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

Santiago, T.C.; Bettany, A. J. E.; Purvis, Ian J.; Brown, Alistair J. P.

doi:10.1093/nar/15.6.2417

Cited by 40 publications

(28 citation statements)

References 39 publications

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“…An earlier study in yeasts (89) found no correlation between mRNA decay rates and poly(A) lengths, an observation supported by the work described here. We found that (i) poly(A)-deficient CYH2 and PGKI mRNAs are extremely stable (Fig.…”

Section: Discussionsupporting

confidence: 90%

“…The significance of such observations is still unclear. It is unlikely that arrested ribosomes simply protect mRNA from nucleases since, in normally growing cells, the ribosome packing density does not differ for stable and unstable mRNAs (89,94). The possibility exists that essential nucleases are metabolically unstable or that mRNA degradation depends on ribosomal translocation through or up to specific mRNA regions (9, 28).…”

Section: Resultsmentioning

confidence: 99%

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Identification and comparison of stable and unstable mRNAs in Saccharomyces cerevisiae.

1990

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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 rpbl-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 alters 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 MATal, were unstable (t112 < 7 min) and 4, including those encoded by ACT) and PGKI, were stable (t112 > 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.Differences in the decay rates of individual mRNAs can have profound effects on the overall levels of expression of specific genes (80,93). Although the potential importance of mRNA stability as a mechanism for regulating gene expression has been recognized (7, 86), the structures and mechanisms involved in the determination of individual mRNA decay rates have yet to be elucidated. As an approach to understanding the determinants of mRNA stability, we have begun to compare the properties of mRNAs in Dictyostelium discoideum which differ significantly in their respective decay rates (94). In this report, we describe our initial efforts to perform a similar analysis of mRNAs in the yeast Saccharomyces cerevisiae. Our objective was the identification of both stable and unstable yeast mRNAs that were encoded by genes which had already been well characterized. Success in such an endeavor would make it possible to explore the structural determinants of mRNA stability, for example, by analyzing the decay rates of mRNAs transcribed from chimeric genes (25,42,43,81,96,97).Decay rates for both the poly(A)+ RNA population and for individual yeast mRNAs have been measured previously by several different functional or chemical assays. Half-lives ranging from 16 to 23 min have been measured for the average turnover rate of the poly(A)+ RNA population, whereas half-lives of individual mRNAs span a broader range from 1 to over 100 min (3,18,19,35,36,46,47,50,52,54,...

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Section: Discussionsupporting

confidence: 90%

Section: Resultsmentioning

confidence: 99%

Identification and comparison of stable and unstable mRNAs in Saccharomyces cerevisiae.

1990

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“…This conclusion is supported by our recent experiments which indicate that the entire set of D. discoideum ribosomal protein mRNAs can exist in the cytoplasm of early developing cells in a stable, but untranslated, form (83). A lack of a relationship between mRNA stability and translatability has also been observed in other experimental systems (38,71). To reconcile these conclusions with the destabilizing effects listed above, we note that all three types of effect lead to aberrant dissociation of mRNA from ribosomes.…”

Section: Discussionsupporting

confidence: 74%

“…Santiago et al (72) inhibited transcription with high concentrations of 1,10-phenanthroline, a chelating agent which affects a number of cellular processes (15,32,37) The possibility that poly(A) tail lengths directly determine mRNA stabilities has been suggested by microinjection experiments with adenylated and deadenylated mRNAs (17,29,46,56) and by experiments with cordycepin-treated cells (90). However, similar microinjection experiments with different poly(A)+ and poly(A)-mRNAs (16,27,48,73) and other experimental approaches (38,58,71,84) (Fig. 7) (58,59,75); (ii) the decay curves of mRNAs with half-lives longer than the 4-h half-life (58,59) for poly(A) shortening are linear, not biphasic (Fig.…”

Section: Discussionmentioning

confidence: 99%

Determinants of mRNA stability in Dictyostelium discoideum amoebae: differences in poly(A) tail length, ribosome loading, and mRNA size cannot account for the heterogeneity of mRNA decay rates.

Shapiro¹,

Herrick²,

Manrow³

et al. 1988

Mol. Cell. Biol.

