Home LiteratureArticle Details
PMID: 7565797 Published · ppublish English Comparative Study Journal Article Research Support, Non-U.S. Gov't Research Support, U.S. Gov't, P.H.S.

Feedback inhibition of the yeast ribosomal protein gene CRY2 is mediated by the nucleotide sequence and secondary structure of CRY2 pre-mRNA.

Molecular and cellular biology ·Vol. 15 ·No. 11 ·1995-11-00 ·Pages 6454-64

Li Z, Paulovich AG, Woolford JL

Abstract

The Saccharomyces cerevisiae CRY1 and CRY2 genes, which encode ribosomal protein rp59, are expressed at a 10:1 ratio in wild-type cells. Deletion or inactivation of CRY1 leads to 5- to 10-fold-increased levels of CRY2 mRNA. Ribosomal protein 59, expressed from either CRY1 or CRY2, represses expression of CRY2 but not CRY1. cis-Acting elements involved in repression of CRY2 were identified by assaying the expression of CRY2-lacZ gene fusions and promoter fusions in CRY1 CRY2 and cry1-delta CRY2 strains. Sequences necessary and sufficient for regulation lie within the transcribed region of CRY2, including the 5' exon and the first 62 nucleotides of the intron. Analysis of CRY2 point mutations corroborates these results and indicates that both the secondary structure and sequence of the regulatory region of CRY2 pre-mRNA are necessary for repression. The regulatory sequence of CRY2 is phylogenetically conserved; a very similar sequence is present in the 5' end of the RP59 gene of the yeast Kluyveromyces lactis. Wild-type cells contain very low levels of both CRY2 pre-mRNA and CRY2 mRNA. Increased levels of CRY2 pre-mRNA are present in mtr mutants, defective in mRNA transport, and in upf1 mutants, defective in degradation of cytoplasmic RNA, suggesting that in wild-type repressed cells, unspliced CRY2 pre-mRNA is degraded in the cytoplasm. Taken together, these results suggest that feedback regulation of CRY2 occurs posttranscriptionally. A model for coupling ribosome assembly and regulation of ribosomal protein gene expression is proposed.

