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At least 523 records · Page 29Linked to original sources
PubMed1996

Regulation of the RNA polymerase I and III transcription systems in response to growth conditions.

To better understand the mechanisms that regulate stable RNA synthesis, we have analyzed the RNA polymerase I and III transcriptional activities of extracts isolated from cells propagated under a variety of conditions. Under balanced growth conditions the levels of both RNA polymerase I- and III-specific transcription increased proportionally with growth rate. Upon nutritional starvation, RNA polymerase I transcription rapidly declined, followed by 5 S rDNA and eventually tDNA transcription. Transcriptional activities in extracts were restored when the nongrowing cultures were resuspended in fresh medium, although growth did not resume. The differential expression of 5 S rDNA and tDNA genes in extracts prepared from cells subjected to partial starvation was traced to a 5 S rDNA-specific inhibitor and not to a defect in any RNA polymerase III transcription factor. Characterization of this inhibitor indicated that it was not 5 S rRNA. It was sensitive to phenol extraction and resistant to RNase, and its target did not appear to be transcription factor IIIA. Not all treatments that slowed or stopped growth down-regulated the stable RNA transcription apparatus. Cells that have been subjected to either energy starvation or cycloheximide treatment still retain the ability to synthesize stable RNA in vitro, suggesting the presence of alternative regulatory mechanisms.

Cell Cycle↗
PubMed2002

Deficient dimerization of human immunodeficiency virus type 1 RNA caused by mutations of the u5 RNA sequences.

The human immunodeficiency virus type 1 (HIV-1) virion contains two copies of genomic RNA that are noncovalently attached along a region at their 5' ends, in which two contact sites have been observed by electron microscopy. One of these sites is believed to be the stem-loop 1 (SL1) sequence which serves as the dimerization initiation site (DIS), and the other site, closer to the 5' end of the viral RNA, may involve the R or U5 RNA sequences. In this study, we present biochemical evidence showing that alteration of the U5 RNA sequence in the context of full-length viral RNA leads to diminished dimerization of virion RNA. In particular, two stretches of GU-rich sequences, which are located at nucleotides (nt) 99 to 108 and nt 112 to 123 within U5, were either deleted or substituted with exogenous sequences. The mutated viruses thus generated all exhibited deficient RNA dimerization. This dimerization deficit was not corrected by second-site mutations that preserved local RNA structures, such as the poly(A) hairpin, and was overcome to only a limited extent by compensatory mutations within Gag; these mutations were identified after long-term culture of the relevant mutant viruses in permissive cell lines and were able to restore viral infectiousness and RNA packaging to wild-type levels. Therefore, these GU sequences do not regulate RNA dimerization by the formation of local secondary structures nor by the maintenance of efficient viral RNA packaging; instead, they may mediate direct RNA-RNA interactions in the dimer structure. In contrast, mutation of palindrome 5'-AAGCUU-3', which resides within R and crowns the poly(A) hairpin, did not affect either RNA dimerization or RNA packaging.

5' Untranslated Regions↗
PubMed2005

Systemic antiviral silencing in plants.

RNA silencing controls numerous developmental processes in eukaryotic organisms from fungi, plants, to animals. In plants as well as in animals, this system of RNA regulation functions as part of an immune response against invading viruses. From transitive RNA silencing to virus-induced gene silencing (VIGS), the systemic effects are proven to be the core of RNA silencing. This article reviews the latest advances in view of the effect of cellular RDR6, an RNA-dependent RNA polymerase (RdRp), on systemic RNA silencing, systemic virus silencing, and discusses the abilities of viral suppressors in modulating RNA silencing efficiency to establish effective infection.

Plant Diseases↗
PubMed2006

Human Immunodeficiency Virus-Type 1 LTR DNA contains an intrinsic gene producing antisense RNA and protein products.

