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At least 469 records · Page 26Linked to original sources

PubMed1998

The solution structure of an RNA loop-loop complex: the ColE1 inverted loop sequence.

BACKGROUND: Replication of the ColE1 plasmid of Escherichia coli is regulated by the interaction of sense and antisense plasmid-encoded transcripts. The antisense RNA I negatively regulates the replication of the plasmid by duplex formation with complementary RNA II. The interaction is initiated by the formation of a double helix between seven-nucleotide loops from each RNA and is stabilized by binding of the RNA one modulator (ROM) protein. The ROM protein is thought to recognize a specific RNA structure, regardless of sequence. RESULTS: The solution structure of a loop-loop complex between model RNA hairpins that resemble RNA I and RNA II has been determined by nuclear magnetic resonance spectroscopy. The model hairpins have loop sequences inverted 5' to 3' relative to the wild-type sequence and were chosen because of their complex's slow dissociation in comparison to the wild type. The complex has continuous stacking from the 3'-side of one stem helix through the loop-loop helix to the other stem helix. One residue from each hairpin has a unique phosphodiester bond which bridges and narrows the major groove. These bridging phosphates are in close proximity to the phosphate groups of the adjacent bases, forming unique structural motifs called phosphate clusters. The purine residue at the 3'-end of the loop-loop helix of one RNA stacks on a purine residue on the 5'-side of the other RNA stem, and there are strong cross-strand stacking interactions between guanine bases in the stem helices adjacent to the loops. CONCLUSIONS: Unique distortions, such as the strong bend and the phosphate clusters flanking the major groove of the loop-loop helix, provide an attractive nonsequence-specific structural feature for recognition by the ROM protein. The structure provides a basis for rationalizing the sequence dependence of the stability of loop-loop interaction.

Bacterial Proteins↗

PubMed2002

Cellular RNA-dependent RNA polymerase involved in posttranscriptional gene silencing has two distinct activity modes.

Recent genetic data suggest that proteins homologous to a plant RNA-dependent RNA polymerase (RdRP) play a central role in posttranscriptional gene silencing (PTGS) in many organisms. We show here that purified recombinant protein QDE-1, a genetic component of PTGS ("quelling") in the fungus Neurospora crassa, possesses RNA polymerase activity in vitro. The full-length enzyme and its enzymatically active C-terminal fragment perform two different reactions on single-stranded RNA templates, synthesizing either extensive RNA chains that form template-length duplexes or approximately 9-21-mer complementary RNA oligonucleotides scattered along the entire template. QDE-1 supports both de novo and primer-dependent initiation mechanisms. These results suggest that several distinct activities of cell-encoded RdRPs can be employed for efficient PTGS in vivo.

Amino Acid Sequence↗

PubMed2004

Single-chain antibodies against a plant viral RNA-dependent RNA polymerase confer virus resistance.

Crop loss due to viral diseases is still a major problem for agriculture today. We present a strategy to achieve virus resistance based on the expression of single-chain Fv fragments (scFvs) against a conserved domain in a plant viral RNA-dependent RNA polymerase (RdRp), a key enzyme in virus replication. The selected scFvs inhibited complementary RNA synthesis of different plant virus RdRps in vitro and virus replication in planta. Moreover, the scFvs also bound to the RdRp of the distantly related hepatitis C virus. T(1) and T(2) progeny of transgenic lines of Nicotiana benthamiana expressing different scFvs either in the cytosol or in the endoplasmic reticulum showed varying degrees of resistance against four plant viruses from different genera, three of which belong to the Tombusviridae family. Virus resistance based on antibodies to RdRps adds another tool to the repertoire for combating plant viruses.

Amino Acid Motifs↗

PubMed1993

2'-O-alkyloligoribonucleotides: probes for studying the biochemistry and cell biology of RNA processing.

Chemical synthesis of 2'-O-alkyloligoribonucleotides has been developed and shown to have important applications in the study of RNA processing and the analysis of structure-function relationships in RNA molecules. Antisense oligonucleotides made of 2'-O-alkyl RNA are nuclease-resistant and form extremely stable and specific hybrids with complementary RNA target sequences. This makes them very useful probes for labelling RNAs, for functional studies on the mechanism of RNA processing reactions and for affinity chromatography of RNA-protein complexes. The use of 2'-O-alkyloligoribonucleotides thus provides an important alternative strategy to immunological methods for biochemists wishing to modify, purify, deplete, inactivate or in situ-label RNAs or RNPs. I very much hope that the work I have described here may have helped to stimulate other workers in the RNA field to consider applying these techniques to further their own research interests.