MeSH Terms
Base Sequence Cell Nucleus/metabolism Cytoplasm/metabolism Fungal Proteins/genetics Gene Expression Regulation, Fungal Homeostasis Hydrogen Bonding Molecular Sequence Data Nucleic Acid Conformation Oligodeoxyribonucleotides/chemistry Protein Biosynthesis RNA Precursors/chemistry,genetics RNA, Fungal/genetics RNA, Messenger/chemistry,genetics Regulatory Sequences, Nucleic Acid Ribosomal Proteins/genetics Ribosomes/metabolism,ultrastructure Saccharomyces cerevisiae/genetics Saccharomyces cerevisiae Proteins Sequence Alignment Sequence Homology, Nucleic Acid
Chemicals
Fungal Proteins Oligodeoxyribonucleotides RNA Precursors RNA, Fungal RNA, Messenger RPS14A protein, S cerevisiae Ribosomal Proteins Saccharomyces cerevisiae Proteins
Authors & Affiliations
3 authors, click to expand affiliations / ORCID
Li Z
Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, USA.
Paulovich A G
Woolford J L
References (72)
72 references, click to expand
  1. The HIV-1 rev trans-activator acts through a structured target sequence to activate nuclear export of unspliced viral mRNA.
    Nature. 1989 Mar 16;338(6212):254-7 PMID: 2784194
  2. Some cis- and trans-acting mutants for splicing target pre-mRNA to the cytoplasm.
    Cell. 1989 May 19;57(4):573-83 PMID: 2655924
  3. A system of shuttle vectors and yeast host strains designed for efficient manipulation of DNA in Saccharomyces cerevisiae.
    Genetics. 1989 May;122(1):19-27 PMID: 2659436
  4. Kluyveromyces lactis maintains Saccharomyces cerevisiae intron-encoded splicing signals.
    Mol Cell Biol. 1989 May;9(5):2208-13 PMID: 2664472
  5. Isolation and characterization of pre-mRNA splicing mutants of Saccharomyces cerevisiae.
    Genes Dev. 1989 Aug;3(8):1206-16 PMID: 2676722
  6. Nuclear pre-mRNA splicing in yeast.
    Yeast. 1989 Nov-Dec;5(6):439-57 PMID: 2694677
  7. PCR and DNA sequencing.
    Biotechniques. 1989 Jul-Aug;7(7):700-8 PMID: 2698653
  8. Escherichia coli ribosomal protein L4 stimulates transcription termination at a specific site in the leader of the S10 operon independent of L4-mediated inhibition of translation.
    J Mol Biol. 1990 May 5;213(1):67-78 PMID: 1692593
  9. The yeast his3 promoter contains at least two distinct elements.
    Proc Natl Acad Sci U S A. 1982 Dec;79(23):7385-9 PMID: 6760196
  10. Molecular cloning and analysis of the CRY1 gene: a yeast ribosomal protein gene.
    Nucleic Acids Res. 1983 Jan 25;11(2):403-20 PMID: 6338478
  11. Messenger RNA for ribosomal proteins in yeast.
    J Mol Biol. 1983 Mar 25;165(1):79-89 PMID: 6341608
  12. A technique for radiolabeling DNA restriction endonuclease fragments to high specific activity.
    Anal Biochem. 1983 Jul 1;132(1):6-13 PMID: 6312838
  13. Altered response to growth rate changes in Kluyveromyces lactis versus Saccharomyces cerevisiae as demonstrated by heterologous expression of ribosomal protein 59 (CRY1)
    Nucleic Acids Res. 1991 Sep 11;19(17):4701-7 PMID: 1891361
  14. Molecular evolution of the mammalian ribosomal protein gene, RPS14.
    Mol Biol Evol. 1991 Jul;8(4):503-14 PMID: 1921707
  15. Random mutagenesis of gene-sized DNA molecules by use of PCR with Taq DNA polymerase.
    Nucleic Acids Res. 1991 Nov 11;19(21):6052 PMID: 1658751
  16. The product of the yeast UPF1 gene is required for rapid turnover of mRNAs containing a premature translational termination codon.
    Genes Dev. 1991 Dec;5(12A):2303-14 PMID: 1748286
  17. The structure and biogenesis of yeast ribosomes.
    Adv Genet. 1991;29:63-118 PMID: 1763709
  18. The yeast omnipotent suppressor SUP46 encodes a ribosomal protein which is a functional and structural homolog of the Escherichia coli S4 ram protein.
    Genetics. 1992 Oct;132(2):375-86 PMID: 1427034
  19. Mutations affecting stability and deadenylation of the yeast MFA2 transcript.
    Genes Dev. 1992 Nov;6(11):2100-11 PMID: 1427074
  20. Splice site choice and splicing efficiency are positively influenced by pre-mRNA intramolecular base pairing in yeast.
    Cell. 1993 Mar 26;72(6):893-901 PMID: 8458083
  21. Mutational analysis of pre-mRNA splicing in Saccharomyces cerevisiae using a sensitive new reporter gene, CUP1.
    Genetics. 1993 Apr;133(4):851-63 PMID: 8462846
  22. Yeast ribosomal protein L1 is required for the stability of newly synthesized 5S rRNA and the assembly of 60S ribosomal subunits.
