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[RNA editing in different genetic systems].

One of the significant amendments to the central dogma of the molecular biology was the discovery of the RNA editing process in different genetic systems. Whereas other forms of co- and posttranscriptional modifications of messenger RNA (mRNA) (capping, polyadenilation, splicing) retain the correspondence of the primary structure of exon and final transcript, RNA editing disturbs this correspondence changing the primary structure of mRNA after its transcription. The variants of RNA-editing mechanisms are various and include site-specific insertions and deletions of one or several nucleotides (insertion-deletion editing) as well as specific modifications of nucleosides such as C-->U and A-->I deamination or U-->C transamination (conversion editing). These mechanisms differ greatly in different genetic systems but they always result in synthesis of functionally valuable proteins from "incorrect" genes and, correspondingly, can play a significant role in regulation of their expression.

Animals↗

Modification of the properties of elongating RNA polymerase by persistent association with nascent antiterminator RNA.

Nascent RNA encoded by putL, a cis-acting antitermination site of bacteriophage HK022, increases readthrough of terminators by directly modifying the transcript elongation complex. To characterize the interaction between the antiterminator RNA and RNA polymerase, we stalled the elongation complex downstream of putL and determined the sensitivity of the transcript to ribonuclease cleavage. Part of PutL RNA was protected from cleavage by wild-type polymerase, but not by a mutant with a defect in put-dependent antitermination. We also exposed the stalled complex to oligonucleotides complementary to putL RNA, restarted transcription, and measured antitermination. Some, but not all, complementary oligonucleotides inhibited antitermination. Finally, cleavage of the RNA between putL and the 3'-end released putL RNA from the stalled complex and prevented antitermination.

Bacterial Proteins↗

A small nucleolar guide RNA functions both in 2'-O-ribose methylation and pseudouridylation of the U5 spliceosomal RNA.

In eukaryotes, two distinct classes of small nucleolar RNAs (snoRNAs), namely the fibrillarin-associated box C/D snoRNAs and the Gar1p-associated box H/ACA snoRNAs, direct the site-specific 2'-O-ribose methylation and pseudouridylation of ribosomal RNAs (rRNAs), respectively. We have identified a novel evolutionarily conserved snoRNA, called U85, which possesses the box elements of both classes of snoRNAs and associates with both fibrillarin and Gar1p. In vitro and in vivo pseudouridylation and 2'-O-methylation experiments provide evidence that the U85 snoRNA directs 2'-O-methylation of the C45 and pseudouridylation of the U46 residues in the invariant loop 1 of the human U5 spliceosomal RNA. The U85 is the first example of a snoRNA that directs modification of an RNA polymerase II-transcribed spliceosomal RNA and that functions both in RNA pseudouridylation and 2'-O-methylation.

Animals↗

Modification of human DNA-dependent RNA polymerase activity by cyclic GMP.

The effect of low concentrations of cyclic GMP (guanosine 3':5'-cyclic monophosphate) on the in vitro enzymatic activities of DNA-dependent RNA polymerases isolated from human peripheral blood lymphocytes has been investigated. In agreement with earlier studies which employed isolated nuclei as the enzyme source, an increase in the activity of partially purified RNA polymerase I is observed in the presence of cyclic GMP (10(-8) to 10(-10)M). RNA polymerase II activity is inhibited by the presence of cyclic GMP at concentrations between 10(-4) and 10(-10)M. RNA polymerase III activity is stimulated in a bimodal fashion by the presence of cyclic GMP with maximal activity noted at 10(-8) to 10(-10) M and 10(-5)M. In addition, [3H]cyclic GMP binds specifically to chromatographic fractions which are known to contain RNA polymerases I, II and III. This binding to RNA polymerases II and III is apprarently less tenacious as demonstrated by dissociation studies. The observations provide additional evidence for a role for cyclic GMP in the regulation of RNA synthesis.

Cyclic AMP↗

ICP22 and the UL13 protein kinase are both required for herpes simplex virus-induced modification of the large subunit of RNA polymerase II.

