Home LiteratureArticle Details
PMID: 2183028 Published · ppublish English Journal Article Research Support, U.S. Gov't, P.H.S.

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

Molecular and cellular biology ·Vol. 10 ·No. 5 ·1990-05-00 ·Pages 2269-84

Herrick D, Parker R, Jacobson A

Abstract

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.

MeSH Terms
Blotting, Northern Codon Cycloheximide/pharmacology Gene Expression Regulation, Fungal/drug effects Genes, Fungal Hot Temperature Molecular Weight Poly A/genetics Protein Biosynthesis Pyrrolidinones/pharmacology RNA Polymerase II/metabolism RNA, Fungal/genetics RNA, Messenger/genetics,metabolism Saccharomyces cerevisiae/genetics,metabolism
Chemicals
Codon Pyrrolidinones RNA, Fungal RNA, Messenger acetopyrrothine Poly A Cycloheximide RNA Polymerase II
Authors & Affiliations
3 authors, click to expand affiliations / ORCID
Herrick D
Department of Molecular Genetics and Microbiology, University of Massachusetts Medical School, Worcester 01655.
Parker R
Jacobson A
References (101)
101 references, click to expand
  1. The sequence of the DNAs coding for the mating-type loci of Saccharomyces cerevisiae.
    Cell. 1981 Nov;27(1 Pt 2):15-23 PMID: 7034964
  2. Individual messenger RNA half lives in Saccharomyces cerevisiae.
    Mol Gen Genet. 1979 Feb 26;170(2):129-35 PMID: 372757
  3. Yeast histone genes show dosage compensation.
    Cell. 1981 May;24(2):377-84 PMID: 7016340
  4. Regulation of messenger RNA stability in mouse erythroleukemia cells.
    J Mol Biol. 1985 Jan 20;181(2):231-9 PMID: 3856689
  5. Cycloheximide resistance in yeast: the gene and its protein.
    Nucleic Acids Res. 1983 May 25;11(10):3123-35 PMID: 6304624
  6. Efficient synthesis of enzymatically active calf chymosin in Saccharomyces cerevisiae.
    Gene. 1983 Sep;24(1):1-14 PMID: 6313478
  7. Codon usage tabulated from the GenBank Genetic Sequence Data.
    Nucleic Acids Res. 1988;16 Suppl:r315-402 PMID: 3368329
  8. Correlation between the abundance of yeast transfer RNAs and the occurrence of the respective codons in protein genes. Differences in synonymous codon choice patterns of yeast and Escherichia coli with reference to the abundance of isoaccepting transfer RNAs.
    J Mol Biol. 1982 Jul 15;158(4):573-97 PMID: 6750137
  9. Codon replacement in the PGK1 gene of Saccharomyces cerevisiae: experimental approach to study the role of biased codon usage in gene expression.
    Mol Cell Biol. 1987 Aug;7(8):2914-24 PMID: 2823108
  10. Eucaryotic RNA polymerase conditional mutant that rapidly ceases mRNA synthesis.
    Mol Cell Biol. 1987 May;7(5):1602-11 PMID: 3299050
  11. Expression of a beta-galactosidase gene containing the ribosomal protein 51 intron is sensitive to the rna2 mutation of yeast.
    Proc Natl Acad Sci U S A. 1983 Jul;80(14):4403-7 PMID: 6308621
  12. Determinants of messenger RNA stability.
    Cell. 1987 Jan 16;48(1):5-6 PMID: 2431794
  13. Lomofungin, an inhibitor of deoxyribonucleic acid-dependent ribonucleic acid polymerases.
    Antimicrob Agents Chemother. 1973 Jun;3(6):723-8 PMID: 4790624
  14. Hybridization of denatured RNA and small DNA fragments transferred to nitrocellulose.
    Proc Natl Acad Sci U S A. 1980 Sep;77(9):5201-5 PMID: 6159641
  15. DNA sequence required for efficient transcription termination in yeast.
    Cell. 1982 Mar;28(3):563-73 PMID: 6280875
  16. The genes for fifteen ribosomal proteins of Saccharomyces cerevisiae.
    J Biol Chem. 1981 Oct 10;256(19):10176-83 PMID: 6268628
  17. Identification of a common nucleotide sequence in the 3'-untranslated region of mRNA molecules specifying inflammatory mediators.