Animals↗

PubMed1989

Loss of tumorigenic potential by human lung tumor cells in the presence of antisense RNA specific to the ectopically synthesized alpha subunit of human chorionic gonadotropin.

A clonal strain of human lung tumor cells in culture (ChaGo), derived from a bronchogenic carcinoma, synthesizes and secretes large amounts of alpha (alpha) and a comparatively lower level of beta (beta) subunit of the glycoprotein hormone, human chorionic gonadotropin (HCG). ChaGo cells lost their characteristic anchorage-independent growth phenotype in the presence of anti-alpha-HCG antibody. The effect of the antibody was partially reversed by addition of alpha-HCG to the culture medium. ChaGo cells were transfected with an expression vector (pRSV-anti-alpha-HCG), that directs synthesis of RNA complementary to alpha-HCG mRNA. The transfectants produced alpha-HCG antisense RNA which was associated with the reduced level of alpha-HCG. Transfectants also displayed several altered phenotypic properties, including altered morphology, less mitosis, reduced growth rate, loss of anchorage-independent growth, and loss of tumorigenicity in nude mice. Treatment of transfectants with 8,bromo-cAMP resulted in increased accumulation of alpha-HCG mRNA, no change in the level of alpha-HCG antisense RNA, release of the inhibition of [3H]thymidine incorporation, and restoration of anchorage-independent growth phenotype. The overexpression of c-myc, observed in ChaGo cells, was unaffected by the reduced level of alpha-HCG. These results suggest that ectopic synthesis of the alpha subunit of HCG plays a functional role in the transformation of these human lung cells.

8-Bromo Cyclic Adenosine Monophosphate↗

PubMed1975

Cellular RNA and influenza-virion RNA are synthesized from different pyrimidine-nucleoside-triphosphate pools in chick-embryo cells.

Chick embryo cells infected with an influenza A (fowl plague) virus have been labelled with (3H)-uridine for different lengths of time. Virion RNA and cellular RNA have been separated by specific hybridization with a surplus of unlabelled viral complementary RNA and RNase digestion. The ratio of the specific radioacticity in the UMP and CMP moieties of both types of RNA has been determined. Since the rate of approach to equilibrium of CMP to UMP labelling of both types of RNA is completely different it is concluded that cellular and virion RNA are synthesized using different pyrimidine nucleoside triphosphate pools.

Animals↗

PubMed1981

Monocistronic transcription is the physiological mechanism of sea urchin embryonic histone gene expression.

We have examined histone gene expression during the early stages of sea urchin embryogenesis. The five histone genes expressed at that time are contained in tandem repetitive segments. It has been suggested that adjacent coding regions and their intervening spacer sequences are transcribed into large polycistronic messenger ribonucleic acid (RNA) precursors. We have subcloned into pBR322 deoxyribonucleic acid (DNA) sequences mapping either in the coding region, the 5' spacer, or the 3' spacer of the H2B histone gene. These clones were used to produce radioiodinated hybridization probes. We measured the steady-state quantity of H2B messenger RNA as well as spacer-specific RNA in the total RNA from embryos taken at various stages of development from fertilization to hatching of blastulae (0 to 22 h post-fertilization). Small amounts of RNA hybridizing to both spacer probes could be found. However, we show that these RNAs form mismatched hybrids with the spacer DNA and therefore cannot originate from the spacers present in the histone genes. We conclude that there is no detectable transcription of the spacer regions on either side of the H2B histone gene. The detection limit for RNA complementary to the 5' spacer sequence corresponds to a maximum of about three RNA molecules per cell, an amount shown to be far less than the projected steady-state pool size of a putative polycistronic transcript, if such a precursor were to be the obligatory transcript of the histone genes. (This conclusion was derived by using the known rates of production of H2B mRNA throughout early development [R. E. Maxson and F. H. Wilt, Dev. Biol., in press].) The physiologically relevant transcript of the histone genes in early development is therefore monocistronic and probably identical to the messenger RNA itself.

Animals↗

PubMed1991

Regulation of polyadenylation of hepatitis delta virus antigenomic RNA.