Herpes simplex virus type 1 (HSV-1) infection alters the phosphorylation of the large subunit of RNA polymerase II (RNAP II), resulting in the depletion of the hypophosphorylated and hyperphosphorylated forms of this polypeptide (known as IIa and IIo, respectively) and induction of a novel, alternatively phosphorylated form (designated IIi). We previously showed that the HSV-1 immediate-early protein ICP22 is involved in this phenomenon, since induction of IIi and depletion of IIa are deficient in cells infected with 22/n199, an HSV-1 ICP22 nonsense mutant (S. A. Rice, M. C. Long, V. Lam, P. A. Schaffer, and C. A. Spencer, J. Virol. 69:5550-5559, 1995). However, depletion of IIo still occurs in 22/n199-infected cells. This suggests either that another viral gene product affects the RNAP II large subunit or that the truncated ICP22 polypeptide encoded by 22/n199 retains residual activity which leads to IIo depletion. To distinguish between these possibilities, we engineered an HSV-1 ICP22 null mutant, d22-lacZ, and compared it to 22/n199. The two mutants are indistinguishable in their effects on the RNAP II large subunit, suggesting that an additional viral gene product is involved in altering RNAP II. Two candidates are UL13, a protein kinase which has been implicated in ICP22 phosphorylation, and the virion host shutoff (Vhs) factor, the expression of which is positively regulated by ICP22 and UL13. To test whether UL13 is involved, a UL13-deficient viral mutant, d13-lacZ, was engineered. This mutant was defective in IIi induction and IIa depletion, displaying a phenotype very similar to that of d22-lacZ. In contrast, a Vhs mutant had effects that were indistinguishable from wild-type HSV-1. Therefore, UL13 but not the Vhs function plays a role in modifying the RNAP II large subunit. To study the potential role of UL13 in viral transcription, we carried out nuclear run-on transcription analyses in infected human embryonic lung cells. Infections with either UL13 or ICP22 mutants led to significantly reduced amounts of viral genome transcription at late times after infection. Together, our results suggest that ICP22 and UL13 are involved in a common pathway that alters RNAP II phosphorylation and that in some cell lines this change promotes viral late transcription.

Animals↗

A tri-hybrid system for the analysis and detection of RNA--protein interactions.

A modification of the two-hybrid system is described for the in vivo reconstruction of specific RNA-protein interactions. In this tri-hybrid system, the DNA binding and transcription activation domains of the yeast transcriptional activator GAL4 are brought together via the interaction of recombinant fusion proteins with a recombinant RNA. The method provides a system for studying RNA-protein interactions with the genetic advantages of the two-hybrid system. It may be used to detect specific RNA-binding proteins or target RNAs from a library of cDNAs, or to analyse the structural specificity of identified RNA-protein interactions.

Binding Sites↗

Mode of transfection influences the stability of ectopically expressed mRNA.

In the study of mRNA metabolism, modified mRNAs are often analyzed after corresponding mRNA expression vectors have been transfected, either transiently or stably, into cells. Two differently transfected templates might be localized in distinct nuclear compartments: in transient transfection they remain in the nucleoplasm while in stable transfection they are integrated in the chromatin. Consequently, nascent transcripts may encounter different environments which may affect the physical state of mRNA and its fate. In this work, we addressed the question whether the two different modes of transfection affect the stability of expressed mRNA. We compared globin mRNA, which is characteristically stable, and globin-delta AU mRNA, which contains the 3' untranslated region of urokinase-type plasminogen activator mRNA and is unstable. In stably transfected cells, these mRNAs were degraded in a manner which mimicked the endogenous mRNA, whereas in transiently transfected cells, the regulated degradation of both mRNAs was impaired. However, when lower amounts of template DNA were used in transient transfection, mRNA was degraded in a manner similar to that of stably expressed mRNA, indicating that mRNA levels affect its stability. To monitor potential differences in the physical state of mRNAs in vivo, we developed a method based on a combination of chemical modification of cellular RNA and a modified RT-PCR. We found that patterns of chemical modification vary with the levels of mRNA expressed. Our results suggest that a proper interaction of mRNA with specific cellular proteins is important for regulated degradation and that overexpression of mRNA destroys such proper stoichiometry.

Animals↗

On the role of exon and intron sequences in trans-splicing utilization and cap 4 modification of the trypanosomatid Leptomonas collosoma SL RNA.

