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At least 19 recordsLinked to original sources
PubMed2001

Hfq is necessary for regulation by the untranslated RNA DsrA.

DsrA is an 85-nucleotide, untranslated RNA that has multiple regulatory activities at 30 degrees C. These activities include the translational regulation of RpoS and H-NS, global transcriptional regulators in Escherichia coli. Hfq is an E. coli protein necessary for the in vitro and in vivo replication of the RNA phage Qbeta. Hfq also plays a role in the degradation of numerous RNA transcripts. Here we show that an hfq mutant strain is defective for DsrA-mediated regulation of both rpoS and hns. The defect in rpoS expression can be partially overcome by overexpression of DsrA. Hfq does not regulate the transcription of DsrA, and DsrA does not alter the accumulation of Hfq. However, in an hfq mutant, chromosome-expressed DsrA was unstable (half-life of 1 min) and truncated at the 3' end. When expressed from a multicopy plasmid, DsrA was stable in both wild-type and hfq mutant strains, but it had only partial activity in the hfq mutant strain. Purified Hfq binds DsrA in vitro. These results suggest that Hfq acts as a protein cofactor for the regulatory activities of DsrA by either altering the structure of DsrA or forming an active RNA-protein complex.

Bacterial Proteins↗
PubMed2005

Implication of CcpN in the regulation of a novel untranslated RNA (SR1) in Bacillus subtilis.

Antisense-RNAs have been investigated in detail over the past 20 years as the principal regulators in accessory DNA elements such as plasmids, phages and transposons. However, only a few examples of chromosomally encoded bacterial antisense RNAs were known. Meanwhile, approximately 70 small non-coding RNAs from the Escherichia coli genome have been found, the functions of the majority of which remain to be elucidated. Only one systematic search has been performed for Gram-positive bacteria, so far. Here, we report the identification of a novel small (205 nt) non-translated RNA--SR1--encoded in the Bacillus subtilis genome. SR1 was predicted by a computational approach and verified by Northern blotting. Knockout or overexpression of SR1 did not affect growth. SR1 was derepressed under conditions of gluconeogenesis, but repressed under glycolytic conditions. Two regulatory levels could be identified, one involving CcpA, the second, more important, involving the recently identified regulator CcpN.

Bacillus subtilis↗
PubMed2005

Small untranslated RNA antitoxin in Bacillus subtilis.

Toxin-antitoxin (TA) modules are pairs of genes in which one member encodes a toxin that is neutralized or whose synthesis is prevented by the action of the product of the second gene, an antitoxin, which is either protein or RNA. We now report the identification of a TA module in the chromosome of Bacillus subtilis in which the antitoxin is an antisense RNA. The antitoxin, which is called RatA (for RNA antitoxin A), is a small (222 nucleotides), untranslated RNA that blocks the accumulation of the mRNA for a toxic peptide TxpA (for toxic peptide A; formerly YqdB). The txpA and ratA genes are in convergent orientation and overlap by ca. 75 nucleotides, such that the 3' region of ratA is complementary to the 3' region of txpA. Deletion of ratA led to increased levels of txpA mRNA and lysis of the cells. Overexpression of txpA also caused cell lysis and death, a phenotype that was prevented by simultaneous overexpression of ratA. We propose that the ratA transcript is an antisense RNA that anneals to the 3' end of the txpA mRNA, thereby triggering its degradation.

3' Untranslated Regions↗
PubMed2003

Inhibition of tumorigenicity by the 5'-untranslated RNA of the human c-myc P0 transcript.

Activity of the independently regulated human c-myc P0 promoter has been associated with the undifferentiated status of leukemia cells as well as the hormone-independent proliferation of breast cancer cells. The P0 transcript is distinguished from the predominant P1 and P2 c-myc mRNAs by an approximately 639-nucleotide extension of the 5'-untranslated region. We hypothesized that this complex 5'-untranslated RNA sequence unique to the P0 transcript may contribute significantly to the composite regulation of the c-myc locus and that enforced intracellular synthesis of the isolated P0 5'-UTR, out of its native sequence context, might amplify or dominantly interfere with its normal regulatory function. Human tumor (HeLa) cells in which the isolated P0 5'-UTR was ectopically expressed displayed a dramatic decrease in anchorage-independent proliferation. Furthermore, P0 5'-UTR-expressing HeLa cells failed to form tumors when inoculated into SCID mice. This loss of tumorigenicity was associated with increases in levels of the c-Myc1 (p67) and c-Myc2 (p64) proteins and a 3- to 5-fold elevation of spontaneous apoptotic index. These results demonstrate that an isolated 5'-untranslated RNA sequence can be attributed potent in trans gene-regulatory and phenotype-altering capabilities and that extrinsic alterations in c-myc regulation can be utilized to reestablish the natural proapoptotic (tumor suppressor) activities associated with this protooncogene.