    Proc Natl Acad Sci U S A. 1986 Mar;83(6):1670-4 PMID: 2419912
  18. In vivo transcription of a eukaryotic regulatory gene.
    EMBO J. 1983;2(12):2179-84 PMID: 6321151
  19. Isolation and sequence of the gene for actin in Saccharomyces cerevisiae.
    Proc Natl Acad Sci U S A. 1980 Jul;77(7):3912-6 PMID: 7001447
  20. Inhibition of yeast ribonucleic acid polymerases by thiolutin.
    J Bacteriol. 1973 Oct;116(1):245-56 PMID: 4583213
  21. Analysis of interferon mRNA in human fibroblast cells induced to produce interferon.
    Proc Natl Acad Sci U S A. 1981 Dec;78(12):7426-30 PMID: 6174973
  22. Translation is required for regulation of histone mRNA degradation.
    Cell. 1987 Feb 27;48(4):615-26 PMID: 3028643
  23. Absence of polyadenylate segment in globin messenger RNA accelerates its degradation in Xenopus oocytes.
    Proc Natl Acad Sci U S A. 1975 Aug;72(8):3065-7 PMID: 1059092
  24. Length heterogeneity in the poly (adenylic acid) region of yeast messenger ribonucleic acid.
    Biochemistry. 1974 Dec 17;13(26):5378-83 PMID: 4611485
  25. Does 3'-terminal poly(A) stabilize human fibroblast interferon mRNA in oocytes of Xenopus laevis?
    Proc Natl Acad Sci U S A. 1978 Oct;75(10):5030-3 PMID: 283411
  26. A conserved AU sequence from the 3' untranslated region of GM-CSF mRNA mediates selective mRNA degradation.
    Cell. 1986 Aug 29;46(5):659-67 PMID: 3488815
  27. Interference of nonsense mutations with eukaryotic messenger RNA stability.
    Proc Natl Acad Sci U S A. 1979 Oct;76(10):5134-7 PMID: 388431
  28. Poly(A) shortening and degradation of the 3' A+U-rich sequences of human c-myc mRNA in a cell-free system.
    Mol Cell Biol. 1988 Apr;8(4):1697-708 PMID: 3380094
  29. Three forms of the 5.8-S ribosomal RNA species in Saccharomyces cerevisiae.
    Eur J Biochem. 1974 Jan 3;41(1):197-202 PMID: 4593336
  30. "A technique for radiolabeling DNA restriction endonuclease fragments to high specific activity". Addendum.
    Anal Biochem. 1984 Feb;137(1):266-7 PMID: 6329026
  31. Fractionation and functional analysis of newly synthesized and decaying messenger RNAs from vegetative cells of Dictyostelium discoideum.
    J Mol Biol. 1979 Mar 5;128(3):371-95 PMID: 439140
  32. Isolation and identification of yeast messenger ribonucleic acids coding for enolase, glyceraldehyde-3-phosphate dehydrogenase, and phosphoglycerate kinase.
    Biochemistry. 1978 Nov 14;17(23):4900-7 PMID: 363146
  33. Messenger RNA for ribosomal proteins in yeast.
    J Mol Biol. 1983 Mar 25;165(1):79-89 PMID: 6341608
  34. Nucleotide sequences of STE2 and STE3, cell type-specific sterile genes from Saccharomyces cerevisiae.
    EMBO J. 1985 Oct;4(10):2643-8 PMID: 16453635
  35. Correlation between the abundance of Escherichia coli transfer RNAs and the occurrence of the respective codons in its protein genes: a proposal for a synonymous codon choice that is optimal for the E. coli translational system.
    J Mol Biol. 1981 Sep 25;151(3):389-409 PMID: 6175758
  36. Inhibitors of ribonucleic acid synthesis in Saccharomyces cerevisiae: decay rate of messenger ribonucleic acid.
    J Bacteriol. 1973 Sep;115(3):889-96 PMID: 4580571
  37. Messenger RNA half-life in Dictyostelium discoideum.
    Dev Biol. 1983 Jan;95(1):239-43 PMID: 6825928
  38. Comparative effects of 1,10-phenanthroline and 1,7-phenanthroline on DNA and RNA synthesis in mouse spleen.
    Life Sci. 1978 Mar;22(11):1007-10 PMID: 642706
  39. Codon usage determines translation rate in Escherichia coli.
    J Mol Biol. 1989 May 20;207(2):365-77 PMID: 2474074
