Individual messenger RNA half lives in Saccharomyces cerevisiae

Impact of Methods on the Measurement of mRNA Turnover

The turnover of the RNA molecules is determined by the rates of transcription and RNA degradation. Several methods have been developed to study RNA turnover since the beginnings of molecular biology. Here we summarize the main methods to measure RNA half-life: transcription inhibition, gene control, and metabolic labelling. These methods were used to detect the cellular activity of the mRNAs degradation machinery, including the exo-ribonuclease Xrn1 and the exosome. On the other hand, the study of the differential stability of mature RNAs has been hampered by the fact that different methods have often yielded inconsistent results. Recent advances in the systematic comparison of different method variants in yeast have permitted the identification of the least invasive methodologies that reflect half-lives the most faithfully, which is expected to open the way for a consistent quantitative analysis of the determinants of mRNA stability.

Examining the relative activity of several dicistrovirus intergenic internal ribosome entry site elements in uninfected insect and mammalian cell lines

Comparisons of the relative activities of 11 intergenic region (IGR) internal ribosome entry site (IRES) elements of insect dicistrovirus with 5' IRES elements of the hepatitis C and encephalomyocarditis viruses were performed in insect and mammalian cells. Dual luciferase assays were performed to determine the most effective dicistrovirus IGR IRES in the lepidopteran cell lines Sf9 (Spodoptera frugiperda) and BmN (Bombyx mori), and the dipteran cell lines S2 (Drosophila melanogaster) and ATC-10 (Aedes aegypti). Evaluation of dual luciferase expression from DNA plasmids and in vitro-transcribed RNA revealed apparent splicing with certain IRES elements. Though IRES activity depended upon the cell line examined, the black queen cell and Drosophila C dicistrovirus intergenic IRES elements were most effective for coupled gene expression in the diverse insect cell lines examined.

Mucor dimorphism

Mucor dimorphism has interested microbiologists since the time of Pasteur. When deprived of oxygen, these fungi grow as spherical, multipolar budding yeasts. In the presence of oxygen, they propagate as branching coenocytic hyphae. The ease with which these morphologies can be manipulated in the laboratory, the diverse array of morphopoietic agents available, and the alternative developmental fates that can be elicited from a single cell type (the sporangiospore) make Mucor spp. a highly propitious system in which to study eukaryotic cellular morphogenesis. The composition and organization of the cell wall differ greatly in Mucor yeasts and hyphae. The deposition of new wall polymers is isodiametric in yeasts and apically polarized in hyphae. Current research has focused on the identity and control of enzymes participating in wall synthesis. An understanding of how the chitosome interacts with appropriate effectors, specific enzymes, and the plasma membrane to assemble chitin-chitosan microfibrils and to deposit them at the proper sites on the cell exterior will be critical to elucidating dimorphism. Several biochemical and physiological parameters have been reported to fluctuate in a manner that correlates with Mucor morphogenesis. The literature describing these has been reviewed critically with the intent of distinguishing between causal and casual connections. The advancement of molecular genetics has afforded powerful new tools that researchers have begun to exploit in the study of Mucor dimorphism. Several genes, some encoding products known to correlate with development in Mucor spp. or other fungi, have been cloned, sequenced, and examined for transcriptional activity during morphogenesis. Most have appeared in multiple copies displaying independent transcriptional control. Selective translation of stored mRNA molecules occurs during sporangiospore germination. Many other correlates of Mucor morphogenesis, presently described but not yet explained, should prove amenable to analysis by the emerging molecular technology.

Identification and comparison of stable and unstable mRNAs in Saccharomyces cerevisiae

We developed a procedure to measure mRNA decay rates in the yeast Saccharomyces cerevisiae and applied it to the determination of half-lives for 20 mRNAs encoded by well-characterized genes. The procedure utilizes Northern (RNA) or dot blotting to quantitate the levels of individual mRNAs after thermal inactivation of RNA polymerase II in an rpb1-1 temperature-sensitive mutant. We compared the results of this procedure with results obtained by two other procedures (approach to steady-state labeling and inhibition of transcription with Thiolutin) and also evaluated whether heat shock alter mRNA decay rates. We found that there are no significant differences in the mRNA decay rates measured in heat-shocked and non-heat-shocked cells and that, for most mRNAs, different procedures yield comparable relative decay rates. Of the 20 mRNAs studied, 11, including those encoded by HIS3, STE2, STE3, and MAT alpha 1, were unstable (t1/2 less than 7 min) and 4, including those encoded by ACT1 and PGK1, were stable (t1/2 greater than 25 min). We have begun to assess the basis and significance of such differences in the decay rates of these two classes of mRNA. Our results indicate that (i) stable and unstable mRNAs do not differ significantly in their poly(A) metabolism; (ii) deadenylation does not destabilize stable mRNAs; (iii) there is no correlation between mRNA decay rate and mRNA size; (iv) the degradation of both stable and unstable mRNAs depends on concomitant translational elongation; and (v) the percentage of rare codons present in most unstable mRNAs is significantly higher than in stable mRNAs.

