Vesicular stomatitis virus mRNA methylation in vivo: effect of cycloleucine, an inhibitor of S-adenosylmethionine biosynthesis, on viral transcription and translation

Modulation of the Antiviral Activity of Poly (A-U) by Ethidium Bromide and Propidium Iodide

The role of ethidium bromide (EB) and propidium iodide (PI) in modulating the antiviral and interferon-inducing activities of poly(adenylate-uridylate) (poly (A-U)) was examined using the human foreskin fibroblast-vesicular stomatitis virus (HSF-VSV) bioassay system in which the concentration of poly (A-U) was fixed at 0.05 mM or 0.2 mM while the EB or PI concentration was varied to produce variable EB (or PI)/ribonucleotide ratios ranging from 1:16 to 2:1. EB, PI and poly (A-U) tested individually were not efficacious antiviral agents. When poly (A-U) was combined with the ethidium bromide or propidium iodide the antiviral activity was potentiated 15- to 22-fold at EB (or PI)/ribonucleotide ratios in the region of 1/4. The interferon-inducing activity of the EB (or PI)/poly (A-U) combinations were equal to the sum of the interferon-inducing activity of the poly (A-U) and the EB or (PI). These results indicate that the EB and PI potentiate the antiviral activity of the poly (A-U) without superinduction of interferon. The direct viral inactivation study demonstrated that EB, PI, poly (A-U) and the EB (or PI)/poly (A-U) combinations did not inactivate the VSV at concentrations near the 50% viral inhibitory dose.

Mapping and significance of the mRNA methylome

Internal methylation of eukaryotic mRNAs in the form of N6-methyladenosine (m(6)A) and 5-methylcytidine (m(5)C) has long been known to exist, but progress in understanding its role was hampered by difficulties in identifying individual sites. This was recently overcome by high-throughput sequencing-based methods that mapped thousands of sites for both modifications throughout mammalian transcriptomes, with most sites found in mRNAs. The topology of m(6)A in mouse and human revealed both conserved and variable sites as well as plasticity in response to extracellular cues. Within mRNAs, m(5)C and m(6)A sites were relatively depleted in coding sequences and enriched in untranslated regions, suggesting functional interactions with post-transcriptional gene control. Finer distribution analyses and preexisting literature point toward roles in the regulation of mRNA splicing, translation, or decay, through an interplay with RNA-binding proteins and microRNAs. The methyltransferase (MTase) METTL3 'writes' m(6)A marks on mRNA, whereas the demethylase FTO can 'erase' them. The RNA:m(5)C MTases NSUN2 and TRDMT1 have roles in tRNA methylation but they also act on mRNA. Proper functioning of these enzymes is important in development and there are clear links to human disease. For instance, a common variant of FTO is a risk allele for obesity carried by 1 billion people worldwide and mutations cause a lethal syndrome with growth retardation and brain deficits. NSUN2 is linked to cancer and stem cell biology and mutations cause intellectual disability. In this review, we summarize the advances, open questions, and intriguing possibilities in this emerging field that might be called RNA modomics or epitranscriptomics.

Effects of the S-adenosylhomocysteine hydrolase inhibitors 3-deazaadenosine and 3-deazaaristeromycin on RNA methylation and synthesis

The effects of 3-deazaaristeromycin and 3-deazaadenosine on RNA methylation and synthesis were examined in the mouse macrophage cell line, RAW264. S-Adenosylhomocysteine accumulated in cells incubated with 3-deazaaristeromycin while S-3-deazaadenosylhomocysteine was the major product in cells incubated with 3-deazaadenosine and homocysteine thiolactone. RNA methylation was inhibited to a similar extent by the accumulation of either S-adenosylhomocysteine or S-3-deazaadenosylhomocysteine, with S-adenosylhomocysteine being a slightly better inhibitor. In mRNA, the synthesis of N6-methyladenosine and N6-methyl-2'-O-methyladenosine were inhibited to the greatest extent, while the synthesis of 7-methylguanosine and 2'-O-methyl nucleosides were inhibited to a lesser extent. Incubation of cells with 100 microM 3-deazaaristeromycin or with 10 microM 3-deazaadenosine and 50 microM homocysteine thiolactone produced little inhibition of mRNA synthesis, even though mRNA methylation was inhibited. In contrast, mRNA synthesis was greatly inhibited by treatment of cells with 100 microM 3-deazaadenosine and the inhibition of synthesis was not correlated with an inhibition of methylation.