Hepatitis delta virus (HDV) is a subviral agent with a small RNA genome that is replicated in the nucleus of an infected cell. During genome replication, there is the synthesis of a complementary RNA, known as the antigenome, and also of a smaller complementary species that is polyadenylated and acts in the cytoplasm as the mRNA for the only known HDV protein, the delta antigen. We have carried out an examination of the cis- and trans-acting elements that regulate the polyadenylation process involved in the synthesis of this mRNA for the delta antigen. Our experimental approach has been to study the processing of nascent antigenomic RNA as it occurs in transfected cells via DNA-directed RNA synthesis, in the absence of genome replication. Three conclusions have been made. (i) The polyadenylation process occurs independent of the functionality of a unique self-cleavage domain located just 3' of the polyadenylation site. (ii) RNA transcripts that proceed beyond the polyadenylation site can be stabilized by the self-cleavage reaction. Thus, a single transcription initiation event can lead not only to the mRNA species but also to at least one more stable RNA species. (iii) If the nascent RNA species can fold on itself, into the so-called rodlike structure, then the presence of the delta antigen leads to a major suppression of polyadenylation. These results are incorporated into a more detailed model of the replication of the HDV genome.

Animals↗

PubMed1983

Molecular induction by phenobarbital of a rat hepatic form of cytochrome P-450: expression of a 4-kilobase messenger RNA.

A differential screening procedure was employed to isolate a cDNA clone corresponding to a major phenobarbital (PB)-inducible form of rat hepatic cytochrome P-450. The G-C homopolymer-tailing technique was utilized to construct a cDNA library in the PstI site of plasmid pBR322. The library represented PB-induced poly(A+)RNA sequences from hepatic polysomes of 150-g male Sprague-Dawley rats. Hybrid-selection experiments against total PB-inducible RNA were performed with plasmid DNA derived from clones enriched in PB-inducible information. The mRNA molecules that specifically hybridized were subjected to in vitro translation, were immunoprecipitated with antibody raised in rabbits against purified cytochrome P-450b (P. E. Thomas, D. Korzeniowski, D. Ryan, and W. Levin (1979) Arch. Biochem. Biophys. 192, 524-532), and were electrophoresed under sodium dodecyl sulfate (SDS)-polyacrylamide gel electrophoretic conditions. One cDNA clone, designated PB-8, contained a 600-bp insert partially coding for a PB-inducible cytochrome P-450 species that comigrated on SDS-gel electrophoresis with highly purified P-450b. A single injection of PB, 15-18 h before sacrifice, increased the level of polysomal poly(A+)RNA complementary to the isolated cDNA clone by approximately 16-fold. Northern blot hybridizations of polysome-derived poly (A+)RNA, electrophoresed in denaturing agarose gels, demonstrated that the size of the mRNA corresponding to the isolated clone was 4 kb. Isolated heteronuclear RNA species demonstrated a time-dependent increase in the synthesis of a similar 4-kb RNA molecule. By genomic blot hybridization to EcoRI-restricted DNA, at least three complementary DNA fragments migrating at 5.1, 3.2, and 2.9 kb were observed with 32P-labeled PB-8 as a probe. These data, together with restriction endonuclease mapping and partial cDNA sequence information of the PB-8 cDNA, suggest that the PB-8 clone represents a previously unreported cDNA clone for a form of cytochrome P-450 inducible by PB.

Animals↗

PubMed1982

Synthesis of RNA segments 1-3 during generation of incomplete influenza A (fowl plague) virus.

Incomplete influenza A virus (fowl plague Dobson strain) was prepared by undiluted passage in primary chick embryo fibroblast cells. Analysis of released virus RNA revealed a deficiency in RNA segments 1-3, characteristic of incomplete virus formation. The virus yield from a high multiplicity infection with standard virus always showed this deficiency, even when analysed as early as 6 hours post-infection, whereas infection at low multiplicity gave rise to virus indistinguishable in RNA composition from the parent virus. The relative amounts of intracellular, non-polyadenylated, complementary RNA (template RNA) were found to reflect accurately the eventual RNA composition of released virus, and were altered in phase with PFU:HAU ratio, throughout a von Magnus cycle.

Animals↗

PubMed1988

Translational control and differential RNA decay are key elements regulating postsegregational expression of the killer protein encoded by the parB locus of plasmid R1.