In trypanosomatid protozoa the biogenesis of mature mRNA involves addition of the spliced leader (SL) sequence from the SL RNA to polycistronic pre-mRNA via trans-splicing. Here we present a mutational analysis of the trypanosomatid Leptomonas collosoma SL RNA to further our understanding of its functional domains important for trans-splicing utilization. Mutant SL RNAs were analyzed for defects in modification of the hypermethylated cap structure (cap 4) characteristic of trypanosomatid SL RNAs, for defects in the first step of the reaction and overall utilization in trans-splicing. Single substitution of the cap 4 nucleotides led to undermethylation of the cap 4 structure, and these mutants were all impaired in their utilization in trans-splicing. Abrogation of the sequence of the Sm-like site and sequences downstream to it also showed cap modification and trans-splicing defects, thus providing further support for a functional linkage between cap modifications and trans-splicing. Further, we report that in L. collosoma both the exon and intron of the SL RNA contribute information for efficient function of the SL RNA in trans-splicing. This study, however, did not provide support for the putative SL RNA-U6 small nuclear RNA (snRNA) interaction at the Sm site like in the nematodes, suggesting differences in the bridging role of U6 in the two trans-splicing systems.

Animals↗

[Addressed modification of the promoter region of DNA in a complex with RNA polymerase by alkylating oligonucleotide derivatives].

Addressed chemical modification of double-stranded DNA unwound with the specific protein has been demonstrated. 4(N-2-chloroethyl-N-methylamino)benzyl-5'-phosphoamides of oligonucleotides d(CG)rC, d(ATCG)rC, d(AATCG)rC, which can serve as primers in the RNA polymerase-catalyzed transcription, alkylated A2 promoter region of pSK-A2 plasmid in its "open" complex with E. coli RNA polymerase.

Alkylating Agents↗

Stimulation of RNA polymerases I and II from mouse L1210 leukemia and Ehrlich ascites carcinoma cells by spermine and spermidine and its modification by ammonium sulfate.

Nuclear RNA polymerases from murine L1210 leukemia and Ehrlich carcinoma cells were stimulated more effectively by spermine than by spermidine. Optimal stimulatory concentrations of spermine and spermidine for Ehrlich polymerases Ia and Ib decreased to physiological values and maximal stimulation increased as the concentration of (NH4)2SO4 was reduced from 0.08 to 0 M. In the presence of 0.062-0.074 M (NH4)2SO4 L1210 polymerases Ia, IIa and IIb were stimulated significantly by both polyamines, whereas, at (NH4)2SO4 concentrations of 0.11-0.17 M, stimulation was suppressed and high concentrations of the polyamines were inhibitory. Similarly, stimulation of Ehrlich solubilized polymerase by polyamines was inhibited by 0.064 M (NH4)2SO4.

Ammonium Sulfate↗

Direct probing of RNA structures and RNA-protein interactions in the HIV-1 packaging signal by chemical modification and electrospray ionization fourier transform mass spectrometry.

RNA hairpins of the HIV-1 packaging signal and their complexes with the nucleocapsid protein p7 (NC) were probed by solvent-accessibility reagents and electrospray ionization-Fourier transform mass spectrometry (ESI-FTMS). The combination of dimethylsulfate, kethoxal, and 1-cyclohexyl-3-(2-morpholinoethyl)-carbodiimide metho-p-toluene sulfonate (CMCT) offers the full range of information on base-pairing and solvent exposure concerning the four more abundant ribonucleotides. ESI-FTMS provides a universal method to achieve a direct and unambiguous characterization of alkylated structures, with no need for the different probe-specific procedures required by established methodologies based on gel electrophoresis. It enables us to streamline the optimization of the conditions for probe administration to minimize the incidence of probe-induced distortion of the structures under investigation. Nucleotides located in the single-stranded loops of hairpins SL2, SL3 and SL4 manifested different levels of protection, which were correlated directly to their conformation and structural surroundings. A common feature noted for all the hairpins was the limited susceptibility observed for the guanine base located at the 5'-end of each tetraloop, which assumes a stacked position upon the last base-pair of the double-stranded stems. The remaining loop bases were found to be clearly accessible by modifying reagents in free RNA, but were effectively protected in the NC-hairpin complexes. While this finding is consistent with the proven participation of SL2 and SL3 loops in interactions with NC, it contrasts with prior suggestions that tetraloop bases in SL4 might not be involved directly in NC binding. Alkylation was detected for stem nucleotides, which are not involved in the normal base-pairing and stacking typical of double-stranded structures, such as adenine 15 of the SL2 triple-base platform. Modification of the blunt ends of the double-stranded stems was found to be absent or extremely limited, due to the annealing stabilization introduced by the presence of G-C pairs at the end of the stems structures. Previously undetected alkylation of guanine 3 and guanine 13 in SL4 provides direct evidence of the destabilizing effects induced by the tandem G.U wobbles on the double-stranded structure of this stem, which is thought to be important for the hairpin's biological function.

Base Sequence↗