BACKGROUND: While viruses have long been shown to capitalize on their limited genomic size by utilizing both strands of DNA or complementary DNA/RNA intermediates to code for viral proteins, it has been assumed that human retroviruses have all their major proteins translated only from the plus or sense strand of RNA, despite their requirement for a dsDNA proviral intermediate. Several studies, however, have suggested the presence of antisense transcription for both HIV-1 and HTLV-1. More recently an antisense transcript responsible for the HTLV-1 bZIP factor (HBZ) protein has been described. In this study we investigated the possibility of an antisense gene contained within the human immunodeficiency virus type 1 (HIV-1) long terminal repeat (LTR). RESULTS: Inspection of published sequences revealed a potential transcription initiator element (INR) situated downstream of, and in reverse orientation to, the usual HIV-1 promoter and transcription start site. This antisense initiator (HIVaINR) suggested the possibility of an antisense gene responsible for RNA and protein production. We show that antisense transcripts are generated, in vitro and in vivo, originating from the TAR DNA of the HIV-1 LTR. To test the possibility that protein(s) could be translated from this novel HIV-1 antisense RNA, recombinant HIV antisense gene-FLAG vectors were designed. Recombinant protein(s) were produced and isolated utilizing carboxy-terminal FLAG epitope (DYKDDDDK) sequences. In addition, affinity-purified antisera to an internal peptide derived from the HIV antisense protein (HAP) sequences identified HAPs from HIV+ human peripheral blood lymphocytes. CONCLUSION: HIV-1 contains an antisense gene in the U3-R regions of the LTR responsible for both an antisense RNA transcript and proteins. This antisense transcript has tremendous potential for intrinsic RNA regulation because of its overlap with the beginning of all HIV-1 sense RNA transcripts by 25 nucleotides. The novel HAPs are encoded in a region of the LTR that has already been shown to be deleted in some HIV-infected long-term survivors and represent new potential targets for vaccine development.

Base Sequence↗
PubMed1987

Effects of cis- and trans-tamoxifen isomers on RNA incorporation of human breast cancer cells.

Cultured T47-D human breast cancer cells were used to investigate growth-inhibiting effects of the antiestrogen, trans-tamoxifen, on [3H]Cyd incorporation into specific classes of nuclear and cytoplasmic RNA. The steroid agonist, 17 beta-estradiol, and the inactive cis isomer of tamoxifen were used as treatment controls to compare antiestrogen-induced changes in RNA metabolism, independent of estrogen receptor-binding properties. Using a 24-hr labeling interval, trans-tamoxifen produced a 1.4- to 4-fold enhanced incorporation into pre-rRNA species (20S, 32-45S), with slight reduction in mature 18S rRNA incorporation, and a 2- to 3-fold increased incorporation into 5S and 5.8S rRNA and 4-4.5S tRNA. Most notable, trans-tamoxifen enhanced incorporation into the less abundant low molecular weight U1, U3, and 7S RNA species by 3- to 6-fold. These findings were associated with an apparent reduction in pre-rRNA content and little change in U1, U3, or 7S RNA levels in antiestrogen-treated cells, suggesting that trans-tamoxifen independently regulates RNA transcription and turnover. The present study provides new rationale for the choice of molecular probes to study trans-tamoxifen effects on synthesis and turnover of specific nuclear and cytoplasmic RNA species.

Breast Neoplasms↗
PubMed1981

Activation of purified hepatoma RNA polymerase I by homologous protein kinase NII.

We have recently purified a cyclic nucleotide-independent, heparin-sensitive nuclear protein kinase (NII) from Morris hepatoma 3924A and demonstrated an apparent relationship of this kinase to the two subunits (Mr = 42,000 and 24,600) of RNA polymerase I. When homogeneous protein kinase NII was recombined with purified homologous RNA polymerase I containing limiting quantities of endogenous kinase, RNA synthesis was stimulated as much as 5-fold during a 90-min incubation. The enhanced RNA synthesis was due to an increase in the average RNA chain length; protein kinase did not alter the number of RNA molecules synthesized by the polymerase. Phosphorylation of RNA polymerase occurred at serine and threonine moieties. Unlike the NII kinase, purified homologous NI kinase did not phosphorylate RNA polymerase I and, as a result, did not alter transcription. These data indicate that 1) RNA polymerase I is activated by protein kinase NII, 2) endogenous protein kinase NII remaining with highly purified RNA polymerase I does not fully phosphorylate RNA polymerase I in vitro, and 3) protein kinase NII is capable of regulating RNA polymerase I activity by preventing premature termination of RNA chains.