    Mol Cell Biol. 1993 May;13(5):2835-45 PMID: 8474444
  23. Pre-mRNA secondary structure and the regulation of splicing.
    Bioessays. 1993 Mar;15(3):165-9 PMID: 8489523
  24. Regulation of RNA processing and transport by a nuclear guanine nucleotide release protein and members of the Ras superfamily.
    EMBO J. 1993 Jul;12(7):2929-37 PMID: 7687541
  25. Stabilization and ribosome association of unspliced pre-mRNAs in a yeast upf1- mutant.
    Proc Natl Acad Sci U S A. 1993 Aug 1;90(15):7034-8 PMID: 8346213
  26. Lack of introns in the ribosomal protein gene S14 of trypanosomes.
    Mol Cell Biol. 1990 Jun;10(6):3284-8 PMID: 2188114
  27. A Neurospora crassa ribosomal protein gene, homologous to yeast CRY1, contains sequences potentially coordinating its transcription with rRNA genes.
    Nucleic Acids Res. 1990 Oct 11;18(19):5759-65 PMID: 1977135
  28. Functional analysis of a duplicated linked pair of ribosomal protein genes in Saccharomyces cerevisiae.
    Mol Cell Biol. 1990 Nov;10(11):6097-100 PMID: 2233736
  29. Depletion of yeast ribosomal proteins L16 or rp59 disrupts ribosome assembly.
    J Cell Biol. 1990 Dec;111(6 Pt 1):2261-74 PMID: 2277060
  30. The production of single-stranded DNA suitable for sequencing using the polymerase chain reaction.
    Biotechniques. 1991 Jan;10(1):24-6 PMID: 2003916
  31. Structural basis for the regulation of splicing of a yeast messenger RNA.
    Cell. 1991 May 31;65(5):797-804 PMID: 2040015
  32. The ribosomal protein L2 in S. cerevisiae controls the level of accumulation of its own mRNA.
    EMBO J. 1991 Aug;10(8):2215-21 PMID: 2065661
  33. Unexpected point mutations activate cryptic 3' splice sites by perturbing a natural secondary structure within a yeast intron.
    Genes Dev. 1991 Jul;5(7):1252-63 PMID: 2065975
  34. Macromolecule synthesis in temperature-sensitive mutants of yeast.
    J Bacteriol. 1967 May;93(5):1662-70 PMID: 5337848
  35. Coordinate regulation of the synthesis of eukaryotic ribosomal proteins.
    Proc Natl Acad Sci U S A. 1976 May;73(5):1547-51 PMID: 775493
  36. Yeast use translational control to compensate for extra copies of a ribosomal protein gene.
    Cell. 1982 Jun;29(2):347-55 PMID: 7116444
  37. Transformation of intact yeast cells treated with alkali cations.
    J Bacteriol. 1983 Jan;153(1):163-8 PMID: 6336730
  38. Ribosomal protein L32 of Saccharomyces cerevisiae regulates both splicing and translation of its own transcript.
    J Biol Chem. 1993 Sep 15;268(26):19669-74 PMID: 8366109
  39. Short artificial hairpins sequester splicing signals and inhibit yeast pre-mRNA splicing.
    Mol Cell Biol. 1993 Nov;13(11):6841-8 PMID: 8413277
  40. Molecular genetics of cryptopleurine resistance in Saccharomyces cerevisiae: expression of a ribosomal protein gene family.
    Genetics. 1993 Nov;135(3):719-30 PMID: 8293976
  41. Regulation of splicing at an intermediate step in the formation of the spliceosome.
    Genes Dev. 1994 Jan;8(2):211-20 PMID: 8299940
  42. The sequence of a cDNA encoding ribosomal protein S14 from the hydrozoan Podocoryne carnea reveals high evolutionary conservation.
    Gene. 1994 Mar 25;140(2):243-6 PMID: 7908274
  43. Commitment of yeast pre-mRNA to the splicing pathway requires a novel U1 small nuclear ribonucleoprotein polypeptide, Prp39p.
    Mol Cell Biol. 1994 Jun;14(6):3623-33 PMID: 8196608
  44. Diverse mechanisms for regulating ribosomal protein synthesis in Escherichia coli.
    Prog Nucleic Acid Res Mol Biol. 1994;47:331-70 PMID: 7517053
  45. Isolation and characterization of Saccharomyces cerevisiae mRNA transport-defective (mtr) mutants.
    J Cell Biol. 1994 Aug;126(3):649-59 PMID: 8045930
  46. Evidence that HIV-1 Rev directly promotes the nuclear export of unspliced RNA.
    EMBO J. 1994 Sep 1;13(17):4105-12 PMID: 8076606
  47. Saccharomyces cerevisiae ribosomal protein L37 is encoded by duplicate genes that are differentially expressed.
    Curr Genet. 1994 Jun;25(6):480-7 PMID: 8082197
  48. Changes in the stem-loop at the 3' terminus of histone mRNA affects its nucleocytoplasmic transport and cytoplasmic regulation.
    Nucleic Acids Res. 1994 Nov 11;22(22):4660-6 PMID: 7984415
  49. Characterization of cis-acting sequences and decay intermediates involved in nonsense-mediated mRNA turnover.
    Mol Cell Biol. 1995 Feb;15(2):809-23 PMID: 7823948