Identification and comparison of stable and unstable mRNAs in Saccharomyces cerevisiae

We developed a procedure to measure mRNA decay rates in the yeast Saccharomyces cerevisiae and applied it to the determination of half-lives for 20 mRNAs encoded by well-characterized genes. The procedure utilizes Northern (RNA) or dot blotting to quantitate the levels of individual mRNAs after thermal inactivation of RNA polymerase II in an rpb1-1 temperature-sensitive mutant. We compared the results of this procedure with results obtained by two other procedures (approach to steady-state labeling and inhibition of transcription with Thiolutin) and also evaluated whether heat shock alter mRNA decay rates. We found that there are no significant differences in the mRNA decay rates measured in heat-shocked and non-heat-shocked cells and that, for most mRNAs, different procedures yield comparable relative decay rates. Of the 20 mRNAs studied, 11, including those encoded by HIS3, STE2, STE3, and MAT alpha 1, were unstable (t1/2 less than 7 min) and 4, including those encoded by ACT1 and PGK1, were stable (t1/2 greater than 25 min). We have begun to assess the basis and significance of such differences in the decay rates of these two classes of mRNA. Our results indicate that (i) stable and unstable mRNAs do not differ significantly in their poly(A) metabolism; (ii) deadenylation does not destabilize stable mRNAs; (iii) there is no correlation between mRNA decay rate and mRNA size; (iv) the degradation of both stable and unstable mRNAs depends on concomitant translational elongation; and (v) the percentage of rare codons present in most unstable mRNAs is significantly higher than in stable mRNAs.

Yeast mutation thought to arrest mRNA transport markedly increases the length of the 3' poly(A) on polyadenylated RNA

In Saccharomyces cerevisiae the function of the RN A1 gene is believed to be required for the transport of newly synthesized mRNA from the nucleus to the cytoplasm. Nuclear poly(A)+ RNAs accumulate and cytoplasmic mRNAs decay after the temperature-sensitive (ts) rna1.1 mutant is shifted from 25 degrees C to 37 degrees C. In this study the 3' poly(A) upon poly(A)+ RNA synthesized after expression of rna1.1 was shown to be appreciably longer than the poly(A) normally present on yeast cytoplasmic mRNA. This increased poly(A) length is due to rna1.1, since it was found only in this mutant after a 25 degrees C to 37 degrees C heat shock, not an intragenic non-ts revertant of rna1.1, wild-type (RN A1+) cells or a RN A1+, rna2.1 mutant subjected to equivalent heat shocks. It may be an indication that the normal shortening of the poly(A) on mRNAs does not occur in the nucleus, but happens only with transport to the cytoplasm. Alterations in the mean size of poly(A) may be a relatively simple marker for mRNA transport defects.

Messenger RNA degradation in Saccharomyces cerevisiae

The analysis of 17 functional mRNAs and two recombinant mRNAs in the yeast Saccharomyces cerevisiae suggests that the length of an mRNA influences its half-life in this organism. The mRNAs are clearly divisible into two populations when their lengths and half-lives are compared. Differences in ribosome loading amongst the mRNAs cannot account for this division into relatively stable and unstable populations. Also, specific mRNAs seem to be destabilized to differing extents when their translation is disrupted by N-terminus-proximal stop codons. The analysis of a mutant mRNA, generated by the fusion of the yeast PYK1 and URA3 genes, suggests that a destabilizing element exists within the URA3 sequence. The presence of such elements within relatively unstable mRNAs might account for the division between the yeast mRNA populations. On the basis of these, and other previously published observations, a model is proposed for a general pathway of mRNA degradation in yeast. This model may be relevant to other eukaryotic systems. Also, only a minor extension to the model is required to explain how the stability of some eukaryotic mRNAs might be regulated.

Two-dimensional gel analysis of yeast proteins: application to the study of changes in the levels of major polypeptides of Saccharomyces cerevisiae depending on the fermentable or nonfermentable nature of the carbon source

Taking advantage of the recent identification of polypeptides of the carbon metabolism machinery on the yeast protein map [1], we applied two-dimensional gel electrophoresis to a study of changes in protein composition of Saccharomyces cerevisiae depending on the fermentable or nonfermentable nature of the carbon source. The levels of the 250 most abundant polypeptides were compared. Thirty-three were found to display markedly increased levels during growth on nonfermentable carbon sources. These 33 polypeptides include 11 mitochondrial polypeptides and polypeptides corresponding to alcohol dehydrogenase II, acetyl-CoA synthetase, phosphoenol pyruvate kinase and hexokinase PI. Sixteen other polypeptides, in contrast, reached their higher levels during growth on fermentable carbon sources. Among these were identified the monomeric subunits of 6 glycolytic enzymes. Collectively the 33 polypeptides of the first class comprised over 30% of the total soluble proteins of cells grown on nonfermentable carbon source and 3% during growth on fermentable carbon source. The protein fraction of the 16 polypeptides of the second class corresponded to 10% and 38%, respectively. Together these results show that two-dimensional gel electrophoresis, when coupled with the identification of polypeptides of the carbon metabolism apparatus, provides a valuable tool for approaching questions concerning carbon metabolism in S. cerevisiae.