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As an approach to understanding the structures and mechanisms which determine mRNA decay rates, we have cloned and begun to characterize cDNAs which encode mRNAs representative of the stability extremes in the poly(A)+ RNA population of Dictyostelium discoideum amoebae. The cDNA clones were identified in a screening procedure which was based on the occurrence of poly(A) shortening during mRNA aging. mRNA half-lives were determined by hybridization of poly(A)+ RNA, isolated from cells labeled in a 32P04 pulse-chase, to dots of excess cloned DNA. Individual mRNAs decayed with unique first-order decay rates ranging from 0.9 to 9.6 h, indicating that the complex decay kinetics of total poly(A)+ RNA in D. discoideum amoebae reflect the sum of the decay rates of individual mRNAs. Using specific probes derived from these cDNA clones, we have compared the sizes, extents of ribosome loading, and poly(A) tail lengths of stable, moderately stable, and unstable mRNAs. We found (i) no correlation between mRNA size and decay rate; (ii) no significant difference in the number of ribosomes per unit length of stable versus unstable mRNAs, and (iii) a general inverse relationship between mRNA decay rates and poly(A) tail lengths. Collectively, these observations indicate that mRNA decay in D. discoideum amoebae cannot be explained in terms of random nucleolytic events. The possibility that specific 3'-structural determinants can confer mRNA instability is suggested by a comparison of the labeling and turnover kinetics of different actin mRNAs. A correlation was observed between the steady-state percentage of a given mRNA found in polysomes and its degree of instability; i.e., unstable mRNAs were more efficiently recruited into polysomes than stable mRNAs. Since stable mRNAs are, on average, "older" than unstable mRNAs, this correlation may reflect a translational role for mRNA modifications that change in a time-dependent manner. Our previous studies have demonstrated both a time-dependent shortening and a possible translational role for the 3' poly(A) tracts of mRNA. We suggest, therefore, that the observed differences in the translational efficiency of stable and unstable mRNAs may, in part, be attributable to differences in steady-state poly(A) tail lengths.We have previously demonstrated that the mRNA population in vegetatively growing amoebae of the cellular slime mold Dictyostelium discoideum decays with complex kinetics, consisting of at least two major components: a rapidly decaying component with a half-life of approximately 50 min, and a long-lived component with a half-life of approximately 10 h (14, 58). Similar complex kinetics have been observed for the decay of poly(A)+ RNA in a variety of other eucaryotic cells (5,25,39,57,77,78,81). It is likely that these complex decay kinetics reflect the sum of the decay rates of individual mRNAs (e.g., in D. discoideum, the most stable mRNAs have half-lives of approximately 10 h and the least stable mRNAs have half-lives which are approximately 10-fold shorter). It has been s...

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“…shown that there is no apparent correlation between mRNA stability and transcript size (14), length of poly(A) tail (14,32), or efficiency of ribosome loading onto the mRNA (32). Even less is known about mRNA turnover during meiosis, primarily because of poor uptake of labeled precursors into cells during sporulation and reincorporation of radioactive isotopes from cells prelabeled during growth (due to RNA degradation during sporulation) (27,36).…”

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confidence: 99%

Early meiotic transcripts are highly unstable in Saccharomyces cerevisiae.

Surosky

Esposito

1992

Mol. Cell. Biol.

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Meiosis in Saccharomyces cerevisiae requires the induction of a large number of genes whose mRNAs accumulate at specific times during meiotic development. This study addresses the role of mRNA stability in the regulation of meiosis-specific gene expression. Evidence is provided below demonstrating that the levels of meiotic mRNAs are exquisitely regulated by both transcriptional control and RNA turnover. The data show that (i) early meiotic transcripts are extremely unstable when expressed during either vegetative growth or sporulation, and (ii) transcriptional induction, rather than RNA turnover, is the predominant mechanism responsible for meiosis-specific transcript accumulation. When genes encoding the early meiotic mRNAs are fused to other promoters and expressed during vegetative growth, their mRNA half-lives, of under 3 min, are among the shortest known in S. cerevisiae. Since these mRNAs are only twofold more stable when expressed during sporulation, we conclude that developmental regulation of mRNA turnover can be eliminated as a major contributor to meiosis-specific mRNA accumulation. The rapid degradation of the early mRNAs at all stages of the yeast life cycle, however, suggests that a specific RNA degradation system operates to maintain very low basal levels of these transcripts during vegetative growth and after their transient transcriptional induction in meiosis. Studies to identify specific cis-acting elements required for the rapid degradation of early meiotic transcripts support this idea. A series of deletion derivatives of one early meiosis-specific gene, SP013, indicate that its mRNA contains determinants, located within the coding region, which contribute to the high instability of this transcript. Translation is another component of the degradation mechanism since frameshift and nonsense mutations within the SP013 mRNA stabilize the transcript.

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

Cited by 40 publications

References 39 publications

Identification and comparison of stable and unstable mRNAs in Saccharomyces cerevisiae.

Identification and comparison of stable and unstable mRNAs in Saccharomyces cerevisiae.

Determinants of mRNA stability in Dictyostelium discoideum amoebae: differences in poly(A) tail length, ribosome loading, and mRNA size cannot account for the heterogeneity of mRNA decay rates.

Early meiotic transcripts are highly unstable in Saccharomyces cerevisiae.

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