  40. Codon usage in yeast: cluster analysis clearly differentiates highly and lowly expressed genes.
    Nucleic Acids Res. 1986 Jul 11;14(13):5125-43 PMID: 3526280
  41. Accumulation of rare and moderately abundant mRNAs in mouse L-cells is mainly post-transcriptionally regulated.
    J Mol Biol. 1984 Oct 5;178(4):869-80 PMID: 6492167
  42. Nucleotide sequence and transcriptional mapping of the yeast pet56-his3-ded1 gene region.
    Nucleic Acids Res. 1985 Dec 9;13(23):8587-601 PMID: 3001645
  43. Cytoplasmic processing of myosin heavy chain messenger RNA: evidence provided by using a recombinant DNA plasmid.
    Proc Natl Acad Sci U S A. 1980 Oct;77(10):5749-53 PMID: 6934508
  44. RNA molecular weight determinations by gel electrophoresis under denaturing conditions, a critical reexamination.
    Biochemistry. 1977 Oct 18;16(21):4743-51 PMID: 911786
  45. Consequences of frameshift mutations at the immunoglobulin heavy chain locus of the mouse.
    EMBO J. 1985 Feb;4(2):351-9 PMID: 3926482
  46. Effects of 1,10-phenanthroline and a zinc complex of 1,10-phenanthroline on nucleic acid synthesis in mouse liver and spleen.
    J Pharmacol Exp Ther. 1978 Apr;205(1):27-32 PMID: 633088
  47. Cell-specific regulation of the c-myc gene by lymphocyte mitogens and platelet-derived growth factor.
    Cell. 1983 Dec;35(3 Pt 2):603-10 PMID: 6606489
  48. Transcriptional regulation of the yeast cytochrome c gene.
    Proc Natl Acad Sci U S A. 1979 Aug;76(8):3627-31 PMID: 226972
  49. High stability of messenger RNA in growing cultured cells.
    Nature. 1972 Nov 10;240(5376):102-4 PMID: 4564814
  50. Globin mRNA species containing poly(A) segments of different lengths. Their functional stability in Xenopus oocytes.
    Eur J Biochem. 1976 Apr 15;64(1):115-21 PMID: 776610
  51. Regulation of c-myc mRNA stability in vitro by a labile destabilizer with an essential nucleic acid component.
    Mol Cell Biol. 1989 May;9(5):1996-2006 PMID: 2747642
  52. Location and sequence of the erf gene of phage P22.
    Virology. 1982 Jun;119(2):422-9 PMID: 6210989
  53. Mode of action of thiolutin, an inhibitor of macromolecular synthesis in Saccharomyces cerevisiae.
    Antimicrob Agents Chemother. 1973 Jun;3(6):729-38 PMID: 4597739
  54. Premature translation termination mediates triosephosphate isomerase mRNA degradation.
    Mol Cell Biol. 1988 Feb;8(2):802-13 PMID: 2832737
  55. Effects of inducer addition and removal upon the level of allophanate hydrolase in Saccharomyces cerevisiae.
    Biochem Biophys Res Commun. 1973 Dec 19;55(4):1100-4 PMID: 4589302
  56. Codon selection in yeast.
    J Biol Chem. 1982 Mar 25;257(6):3026-31 PMID: 7037777
  57. Control of biologically active interleukin 2 messenger RNA formation in induced human lymphocytes.
    Proc Natl Acad Sci U S A. 1984 May;81(9):2601-5 PMID: 6609365
  58. Temperature-sensitive yeast mutant defective in ribonucleic acid production.
    J Bacteriol. 1969 Sep;99(3):807-14 PMID: 5370278
  59. The a-factor pheromone of Saccharomyces cerevisiae is essential for mating.
    Mol Cell Biol. 1988 Mar;8(3):1309-18 PMID: 3285180
  60. Structure of polyadenylic acid in the ribonucleic acid of Saccharomyces cerevisiae.
    J Bacteriol. 1979 May;138(2):542-51 PMID: 374394
  61. A rapid alkaline extraction procedure for screening recombinant plasmid DNA.
    Nucleic Acids Res. 1979 Nov 24;7(6):1513-23 PMID: 388356
  62. Identification and regulation of a gene required for cell fusion during mating of the yeast Saccharomyces cerevisiae.
    Mol Cell Biol. 1987 Aug;7(8):2680-90 PMID: 3313002
  63. Posttranscriptional regulation of c-fos mRNA expression.
