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Effects of polynucleotides on production and activity of streptolysin S.

Activity of various natural and synthetic polynucleotides as a carrier for streptolysin S was tested in a resting cell system. As the carrier, intact molecules of MS2 RNA, E coli tRNA or rat liver RNA were almost inactive, whereas RNase I core of these RNAs, especially the core fractions eluted from DEAE-cellulose column at higher NaCl concentrations, effectively induced production of the extracellular hemolysin. The carrier activity of yeast RNA was significantly enhanced by simultaneous addition of RNase I, to the streptococcal suspension. Preincubation of yeast RNA with growing streptococci or a protein fraction from the bacterial culture supernatant increased its carrier activity. Evidences were obtained suggesting involvement of streptococcal nuclease in the enhancement of the carrier effect. Production of the streptococcal hemolysin was markedly promoted by polyguanylic acid but neither by polyadenylic acid, polycytidylic acid nor by polyuridylic acid. Like trypan blue, polyguanylic acid exerted potent inhibitory effect on hemolytic activity of streptolysin S complex. Similar but less marked effect was observed with certain RNase I core fractions of rat liver RNA. Some data concerning effect of polynucleotides on stability of the hemolysin were also presented.

Animals↗

A specific monovalent metal ion integral to the AA platform of the RNA tetraloop receptor.

Metal ions are essential for the folding and activity of large catalytic RNAs. While divalent metal ions have been directly implicated in RNA tertiary structure formation, the role of monovalent ions has been largely unexplored. Here we report the first specific monovalent metal ion binding site within a catalytic RNA. As seen crystallographically, a potassium ion is coordinated immediately below AA platforms of the Tetrahymena ribozyme P4-P6 domain, including that within the tetraloop receptor. Interference and kinetic experiments demonstrate that potassium ion binding within the tetraloop receptor stabilizes the folding of the P4-P6 domain and enhances the activity of the Azoarcus group I intron. Since a monovalent ion binding site is integral to the tetraloop receptor, a tertiary structural motif that occurs frequently in RNA, monovalent metal ions are likely to participate in the folding and activity of a wide diversity of RNAs.

Adenine↗

New synthetic peptides can enhance gene expression of key antioxidant defense enzymes in vitro and in vivo.

Neurodegenerative, cardiovascular, and age-related disorders have been attributed to the cellular damage caused by elevated production of reactive oxygen species (ROS) and free radicals (FRs). These cannot be adequately defended by existing levels of key antioxidant enzymes. Two peptides, 8 and 14 amino acids long, were synthesized and found to up-regulate, at nanomolar concentrations, superoxide dismutase (SOD) and catalase (CAT) m-RNAs (9- to 12-fold) within 3 h, and then elevate by 5- to 10-fold the protein levels of SOD, CAT, and glutathione peroxidase (GPX) in rat primary cortical cultures. Kinetic studies showed that the peptide up-regulation of all three enzymes appears to be a coordinated process which occurs in vitro and in vivo. We also found that ischemia alone, without added drugs, can lead to enhanced gene expression of SOD, CAT, and GPX. This suggests that the CNS can initiate its own "defense" against ROS and FR. Thus, our peptides may activate such systems, as well as AP-1 transcription factor, reported in earlier findings to lead to "repair" (growth) of injured cells.

Animals↗

Protein kinase A regulates nicotinic cholinergic receptors and subunit messenger ribonucleic acids in PC 12 cells.

To delineate mechanisms regulating the expression of neuronal nicotinic cholinergic receptors (nAcChRs), we studied the cAMP-dependent second messenger system. PC 12 cells were grown in (Bu)2cAMP (0.001-1.0 mM) or vehicle for 7 days, and specific [3H] nicotine binding was measured. (Bu)2cAMP (0.1 mM) increased specific binding 2- and 4-fold at 3 and 7 days, respectively, whereas 1.0 mM enhanced binding 4-fold at both time intervals. Cells grown in 8-bromo-cAMP (1.0 mM) showed a 2-fold increase in [3H]nicotine binding at 3 days. Forskolin (10-100 microM), in combination with isobutyl-methylxanthine (1.0 mM), enhanced [3H]nicotine binding 2- to 3-fold at 7 days; forskolin or isobutyl-methylxanthine alone had no effect. Specific [3H] nicotine binding to PC 12 cell mutants (A126.1B2 and A123.7), deficient in cAMP-responsive protein kinase A types I and II, were unaffected by (Bu)2cAMP. Northern gel analysis of nAcChR subunit messenger RNAs showed that the alpha-3, alpha-5, and beta-4 subunits were significantly decreased by (Bu)2cAMP at 4 h. However, (Bu)2cAMP caused an increase in the beta-2 messenger RNA transcript at 4 h, which returned to baseline by 24 h. These studies indicate that the cAMP-protein kinase A system regulates expression of nAcChR by PC 12 cells. These studies also suggest that enhancement of [3H]nicotine binding by activated protein kinase A may not involve synthesis of new receptor subunit proteins.