Animals↗
PubMed2003

Differential subnuclear localization of RNA strands of opposite polarity derived from an autonomously replicating viroid.

The wide variety of RNAs produced in the nucleus must be localized correctly to perform their functions. However, the mechanism of this localization is poorly understood. We report here the differential subnuclear localization of RNA strands of opposite polarity derived from the replicating Potato spindle tuber viroid (PSTVd). During replication, (+)- and (-)-strand viroid RNAs are produced. We found that in infected cultured cells and plants, the (-)-strand RNA was localized in the nucleoplasm, whereas the (+)-strand RNA was localized in the nucleolus as well as in the nucleoplasm with distinct spatial patterns. Furthermore, the presence of the (+)-PSTVd in the nucleolus caused the redistribution of a small nucleolar RNA. Our results support a model in which (1) the synthesis of the (-)- and (+)-strands of PSTVd RNAs occurs in the nucleoplasm, (2) the (-)-strand RNA is anchored in the nucleoplasm, and (3) the (+)-strand RNA is transported selectively into the nucleolus. Our results imply that the eukaryotic cell has a machinery that recognizes and localizes the opposite strands of an RNA, which may have broad ramifications in the RNA regulation of gene expression and the infection cycle of pathogenic RNAs and in the development of RNA-based methods to control gene expression as well as pathogen infection.

Cell Nucleolus↗
PubMed1993

Analysis of establishment phase replication of the plasmid ColE1.

The replication regulatory mechanisms by which the small, multicopy plasmid ColE1 maintains a constant steady-state copy number have been extensively characterized by a combination of in vivo genetics and in vitro biochemistry. We have extended the analysis of replication control into the "establishment" phase of replication, when ColE1-directed replicons replicate more than once per cell generation and the intracellular concentrations of plasmid-encoded replication regulatory elements are changing. To study establishment phase replication, in which plasmid-directed replicons amplify from an initially low concentration to the characteristic, steady-state concentration, bacteriophage-plasmid hybrids, termed phasmids, were constructed. Phasmids were shown to exhibit stability, segregation, and incompatibility properties similar to those of the parent plasmid. Establishment phase replication was analyzed by measuring the number of phasmids per cell as a function of time after infection. We observed a linear increase in phasmid concentration until the steady-state concentration characteristic of the ColE1 plasmid component of the hybrid was reached. The number of cell doublings required for the phasmid concentration to reach steady-state was inversely related to cell growth rate. The observed amplification kinetics imply that the frequency of replication initiation per phasmid continually decreases until steady-state is reached. Kinetics of establishment phase amplification were sensitive to rate of expression of RNA II. A phasmid containing an up mutation in the RNA II promoter amplified at a 15-fold faster rate than the wild-type phasmid. Concentration of the ColE1 replication negative regulator (RNA I) was proportional to phasmid concentration throughout the amplification phase. These results suggest that the same elements that regulate steady-state replication also control establishment phase replication.

Bacteriocin Plasmids↗
PubMed2006

The guanosine tetraphosphate (ppGpp) alarmone, DksA and promoter affinity for RNA polymerase in regulation of sigma-dependent transcription.