5' Untranslated Regions↗
PubMed2006

The small untranslated RNA SR1 from the Bacillus subtilis genome is involved in the regulation of arginine catabolism.

Whereas about 70 small non-coding RNAs have been found in the Escherichia coli genome, relatively little is known about regulatory RNAs from Gram-positive bacteria. Here, we demonstrate that the recently identified small untranslated RNA SR1 from the Bacillus subtilis genome is a regulatory RNA involved in fine-tuning of arginine catabolism. 2D protein gel electrophoresis indicated three possible SR1 targets that are regulated by the transcriptional activator AhrC, which was shown to be the primary target of SR1. In vitro pairing studies and an in vivo reporter gene test demonstrated a specific interaction between SR1 and ahrC mRNA. This interaction did not lead to degradation of ahrC mRNA, but inhibited translation at a post-initiation stage. Our data show that the Hfq chaperone was not required for the stabilization of SR1 in vivo. The amount of SR1 was increased upon addition of l-arginine and l-ornithine, but not l-citrulline or l-proline.

Arginine↗
PubMed2005

Characterization of the small untranslated RNA RyhB and its regulon in Vibrio cholerae.

Numerous small untranslated RNAs (sRNAs) have been identified in Escherichia coli in recent years, and their roles are gradually being defined. However, few of these sRNAs appear to be conserved in Vibrio cholerae, and both identification and characterization of sRNAs in V. cholerae remain at a preliminary stage. We have characterized one of the few sRNAs conserved between E. coli and V. cholerae: RyhB. Sequence conservation is limited to the central region of the gene, and RyhB in V. cholerae is significantly larger than in E. coli. As in E. coli, V. cholerae RyhB is regulated by the iron-dependent repressor Fur, and it interacts with the RNA-binding protein Hfq. The regulons controlled by RyhB in V. cholerae and E. coli appear to differ, although some overlap is evident. Analysis of gene expression in V. cholerae in the absence of RyhB suggests that the role of this sRNA is not limited to control of iron utilization. Quantitation of RyhB expression in the suckling mouse intestine suggests that iron availability is not limiting in this environment, and RyhB is not required for colonization of this mammalian host by V. cholerae.

Bacterial Proteins↗
PubMed1997

Multiple biological roles associated with the Rous sarcoma virus 5' untranslated RNA U5-IR stem and loop.

The 5' untranslated region of Rous sarcoma virus (RSV) RNA is a highly ordered structure involved in multiple processes in the viral replication cycle. One of these structures, referred to as the U5-IR stem, is located immediately upstream of the 5' end of the primer binding site. Disruption of its base pairing results in a decrease in initiation of reverse transcription (D. Cobrinik, A. Aiyar, Z. Ge, M. Katzman, H. Huang, and J. Leis, J. Virol. 65:3864-3872, 1991). In the present study, the length of the U5-IR stem structure has been extended by insertions of different sequences which decrease the efficiency of reverse transcription, in vivo and in vitro. Reverse transcription is rescued partially by placing single-stranded bulges into the middle of the extended duplexes. Nucleotide substitutions or insertions into the loop region of the U5-IR stem also decrease the efficiency of reverse transcription, suggesting that these sequences may specifically interact with reverse transcriptase. Surprisingly, all of the extended stem mutations cause significant RNA packaging defects. In contrast, nucleotide insertions or base substitutions in the U5-IR loop do not affect RNA packaging. These data indicate that the reverse transcription initiation complex and RNA packaging apparatus are influenced by the same region of RSV RNA and that each process is differentially sensitive to changes in sequence and/or secondary structure.

Animals↗
PubMed1996

RNA-binding proteins of 37/38 kDa bind specifically to the barley chloroplast psbA 3'-end untranslated RNA.