    Nucleic Acids Res. 1987 Feb 25;15(4):1643-59 PMID: 3103102
  64. Rapid cytoplasmic turnover of c-myc mRNA: requirement of the 3' untranslated sequences.
    Mol Cell Biol. 1987 Dec;7(12):4513-21 PMID: 3325826
  65. Regulation of messenger RNA stability in eukaryotic cells.
    Bioessays. 1987 May;6(5):221-6 PMID: 3606588
  66. Lariat structures are in vivo intermediates in yeast pre-mRNA splicing.
    Cell. 1984 Dec;39(3 Pt 2):611-21 PMID: 6096014
  67. Unstable beta-globin mRNA in mRNA-deficient beta o thalassemia.
    Cell. 1981 Dec;27(3 Pt 2):543-53 PMID: 6101206
  68. Iron-responsive elements: regulatory RNA sequences that control mRNA levels and translation.
    Science. 1988 May 13;240(4854):924-8 PMID: 2452485
  69. RNA synthesis and control of cell division in the yeast S. cerevisiae.
    Cell. 1978 Aug;14(4):951-8 PMID: 99247
  70. Determinants that contribute to cytoplasmic stability of human c-fos and beta-globin mRNAs are located at several sites in each mRNA.
    Mol Cell Biol. 1988 Aug;8(8):3244-50 PMID: 3211141
  71. Regulation of c-fos gene expression in hamster fibroblasts: initiation and elongation of transcription and mRNA degradation.
    Nucleic Acids Res. 1987 Jul 24;15(14):5657-67 PMID: 3615200
  72. The stem-loop structure at the 3' end of histone mRNA is necessary and sufficient for regulation of histone mRNA stability.
    Mol Cell Biol. 1987 Dec;7(12):4557-9 PMID: 3437896
  73. Nucleotide sequence of the tcml gene (ribosomal protein L3) of Saccharomyces cerevisiae.
    J Bacteriol. 1983 Jul;155(1):8-14 PMID: 6305925
  74. Structure of a yeast pheromone gene (MF alpha): a putative alpha-factor precursor contains four tandem copies of mature alpha-factor.
    Cell. 1982 Oct;30(3):933-43 PMID: 6754095
  75. Transcriptional and translational expression of a chimeric bacterial-yeast plasmid in yeasts.
    Gene. 1980 Oct;11(1-2):11-9 PMID: 7002730
  76. Inhibition of protein synthesis stabilizes histone mRNA.
    Mol Cell Biol. 1984 Oct;4(10):2082-90 PMID: 6209555
  77. Lomofungin, an inhibitor of ribonucleic acid synthesis in yeast protoplasts: its effect on enzyme formation.
    Antimicrob Agents Chemother. 1973 Jun;3(6):716-22 PMID: 4790623
  78. A single gene from yeast for both nuclear and cytoplasmic polyadenylate-binding proteins: domain structure and expression.
    Cell. 1986 Jun 20;45(6):827-35 PMID: 3518950
  79. Structure and function of the yeast URA3 gene. Differentially regulated expression of hybrid beta-galactosidase from overlapping coding sequences in yeast.
    J Mol Biol. 1983 Nov 15;170(4):883-904 PMID: 6315953
  80. Messenger RNA stability in Dictyostelium discoideum: does poly(A) have a regulatory role?
    J Mol Biol. 1980 Aug 5;141(2):99-118 PMID: 7441754
  81. 1,10-Phenanthroline-cuprous ion complex, a potent inhibitor of DNA and RNA polymerases.
    Biochem Biophys Res Commun. 1978 Feb 28;80(4):1025-32 PMID: 346019
  82. Effects of ethylenediaminetetraacetic acid and 1,10-phenanthroline on cell proliferation and DNA synthesis of Ehrlich ascites cells.
    Cancer Res. 1980 Nov;40(11):4092-9 PMID: 6781741
  83. Removal of poly(A) and consequent degradation of c-fos mRNA facilitated by 3' AU-rich sequences.
    Nature. 1988 Nov 24;336(6197):396-9 PMID: 3194021
  84. mRNA decay rates in late-developing Dictyostelium discoideum cells are heterogeneous, and cyclic AMP does not act directly to stabilize cell-type-specific mRNAs.
    Mol Cell Biol. 1988 Oct;8(10):4088-97 PMID: 2847029
  85. Faithful cell-cycle regulation of a recombinant mouse histone H4 gene is controlled by sequences in the 3'-terminal part of the gene.