The RNA polymerase-binding protein DksA is a cofactor required for guanosine tetraphosphate (ppGpp)-responsive control of transcription from sigma70 promoters. Here we present evidence: (i) that both DksA and ppGpp are required for in vivo sigma54 transcription even though they do not have any major direct effects on sigma54 transcription in reconstituted in vitro transcription and sigma-factor competition assays, (ii) that previously defined mutations rendering the housekeeping sigma70 less effective at competing with sigma54 for limiting amounts of core RNA polymerase similarly suppress the requirement for DksA and ppGpp in vivo and (iii) that the extent to which ppGpp and DksA affect transcription from sigma54 promoters in vivo reflects the innate affinity of the promoters for sigma54-RNA polymerase holoenzyme in vitro. Based on these findings, we propose a passive model for ppGpp/DksA regulation of sigma54-dependent transcription that depends on the potent negative effects of these regulatory molecules on transcription from powerful stringently regulated sigma70 promoters.

DNA-Directed RNA Polymerases↗
PubMed1994

Effect of in utero ethanol exposure on the postnatal ontogeny of insulin-like growth factor-1, and type-1 and type-2 insulin-like growth factor receptors in the rat brain.

There is convincing evidence that alcohol consumption during pregnancy causes major CNS abnormalities; however, the molecular and cellular basis of these dysfunctions is currently not understood. This study examined the effects of prenatal ethanol exposure on the expression of insulin-like growth factor-1 messenger RNA and type-1 and type-2 receptor protein and messenger RNA expression in the developing rat brain. Mothers were maintained on an ethanol containing liquid diet from day 2 of pregnancy through parturition and the offspring were killed at birth, 10, 20 and 40 days of age. Insulin-like growth factor-1 messenger RNA, and insulin-like growth factor receptors demonstrated developmentally dependent expression in specific brain regions throughout the postnatal period of CNS maturation. Insulin-like growth factor-1 gene expression in the brain, as analysed by dot-blot hybridization, was greatest at birth, and decreased 61% in ad libitum and pair-fed animals by 20 days of age. In contrast, ethanol-treated animals exhibited only a 25% decrease in insulin-like growth factor-1 messenger RNA levels during the same period. This delay in insulin-like growth factor-1 messenger RNA maturation may be related to a developmental delay in CNS development in the prenatally ethanol exposed offspring. Prenatal ethanol exposure did not alter the observed localization of insulin-like growth factor-1 messenger RNA. While alterations were observed in long-term insulin-like growth factor-1 messenger RNA regulation, quantitative receptor autoradiography and in situ hybridization demonstrated no alterations in either type-1 or type-2 insulin-like growth factor receptor populations in ethanol-treated animals. Changes in hepatic and plasma insulin-like growth factor-1 and insulin-like growth factor-binding protein regulation have also been observed in these animals, suggesting changes in protein translation and the autocrine/paracrine actions of this peptide. The present study demonstrated that insulin-like growth factor-1 messenger RNA and insulin-like growth factor receptors are regionally expressed during early postnatal development and that ethanol administration influenced the long-term regulation of insulin-like growth factor messenger RNA levels in the brain without affecting either its localization or insulin-like growth factor receptor populations.(ABSTRACT TRUNCATED AT 400 WORDS)

Aging↗
PubMed1970

The effect of feeding with a tryptophan-free amino acid mixture on rat liver magnesium ion-activated deoxyribonucleic acid-dependent ribonucleic acid polymerase.