The stability of the psbA mRNA increases during barley chloroplast development eventually reaching a half-life of over 40 h. Translation of psbA mRNA is also regulated in a complex way. Sequence-specific RNA binding proteins may modulate the translation or stability of the psbA mRNA during chloroplast development. UV cross-linking assays revealed that chloroplast proteins of 37 and 38 kDA bind specifically to the 3' end of psbA transcripts and not to the 5' end of psbA or rbcL transcripts. The two RNA-binding proteins were partially purified by ammonium sulfate precipitation followed by heparin agarose chromatography. Deletion and site-directed mutation analysis demonstrated that the 37/38RNPs bind in a 30 nucleotide region immediately downstream from the translation termination codon and upstream of sequences capable of forming a stem-loop structure in the 3' end of psbA transcripts. Single-base changes that diminish the binding of the 37RNP also reduce binding of the 38RNP suggesting that these proteins may bind as a heterodimer. The 37/38RNPs that bind within the 3' end of psbA transcripts could modulate transcription termination, translation or mRNA stability.

Base Sequence↗
PubMed2006

Structural characterization of the 5' untranslated RNA of hepatitis C virus by vibrational spectroscopy.

Raman and FTIR spectroscopy have been used to characterize the structure of 5'untranslated region (5'UTR, 342-mer RNA) of the HCV genome. The study of the 750-850 cm(-1) Raman spectral domain of the ribose-phosphate backbone reveals that the percentage of nucleobases involved in double helix-loop junctions is 19+/-1%, which is very close to that of a theoretical secondary structure model (18.7%) proposed on the basis of comparative sequence analysis and thermodynamic modelling. In addition, about 68+/-2% of the bases are helically ordered having C(3')-endo ribofuranose pucker. FTIR-monitored H/D exchange provides the following results: (a) base-paired guanine and cytosine nucleobases show the lowest rate of isotopic exchange, and some synchronous intensity changes of marker bands of A.U pair and single stranded adenine are consistent with the presence of A(*)A.U triplets; (b) the vibrational coupling between the ribose ether C-O stretching and 2'OH bending motions reveals that helical regions of 5'UTR RNA are characterized by hydrogen bonding between the 2'OH ribose groups and the ether oxygen atoms of neighbouring ribose residues.

5' Untranslated Regions↗
PubMed1993

A phylogenetically conserved sequence within viral 3' untranslated RNA pseudoknots regulates translation.

Both the 68-base 5' leader (omega) and the 205-base 3' untranslated region (UTR) of tobacco mosaic virus (TMV) promote efficient translation. A 35-base region within omega is necessary and sufficient for the regulation. Within the 3' UTR, a 52-base region, composed of two RNA pseudoknots, is required for regulation. These pseudoknots are phylogenetically conserved among seven viruses from two different viral groups and one satellite virus. The pseudoknots contained significant conservation at the secondary and tertiary levels and at several positions at the primary sequence level. Mutational analysis of the sequences determined that the primary sequence in several conserved positions, particularly within the third pseudoknot, was essential for function. The higher-order structure of the pseudoknots was also required. Both the leader and the pseudoknot region were specifically recognized by, and competed for, the same proteins in extracts made from carrot cell suspension cells and wheat germ. Binding of the proteins is much stronger to omega than the pseudoknot region. Synergism was observed between the TMV 3' UTR and the cap and to a lesser extent between omega and the 3' UTR. The functional synergism and the protein binding data suggest that the cap, TMV 5' leader, and 3' UTR interact to establish an efficient level of translation.

Base Sequence↗
PubMed1990

The ompA 5' untranslated RNA segment functions in Escherichia coli as a growth-rate-regulated mRNA stabilizer whose activity is unrelated to translational efficiency.

The 5' untranslated region (UTR) of the long-lived Escherichia coli ompA message can function in vivo as an mRNA stabilizer. Substitution of this ompA mRNA segment for the corresponding segment of the labile bla gene transcripts prolongs their lifetime by a factor of 6. We show here that the function of this ompA mRNA stabilizer requires the presence of a 115-nucleotide ompA RNA segment that lies upstream of the ribosome-binding site. Although deletion of this segment reduced the half-life of the ompA transcript by a factor of 5, its absence had almost no effect on the translational efficiency of ompA mRNA. Like the ompA transcript, but unlike bla mRNA, hybrid ompA-bla messages containing the complete ompA 5' UTR were significantly less stable under conditions of slow bacterial growth. We conclude that the stabilizing activity of the ompA 5' UTR is growth rate regulated and that the mechanism of mRNA stabilization by this RNA segment is not related to the spacing between translating ribosomes.

