Selective Degradation of Newly Synthesized Nonmessenger Simian Virus 40 Transcripts

By pretreating simian virus 40-infected BSC-1 cells with glucosamine, [(3)H]uridine labeling of both cellular and viral RNA can be halted instantaneously by addition of cold uridine. We have studied the fate of pulse-labeled viral RNA from cells at 45 h postinfection under these conditions. During a 5-min period of labeling, both the messenger and nonmessenger regions of the late strand were transcribed. After various chase periods, nuclear viral species which sediment at 19, 17.5, and 16S were observed. Nuclear viral RNA decays in a multiphasic manner. Of the material present at the beginning of the chase period, 50% was degraded rapidly with a half-life of 8 min (initial processing). This rapidly degraded material was that fraction of the late strand which did not give rise to stable late mRNA species. Forty percent was transported to the cytoplasm, and 10% remained in the nucleus as material which sedimented in the 2 to 4S region. These 2 to 4S viral RNAs had a half-life of 3 h, and hybridization studies suggest that they are in part coded for by the late-strand nonmessenger region and are derived from the initial nuclear processing step. Another part is coded for by the late-strand messenger region and may be generated by some subsequent nuclear cleavages of 19S RNA into 17.5 and 16S RNAs. Transport of nuclear viral RNA into the cytoplasm was detected after a 5-min pulse and a 7-min chase. The maximum amount of labeled viral RNA was accumulated in the cytoplasm after a 30-min to 1-h chase. At least two viral cytoplasmic species were observed. Kinetic data suggest that 19S RNA is transported directly from the nucleus. Whether cytoplasmic 16S is formed by cleavage of 19S RNA in the cytoplasm is not clear. The half-lives of cytoplasmic 19 and 16S RNAs can be approximated as 2 and 5 h, respectively.     

A precursor of globin messenger RNA

The size of pulse-labeled globin messenger RNA nucleotide sequences was investigated, to determine whether newly transcribed globin mRNA molecules are larger than steady-state globin mRNA. Molecular hybridization techniques were used to compare directly the sedimentation of steady-state (unlabeled) and pulse-labeled (radioactive) globin mRNA sequences in the same analytical sucrose gradient. In gradients containing 98% formamide, radioactive globin mRNA sequences from mouse fetal liver cells labeled for 15 to 20 minutes with [³H]uridine sediment in a broad band with a peak at approximately 14 S, while steady-state globin mRNA sediments at 10 S. The large radioactive RNA can be recovered from one gradient and recentrifuged in a second gradient, in which it again sediments in a broad band with a peak at 14 S. The large radioactive RNA is cleaved to 10 S during a 75-minute “chase” with either actinomycin D or unlabeled uridine plus cytidine. The estimated half-life of the precursor is 45 minutes or less under these conditions. A covalent RNA precursor larger than 18 S with a similar turnover rate is not observed.     

Biosynthesis and stability of globin mRNA in cultured erythroleukemic friend cells

Biosynthesis and stability of the mRNA population in DMSO-induced Friend erythroleukemic cells were studied after labeling the RNA with ³H-uridine and then chasing it with nonlabeled uridine. Globin RNA metabolism was studied by hybridization to excess complementary DNA covalently coupled to oligo(dT)-cellulose. After a labeling period of 120 min, 2–4% of the poly(A)-containing labeled RNA was in globin RNA; it decayed with a half-life of 16–17 hr. The rest of the poly(A)-containing RNA was composed of two kinetic populations: 85–90% decayed with a half-life of about 3 hr, while 10% decayed with a half-life of about 37 hr. The portion of globin RNA in labeled poly(A)-containing RNA behaved in an unexpected fashion during the chase period. During the initial chase period, the percentage of globin RNA increased rapidly, reaching a maximum of about 15% at 20 hr, but if subsequently declined gradually.Based on these findings, a model was built that describes the changes in the proportion of globin mRNA in poly(A)-containing RNA during continuous synthesis and after chase of the labeled RNA. It appears that if the parameters described remain constant during the maturation of erythroblasts, then this model would not account for the almost exclusive presence of globin RNA in the reticulocyte. By far the most effective way to achieve this high level of globin RNA is the destabilization of the mRNA population which is more stable than globin RNA, and not the stabilization of globin RNA itself.     