Adenylyl Cyclases↗

Inability of Agrobacterium tumefaciens ribosomes to translate in vivo mRNAs containing non-Shine-Dalgarno translational initiators.

Numerous data accumulated during the last decade have shown that the Shine-Dalgarno (SD) sequence is not a unique initiator of translation for Escherichia coli. Several other sequences, mostly of viral origin, have demonstrated their capability of either enhancing or initiating translation in vivo. A phage T7 gene 10 sequence, called "epsilon" (epsilon), has shown its high enhancing activity on translation in both Escherichia coli and Agrobacterium tumefaciens cells. In this study the epsilon, together with three other nucleotide sequences derived from the 5' non-translated regions of tobacco mosaic virus (TMV), papaya mosaic virus (PMV) and clover yellow mosaic virus (CYMV) RNAs are tested for translation initiation activity in A. tumefaciens cells. The obtained results indicate that none of them was capable of initiating translation in vivo of chloramphenicol acetyltransferase (CAT) mRNA. To determine whether their inactivity was related with structural differences in the ribosomal protein S1, the rpsA gene (coding for S1 protein in E. coli) was co-expressed in A. tumefaciens together with the cat gene placed under the translational control of the above sequences. Our results showed that the rpsA gene product did not make any of the four viral enhancers active in A. tumefaciens cells. The inability of A. tumefaciens ribosomes to translate mRNAs devoid of SD sequences indicates for a substantial difference in the ribosome structure of the two Gram negative bacteria E. coli and A. tumefaciens.

5' Untranslated Regions↗

Enhanced resolution of circular and linear molecular forms of viroid and viroid-like RNA by electrophoresis in a discontinuous-pH system.

A discontinuous-pH polyacrylamide gel electrophoresis system is described. An increase in the pH differential between the gel and the running buffer enhances the separation of low molecular weight circular and linear RNA molecules. Highly purified preparations of the circular form of viroids can be obtained with this procedure. Since all the linear RNAs of similar molecular weight migrate with the front, a relatively clean background can be obtained even when crude extracts are used. This facilitates an improved separation and identification of similarly sized viroid-like RNAs. The conditions of electrophoresis in low salt and 8 M urea also permit the effective transfer of RNA molecules directly to nylon-based membranes without any additional denaturation treatment.

Electrophoresis, Polyacrylamide Gel↗

Molecular organization of a Drosophila puff site that responds to ecdysone.

The 68C locus in the polytene chromosomes of Drosophila melanogaster salivary glands is puffed during the last half of the third larval instar and harbors the structural gene for sgs3, one of the glue polypeptides synthesized by the glands during this period. This puff regresses in response to the steroid hormone ecdysone. We have isolated a set of overlapping cloned segments that define approximately 50 kb of DNA at the 68C puff locus. Three polysomal poly(A)+ RNAs that are abundant in the salivary glands during the intermolt-puff stage are transcribed from three genes (II, III and IV) that map near the center of the cloned DNA in a 5 kb cluster region. These are the only transcripts from the 50 kb of 68C DNA detectable in these glands, and they are undetectable in other larval tissues at this stage, or in whole animals at other stages of development. Correlative criteria indicate that gene IV, which yields an RNA of 1.1 kb, is the structural gene for sgs3. Genes II and III, which yield RNAs of 0.36 kb and 0.32 kb, respectively, are oppositely oriented so that their promoters are adjacent, suggesting that this pair may form a single regulated unit, a suggestion that is enhanced by the fact that the pair is bounded by an inverted repeat of 0.3 kb elements. The possible, but as yet unidentified, functions of this gene pair are discussed. A 9.2 kb element belonging to a family of transposable elements called roo is inserted adjacent to the 5 kb cluster region in some but not other D. melanogaster strains. This insertion has no obvious effect on the transcription of genes II, III and IV. Although roo elements yield a 9 kb poly(A)+ RNA in embryos, no roo transcripts were detected in intermolt salivary glands, whether they do or do not contain an element at the 68C puff site.