1. The Widnell & Tata (1966) assay method for Mg(2+)-activated DNA-dependent RNA polymerase was used for initial-velocity determinations of rat liver nuclear RNA polymerase. One unit (U) of RNA polymerase was defined as that amount of enzyme required for 1 mmol of [(3)H]GMP incorporation/min at 37 degrees C. 2. Colony fed rats were found to have a mean RNA polymerase activity of 65.9muU/mg of DNA and 18h-starved rats had a mean activity of 53.2muU/mg of DNA. Longer periods of starvation did not significantly decrease RNA polymerase activity further. 3. Rats that had been starved for 18h were used for all feeding experiments. Complete and tryptophan-deficient amino acid mixtures were given by stomach tube and the animals were killed 15-120min later. The response of RNA polymerase to the feeding with the complete amino acid mixture was rapid and almost linear over the first hour of feeding, resulting in a doubling of activity. The activity was still elevated above the starvation value at 120min after feeding. The tryptophan-deficient amino acid mixture produced a much less vigorous response about 45min after the feeding, and the activity had returned to the starvation value by 120min after the feeding. 4. The response of RNA polymerase to the feeding with the complete amino acid mixture was shown to occur within a period of less than 5min to about 10min after the feeding. 5. Pretreatment of the animals with puromycin or cycloheximide was found to abolish the 15min RNA polymerase response to the feeding with the complete amino acid mixture, but the activity of the controls was unaffected. 6. The characteristics of the RNA polymerase from 18h-starved animals and animals fed with the complete or incomplete amino acid mixtures for 1h were examined. The effects of Mg(2+) ions, pH, actinomycin D and nucleoside triphosphate omissions were determined. The [Mg(2+)]- and pH-activity profiles of the RNA polymerase from the animal fed with the complete mixture appeared to differ from those of the enzyme from the other groups, but this difference is probably not significant. 7. [5-(3)H]Orotic acid incorporation by rat liver nuclei in vivo was shown to be affected by the amino acid mixtures in a similar manner to the RNA polymerase. 8. The tryptophan concentrations of plasma and liver were determined up to 120 min after feeding with the amino acid mixtures. Feeding with the complete mixture produced a rapid increase in free tryptophan concentrations in both plasma and liver, but feeding with the incomplete mixture did not alter the plasma concentration. The liver tryptophan concentration increased at about 45min after feeding with the tryptophan-deficient diet. 9. There was a good correlation between the liver tryptophan concentration and RNA polymerase activity in all groups of animals. 10. It was concluded that the rat liver nucleus responded to an increase in amino acid supply by increased synthesis of RNA as a result of synthesis of RNA polymerase de novo. The correlation of tryptophan concentration and RNA polymerase activity appears to reflect the general amino acid concentration required to support hepatic protein synthesis and to produce new RNA polymerase. This new polymerase appears to differ from the basal RNA polymerase by its rapid synthesis and destruction, which may be a means of regulating RNA synthesis by the amino acid concentration in the liver.

Amino Acids↗
PubMed1999

Parathyroid hormone-related protein interacts with RNA.

Parathyroid hormone-related protein (PTHrP) is a secreted protein that acts as an autocrine and paracrine mediator of cell proliferation and differentiation. In addition to its biological activity that is mediated through signal transduction cascades, there is evidence for an intracellular role for PTHrP in cell cycle progression and apoptosis. These effects are mediated through a mid-region nuclear targeting sequence (NTS) that localizes PTHrP to the region of the nucleolus where ribonucleoprotein complexes form in vivo. In this work, we show that endogenous, transfected, and in vitro translated PTHrP proteins bind homopolymeric and total cellular RNAs at salt concentrations up to 1 M. A peptide representing the PTHrP NTS was effective in competing with the wild-type protein for RNA binding, whereas a similar peptide representing the nucleolin NTS was not. Site-directed mutagenesis revealed that the binding of PTHrP to RNA was direct and was dependent on preservation of a core GXKKXXK motif, embedded in the PTHrP NTS, which is shared with other RNA-binding proteins. The current observations are the first to document RNA binding by a secreted cellular protein and predict a role for PTHrP in regulating RNA metabolism that may be related to its localization in the nucleolus of cells in vivo.

Amino Acid Sequence↗
PubMed2006

Homologous gene sequences mediate transcription-domain formation.