Bacterial Outer Membrane Proteins↗
PubMed2003

The 5'-untranslated RNA of the human dhfr minor transcript alters transcription pre-initiation complex assembly at the major (core) promoter.

The human dhfr minor transcript is distinguished from the predominant dhfr mRNA by an approximately 400 nucleotide extension of the 5'-untranslated region, which corresponds to the major (core) promoter DNA (its template). Based on its unusual sequence composition, we hypothesized that the minor transcript 5'-UTR might be capable of altering transcription pre-initiation complex assembly at the core promoter, through direct interactions of the RNA with specific regulatory polypeptides or the promoter DNA itself. We found that the minor transcript 5'-UTR selectively sequesters transcription factor Sp3, and to a lesser extent Sp1, preventing their binding to the dhfr core promoter. This allows a third putative transcriptional regulatory protein, which is relatively resistant to sequestration by the minor transcript RNA, the opportunity to bind the dhfr core promoter. The selective sequestration of Sp3 > Sp1 by the minor transcript 5'-UTR involves an altered conformation of the RNA, and a structural domain of the protein distinct from that required for binding to DNA. As a consequence, the minor transcript 5'-UTR inhibits transcription from the core promoter in vitro (in trans) in a concentration-dependent manner. These results suggest that the dhfr minor transcript may function in vivo (in cis) to regulate the transcriptional activity of the major (core) promoter.

5' Untranslated Regions↗
PubMed2006

Control of Listeria monocytogenes virulence by 5'-untranslated RNA.

The Gram-positive bacterium Listeria monocytogenes uses a wide range of virulence factors for its pathogenesis. Expression of five of these factors has previously been shown to be subjected to post-transcriptional regulation as a result of their long 5'-untranslated region (5'-UTR). We have investigated the presence of 5'-UTRs among the other known virulence genes and genes that encode putatively virulence-associated surface proteins. Our results strongly suggest that L. monocytogenes controls many of its virulence genes by a mechanism that involves the 5'-UTR. These findings further emphasize the importance of post-transcriptional control for L. monocytogenes virulence.

5' Untranslated Regions↗
PubMed1995

Characterization and regulatory effect of gamma-glutamyltransferase messenger RNA untranslated regions in human leukemia.

In this paper we report the presence and function of the 5' untranslated region (5'UTR) from the mRNA encoding human gamma-glutamyltransferase (GGT) in three different hematopoietic cell lines (HL-60, U-937 and K-562) as well as in the RNA of the leukocyte fraction from six acute lymphoblastic leukemias (ALL). Results obtained by RNase protection analysis demonstrate the presence of a unique form of 5'UTR expressed in most human tissues. In order to investigate the possible role of this type of sequence on regulation of GGT in hematopoietic cells, plasmid constructs carrying human hepatoma GGT 5'UTR and a luciferase reporter gene were transfected into the three blood cell lines. Compared to control untransfected cells, transfected HL-60 and K-562 showed a decrease in reporter gene activity of 51 and 73%, respectively. In contrast, transfected U-937 showed a 139% increase of reporter gene activity. Results were compared to GGT activity in the relevant cells and we concluded that the 5'UTR appears to have a regulatory role in GGT expression as a tissue-specific modulator of translation.

Base Sequence↗
PubMed2000

The gcvB gene encodes a small untranslated RNA involved in expression of the dipeptide and oligopeptide transport systems in Escherichia coli.

The Escherichia coli gcvB gene encodes a small RNA transcript that is not translated in vivo. Transcription from the gcvB promoter is activated by the GcvA protein and repressed by the GcvR protein, the transcriptional regulators of the gcvTHP operon encoding the enzymes of the glycine cleavage system. A strain carrying a chromosomal deletion of gcvB exhibits normal regulation of gcvTHP expression and glycine cleavage enzyme activity. However, this mutant has high constitutive synthesis of OppA and DppA, the periplasmic-binding protein components of the two major peptide transport systems normally repressed in cells growing in rich medium. The altered regulation of oppA and dppA was also demonstrated using oppA-phoA and dppA-lacZ gene fusions. Although the mechanism(s) involving gcvB in the repression of these two genes is not known, oppA regulation appears to be at the translational level, whereas dppA regulation occurs at the mRNA level.