A characterization of globin mRNA sequences in the nucleus of duck immature red blood cells

Studies were performed with duck immature red blood cells to identify and characterize the globin mRNA sequences in nuclear RNA. Annealing of ³H-globin cDNA to unlabeled nuclear RNA has identified three distinct size classes of nuclear RNA molecules containing globin mRNA sequences. The largest size class contained 1–2% of total nuclear globin mRNA sequences and sedimented through 85% formamide-sucrose gradients at the same rate as 28S ribosomal RNA. Chromatography on oligo(dT)-cellulose indicated that most of these molecules are not polyadenylated. The bulk of nuclear globin mRNA sequences (70%) was contained in polyadenylated RNA molecules which sedimented at 16.5S. The remainder of nuclear globin mRNA sequences (～30%) was detected in molecules sedimenting at 10S (the position of cytoplasmic globin mRNA).To determine whether a precursor-product relationship exists between these nuclear molecules and cytoplasmic globin mRNA, pulse-label and chase experiments were performed. Labeled globin mRNA sequences were assayed by annealing to globin cDNA-cellulose. Labeled 28S nuclear globin RNA sequences could not be detected, perhaps due to technical reasons. 16.5S nuclear globin RNA was labeled and chased into cytoplasmic globin mRNA sequences. The half-life of 16.5S nuclear globin RNA was estimated to be less than 30 min. These results demonstrate that in duck immature red blood cells, globin mRNA is transcribed as a larger precursor. Furthermore, size characterization of this precursor during pulse-label and chase periods suggests that it is processed within the nucleus to 10S globin RNA.     

Kinetics of synthesis of cytoplasmic messenger-like RNA not associated with ribosomes in HeLa cells

The turn-over of cytoplasmic messenger-like RNA not associated with polyribosomes as well as that of polyribosomal mRNA was investigated by labelling with [3H]uridine in conditions of arrested ribosomal RNA and mitochondrial RNA synthesis. The synthesis of ribosomal RNA was inhibited with toyokamycin and that of mitochondrial RNA with ethidium bromide. In both accumulation kinetics and actinomycin-D-chase experiments, cytoplasmic messenger-like ribonucleoprotein particles and polyribosomes were fractionated by buoyant density centrifugation in CsCl gradients. The half-life of free m1RNA was found to be of 1--2 h whereas the bulk of polyribosomal mRNA was stable over the time period considered (up to 8 h) but with a minor short-lived component. Purification of RNA from polyribosomes labelled under the same conditions and fractionation of it into polyadenylated and non-polyadenylated fractions showed that this short-lived minor component of half-life less than 1 h is non-polyadenylated.     

Messenger RNA in HeLa cells: kinetics of formation and decay

The polyadenylic acid-containing messenger RNA fraction of HeLa cells was measured by its affinity for oligedeoxythymidylate cellulose. Both the kinetics of initial labeling and the decay after a brief pulse of incorporation were examined.The kinetics of decay are complex, but can be approximated by assuming two populations; a short-lived species with a half-life of seven hours and a long-lived component with a half-life of 24 hours. It is estimated that the short-lived material comprises 33% of total cellular mRNA, while the relatively stable species amounts to 67% of the steady-state mRNA content.The two mRNA components with different decay times were observed simultaneously in the same cell population by measuring decay of 24-hour old mRNA labeled with ¹⁴C and RNA briefly labeled with ³H. The old mRNA had only a 24-hour decay component, while the new mRNA was biphasic. The decay of old and new mRNA was also observed after RNA synthesis was inhibited with actinomycin. Again, old mRNA decayed more slowly than recently labeled material. However, both decay times are significantly shorter in the presence of actinomycin and correspond to half-lives of approximately 4 and 12 hours.There is a small but significant difference in sedimentation distribution of new and old mRNA, the old mRNA sedimenting more slowly than new material, suggesting that the more stable species has a lower average molecular weight.The steady-state content of mRNA in HeLa cells amounts to 5.5% of the ribosomal RNA, or more than twice the amount of messenger RNA estimated to be on hemoglobin-synthesizing polyribosomes.     

