Escherichia coli RNAse 3 cleaves HeLa cell nuclear RNA

The accessibility of phage MS2 RNA to structure specific nucleases in various conditions

The accessibility of ds- and ss-segments of phage MS2 RNA to ds- and ss-specific nucleases (RNase III, nuclease SV and nuclease S1) was studied. The results show that the RNA has hydrolysis sites for all the nucleases used. These sites are unvariable in a wide range of the conditions (ionic strength, pH, bivalent cations and temperature) and are not changed also after denaturation-renaturation of the RNA. This testifies that the distribution and interactions of ds- and ss-segments in the whole molecule are very specific and stable.

Double-stranded RNA specific nuclease from germinating embryos of Pennisetum typhoides

A double-stranded RNA specific nuclease (ds RNase) has been purified from the pearl millet Pennisetum typhoides. The purification involved S-30 preparation from the germinating embryos, DEAE-cellulose and DNA-cellulose chromatography. The partially pure enzyme preferentially solubilized the synthetic double-stranded polynucleotide [3H]poly(rA) . poly(rU); the degradation of [3H]poly(rC) was fourteen fold lower under the same assay conditions. Furthermore, the ds RNase activity was inhibited to an extent of 58% by ethidium bromide, which is known to intercalate with double-stranded RNAs. Active sulfhydryl groups were found to be necessary for the ds RNase activity since the enzyme action was inhibited by N-ethylmaleimide. Ethidium bromide and N-ethyl-maleimide did not significantly inhibit the ss RNase activity. In contrast, diethyl pyrocarbonate inhibited ss RNase activity completely and ds RNase by 58%. Heating the enzyme for 20 min at 50 degrees C resulted in drastic loss of both enzyme activities. The ds RNase showed maximum activity in the pH range of 6.5 to 7.5. The enzyme acts in vitro on E. coli 30S precursor ribosomal RNA and the cleavage products migrated in the region of mature 23S and 16S rRNAs.

Partial purification and characterization of a double-stranded RNA-specific nuclease from human placenta

A double-stranded RNA-specific nuclease (ds RNase) has been isolated and partially purified from human placenta by DEAE-cellulose and DNA-cellulose column chromatography. Denatured DNA-cellulose retained most of the single-stranded RNA-specific nuclease (ss RNase) activity, whereas the ds RNase came out in the void volume. N-ethylmaleimide at a concentration of 5 mM, selectively inhibited ds RNase activity by 60% under the conditions in which the ss RNase activity was inhibited to an extent of 7%. The ds RNase was specifically inhibited by Penicillium chrysogenum viral ds RNA and by ethidium bromide. The partially purified ds RNase showed requirements for Mg+ whereas Mn2+ and NH4+ ions were inhibitory. The DEAE-enzyme cleaved 32P-labelled 45S ribosomal precursor RNAs from Yoshida ascites sarcoma cells into species that had similar electrophoretic mobilities as the mature rRNAs.

Recognition signals for mouse pre-rRNA processing. A potential role for U3 nucleolar RNA

In order to identify signals for rRNA processing in eukaryotes, mouse pre-rRNA sequence features around four cleavage sites have been analyzed. No consensus sequence can be recognized when the four boundary regions are examined. Unlike mature rRNA termini, distal sequences of precursor-specific domains cannot participate in stable duplex with adjacent regions. The extensive divergence of precursor-specific sequences during evolution also applies to nucleotides adjacent to cleavage sites, with a significant exception for a conserved segment immediately downstream 5.8S rRNA. A specific role is proposed for U3 nucleolar RNA in the conversion of 32S pre-rRNA into mature 28S rRNA, through base-pairing with precursor-specific sequences at the boundaries of excised domains.

Effect of toyocamycin on oncornaviral production by acutely infected cells

The adenosine analogue toyocamycin incorporates into the RNA species of mammalia cells and abolishes at low concentrations of the processing of 45S preribosomal nucleolar RNA into the mature 28 and 18S cytoplasmic ribosomal RNAs. We have previously shown that toyocamycin depresses the production of the Friend leukemia viral complex by chronically infected cells. In this article, we report the study of the action of the drug on viral RNA in acutely infected cells. We found that, although abolishing viral production, the incorporation of toyocamycin does not inhibit the formation of mature viral messenger RNAs nor prevent the synthesis of specific viral proteins. These results are obtained at concentrations of analogue sufficient to abolish the appearance of mature cytoplasmic ribosomal RNA.

Localisation of an endonuclease specific for double-stranded RNA within the nucleolus and its implication in processing ribosomal transcripts

Nucleoli of both chick embryos and mouse Ehrlich ascites cells contain an enzymatic activity that is very similar to RNase DII, an enzyme isolated from total chick embryos for its ability to degrade double-stranded RNA. The enzyme can be extracted by low salt/EDTA from nucleoli and is associated with pre-ribosomal 80-S and 55-S particles. Under ionic conditions which are inhibitory for the nucleolytic activity the transcript in vitro of nucleoli is not processed and sediments around 45 S. Under salt conditions which are optimal for the nucleolar enzyme the nucleolar transcripts are cleaved to distinct intermediate-sized molecules. Addition of the chicken RNase DII or RNase III to the nucleolar transcription system results in a similar shift of the chain length of the RNA molecules. It is concluded that a nucleolar RNase recognizing double-stranded regions in the pre-ribosomal RNA is involved in the maturation of ribosomal RNA.

