we examined the localization of vascular endothelial growth factor (VEGF) and the changes in VEGF mRNA expression in various regions of the oviduct in fertile women throughout the ovulatory cycle. Oviduct tissue was collected from 22 women undergoing laparoscopic tubal sterilization or hysterectomy for a benign gynecological condition. Oviduct sections were divided into isthmus, ampullary, and infundibular regions. Serial cross sections were analyzed for the presence of VEGF by specific immunohistochemical staining. The mucosal layer was isolated, and a semiquantitative reverse transcription polymerase chain reaction was performed. Immunohistochemical study revealed VEGF in the oviduct luminal epithelium, smooth muscle cells, and blood vessels within the oviduct. VEGF mRNA expression in oviduct was the highest during the periovulatory stage, and the expression in the ampullary and infundibular regions was higher than that in the isthmus. There was a significant positive correlation between serum FSH and LH concentrations and VEGF mRNA expression. There was no significant correlation between serum estradiol and progesterone concentrations and VEGF mRNA expression. These results suggest that VEGF in human oviduct may play an important role related the early reproductive events, which occur predominantly in the ampulla during the periovulatory phase when serum FSH and LH concentrations are high.

Estradiol↗
PubMed2005

Modulation of hepatitis C virus RNA abundance by a liver-specific MicroRNA.

MicroRNAs are small RNA molecules that regulate messenger RNA (mRNA) expression. MicroRNA 122 (miR-122) is specifically expressed and highly abundant in the human liver. We show that the sequestration of miR-122 in liver cells results in marked loss of autonomously replicating hepatitis C viral RNAs. A genetic interaction between miR-122 and the 5' noncoding region of the viral genome was revealed by mutational analyses of the predicted microRNA binding site and ectopic expression of miR-122 molecules containing compensatory mutations. Studies with replication-defective RNAs suggested that miR-122 did not detectably affect mRNA translation or RNA stability. Therefore, miR-122 is likely to facilitate replication of the viral RNA, suggesting that miR-122 may present a target for antiviral intervention.

Animals↗
PubMed2006

Hepatitis C virus RNA replication is regulated by FKBP8 and Hsp90.

Hepatitis C virus (HCV) nonstructural protein 5A (NS5A) is a component of viral replicase and is well known to modulate the functions of several host proteins. Here, we show that NS5A specifically interacts with FKBP8, a member of the FK506-binding protein family, but not with other homologous immunophilins. Three sets of tetratricopeptide repeats in FKBP8 are responsible for interactions with NS5A. The siRNA-mediated knockdown of FKBP8 in a human hepatoma cell line harboring an HCV RNA replicon suppressed HCV RNA replication, and this reduction was reversed by the expression of an siRNA-resistant FKBP8 mutant. Furthermore, immunoprecipitation analyses revealed that FKBP8 forms a complex with Hsp90 and NS5A. Treatment of HCV replicon cells with geldanamycin, an inhibitor of Hsp90, suppressed RNA replication in a dose-dependent manner. These results suggest that the complex consisting of NS5A, FKBP8, and Hsp90 plays an important role in HCV RNA replication.

Antiviral Agents↗
PubMed1992

Replication control of plasmid R1: RepA synthesis is regulated by CopA RNA through inhibition of leader peptide translation.

The replication frequency of plasmid R1 is post-transcriptionally controlled by an antisense RNA, CopA, that binds to the leader region in the RepA mRNA, CopT, and ultimately inhibits the synthesis of the replication initiator protein RepA. We present results demonstrating that CopA controls RepA synthesis indirectly. A reading frame for a 24 amino acid leader peptide (Tap, translational activator peptide) is located in the region between the copA and repA genes. A translational fusion between the tap and lacZ genes was used to demonstrate that tap is translated and controlled by CopA. Stop codons (UAA, UAG and UGA) introduced at three different positions within the tap gene led to a severe decrease in repA expression. Specific suppression of the stop codons reversed the effect. This indicates that tap translation is required for RepA synthesis. Phylogenetic comparisons between IncFII-like plasmids, together with previous in vitro and in vivo results (Ohman and Wagner, 1989, 1991), suggest that a stable RNA stem-loop structure sequesters the repA ribosome binding site irrespective of CopA-CopT duplex formation. The results presented here show that ribosomes translating the tap reading frame have to terminate close to the start codon of repA to permit reinitiation (direct translational coupling), and that transient disruption of the inhibitory RNA stem-loop is insufficient for activation of repA translation. The possibility that direct translational coupling is required because of a suboptimal repA RBS cannot be excluded.(ABSTRACT TRUNCATED AT 250 WORDS)

Bacterial Proteins↗
PubMed1995

Differential regulation of two related RNA-binding proteins, iron regulatory protein (IRP) and IRPB.