  50. Effects of secondary structure on pre-mRNA splicing: hairpins sequestering the 5' but not the 3' splice site inhibit intron processing in Nicotiana plumbaginifolia.
    EMBO J. 1995 Jan 16;14(2):377-88 PMID: 7835348
  51. Regulation of human RPS14 transcription by intronic antisense RNAs and ribosomal protein S14.
    Genes Dev. 1995 Feb 1;9(3):304-16 PMID: 7867928
  52. Turnover mechanisms of the stable yeast PGK1 mRNA.
    Mol Cell Biol. 1995 Apr;15(4):2145-56 PMID: 7891709
  53. Regulation and intracellular localization of Saccharomyces cerevisiae strand exchange protein 1 (Sep1/Xrn1/Kem1), a multifunctional exonuclease.
    Mol Cell Biol. 1995 May;15(5):2728-36 PMID: 7739553
  54. A comprehensive set of sequence analysis programs for the VAX.
    Nucleic Acids Res. 1984 Jan 11;12(1 Pt 1):387-95 PMID: 6546423
  55. Regulation of the synthesis of ribosomes and ribosomal components.
    Annu Rev Biochem. 1984;53:75-117 PMID: 6206783
  56. Structure and organization of two linked ribosomal protein genes in yeast.
    Nucleic Acids Res. 1984 Oct 11;12(19):7345-58 PMID: 6387623
  57. Expression of two Xenopus laevis ribosomal protein genes in injected frog oocytes. A specific splicing block interferes with the L1 RNA maturation.
    J Mol Biol. 1984 Dec 25;180(4):987-1005 PMID: 6084725
  58. mRNA splicing efficiency in yeast and the contribution of nonconserved sequences.
    Cell. 1985 May;41(1):119-26 PMID: 3888403
  59. Saccharomyces cerevisiae coordinates accumulation of yeast ribosomal proteins by modulating mRNA splicing, translational initiation, and protein turnover.
    Mol Cell Biol. 1985 Jun;5(6):1512-21 PMID: 3897837
  60. Autogenous regulation of splicing of the transcript of a yeast ribosomal protein gene.
    Proc Natl Acad Sci U S A. 1986 Aug;83(16):5854-7 PMID: 3526341
  61. Effect of RP51 gene dosage alterations on ribosome synthesis in Saccharomyces cerevisiae.
    Mol Cell Biol. 1985 Dec;5(12):3429-35 PMID: 3915776
  62. Primary structure of human ribosomal protein S14 and the gene that encodes it.
    Mol Cell Biol. 1986 Aug;6(8):2774-83 PMID: 3785212
  63. Yeast shuttle and integrative vectors with multiple cloning sites suitable for construction of lacZ fusions.
    Gene. 1986;45(3):299-310 PMID: 3026915
  64. Structure and expression of the Saccharomyces cerevisiae CRY1 gene: a highly conserved ribosomal protein gene.
    Mol Cell Biol. 1987 May;7(5):1764-75 PMID: 3037334
  65. The accumulation of three yeast ribosomal proteins under conditions of excess mRNA is determined primarily by fast protein decay.
    Mol Cell Biol. 1988 Jan;8(1):169-75 PMID: 3275866
  66. Plasmid construction by homologous recombination in yeast.
    Gene. 1987;58(2-3):201-16 PMID: 2828185
  67. Rapid and efficient site-specific mutagenesis without phenotypic selection.
    Methods Enzymol. 1987;154:367-82 PMID: 3323813
  68. The cellular level of yeast ribosomal protein L25 is controlled principally by rapid degradation of excess protein.
    Curr Genet. 1986;10(10):733-9 PMID: 3329033
  69. Depletion of Saccharomyces cerevisiae ribosomal protein L16 causes a decrease in 60S ribosomal subunits and formation of half-mer polyribosomes.
    Genes Dev. 1988 Feb;2(2):160-72 PMID: 3282992
  70. Ribosomal protein L2 in Saccharomyces cerevisiae is homologous to ribosomal protein L1 in Xenopus laevis. Isolation and characterization of the genes.
    J Biol Chem. 1988 May 5;263(13):6188-92 PMID: 2834365
  71. Ribosomal protein synthesis is not regulated at the translational level in Saccharomyces cerevisiae: balanced accumulation of ribosomal proteins L16 and rp59 is mediated by turnover of excess protein.
    Genes Dev. 1988 Jun;2(6):664-76 PMID: 3047007
  72. Ribosomal protein S14 is encoded by a pair of highly conserved, adjacent genes on the X chromosome of Drosophila melanogaster.
    Mol Cell Biol. 1988 Oct;8(10):4314-21 PMID: 3141788
Article Info
Journal
Molecular and cellular biology
Abbr.
Mol Cell Biol
ISSN
0270-7306
DOI
10.1128/MCB.15.11.6454
Published
1995-11-00
Pages
6454-64
Language
English
Region
United States
NLM ID
8109087
PMCID
PMC230896
Subset
IM
Grants
NCI NIH HHS · CA-01000 · United States
NIGMS NIH HHS · GM28301 · United States
External Links
PubMed source DOI: 10.1128/MCB.15.11.6454 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: product@genelibs.com

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