    Proc Natl Acad Sci U S A. 1985 Jul;82(13):4389-93 PMID: 3925455
  86. Histone H2B genes of yeast encode two different proteins.
    Cell. 1980 Dec;22(3):799-805 PMID: 7006833
  87. Messenger RNA stability in Saccharomyces cerevisiae: the influence of translation and poly(A) tail length.
    Nucleic Acids Res. 1987 Mar 25;15(6):2417-29 PMID: 3550698
  88. Mild temperature shock affects transcription of yeast ribosomal protein genes as well as the stability of their mRNAs.
    Nucleic Acids Res. 1988 Aug 25;16(16):7917-29 PMID: 3047675
  89. 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.
    Mol Cell Biol. 1988 May;8(5):1957-69 PMID: 2898728
  90. A stem-loop in the 3' untranslated region mediates iron-dependent regulation of transferrin receptor mRNA stability in the cytoplasm.
    Cell. 1988 Jun 3;53(5):815-25 PMID: 3370673
  91. An analysis of the rate of metallothionein mRNA poly(A)-shortening using RNA blot hybridization.
    Nucleic Acids Res. 1985 Nov 25;13(22):7929-43 PMID: 2866488
  92. Sequence-specific adenylations and deadenylations accompany changes in the translation of maternal messenger RNA after fertilization of Spisula oocytes.
    J Mol Biol. 1983 May 25;166(3):309-27 PMID: 6854649
  93. The turnover of messenger RNA.
    Sci Am. 1989 Apr;260(4):48-55 PMID: 2648565
  94. Turnover of polyadenylate-containing ribonucleic acid in Saccharomyces cerevisiae.
    J Bacteriol. 1976 Feb;125(2):595-600 PMID: 1107326
  95. Structure of a split yeast gene: complete nucleotide sequence of the actin gene in Saccharomyces cerevisiae.
    Proc Natl Acad Sci U S A. 1980 May;77(5):2546-50 PMID: 6994099
  96. Preparative and analytical purification of DNA from agarose.
    Proc Natl Acad Sci U S A. 1979 Feb;76(2):615-9 PMID: 284385
  97. The c-fos transcript is targeted for rapid decay by two distinct mRNA degradation pathways.
    Genes Dev. 1989 Jan;3(1):60-72 PMID: 2496006
  98. Escherichia coli ribosomes translate in vivo with variable rate.
    EMBO J. 1984 Dec 1;3(12):2895-8 PMID: 6396082
  99. Evidence the yeast STE3 gene encodes a receptor for the peptide pheromone a factor: gene sequence and implications for the structure of the presumed receptor.
    Proc Natl Acad Sci U S A. 1986 Mar;83(5):1418-22 PMID: 3006051
  100. The yeast alpha-factor receptor: structural properties deduced from the sequence of the STE2 gene.
    Nucleic Acids Res. 1985 Dec 9;13(23):8463-75 PMID: 3001640
  101. Codon usage can affect efficiency of translation of genes in Escherichia coli.
    Nucleic Acids Res. 1984 Sep 11;12(17):6663-71 PMID: 6091031
Article Info
Journal
Molecular and cellular biology
Abbr.
Mol Cell Biol
ISSN
0270-7306
DOI
10.1128/mcb.10.5.2269-2284.1990
Published
1990-05-00
Pages
2269-84
Language
English
Region
United States
NLM ID
8109087
PMCID
PMC360574
Subset
IM
Grants
NIGMS NIH HHS · R01 GM027757 · United States
NIGMS NIH HHS · GM11479 · United States
NIGMS NIH HHS · GM27757 · United States
External Links
PubMed source DOI: 10.1128/mcb.10.5.2269-2284.1990 PMC Full Text View journal details
Analysis Services
Analysis Services

Contact

No. 2 Wenbo Road, Zhangqiu District, Jinan, Shandong

Qilu Normal University · Genelibs Bioinformatics Lab

750 Shunhua Rd, Jinan

2F, Bldg F, University Science Park

Tel: 0531-88819269

WeChat Official Account

Follow our WeChat subscription account for real-time updates and the latest in medical and biological research.


Business Email

E-mail: [email protected]

Copyright © 2026.Genelibs Jinan Honghui Biotechnology Co., Ltd. 鲁ICP备20007159号-2