Messenger RNA stability in Saccharomyces cerevisiae: the influence of translation and poly(A) tail length

A comparison between the half-lives of 10 specific yeast mRNAs and their distribution within polysomes (fractionated on sucrose density gradients) was used to test the relationship between mRNA translation and degradation in the eukaryote Saccharomyces cerevisiae. Although the mRNAs vary in their distribution across the same polysome gradients, there is no obvious correlation between the stability of an mRNA and the number of ribosomes it carries in vivo. This suggests that ribosomal protection against nucleolytic attack is not a major factor in determining the stability of an mRNA in yeast. The relative lengths of the poly(A) tails of 9 yeast mRNAs were analysed using thermal elution from poly(U)-Sepharose. No dramatic differences in poly(A) tail length were observed amongst the mRNAs which could account for their wide ranging half-lives. Minor differences were consistent with shortening of the poly(A) tail as an mRNA ages.

The relationship between mRNA stability and length in Saccharomyces cerevisiae

A rapid and convenient procedure has been developed for the measurement of mRNA half-life in S.cerevisiae using the transcriptional inhibitor, 1,10-phenanthroline. A range of half-lives from 6.6 +/- 0.67 minutes to over 100 minutes, relative to the stability of the 18S rRNA control, has been obtained for fifteen mRNAs. They include the pyruvate kinase and actin mRNAs, as well as 13 randomly picked mRNAs of unknown function. The mRNAs clearly fall into two populations when their lengths and half-lives are analysed; one population is considerably more stable than the other when mRNAs of similar length are compared. Also, within each population, there is an inverse relationship between mRNA length and half-life. These results suggest that mRNA length and at least one additional factor strongly influence mRNA stability in yeast.

Differential stability of Drosophila embryonic mRNAs during subsequent larval development

The relative stabilities of specific embryonic mRNAs that persist in Drosophila melanogaster larvae were determined using an approach that combined RNA density labeling with cell-free translation. Unlike the other methods commonly used to measure the decay of individual mRNAs, the density labeling approach does not depend on the use of transcriptional inhibitors or on the measurement of precursor pool specific activities. Using this approach, we have determined that different embryonic mRNA species persist for varying periods during subsequent development, with half-lives ranging from approximately 2 to approximately 30 h. The embryonic histone mRNAs are relatively unstable; they are no longer detectable by 9 h of larval development. By 41 h of larval development, 90% of the nonhistone mRNAs assayed have decayed considerably; computerized scanning densitometry of translation products indicates that these transcripts are not decaying as members of discrete half-life classes. The persisting mRNAs that remain are very long-lived; their in vitro translation products can still be detected after 91 h of larval development. We have tentatively identified the mRNAs that encode actin, tropomyosin, and tubulin as members of this stable mRNA population. Although embryonic mRNAs do fall into these three broad classes of stability, they appear to decay with a continuum of half-lives. Because the range of half-lives is so great, mRNA stability is probably an important factor controlling mRNA abundance during Drosophila development.

Regulation of cytoplasmic mRNA prevalence in sea urchin embryos. Rates of appearance and turnover for specific sequences

Complementary DNA clones representing cytoplasmic poly(A) RNAs of sea urchin embryos were hybridized with metabolically labeled cytoplasmic RNA preparations and the rates of appearance and of decay for each transcript species were determined at the blastula-gastrula stage of development. The prevalence of the transcripts chosen for this study ranged, on average, from about one molecule per cell to a few hundred molecules per cell. The embryos were labeled continuously for 18 hours with [3H]guanosine, beginning at 24 hours post-fertilization. The amount of cytoplasmic [3H]poly(A) RNA that hybridized to each cloned sequence was determined and the specific activity of the [3H]GTP pool was measured in the same embryos. Rate constants for the entry of each transcript species into the cytoplasm, and for its decay were extracted from these data. The embryo transcript species identified by the cloned probes displayed a range of stabilities. Half-lives of only a few hours were measured both for a very rare sequence and for a moderately prevalent sequence. Other newly synthesized transcripts, including sequences that first appear during embryonic development, as well as sequences also represented in maternal RNA, are far more stable. We conclude that cytoplasmic RNA turnover rate is a major variable in the determination of the cytoplasmic level of expression of embryo genes. The entry rates of the transcripts into the cytoplasm also varied, from a few molecules per embryo per minute to several hundred, depending on the sequence. By comparing the mass of transcripts of a given sequence in the embryo to the mass of transcripts of that sequence accumulating as a result of new synthesis, the point at which embryo transcription accounts for the major fraction of the cytoplasmic molecules could be estimated. This calculation showed that for some sequences maternal transcripts persist well beyond gastrulation, while other embryo poly(A) RNA species are largely the product of transcription in the embryo nuclei from the blastula stage onwards. There is no single stage at which all maternal transcripts are suddenly replaced by newly synthesized embryo transcripts. Primary transcription rates were measured for two sequences by determining accumulation of label in these RNA species soon after addition of [3H]guanosine to the cultures. Comparing these rates to the cytoplasmic entry rates, we did not detect a significantly greater nuclear transcription of the sequence homologous to the cloned probe.