The parB locus of plasmid R1, which mediates plasmid stability via postsegregational killing of plasmid-free cells, encodes two genes, hok and sok. The hok gene product is a potent cell-killing protein. The hok gene is regulated at the translational level by the sok gene-encoded repressor, a small anti-sense RNA complementary to the hok mRNA. The hok mRNA is extraordinarily stable, while the sok RNA decays rapidly. The mechanism of postsegregational killing is explained by the following model; the sok RNA molecule rapidly disappears in cells that have lost a parB-carrying plasmid, leading to translation of the stable hok mRNA. Consequently, the Hok protein is synthesized and killing of the plasmid-free cell follows.

Base Sequence↗

PubMed1992

RNA-DNA hybridization promoted by E. coli RecA protein.

RecA protein of E. coli plays a central regulatory role that is induced by damage to DNA and results in the inactivation of LexA repressor. In vitro, RecA protein binds preferentially to single-stranded DNA to form a nucleoprotein filament that can recognize homology in naked duplex DNA and promote extensive strand exchange. Although RecA protein shows little tendency at neutral pH to bind to RNA, we found that it nonetheless catalyzed at 37 degrees C the hybridization of complementary RNA and single-stranded DNA sequences. Hybrids made by RecA protein at 37 degrees C appeared indistinguishable from ones prepared by thermal annealing. RNA-DNA hybridization by RecA protein at neutral pH required, as does RecA-promoted homologous pairing, optimal conditions for the formation of RecA nucleoprotein filaments. The cosedimentation of RNA with those filaments further paralleled observations made on the formation of networks of nucleoprotein filaments with double-stranded DNA, an instrumental intermediate in homologous pairing in vitro. These similarities with the pairing reaction support the view that RecA protein acts specifically in the hybridization reaction.

Bacterial Proteins↗

PubMed1992

Nucleotide sequence and coding strategy of the Uukuniemi virus L RNA segment.

The complete nucleotide sequence of the L RNA segment of Uukuniemi virus has been determined from cloned cDNA. The L RNA is 6423 nucleotides in length, and is of negative polarity. The viral-complementary RNA contains a single large open reading frame of 2104 codons which corresponds to the L protein (M(r) 241039). Comparison with the L protein sequences of other members of the Bunyaviridae showed homology with the Rift Valley fever phlebovirus L protein (38% amino acid identity), but no detectable similarity with bunyavirus, hantavirus or tospovirus L proteins. These data lend further support for the recent reclassification of uukuviruses and phleboviruses into the same genus, Phlebovirus, in the family Bunyaviridae. The L RNA sequence completes the determination of the Uukuniemi virus genome: since the M RNA segment is 3229 and the S RNA segment 1720 nucleotides, the whole genome comprises 11372 nucleotides.

Amino Acid Sequence↗

PubMed2006

Structure of an RNA duplex r(GGCGBrUGCGCU)2 with terminal and internal tandem G.U base pairs.

The crystal structure of a self-complementary RNA duplex r(GGCG(Br)UGCGCU)(2) with terminal G.U and internal tandem G.U base pairs has been determined at 2.1 Angstroms resolution. The crystals belong to the tetragonal space group P4(3), with unit-cell parameters a = b = 37.69, c = 96.28 Angstroms and two duplexes in the asymmetric unit. The two strands of each duplex are related by a pseudodyad axis. The structure was refined to final R(work) and R(free) values of 20.9 and 25.3%, respectively. The duplexes stack in an end-to-end manner, forming infinite columns along the c axis. This is the first structural study of an RNA duplex containing G.U pairs at the termini. The stacking overlaps of the terminal G.U base pairs with their adjacent Watson-Crick base pairs are larger than those of Watson-Crick base pairs of the 5'-YR-3'/3'-RY-5' type. The terminal G.U base pairs of neighbouring duplexes are also stacked with each other. An alternating underwound-overwound pattern of the twist angles is seen at each step along the duplex. This observation is typical for internal tandem G.U pairs, while the terminal G.U base pairs exhibit high twist angles with the adjacent Watson-Crick pairs. The 3'-side of U of the internal G.U base pair, which is unstacked, appears to be stabilized by pi-cation interaction with an Mg(2+) ion.

Base Pairing↗

PubMed1963

TRANSCRIPTION IN VIVO OF DNA FROM BACTERIOPHAGE SP8.

The DNA of bacteriophage SP8, when denatured, yields two components differing in buoyant density in cesium chloride gradients and separable by chromatography on a column of methylated bovine serum albumin and kieselguhr. The denser of the two strands (H) contains more pyrimidines and fewer purines than the lighter (L) strand. Only the H strand forms hybrids with the RNA synthesized by the infected host. The L strand is capable of annealing with complementary RNA synthesized in vitro with it as primer in reactions catalyzed by RNA polymerase. During the vegetative development of phage, host-specific messenger RNA is also synthesized.