Chromosome Mapping↗

Extraordinarily slow binding of guanosine to the Tetrahymena group I ribozyme: implications for RNA preorganization and function.

The Tetrahymena ribozyme derived from the self-splicing group I intron binds a 5'-splice site analog (S) and guanosine (G), catalyzing their conversion to a 5'-exon analog (P) and GA. Herein, we show that binding of guanosine is exceptionally slow, limiting the reaction at near neutral pH. Our results implicate a conformational rearrangement on guanosine binding, likely because the binding site is not prearranged in the absence of ligand. The fast accommodation of guanosine (10(2) to 10(3) x s(-1)) and prior structural data suggest local rather than global rearrangements, raising the possibility that folding of this and perhaps other large RNAs is not fully cooperative. Guanosine binding is accelerated by addition of residues that form helices, referred to as P9.0 and P10, immediately 5' and 3' to the guanosine. These rate enhancements provide evidence for binding intermediates that have the adjacent helices formed before accommodation of guanosine into its binding site. Because the ability to form the P9.0 and P10 helices distinguishes the guanosine at the correct 3'-splice site from other guanosine residues, the faster binding of the correct guanosine can enhance specificity of 3'-splice site selection. Thus, paradoxically, the absence of a preformed binding site and the resulting slow guanosine binding can contribute to splicing specificity by providing an opportunity for the adjacent helices to increase the rate of binding of the guanosine specifying the 3'-splice site.

Animals↗

Purification and characterization of the Pac1 ribonuclease of Schizosaccharomyces pombe.

The pac1+ gene of the fission yeast Schizosaccharomyces pombe is essential for viability and its overexpression induces sterility and suppresses mutations in the pat1+ and snm1+ genes. The pac1+ gene encodes a protein that is structurally similar to RNase III from Escherichia coli, but its normal function is unknown. We report here the purification and characterization of the Pac1 protein after overexpression in E. coli. The purified protein is a highly active, double-strand-specific endoribonuclease that converts long double-stranded RNAs into short oligonucleotides and also cleaves a small hairpin RNA substrate. The Pac1 RNase is inhibited by a variety of double- and single-stranded polynucleotides, but polycytidylic acid greatly enhances activity and also promotes cleavage specificity. The Pac1 RNase produces 5'-phosphate termini and requires Mg2+; Mn2+ supports activity but causes a loss of cleavage specificity. Optimal activity was obtained at pH 8.5, at low ionic strength, in the presence of a reducing agent. The enzyme is relatively insensitive to N-ethylmaleimide but is strongly inhibited by ethidium bromide and vanadyl ribonucleoside complexes. The properties of the Pac1 RNase support the hypothesis that it is a eukaryotic homolog of RNase III.

Amino Acid Sequence↗

The topology of bulges in the long stem of the flavivirus 3' stem-loop is a major determinant of RNA replication competence.

All flavivirus genomes contain a 3'terminal stem-loop secondary structure (3'SL) formed by the most downstream approximately 100 nucleotides (nt) of the viral RNA. The 3'SL is required for virus replication and has been shown to bind both virus-coded and cellular proteins. Results of the present study using an infectious DNA for WN virus strain 956 initially demonstrated that the dengue virus serotype 2 (DEN2) 3'SL nucleotide sequence could not substitute for that of the WN 3'SL to support WN genome replication. To determine what WN virus-specific 3'SL nucleotide sequences were required for WN virus replication, WN virus 3'SL nucleotide sequences were selectively deleted and replaced by analogous segments of the DEN2 3'SL nucleotide sequence such that the overall 3'SL secondary structure was not disrupted. Top and bottom portions of the WN virus 3'SL were defined according to previous studies (J. L. Blackwell and M. A. Brinton, J. Virol. 71:6433-6444, 1997; L. Zeng, L., B. Falgout, and L. Markoff, J. Virol. 72:7510-7522, 1998). A bulge in the top portion of the long stem of the WN 3'SL was essential for replication of mutant WN RNAs, and replication-defective RNAs failed to produce negative strands in transfected cells. Introduction of a second bulge into the bottom portion of the long stem of the wild-type WN 3'SL markedly enhanced the replication competence of WN virus in mosquito cells but had no effect on replication in mammalian cells. This second bulge was identified as a host cell-specific enhancer of flavivirus replication. Results suggested that bulges and their topological location within the long stem of the 3'SL are primary determinants of replication competence for flavivirus genomes.