Base Sequence↗
PubMed2003

Neuronal untranslated BC1 RNA: targeted gene elimination in mice.

Despite the potentially important roles of untranslated RNAs in cellular form or function, genes encoding such RNAs have until now received surprisingly little attention. One such gene encodes BC1 RNA, a small non-mRNA that is delivered to dendritic microdomains in neurons. We have now eliminated the BC1 RNA gene in mice. Three independent founder lines were established from separate embryonic stem cells. The mutant mice appeared to be healthy and showed no anatomical or neurological abnormalities. The gross brain morphology was unaltered in such mice, as were the subcellular distributions of two prototypical dendritic mRNAs (encoding MAP2 and CaMKIIalpha). Due to the relatively recent evolutionary origin of the gene, we expected molecular and behavioral consequences to be subtle. Behavioral analyses, to be reported separately, indicate that the lack of BC1 RNA appears to reduce exploratory activity.

Animals↗
PubMed1998

Mammalian X chromosome inactivation.

X chromosome inactivation in mammals requires expression of the gene Xist, which maps to the X chromosome inactivation centre (Xic) and encodes an untranslated RNA. Truncation of Xist RNA by gene targeting is lethal for female embryos and prevents the inactivation of the X chromosome carrying the deletion. This indicates that Xist RNA is necessary for initiation and propagation of the inactivation process. Xist is transcribed from the inactive X and its expression is silenced by DNA methylation, suggesting that methylation is crucial for shielding the active X chromosome against the inactivation process. Gene transfer experiments using transgenes the size of yeast artificial chromosomes have determined that a 450 kb fragment of DNA carrying Xist acts as an inactivation centre and is sufficient for initiation, propagation and maintenance of the inactive state. The elements for counting and choosing X chromosomes are part of the transgene. We have shown that X inactivation is mediated by a post-translational mechanism, i.e. the stabilization of Xist RNA, rather than by the regulation of the Xist promoter.

Animals↗
PubMed2002

The sheep (Ovis aries) H19 gene: genomic structure and expression patterns, from the preimplantation embryo to adulthood.

H19, which is one of the most abundantly expressed imprinted genes during mammalian embryonic and foetal development, has been cloned from a ruminant. The sheep (Ovis aries) gene contains five exons interspersed by four exceptionally small introns; only short stretches of the nucleotide sequence, particularly in exon 1, show good homology with the human gene. The size of the exons and introns and the sequences around the splice junctions however, are well conserved between the species. The gene encodes a approximately 2.6 kb transcript which contains several potential short open reading frames, none of which is conserved between the ovine and human or murine transcripts, supporting a previous hypothesis that the gene product is the untranslated RNA itself. H19 mRNA is highly abundant in most ovine embryonic and foetal tissues of mesodermal and endodermal origins but was not detected in tissues of ectodermal origin such as the trophectoderm and the foetal brain. Expression of H19 in the extraembryonic membranes was detected only after the ovine conceptus began attachment to the endometrium and the embryo itself had undergone early organogenesis. This may be regarded as the first step in implantation; thus, in comparison with the mouse, the initiation of H19 expression appears to be determined by the timing of implantation rather than by the stage of development of the embryo itself. In most tissues, H19 expression is temporally linked to IGF2, a major foetal growth factor. The exceptions were the elongated blastocyst, the trophectoderm and brain, where low levels of IGF2 were observed in the absence of detectable H19. The abundance of H19 mRNA was in general, directly correlated with IGF2 mRNA abundance in mesodermal and endodermal tissues, suggesting that the two ovine genes share common regulatory elements that co-ordinately regulate their expression. Though both are generally regarded as embryonic and foetal genes, their expression was still maintained at a fairly high level in the adult sheep liver, lung, skeletal muscle, adrenal gland and kidney, suggesting that these organs are significant sources of IGF II in the adult.

Animals↗