Changes in RNA in relation to growth of the fibroblast: II. The lifetime of mRNA,rRNA, and tRNA in resting and growing cells

The stabilities of the principal classes of RNA have been studied in resting and exponentially growing mouse fibroblast lines 3T6 and 3T3. Cytoplasmic mRNA, labeled with tritiated uridine and isolated by virtue of its poly A content, is equally stable in resting and growing cells, displaying a half-life of about 9 hr. We conclude that the accumulation of poly A(+) mRNA during transition from resting to growing state is due not to an increase in its stability, but to an increase in its rate of formation.The stability of cytoplasmic rRNA was measured after labeling with ³H-methyl-methionine. In agreement with the results of previous studies, we found that rRNA is stable in growing cells and unstable in resting cells. Quite unexpectedly, the 18S and 28S rRNA of resting cultures were found to differ appreciably in turnover rate. In both 3T6 and 3T3, the half-life of 28S RNA is about 50 hr, and that of 18S RNA about 72 hr. For this reason, though growing cells should synthesize the two ribosomal subunits in equal numbers, resting cells should synthesize more of the larger subunits than of the smaller. tRNA is unstable under all conditions. Its half-life is 36 hr in resting cells and about 60 hr in growing cells.     

Effect of 5-fluorouracil on the synthesis and stability of ribosomal RNA in Saccharomyces carlsbergensis

A study has been made of the effects of 5-fluorouracil on the synthesis and stability of ribosomal RNA in yeast. The analog causes ribosomal precursor RNA to accumulate. Mature ribosomal RNA species synthesized in the presence of 5-fluorouracil are unstable and are degraded. Pulse chase experiments showed that the 26 S ribosomal RNA is more rapidly degraded than the 17 S component, explaining our observations that in long term experiments apparently less 26 S than 17 S ribosomal RNA is formed. Possible reasons for the instability of ribosomal RNA containing 5-fluorouracil are discussed.     

Alterations in the Distribution of Labeled Ribonucleic Acid in Polyribosomes from Escherichia coli Infected with Bacteriophage R17

The distribution of labeled ribonucleic acid (RNA) associated with polysomes from Escherichia coli infected with the bacteriophage R17 was investigated. Pulse-labeling of RNA for 15 sec with (3)H-uridine resulted in increased labeling of the RNA associated with larger polysomes from infected cells as compared to control cells. Analysis of the RNA indicated that the increased labeling of large polysomes resulted from the presence of labeled double-stranded viral RNA. Other species of 15-sec pulse-labeled RNA entered into polysome formation in both infected and control cells. On the other hand, pulse-labeling of cultures for 15 sec with (3)H-uridine followed by a 5-min chase with unlabeled uridine resulted in a greater decrease in the amount of labeled RNA associated with large polysomes from infected cells as compared to control cells. This decreased labeling of large polysomes from infected cells was accompanied by an increased amount of label associated with the monomer to trimer regions. Analysis of RNA labeled under pulse-chase conditions indicated that virus infection resulted in an increased amount of heterogeneous 5 to 15S RNA in both the monomer to trimer and ribosomal subunit-soluble regions of the polysome profile. Labeled 5 to 15S RNA extracted directly from infected cells under pulse-chase conditions, without prior polysome fractionation, was characterized by a shift toward a distribution of smaller polynucleotides.     

Characterization of the Rapidly Labeled Hybridizable RNA Synthesized in L5178Y Mouse Leukemic Cells: Hybridization Lifetime Studies

An attempt is made to characterize the rapidly labeled hybridizable RNA of L5178Y mouse leukemic cells which has been shown to have similar base sequences when synthesized in two different stages of the cell cycle. The size of rapidly labeled RNA molecules was heterogeneous. For labeling times of 20 min or less, the per cent of hybridization was maximal. With longer labeling times, the per cent of hybridization decreased as radioactivity appeared in long-lived species of low hybridization efficiency; the radioactivity profile resembled the optical density profile in sucrose gradients. The lifetime of newly synthesized hybridizable RNA was studied by pulse labeling exponentially growing cells and then “chasing” with nonradioactive uridine. The per cent of hybridization was studied as a function of chase time. Three RNA groups, which comprised different proportions of rapidly labeled hybridizable RNA, were distinguished. The short-lived group had a half-life of 10 min, much less than the values reported in the literature for messenger RNA of mammalian cells. The half-life of 1-1½ hr observed for a medium-lived group more closely corresponds to that of messenger RNA. A long-lived group had a half-life of approximately 20 hr. Specific activity measurements during chase indicate the presence of a “pool” of labeled uridine derivatives. The uridine of this pool appears to be nonexchangeable with but dilutable by exogenous uridine. A nontoxic concentration of actinomycin D was added to the chase media in an attempt to block the “pool effect”. A rapidly degradable RNA was demonstrable both by specific activity and per cent of hybridization measurements.     