In vitro methylation of undermethylated yeast poly(A)-rich RNA using mRNA(guanine-7-)-methyltransferase purified from wheat germ or yeast

By crossing two strains of Saccharomyces cerevisiae deficient for each of the two methionine adenosyltransferase isoenzymes (ATP: L-methionine S-adenosyltransferase EC 2.5.1.6) respectively, we have constructed a strain strictly auxotrophic for S-adenosylmethionine and used it as a source of undermethylated mRNA suitable for in vitro transmethylation studies. RNA has been phenol-extracted from yeast cells shifted down to S-adenosylmethionine-free medium for 90 min and poly(A)-rich RNA has been prepared by oligo(dT)-cellulose chromatography. Upon incubation in vitro in the presence of methyl-labeled S-adenosylmethionine and mRNA (guanine-7-)-methyltransferase purified from wheat germ or yeast, undermethylated poly(A)-rich RNA became significantly labeled as compared to non-starved cells from the same strain, or from a wild-type control. Cap structures were resolved by paper chromatography afer T2 and P1 RNase digestion, and shown to be a mixture of m7G5'ppp5'G and m7G5'ppp5'A, irrespective of the enzyme source, in agreement with earlier in vivo studies in yeast mRNA capping and methylation.

Methylations of adenosine residues (m6A) in pre-mRNA are important for formation of late simian virus 40 mRNAs

Cycloleucine, a competitive inhibitor of methionine transferase was used to generate in vivo partially methylated mRNA in SV40-infected BSC-1 cells. Cycloleucine at 0.5 mg/ml causes more than a 30% decrease in internal m6As of late SV40 mRNA with only minor effect on the dimethyladenosine of the 5' caps m7GpppmAm. After treatment with 2 and 5 mg/ml of cycloleucine, internal m6As were reduced by 10- and 100-fold, respectively. The inhibition of BSC-1 mRNA methylations paralleled that observed for late SV40 mRNAs. In cells exposed to 2 mg/ml cycloleucine production of late SV40 mRNA was inhibited by 80% whereas the amount of SV40 nuclear RNA was only slightly reduced. Size fractionation of SV40 nuclear RNA from cycloleucine-treated cells revealed a loss of SV40 19 S RNA with a corresponding increase of fragmented RNA sedimenting between 11 to 5 S, so that the total amount of SV40 RNA in the nucleus was almost unchanged. Analysis of viral transcription complexes from cells treated with cycloleucine indicated that SV40 transcription was not affected by cycloleucine. SV40-transformed cells, in contrast to BSC-1 cells, were able to process and transport undermethylated RNA. When transformed cells were treated with 2 mg/ml cycloleucine no changes in quantities or size of cytoplasmic and nuclear RNA were detected. The data argues for a role of internal m6A moieties in modulating the processing-linked transport of mRNA from the nucleus to the cytoplasm of nontransformed cells. Transformed cells may escape these controls due to structural alterations in their perinuclear regions.

Effect of inhibitors of methylation on early and late interferon synthesis in bovine kidney cell cultures

In virus infected bovine kidney cell cultures mainly late interferon is produced starting at about 4 hr after infection. Poly rI:poly rC induced cells as well as interferon pretreated virus infected cells produce early interferon starting immediately after induction. In infected cells the proportion of early interferon increases with time of interferon pretreatment, while late interferon is decreasing. Production of late interferon is selectively inhibited by cycloleucine, an inhibitor of S-adenosylmethionine (SAM) biosynthesis, whereas early interferon synthesis is not affected by the drug. Likewise, late interferon production is reduced much stronger than early interferon production by a combination of adenosine, L-homocysteine thiolactone, and erythro-9[3-(2-hydroxynonyl)]-adenine (EHNA) inducing in cells an accumulation of S-adenosylhomocysteine which inhibits SAM mediated methylation reactions. Inhibition of late interferon synthesis by cycloleucine is time and dose dependent and partially reversible. Cycloheximide equally blocks both early and late interferon production. Inhibition of incorporation of methyl groups into cellular RNA by the methylation inhibitors used is demonstrated by labeling with [methyl-3H] methionine and 3H-uridine. The results indicate that the synthesis of functional mRNA for early and late interferon is differentially sensitive to inhibition of methylation. The data suggest that, if early and late interferon is coded by the same structural gene, two different pathways are available for the cell to synthesize one species of mRNA.