Stabilization of adenovirus nuclear RNA by intercalating drugs

The effect of the intercalating drugs proflavine, ethidium bromide and daunomycin on the rate of degradation of newly synthesized adenovirus RNA was examined. As shown previously for heterogeneous nuclear RNA (HnRNA) and 45 S precursor ribosomal RNA (pre-rRNA), proflavine immediately stabilizes newly synthesized adenovirus RNA, while ethidium bromide stabilizes the RNA after a 30--60 min lag period. In contrast to its effect on HnRNA and pre-rRNA, daunomycin also stabilizes newly synthesized adenovirus RNA. These results are consistent with the hypothesis that the processing of late adenovirus nuclear RNA involves cleavage of base-paired regions by specific cellular nucleases.

In vitrocleavage of 45S pre-ribosomal RNA and of giant heterogeneous RNA extracted from human leukemic cells

45S ribosomal precursor RNA and large heterogeneous RNA molecules (greater than 45S) extracted from human leukemic cells were incubated in vitro with purified RNase III, which specifically attacks double-helical RNA regions. About 50% of the ribosomal precursor was cleaved into two major fragments sedimenting at 28S and 32S respectively. A limited number of cleavages was also introduced in about 40% of heterogeneous RNA molecules sedimenting faster than 45S, causing a partial 'shift' to a polydisperse distribution in the 10S-45S range.

Partial purification of a double-stranded RNA specific ribonuclease (RNAse D) from Krebs II ascites cells

In a search for eucaryotic enzymes which might process the heterogenous nuclear RNA (HnRNA) from animal cells into messenger RNA, a ribonuclease called RNAse D analogous to E. coli RNAse III in its ability to cleave specifically synthetic or viral double-stranded polyribonucleotides has been detected and extensively purified from the cytosol of Krebs II mouse ascites cells. The purification procedure involved cellular fractionation followed by DEAE-and CM-cellulose chromatography and resulted in an RNAas D preparation contaminated with trace amounts of single-strand specific RNAse (equivalent to less than 0.3 ng per ml) as assayed against poly (rC). Significant levels of RNAse H activity against poly (rA)-poly (dT) were still present in these preparations.

Isolation and characterization of two alkaline ribonucleases from calf serum

Treatment of calf serum at 60 degrees C and pH 3.5 followed by chromatography on carboxymethyl (CM) cellulose resulted in the separation of two major peaks of alkaline RNAse activity. One was eluted from CM-cellulose at 0.075 M KCl with an overall purification of 5400-fold and the other was eluted at 0.25 M KCl with a 6700-fold purification. The RNAse eluted from CM-cellulose at 0.075 M KCl was almost completely inhibited by anti-RNAse A serum and by the endogenous RNAse inhibitor and a 33% inhibition was observed in the presence of 5 mM MgCl2. This enzyme seems to be similar or identical to RNAse A. The other RNAse, eluted from CM-cellulose at 0.25 M KCl was not inhibited by anti-RNAse A or 5 mM MgCl2 and was much less sensitive to the endogenous inhibitor. Both enzymes degraded RNA endonucleolytically and the nucleoside monophosphates obtained after partial hydrolysis of RNA by the two serum RNAases were primarily 2'- or 3' -CMP and 2'- or 3' -UMP. Poly(A), native DNA and denatured DNA were degraded slowly or not at all. The RNAase A-like enzyme degraded poly(C) at a significantly faster rate, and poly(U) at a slower rate, than RNA. However, the other serum RNAase was more active with poly(U) than with RNA and almost inactive with poly(C) as the substrate.

Substrate specificity of Salmonella typhimurium RNAase III and the nature of products formed

RNAase III, an endonuclease specific for double-stranded substrates, has been obtained in a highly purified form from extracts of Salmonella typhimurium. Poly (I-C) and a mixture of poly(A) and poly(U) (1 : 1), the latter in presence of 5 mM Mg2+, act as excellent substrates. Poly(I-C) is only partially hydrolysed by RNAase III and the product or products are acted upon by both RNAase I and RNAase II indicating that the products may be oligonucleotides. This conclusion is supported by two-dimensional chromatography on DEAE paper.

Cleavage of adenovirus messenger RNA and of 28S and 18S ribosomal RNA by RNase III

Escherichia coli ribonuclease III cleaves adenovirus messenger RNA and mammalian 28S and 18S ribosomal RNA. Fragmentation is not random, but in each case a specific collection of products is generated. This points to the potential use of the enzyme as a tool for specific fragmentation of RNA. Cleavage by RNase III abolishes the capability of adenovirus messenger RNA to direct cell-free synthesis of virus polypeptides.

30 S pre-ribosomal RNA of Escherichia coli:primary and secondary processing

The metabolism of newly-formed labeled 30 S pre-ribosomal RNA was studied in the Escherichia coli mutant strain AB301-105. Detailed kinetic analysis in rifampicin-treated cells showed that precursors of 23 S and 16 S rRNA are formed from the 30 S RNA species, even in phosphate-limited cultures. To establish the order fo segments along 30 S pre-rRNA, it was allowed to accumulate in replicate chloramphenicol-treated cultures, and pulse-labeled after the addition of rifampicin in segments that progressively contained more 3'-distal label with time. The purified RNAs from the various cultures were then cleaved to a limited extent by RNAase III; the specific activity of the fragments yielded an order from the 5'-end of 17.5S-X-25S, where X refers to some of the sequences released as additional small fragments. More extensive treatment the 25-S and 17.5-S pre-rRNA chains with RNAase III yielded additional fragments and produced RNA species with the mobility of the 23-S and 16-S RNA precursors made in normal cells treated with chloramphenicol. A processing scheme is suggested that distinguishes between early, site-specific cleavage of recognition sites in the RNA itself ('primary processing'), and later, "secondary processing' reactions. The secondary processing reactions are blocked chloramphenicol-treated wild-type cells.