Nucleotide pools of Novikoff rat hepatoma cells growing in suspension culture. II. Independent snucleotide pools for nucleic acid synthesis

Novikoff rat hepatoma cells (subline NlSl-67) in suspension culture incorporate ³H-5-uridine into the acid-soluble nucleotide pool more rapidly than into RNA, resulting in the accumulation of labeled UTP in the cells. When labeled uridine is removed from the medium after 20 minutes or 4.75 hours of labeling, the rate of incorporation of label from the nucleotide pool into RNA decreases to less than 10% of the original rate within five to ten minutes, in spite of the presence of a large pool of labeled UTP in the cells, and incorporation ceases completely if an excess of unlabeled uridine is present during the chase. Upon addition of ¹⁴C-uridine to ³H-uridine pulse-labeled, chased cells, the ¹⁴C begins to be incorporated into RNA without delay and at a rate predetermined by the concentration of ¹⁴C-uridine in the medium and without affecting the fate of the free ³H-nucleotides labeled during the pulse-period. The results are interpreted to indicate that uridine is incorporated into at least two different pools, only one of which serves as primary source of nucleotides for RNA synthesis. During active synthesis of RNA, the latter pool of free nucleotides is very small and rapidly exhausted when uridine is removed from the medium. However, UTP accumulates in this pool when cells are labeled at 4–6°, since at this temperature RNA synthesis is blocked while uridine is still phosphorylated by the cells, and the UTP is rapidly incorporated into RNA during a subsequent ten-minute chase at 37°. From these types of experiments it is estimated that only 20–25% of the total uridine nucleotides formed in the cells from uridine in the medium is directly available for RNA synthesis and that the remainder becomes available only at a slow rate. Evidence is presented which suggests that one uridine nucleotide pool is located in the cytoplasm and another in the nucleus and that mainly the nuclear pool supplies nucleotides for RNA synthesis. The size of the latter pool is under strict regulatory control, since preincubation of the cells with 0.5 mM unlabeled uridine has little or no effect on the subsequent incorporation of ³H-uridine, although it results in an increase of the overall cellular uridine nucleotide content to at least 5 mM. Other results indicate that adenosine is also incorporated into two independent nucleotide pools, whereas the cells normally appear to possess a single thymidine nucleotide pool.     

Stability of globin mRNA in terminally differentiating murine erythroleukemia cells

The stability of globin mRNA in terminally differentiating MEL cells has been reevaluated. Previously, it had been reported that globin mRNA has a half-life of approximately 17 hr in terminally differentiating MEL cells. We show that the previous measurements of this parameter were confounded by physical instability of differentiating MEL cells. By using culture conditions that physically stabilize end-stage cells we show that the stability of globin mRNA in terminally differentiating MEL cells is equal to the value observed for ribosomal RNA, a half-life greater than 60 hr.     

Messenger RNA turnover in mouse L cells

The turnover of polyadenylic acid-containing messenger RNA and histone messenger RNA, which lacks poly(A), was studied in exponentially growing mouse L cells by measuring the kinetics of approach to steady-state uridine labeling. Constant specific activity of precursor pools was verified by showing that the data for stable RNA components, like ribosomal RNA and transfer RNA, follow theoretically predictable curves. In agreement with a previous report by Greenberg (1972), the data for poly(A)-containing mRNA (poly(A)(+)mRNA) follow theoretical curves for a class of molecules turning over with first-order (stochastic) kinetics. Cells growing with doubling times of 13·5 hours at 37 °C and 41 hours at 30 °C exhibited mean lifetimes for their poly(A)(+)mRNA of 15 hours and 42 hours, respectively, suggesting a parallelism between growth and turnover rates. The kinetic data for histone mRNA are not indicative of a stochastic process. Rather, they suggest an age-dependent decay or a zero-order (ordered) turnover with a mean lifetime of about six hours. One model, which gave a good fit to the data, considers that the histone messages persist for a fixed duration of the cell cycle, e.g. the DNA synthetic phase, and are then destroyed in a “sensitive period” after this phase. These results are discussed with regard to the possible implications of the poly(A) sequences in messenger RNA aging.