The organisation of transcription in the mammalian nucleus is a topic of particular interest because of its relevance to gene regulation. RNA polymerase II transcription occurs at hundreds of sites throughout the nucleoplasm. Recent data indicate that coordinately regulated genes can localise to shared transcription sites. Other transcribed sequences have also been shown to cluster in the nucleus. The ribosomal RNA genes cluster in the nucleoli. Similarly, transiently transfected plasmids and dsDNA viruses form transcription domains (TDs) containing multiple templates. Intriguingly, plasmids expressing beta-globin gene sequences recruit the endogenous beta-globin loci to their TDs. In light of this observation, we have investigated plasmid TDs as a model for gene recruitment. We find that TD formation is dependent on the presence of homologous gene sequences. Plasmids containing non-homologous gene sequences form separate TDs, independent of homology in the backbone or promoter sequences. TD formation is also favoured by low plasmid concentrations. This effect is sequence-specific and high concentrations of one plasmid do not disrupt domain formation by non-homologous plasmids in the same cell. We conclude that recruitment into TDs is an active process that is driven by homologies between transcribed sequences and becomes saturated at high copy numbers.

Base Sequence↗
PubMed2002

Alternative splicing of the 5'-sequences of the mouse EAAT2 glutamate transporter and expression in a transgenic model for amyotrophic lateral sclerosis.

Glutamate-mediated neurotoxicity and a reduced expression of the excitatory amino acid transporter 2 (EAAT2) have been described in the pathogenesis of several acute and chronic neurological conditions. EAAT2 is the major carrier of glutamate in the mammalian brain. However, the principles of EAAT2 expression regulation are not fully understood. For the human brain, extensive alternative splicing of the EAAT2 RNA has been shown. To delineate the complex RNA regulation of EAAT2 we investigated whether the murine species is a suitable model for the study of EAAT2 splicing events. We identified five splice variants (mEAAT2/5UT1-5) encoding different 5'-untranslated sequences and two distinct N-termini of the putative EAAT2 polypeptide. In the murine CNS we found a region-specific expression pattern of the novel 5'-variants of EAAT2 as shown by in situ hybridization, dot blotting and competitive reverse transcription polymerase chain reaction. Furthermore, we performed an expression analysis of the EAAT2 splice variants in the spinal cord of a transgenic model (SOD1G93A) of amyotrophic lateral sclerosis, a motor neurone disease for which altered splicing of EAAT2 has been discussed. We found an increased expression of mEAAT2/5UT4 and a reduction of mEAAT2/5UT5 in the early course of the disease. We conclude that alternative splicing of 5'-sequences may contribute to the regional expression of the EAAT2 RNA and was altered in the pre-symptomatic stage of the SOD1G93A-mouse model for amyotrophic lateral sclerosis.

5' Untranslated Regions↗
PubMed2004

Effects and side-effects of viral RNA silencing suppressors on short RNAs.

In eukaryotes, short RNAs play a crucial regulatory role in many processes including development, maintenance of genome stability and antiviral responses. These different but overlapping RNA-guided pathways are collectively termed 'RNA silencing'. To counteract an antiviral RNA silencing response, plant viruses express silencing suppressor proteins. Recent results have shown that silencing suppressors operate by modifying the accumulation and/or activity of short RNAs involved in the antiviral response. Because RNA silencing pathways intersect, silencing suppressors can also inhibit other short-RNA-regulated pathways. Thus, suppressors contribute to viral symptoms. These findings fuel further research to test whether certain symptoms caused by animal viruses are also manifestations of altered RNA regulatory pathways.

Cysteine Endopeptidases↗
PubMed1994

Intragenic sequences of the human glucocorticoid receptor complementary DNA mediate hormone-inducible receptor messenger RNA down-regulation through multiple mechanisms.