Bacillus subtilis↗

PubMed2000

Growth-associated protein-43 messenger ribonucleic acid expression in gonadotropin-releasing hormone neurons during the rat estrous cycle.

We have shown previously at the ultrastructural level that morphological changes occur in the external zone of the median eminence allowing certain GnRH nerve terminals to contact the pericapillary space on the day of proestrus. The present study was designed to determine whether the intrinsic determinant of neuronal outgrowth, growth-associated protein-43 (GAP-43), was expressed in GnRH neurons of adult female rats, and whether its expression varied throughout the estrous cycle. To accomplish this, we perfusion-fixed groups of adult female rats at 0800 and 1600 h on diestrous day 2 (diestrous II), at 0800 h and 1600 h on proestrus, and at 0800 and 1600 h on estrus (n = 4 rats/group) and used double labeling in situ hybridization and quantification to compare the levels of GAP-43 messenger RNA (mRNA) in cells coexpressing GnRH mRNA. GnRH mRNA was detected with an antisense complementary RNA (cRNA) probe labeled with the hapten digoxigenin, whereas the GAP-43 cRNA probe was labeled with 35S and detected by autoradiography. In addition, GAP-43 protein was identified with immunohistochemistry in the median eminence. The results show that many GnRH neurons expressed GAP-43 mRNA and that GAP-43 protein was present in many GnRH axon terminals in the outer layer of the median eminence. The number of GnRH neurons expressing GAP-43 mRNA was significantly higher on proestrus (64 +/- 5%) than on diestrous II (40 +/- 2%; P < 0.001) or on estrus (45 +/- 8%; P < 0.05), and the GAP-43 mRNA levels in GnRH neurons also varied as a function of time of death during the estrous cycle. The GAP-43 mRNA levels in GnRH neurons were higher on proestrus and estrus than on diestrous II (P < 0.05). These data show that 1) GAP-43 is expressed in adult GnRH neurons; 2) GAP-43 mRNA expression in GnRH neurons fluctuates during the estrous cycle; and 3) GAP-43 mRNA content in GnRH neurons is highest on the day of proestrus, before and during the onset of the LH surge. These observations suggest that the increased GAP-43 mRNA expression in GnRH neurons on the day of proestrus could promote the outgrowth of GnRH axon terminals to establish direct neurovascular contacts in the external zone of the median eminence and thus facilitate GnRH release into the pituitary portal blood.

Animals↗

PubMedDate not supplied

Analysis of specific interactions between influenza virus and cells of different sensitivity. Note 1. Analysis of influenza virus-specific RNA synthesis nonpermissive amniotic cells.

Virus-specific RNA synthesis was studied in amniotic AO cells nonpermissive for influenza virus. Syntheses of complementary RNA were found to be greatly reduced in AO cells, as compared with the sensitive MDCK cells. Only primary transcription takes place in AO cells, resulting in the production of poly-A RNAs serving as a template for the synthesis of virus-specific polypeptides. The synthesis of virion-type RNA is absent, since no synthesis of nonpoly-A transcripts (which are the templates for the synthesis of the respective RNA) could be made evident in the resistant AO cells.

Amnion↗

PubMed1994

Reduced malignancy of ras-transformed NIH 3T3 cells expressing antisense osteopontin RNA.

Osteopontin (OPN) is a secreted, calcium-binding phosphoprotein that frequently has been associated with the transformed phenotype. To clarify the function of OPN in tumor cells, we designed experiments to: (a) express antisense OPN RNA in murine PAP2 cells (metastatic, ras-transformed NIH 3T3 cells) and (b) examine the effects of antisense OPN expression on the tumorigenic and metastatic properties of the cells. PAP2 cells were transfected with pNMH-asOPN, an inducible, mammalian expression vector that can generate antisense OPN RNA complementary to the OPN mRNA. Two clones have been identified that expressed antisense OPN RNA in vitro. While reduced OPN protein secretion was not detected when the cells were grown in vitro, the in vivo expression of antisense OPN RNA was associated with reduced tumorigenicity. Tumors that did arise, with greatly extended lag time, had lost expression of antisense OPN RNA in vivo, suggesting that antisense OPN RNA expression was associated with reduced tumorigenicity of these cells.

3T3 Cells↗