The iron regulatory protein (IRP) is a cytoplasmic RNA-binding protein that regulates cellular iron metabolism at the posttranscriptional level. IRP is an unusual bifunctional molecule: in iron-replete cells it predominantly exists as a 4Fe-4S protein and exhibits aconitase enzymatic activity, whereas apo-IRP prevails in iron-starved cells and binds to iron-responsive elements (IREs), structural motifs within the untranslated regions of mRNAs involved in iron metabolism. A related protein with iron-regulated IRE-binding activity, IRPB, was previously identified in rodent cells. IRE-binding by IRP and IRPB is induced by iron deprivation and nitric oxide (NO). Controversial hypotheses have proposed that the induction of IRE-binding activity by iron results either from de novo synthesis of the apo-protein or from a posttranslational conversion of the Fe-S to the apo-protein form. This prompted a detailed analysis of how iron and NO regulate the RNA-binding activities of IRP and IRPB. We demonstrate that IRP is a relatively stable protein (half-life > 12 h). The induction of IRE-binding does not require de novo protein synthesis but results from conversion of Fe-S IRP to apo-IRP. In contrast, IRPB appears less stable in nonstarved cells (half-life approximately 4-6 h) and must be synthesized de novo following iron starvation. Our results furthermore reveal that two RNA-binding proteins with close structural and functional similarities that respond to the same cellular signals are regulated by predominantly different mechanisms.

Animals↗
PubMed2005

Butyrate suppresses tumor necrosis factor alpha production by regulating specific messenger RNA degradation mediated through a cis-acting AU-rich element.

OBJECTIVE: To study the capacity of butyrate to inhibit production of tumor necrosis factor alpha (TNFalpha) in macrophage-like synoviocytes (MLS) from patients with rheumatoid arthritis (RA), in human peripheral monocytes, and in murine RAW264.7 macrophages. METHODS: The concentrations of TNFalpha in culture supernatants of these cells were measured using enzyme-linked immunosorbent assay. The expression levels of various messenger RNAs (mRNA), such as those for TNFalpha, the mRNA-binding protein TIS11B, and luciferase, were measured using real-time quantitative polymerase chain reaction. The in vitro effects of butyrate on transcriptional regulation were evaluated by transfection with various reporter plasmids in RAW264.7 macrophages. The effects of TIS11B on TNFalpha expression were examined using an overexpression model of TIS11B in RAW264.7 cells. RESULTS: Butyrate suppressed TNFalpha protein and mRNA production in MLS and monocytes, but paradoxically enhanced transactivation of the TNFalpha promoter. Expression of the AU-rich element (ARE)-binding protein TIS11B was up-regulated by butyrate. Induction of TNFalpha mRNA by lipopolysaccharide was significantly inhibited when TIS11B was overexpressed. Butyrate facilitated the degradation of luciferase transcripts containing the 3'-untranslated region (3'-UTR) of TNFalpha, and this effect was dependent on the ARE in the 3'-UTR that is known to be involved in the regulation of mRNA degradation. CONCLUSION: These results indicate that butyrate suppresses TNFalpha expression by facilitating mRNA degradation mediated through a cis-acting ARE. Butyrate has the ability to regulate TNFalpha at the mRNA level and is therefore a potential therapeutic drug for RA patients.

3' Untranslated Regions↗
PubMed2000

5-Aza-2'-deoxycytidine leads to down-regulation of aberrant p16INK4A RNA transcripts and restores the functional retinoblastoma protein pathway in hepatocellular carcinoma cell lines.