3' Untranslated Regions↗

Transforming growth factor-beta receptor types I and II in cultured porcine leydig cells: expression and hormonal regulation.

The steroidogenic activity of testicular Leydig cells is controlled both by the pituitary hormone (LH) and by growth factors such as transforming growth factor-beta peptides (TGFbeta1, -2, and -3; inhibin/activin; and anti-Mullerian hormone). By using primary cultures of porcine Leydig cells as a model, the aim of the study was to identify and characterize the TGFbeta receptors and to study their regulation by LH/hCG. TGFbeta receptors have been identified and characterized through three different approaches, including cross-linking experiments and Western and Northern blotting analyses. In cross-linking experiments, labeled TGFbeta was shown to bind to three different molecular species of 300, 80, and 53 kDa, which may correspond to the protein betaglycan (also known as TGFbeta type III receptor) and TGFbeta type II and I receptors (TGFbetaRII and TGFbetaRI), respectively. The presence of TGFbetaRI and -RII was further demonstrated by Western blotting analysis using specific polyclonal antibodies. Finally, the expression of betaglycan, TGFbetaRII, and TGFbetaRI messenger RNAs, was confirmed by Northern blotting analysis, as shown by the presence of 6.4-, 4.6-, and 5.8-kb messenger RNAs, respectively. By using a RT-PCR approach, the mediators of the TGFbeta signal, Smads 1-7, were also detected in cultured Leydig cells. TGFbetaRI and TGFbetaRII protein levels were enhanced by hCG/LH in a dose-dependent (maximal effect with 0.3 ng/ml hCG) and time-dependent (maximal effect observed after 48 h of hCG treatment) manner. Furthermore, to determine whether the stimulatory effect of LH/hCG was mediated by testosterone, use was made of aminogluthetimide, an inhibitor of cytochrome P450scc. The inhibition oftestosterone formation did not affect the stimulatory effect of LH/hCG on TGFbetaRI and -RII levels, suggesting that the gonadotropin action is not mediated by the steroid hormone. Together, the present findings demonstrate that the TGFbeta receptors are expressed and are under hormonal (gonadotropin) control in cultured porcine Leydig cells.

Aminoglutethimide↗

Defective c-myc and c-myb RNA turnover in acute myeloid leukemia cells.

Dysregulated expression of the c-myc and c-myb protooncogenes has been implicated in the pathogenesis of acute myeloid leukemia (AML). To elucidate mechanisms of c-myc dysregulation in AML cells, we studied c-myc RNA turnover in peripheral blood blasts from eight patients using actinomycin D transcription blockade. Rapid c-myc RNA turnover was seen in cells from six patients, with half-lives of approximately 30 minutes, similar to those reported in normal myeloid cells, in HL-60 cells, and in other cell lines. c-myc RNA turnover was prolonged in cells of the other two patients, with half-lives of greater than 75 minutes. c-fos RNA turnover was rapid in blasts from all eight patients, with half-lives of approximately 15 minutes. Stabilization of GM-CSF transcripts was not observed. In contrast, c-myb RNA half-lives were greater than 75 minutes in cells of the two patients with prolonged c-myc RNA turnover, as compared to 30 minutes in cells of the other six patients. Enhanced stability of both c-myc and c-myb RNA species suggests that a defect exists in a trans-acting factor that destabilizes both of these normally labile RNAs. Incomplete correlation between c-myc RNA levels and half-lives indicates regulation of c-myc expression at the level of transcription or nuclear transport in addition to posttranscriptional regulation.

Adult↗

Purification and characterization of a high molecular weight ribonuclease from human milk.