Identification of the purC gene product of Escherichia coli

The purC region of the Escherichia coli chromosome was isolated from in vivo-derived lambda transducing bacteriophages and cloned in high-copy-number plasmids. The product of the purC gene, phosphoribosylaminoimidazolesuccinocarboxamide synthetase, was identified as a protein with an Mr of ca. 27,000. The level of the protein is increased by more than 60-fold in strains carrying the gene on a high-copy-number plasmid. Purine addition represses the enzyme level in both plasmid- and non-plasmid-containing strains.

Quantitative analysis of the heat shock response of Saccharomyces cerevisiae

Transient protein synthesis in Saccharomyces cerevisiae, after shift from 21-23 degrees C to 37 degrees C, was quantitatively analyzed. Pulse-labeled proteins were separated by two-dimensional gel electrophoresis, and autoradiograms of the gels were analyzed by a recently described method involving a computer-coupled film scanning system. In this way, the rate of incorporation of L-[35S]methionine into approximately 500 proteins was followed. The synthesis of more than 80 of these proteins was transiently induced at 37 degrees C, with about 20 being classified as major heat shock proteins (defined as those whose rate of labeling was increased at least eightfold at some time during the response). The synthesis of more than 300 of the proteins was transiently repressed at 37 degrees C, and several general temporal patterns of repression could be distinguished. The influence of temperature-sensitive mutations affecting RNA synthesis and transport on the heat shock response was also examined. A protein whose induction in response to heat shock has a post-transcriptional component could be identified. As previously pointed out, the heat shock repression of certain proteins is so rapid that it also must involve post-transcriptional effects.

Growth-rate-dependent adjustment of ribosome function in chemostat-grown cells of the fungus Mucor racemosus

The dimorphic fungus Mucor racemosus was grown as a yeast in a chemostat. Cellular growth rates were varied over a fourfold range under an atmosphere of N2 and over an eightfold range under CO2. Under either atmosphere, an increase in the cellular growth rate resulted in increases in (i) the cellular ribosome concentration, (ii) the percentage of ribosomes active in protein synthesis, and (iii) the rate of polypeptide chain elongation. The rate of protein synthesis in this organism can therefore be regulated by adjustment of all of these mechanisms.

Mistranslation in cells infected with the bacteriophage MS2: direct evidence of Lys for Asn substitution

The coat protein of the bacteriophage MS2 was found to show an increased level of charge heterogeneity when synthesized in Escherichia coli starved for Asn or Lys. No such increase was found when the host was starved for Arg, His Ile or Pro. This is the pattern predicted by "two-out-of-three" codon misreading in the coat protein gene. In the case of Asn starvation, direct measurements of the relative incorporation of Lys demonstrate that the observed charge heterogeneity is the result of mistranslation. Asn starvation increased the error frequency in coat protein to over 0.3 mistake per asparagine codon. The small amount of charge heterogeneity seen in unstarved cells seems also to be the result of misreading Asn codons.

Alterations in translatable ribonucleic acid after heat shock of Saccharomyces cerevisiae

Changes in populations of translatable messenger ribonucleic acids (mRNA's) after heat shock of Saccharomyces cerevisiae were examined and found to correlate very closely with transient alterations in patterns of in vivo protein synthesis. Initial changes included an increase in translatable species coding for polypeptides synthesized during heat shock; this increase was found to be dependent on transcription but did not require ongoing protein synthesis. A decrease was observed in the level of translatable mRNA's coding for polypeptides whose synthesis was repressed after heat shock. This decrease was much more rapid than can be explained solely by termination of transcription. Requirements for this rapid loss of RNA from the translatable pool included both transcription and an active rna1 gene product but not protein synthesis. After the initial changes in translatable RNA induced by heat shock, the patterns of both in vivo and in vitro translation products began to revert to the preshock levels. This recovery period, unlike the earlier changes, was dependent upon a requisite period of protein synthesis.