Glucocorticoid receptors (GR) are ligand-dependent transcription factors that play a critical role in the endocrine control of cell growth, differentiation, and death. These steroid receptors are widely recognized to undergo down-regulation after exposure to ligand in cell cultures and animals, including humans. This reduction in cellular receptor levels leads to insensitivity to subsequent hormone administration. The mechanisms controlling homologous down-regulation of the GR are, however, poorly understood. We have previously shown (1) that a transfected human GR (hGR) complementary DNA (cDNA) contains sequences that are sufficient to recapitulate the down-regulation of both hGR messenger RNA (mRNA) and protein seen in vivo. We have now evaluated potential mechanisms involved in the hormonal regulation of the hGR mRNA and, further, have identified an intragenic domain of the hGR cDNA that contains the down-regulatory signal. Glucocorticoid treatment of COS-1 cells expressing a transfected hGR cDNA resulted in down-regulation of the hGR mRNA in the presence of cycloheximide or actinomycin-D, suggesting that a glucocorticoid-inducible protein was not essential for down-regulation. We show that prolonged receptor occupation by ligand leads to increased GR mRNA turnover, and furthermore, that either the agonist dexamethasone or the antagonist RU486 decreased transcription of the hGR cDNA. To resolve which receptor cDNA sequences are critical in down-regulation, a cotransfection strategy was employed in which a series of hGR cDNA deletion mutants was transfected in conjunction with the full-length hGR cDNA. The effects of glucocorticoid on the regulation of receptor mRNAs encoded by the mutant receptor cDNAs were examined. Deletions within the 5' half of the receptor cDNA produced transcripts that were susceptible to glucocorticoid-mediated down-regulation, whereas deletion of sequences located in the 3'-end of the receptor-coding sequence (corresponding to amino acids 550-697) resulted in receptor transcripts that were only minimally down-regulated by glucocorticoid. Together these studies indicate that multiple mechanisms control GR mRNA abundance, and an intragenic element within the ligand-binding domain is critical for this down-regulation.

Animals↗
PubMed2004

The chromatin remodeling complex NoRC and TTF-I cooperate in the regulation of the mammalian rRNA genes in vivo.

The transcription termination factor (TTF)-I is a multifunctional nucleolar protein that terminates ribosomal gene transcription, mediates replication fork arrest and regulates RNA polymerase I transcription on chromatin. TTF-I plays a dual role in rDNA regulation, being involved in both activation and silencing of rDNA transcription. The N-terminal part of TTF-I contains a negative regulatory domain (NRD) that inhibits DNA binding. Here we show that interactions between the NRD and the C-terminal part of TTF-I mask the DNA-binding domain of TTF-I. However, interaction with TIP5, a subunit of the nucleolar chromatin remodeling complex, NoRC, recovers DNA-binding activity. We have mapped the protein domains that mediate the interaction between TTF-I and TIP5. The association of TIP5 with the NRD facilitates DNA binding of TTF-I and leads to the recruitment of NoRC to the rDNA promoter. Thus, TTF-I and NoRC act in concert to silence rDNA transcription.

Animals↗
PubMed2003

Identification of the Hfq-binding site on DsrA RNA: Hfq binds without altering DsrA secondary structure.

DsrA RNA regulates the translation of two global regulatory proteins in Escherichia coli. DsrA activates the translation of RpoS while repressing the translation of H-NS. The RNA-binding protein Hfq is necessary for DsrA to function in vivo. Although Hfq binds to DsrA in vitro, the role of Hfq in DsrA-mediated regulation is not known. One hypothesis was that Hfq acts as an RNA chaperone by unfolding DsrA, thereby facilitating interactions with target RNAs. To test this hypothesis, we have examined the structure of DsrA bound to Hfq in vitro. Comparison of free DsrA to DsrA bound to Hfq by RNase footprinting, circular dichroism, and thermal melt profiles shows that Hfq does not alter DsrA secondary structures, but might affect its tertiary conformation. We identify the site on DsrA where Hfq binds, which is a structural element in the middle of DsrA. In addition, we show that although long poly(U) RNAs compete with DsrA for binding to Hfq, a short poly(U) stretch present in DsrA is not necessary for Hfq binding. Finally, unlike other RNAs, DsrA binding to Hfq is not competed with by poly(A) RNA. In fact, DsrA:poly(A):Hfq may form a stable ternary complex, raising the possibility that Hfq has multiple RNA-binding sites.

Bacterial Outer Membrane Proteins↗