We have purified a high molecular weight ribonuclease (hmRNase) from human milk by a two-step column chromatographic procedure and characterized the enzyme. The molecular mass of hmRNase is 80 kDa as determined from SDS-polyacrylamide gel electrophoresis. The pH optimum of the enzyme is in the range of 7.5-8.0, similar to other secretory RNases. hmRNase is pyrimidine-specific and cleaves the phosphodiester bond 3' to a pyrimidine residue. It selectively degrades the pyrimidine strand in poly(rA):poly(rU) and poly(dA):poly(rU) double stranded substrates. The extent of degradation for naturally occurring RNAs vary in the order tRNA < rRNA < mRNA at low enzyme concentrations. hmRNase shows allosteric behavior with positive cooperativity in its reaction on polynucleotide substrates. The activity of the enzyme is enhanced in the presence of monoribonucleotides. Antiserum obtained against purified hmRNase did not cross-react with low molecular weight RNase which is also present in milk. In addition, an immunologically cross-reacting species could not be detected in the serum, suggesting the origin of hmRNase in the mammary gland but not blood.

Amino Acids↗

The doublesex splicing enhancer components Tra2 and Rbp1 also repress splicing through an intronic silencer.

The activation of sex-specific alternative splice sites in the Drosophila melanogaster doublesex and fruitless pre-mRNAs has been well studied and depends on the serine-arginine-rich (SR) splicing factors Tra, Tra2, and Rbp1. Little is known, however, about how SR factors negatively regulate splice sites in other RNAs. Here we examine how Tra2 blocks splicing of the M1 intron from its own transcript. We identify an intronic splicing silencer (ISS) adjacent to the M1 branch point that is sufficient to confer Tra2-dependent repression on another RNA. The ISS was found to function independently of its position within the intron, arguing against the idea that bound repressors function by simply interfering with branch point accessibility to general splicing factors. Conserved subelements of the silencer include five short repeated sequences that are required for Tra2 binding but differ from repeated binding sites found in Tra2-dependent splicing enhancers. The ISS also contains a consensus binding site for Rbp1, and this protein was found to facilitate repression of M1 splicing both in vitro and in Drosophila larvae. In contrast to the cooperative binding of SR proteins observed on the doublesex splicing enhancer, we found that Rbp1 and Tra2 bind to the ISS independently through distinct sequences. Our results suggest that functionally synergistic interactions of these SR factors can cause either splicing activation or repression.

Animals↗

roX RNAs are required for increased expression of X-linked genes in Drosophila melanogaster males.

The male-specific lethal (MSL) ribonucleoprotein complex is necessary for equalization of X:A expression levels in Drosophila males, which have a single X chromosome. It binds selectively to the male X chromosome and directs acetylation of histone H4 at lysine 16 (H4Ac16), a modification linked to elevated transcription. roX1 and roX2 noncoding RNAs are essential but redundant components of this complex. Simultaneous removal of both roX RNAs reduces X localization of the MSL proteins and permits their ectopic binding to autosomal sites and the chromocenter. However, the MSL proteins still colocalize, and low levels of H4Ac16 are detected at ectopic sites of MSL binding and residual sites on the X chromosome of roX1- roX2- males. Microarray analysis was performed to reveal the effect of roX1 and roX2 elimination on X-linked and autosomal gene expression. Expression of the X chromosome is decreased by 26% in roX1- roX2- male larvae. Enhanced expression could not be detected at autosomal sites of MSL binding in roX1- roX2- males. These results implicate failure to compensate X-linked genes, rather than inappropriate upregulation of autosomal genes at ectopic sites of MSL binding, as the primary cause of male lethality upon loss of roX RNAs.

Animals↗

Discordant expression of the immediate-early 1 and 2 gene regions of human cytomegalovirus at early times after infection involves posttranscriptional processing events.