The inactivation of the cyclin-dependent kinase 4 and 6 (CDK4/6) inhibitor p16INK4A may be caused by gene deletion, mutation or promoter hypermethylation. We have previously reported that p16INK4A in hepatocellular carcinoma (HCC) tissues and cell lines is inactivated predominantly by promoter hypermethylation rather than genomic aberrations. In the present experiments, we have studied the effects of the demethylating agent, 5-aza-2'-deoxycytidine (5-AZA/decitabine), on the expression of aberrant p16INK4A RNA transcripts and the CDK-retinoblastoma gene pathway in HCC cell lines with p16INK4A promoter hypermethylation. The expression of aberrant p16INK4A RNA transcripts was down-regulated and p16INK4A protein was strongly re-expressed in the HCC cell lines, SNU 354, 398, 423 and 475 after 5-AZA/decitabine treatment for 5 days. The re-expressed p16INK4A was functional, because it bound to and inhibited CDK4 kinase activity, and increased the concentrations of the hypophosphorylated form of retinoblastoma protein (pRB) in cells with a wild type RB gene. Moreover, treatment with the demethylating agent led not only to G1 cell cycle arrest, but also to the increased expression of the senescence-associated marker beta-galactosidase. This up-regulation of p16INK4A mRNA and protein correlated with demethylation of the p16INK4A promoter, and with the down-regulation or disappearance of aberrant p16INK4A transcripts. These results suggest that the aberrant p16INK4A RNA transcript can be transcribed from the methylated p16INK4A gene, and endogenous reactivation of functional p16INK4A mRNA by a demethylating agent can restore the pRB pathway in HCC, and foster the terminal differentiation of the malignant cells. Therefore, demethylating agents, such as 5-AZA/decitabine, may have potential in the treatment of HCC.

Azacitidine↗
PubMed1999

Sequencing and exon mapping of the inositol 1,4,5-trisphosphate receptor cDNA from Drosophila embryos suggests the presence of differentially regulated forms of RNA and protein.

A single gene appears to code for the inositol 1,4,5-trisphosphate receptor (itpr) in Drosophila melanogaster, as compared to three known genes in mammals. Expression of the itpr gene in Drosophila occurs in a wide range of tissues and developmental stages, suggesting its requirement during diverse cellular and physiological processes. A head cDNA for the Drosophila IP3R has previously been cloned and sequenced. Here we present and analyse the sequence of cDNAs encoding the complete IP3R, obtained from embryonic stages. The embryonic cDNA is 10525bp long and is a splice variant of the head cDNA. It differs from the latter in three main respects. It has longer 5' and 3' untranslated regions, two potential casein kinase II sites are missing in the embryo form and it contains an alternate exon which results in the replacement of three residues (VHF) in the head form by five residues (GVGHSV) in the embryo form. The significance of these changes is discussed. An exon-intron map of the gene derived from sequencing of intron-containing genomic fragments is also presented. The gene has a total of 11 introns, of which more than half are clustered in a region of the modulatory domain of the IP3R.

Animals↗
PubMed1979

Ribosome biosynthesis in Tetrahymena thermophila. III. Regulation of ribosomal RNA degradation in growing and growth arrested cells.

We have measured the turnover rate of ribosomal RNA in exponentially growing Tetrahymena thermophila cells, cells entering the plateau phase of growth, and nutrient-deprived (starved) cells. Ribosomal RNA is stable in cells in early log phase growth but it begins to turnover as the cells begin a deceleratory growth phase prior to entering a plateau state. Likewise, rRNA in cells transferred from early log phase growth to a starvation medium begins to be degraded immediately upon starvation. In both cases the degradation of rRNA exhibits biphasic kinetics. A rapid initial exponential degradation with a half time of nine and one-half hours lasting for six hours is followed by a slower exponential degradation with a half-life of 35 hours. When starved cells are transferred to fresh growth medium turnover of rRNA ceases. The evidence presented suggests that the alteration in degradation rate is a regulated process which is most likely independent of the cell cycle.

Animals↗
PubMed2005

Regulation of endothelial nitric oxide synthase by small RNA.

Repeats (27-nt) in intron 4 have been shown to play a cis-acting role in endothelial nitric oxide synthase (eNOS) promoter activity. We hypothesize that the 27-nt repeats could be the source of small nuclear RNA specifically regulating eNOS expression. In this study, we used synthesized 27-nt RNA duplex and found that the eNOS gene transcriptional efficiency was reduced 63% (0.047 +/- 0.009 vs. 0.126 +/- 0.015, P < 0.01) by nuclear run-on assay. In endothelial cells transfected with the 27-nt small RNA duplex, we found that the eNOS mRNA and protein levels were decreased by >64% (P < 0.01). Conversely, a randomly selected 27-nt from luciferase gene had no effect on the eNOS expression. Furthermore, this eNOS silencing effect appeared to be reversible under the stimulation of vascular endothelial growth factor (10 ng/ml), which is known to up-regulate eNOS expression. Using in situ hybridization and Northern blotting, we observed the presence of endogenous eNOS intron 4-derived 27-nt small RNA, which was confined to the nucleus. In summary, we demonstrated that intron-based microRNAs in eNOS can induce significant gene specific transcriptional suppression, which could be an effective negative feedback regulator for gene expression.

Cells, Cultured↗
PubMed1996

Androgen regulation of ribosomal RNA synthesis in LNCaP cells and rat prostate.

Androgen-dependent growth of prostate tissue has been well documented. An additional prerequisite for cellular growth is the accumulation of ribosomes. It is thus reasonable to hypothesize that ribosomal DNA (rDNA) transcription in prostate tissue must be stimulated by androgen either directly or indirectly. This hypothesis was tested using both LNCaP cells, an androgen-dependent tissue culture line and in a rat animal model. Nuclear run-on assays confirmed that the administration of DHT to LNCaP cells resulted in a two- to three-fold increase in the rate of rRNA synthesis when compared to cells maintained in the absence of androgen. Enzymatic analysis and Western blots were carried out to measure the amount (activity and mass) of RNA polymerase I in DHT treated LNCaP cells. These assays demonstrated that neither the catalytic activity of RNA polymerase I nor the amount of the enzyme varied in response to DHT. However, Western blots revealed that the amount of the auxiliary RNA polymerase I transcription factor UBF, was significantly increased (two- to three-fold) in cells grown in the presence of DHT. Similar experiments were carried out with prostatic tissue obtained from orchiectomized rats maintained on either placebo or testosterone pellets. In this model, both the catalytic activity as well as the amount of RNA polymerase I protein decreased. However, in agreement with the tissue culture model, UBF protein decreased in prostates from orchiectomized rats and was maintained in animals supplemented with testosterone. These lines of evidence are consistent with the hypothesis that androgens stimulate rRNA synthesis by increasing the quantities of the components of the rDNA transcription system.

Animals↗
PubMed2006

Calmodulin interacts with and regulates the RNA-binding activity of an Arabidopsis polyadenylation factor subunit.

The Arabidopsis (Arabidopsis thaliana) gene that encodes the probable ortholog of the 30-kD subunit of the mammalian cleavage and polyadenylation specificity factor (CPSF) is a complex one, encoding small (approximately 28 kD) and large (approximately 68 kD) polypeptides. The small polypeptide (AtCPSF30) corresponds to CPSF30 and is the focus of this study. Recombinant AtCPSF30 was purified from Escherichia coli and found to possess RNA-binding activity. Mutational analysis indicated that an evolutionarily conserved central core of AtCPSF30 is involved in RNA binding, but that RNA binding also requires a short sequence adjacent to the N terminus of the central core. AtCPSF30 was found to bind calmodulin, and calmodulin inhibited the RNA-binding activity of the protein in a calcium-dependent manner. Mutational analysis showed that a small part of the protein, again adjacent to the N terminus of the conserved core, is responsible for calmodulin binding; point mutations in this region abolished both binding to and inhibition of RNA binding by calmodulin. Interestingly, AtCPSF30 was capable of self-interactions. This property also mapped to the central conserved core of the protein. However, calmodulin had no discernible effect on the self-association. These results show that the central portion of AtCPSF30 is involved in a number of important functions, and they raise interesting possibilities for both the interplay between splicing and polyadenylation and the regulation of these processes by stimuli that act through calmodulin.

Amino Acid Sequence↗
PubMed1994

Expression of lactase-phlorizin hydrolase in sheep is regulated at the RNA level.

Lactase-phlorizin hydrolase (LPH) is expressed on the intestinal brush border and is responsible for the hydrolysis of lactose, the chief sugar in mammalian milk. The enzyme activity of LPH peaks soon after birth in most mammals and declines to much lower levels before adolescence. The molecular basis of this pattern of expression has not been clearly established. We have measured relative amounts of LPH mRNA in intestine from sheep with ages across a developmental spectrum, including third trimester fetal lambs, newborn lambs and adult sheep. LPH mRNA levels in the jejunum decline approximately 50-fold between infancy and adulthood, in parallel with the reduction in both lactase specific activity and immunologically reactive lactase protein expression in sheep jejunum. LPH mRNA is present in high concentration in the duodenum of newborn lambs, but steadily declines by day 34 and is dramatically reduced in adults. Because the changes in LPH mRNA, protein, and enzymic activity are generally parallel, we conclude that the developmental regulation of LPH in sheep is probably mediated primarily at the mRNA level.

Aging↗