Expression of the immediate-early 1 and 2 (IE-1 and IE-2) gene region of human cytomegalovirus (HCMV) was studied during initial phases of the replicative cycle. Accumulation of RNA from IE-1 and -2 was found to be differential. Transcripts from IE-2 reached peak levels very early in infection between 3 and 5 h, whereas IE-1 RNA peak levels were detected later, between 6 and 8 h. A strong decrease in steady-state levels of a 2.2-kb IE-2 RNA was observed at a time when IE-1 transcripts showed a further increase in abundance. Northern (RNA) blot experiments revealed that expression of both the IE-1 RNA and the 2.2-kb IE-2 transcript is controlled by the IE-1 enhancer-promoter. Nuclear run-on experiments demonstrated equal rates of primary transcription for IE-1 and -2 at a time when different steady-state levels of RNA were observed. Concomitant with down-regulation of IE-2 RNAs, a decrease in the size of the IE-1 transcript was detected. At 2 to 5 h after infection the IE-1 transcript migrated at 1.95 kb, whereas later in the replicative cycle the RNA was found at 1.8 kb. RNase H blot analysis revealed that this size discrepancy is due to a shorter poly(A) tail of the IE-1 RNA at early times after infection. These experiments suggest that in addition to transcriptional regulation, specific posttranscriptional mechanisms are involved in controlling expression from the IE-1 and -2 gene region of HCMV.

Antigens, Viral↗

Breakage of resistance to Cucumber mosaic virus by co-infection with Zucchini yellow mosaic virus: enhancement of CMV accumulation independent of symptom expression.

Resistance to the cucumovirus Cucumber mosaic virus (CMV) in cucumber cv. Delila was manifested as a very low level of accumulation of viral RNA and capsid protein, and an absence of CMV-induced symptoms. In addition, resistance was observed at the single cell level, with a reduction in accumulation of CMV RNAs, compared to accumulation in cells of the susceptible cucumber cv. Bet Alpha. Resistance to CMV in cv. Delila was broken by co-infection with the potyvirus Zucchini yellow mosaic virus (ZYMV). Resistance breakage in cv. Delila plants was manifested by an increase in the accumulation of (+) and (-) CMV RNA as well as CMV capsid protein, with no increase in the level of accumulation of ZYMV. Resistance breakage in the resistant cultivar by ZYMV also occurred at the single cell level. Thus, synergistic interactions known to occur between a potyvirus and a cucumovirus led to resistance breakage during a double infection. However, resistance breakage was not accompanied by an increase in disease symptoms beyond those induced by ZYMV itself. On co-inoculation with an asymptomatic variant of ZYMV-AG an enhancement of CMV infection occurred without disease manifestation. Consequently, intensification of viral RNA and capsid protein accumulation can occur without a corresponding increase in disease development, suggesting that different host genes regulate viral accumulation and disease development in the CMV-resistant cucumber plants.

Capsid Proteins↗

Neuronal death and neurotrophin gene expression: long-lasting stimulation of neurotrophin-3 messenger RNA in the degenerating CA1 and CA4 pyramidal cell layers.

Neurotrophin-3 has been characterized as the product of a gene cloned by homology with nerve growth factor and brain-derived neurotrophic factor. Recombinant neurotrophin-3, like nerve growth factor and brain-derived neurotrophic factor, has been shown to enhance survival and differentiation of specific neuronal populations in vitro. However, little is known about its function and regulation in vivo. Both brain-derived neurotrophic factor and nerve growth factor messenger RNAs increased in adult rat brain, in a wide range of excitatory paradigms. In contrast, neurotrophin-3 messenger RNA decreased in some of them. Neurotrophin-3 is the most highly expressed neutrophic factor in immature areas of the central nervous system. However, no stimulation of its expression in the mature central nervous system, either in physiological or pathological conditions, has been described to date. This behaviour suggests that neurotrophin-3 could be involved in biological roles different from the prototypes nerve growth factor and brain-derived neurotrophic factor. Excitatory amino acid receptor-mediated neurotoxicity (excitotoxicity) is believed to contribute to neuronal loss in a wide range of neurodegenerative conditions (for a review, see Ref. 17). Moreover, locally increased levels of the endogenous excitotoxin quinolinic acid may be involved in the natural development of neurodegenerative diseases. The unilateral intrahippocampal injection of 120 nmol of quinolinic acid induced seizures together with local neurodegeneration in specific cell layers. In situ hybridization histochemistry was used to analyse the spatiotemporal pattern of expression of neurotrophin-3. As in other excitotoxic paradigms, neurotrophin-3 messenger RNA clearly decreased, nearly disappearing, in the contralateral hippocampus.(ABSTRACT TRUNCATED AT 250 WORDS)

Animals↗