Structure and organization of two linked ribosomal protein genes in yeast

Molenaar, C. M. T.; Woudt, Lambertus P.; Jansen, Antonius E.M.; Mager, Willem H.; Planta, Rudi J.; Donovan, David M.; Pearson, Nancy J.

doi:10.1093/nar/12.19.7345

Cited by 75 publications

(25 citation statements)

References 34 publications

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“…Both genes are active in the genome as well, since disruption of either still permits growth (C. Kruse and J. Warner, unpublished data). The two genes for rpSl (1) and rp28 (22) are also known to be active.…”

Section: Methodsmentioning

confidence: 99%

“…In all cases the transcription was proportional to the copy number times the rate of transcription of the host's genes. Yeasts carry single genes for some ribosomal proteins, e.g., TCMJ, CYH2, and RPL32, and duplicate genes for others, e.g., RPSIO, RP(29) (21), RP(51) (1), RP (28), and RPS16A (22). When extra copies of a duplicated gene are introduced into the yeast cell, the increased synthesis of mRNA is proportional only to half the copy number (Table 3).…”

Section: Methodsmentioning

confidence: 99%

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Saccharomyces cerevisiae coordinates accumulation of yeast ribosomal proteins by modulating mRNA splicing, translational initiation, and protein turnover.

et al. 1985

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The rate of accumulation of each ribosomal protein is carefully regulated by the yeast cell to provide the equimolar ratio necessary for the assembly of the ribosome. The mechanisms responsible for this regulation have been examined by introducing into the yeast cell extra copies of seven individual ribosomal protein genes carried on autonomously replicating plasmids. In each case studied the plasmid-borne gene was transcribed to the same degree as the genomic gene. Nevertheless, the cell maintained a balanced accumulation of ribosomal proteins, using a variety of methods other than transcription. (i) Several ribosomal proteins were synthesized in substantial excess. However, the excess ribosomal protein was rapidly degraded. (ii) The excess mRNA for two of the ribosomal protein genes was translated inefficiently. We provide evidence that this was due to inefficient initiation of translation. (iii) The transcripts derived from two of the ribosomal protein genes were spliced inefficiently, leading to an accumulation of precursor RNA. We present a model which proposes the autogenous regulation of mRNA splicing as a eucaryotic parallel of the autogenous regulation of mRNA translation in procaryotes. Finally, the accumulation of each ribosomal protein was regulated independently. In no instance did the presence of excess copies of the gene for one ribosomal protein affect the synthesis of another ribosomal protein.The ribosome is undoubtedly the most thoroughly understood organelle of the cell (2, 37, 38). It has two subunits. The smaller is composed of one RNA molecule and 20 to 30 proteins; the larger is composed of two RNA molecules and 35 to 50 proteins. With only one or two exceptions (e.g., L7/L12), there is a single molecule of each comnonent in each Escherichia coli ribosome (11) and there is no reason to believe that eucaryotic ribosomes will be different.Our interest is centered on the synthesis of the ribosome, in particular, on the mechanisms used by the cell to ensure an adequate supply of each component used for assembly without needless accumulation of excess components (7,36). In short, we view efficient synthesis of ribosomes as a problem of molecular inventory control. That the cell can carry out this process effectively was apparent from earlier studies on both RNA (33) and proteins (9) showing that no more than 10% excess of any ribosomal component was synthesized. Since the assembly of ribosomes is presumably limited by the availability of the least abundant component, there is little margin for error.

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Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Saccharomyces cerevisiae coordinates accumulation of yeast ribosomal proteins by modulating mRNA splicing, translational initiation, and protein turnover.

et al. 1985

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“…Again for S. cerevisiae, a particular level of rp synthesis is achieved by coordinate adjustments in the abundance of all rp mRNAs, probably by changes in rp gene transcription (7,13,18). This balanced and coordinated expression of yeast rp genes is striking considering the large number of transcription units involved (probably more than 100) and the fact that some rp mRNAs are products of single-copy genes (8,33) while other rp mRNAs are derived by transcription of a pair of duplicate genes (2,30,35,49 ally inactive, presumably due to an absence of TUF factor interaction (23,36,40,51). Conversely, insertion of UAS,pg sequences reactivates transcription (36,50).…”

mentioning

confidence: 99%

Constitutive transcription of yeast ribosomal protein gene TCM1 is promoted by uncommon cis- and trans-acting elements.

Hamil¹,

Nam²,

Fried³

1988

Mol. Cell. Biol.

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The DNA sequence UAST (TCGTTTTGTACGTTTTTCA) was found to mediate transcription of yeast ribosomal protein gene TCMI. UAST was defined as a transcriptional activator on the basis of loss of transcription accompanying deletions of all or part of UAST, orientation-independent restoration of transcription promoted by a synthetic UAST oligomer inserted either into TCM1 or into the yeast CYCI gene lacking its transcriptional activation region, and diminished transcription following nucleotide alterations in UAST. UAST bound in vitro to a protein denoted TAF (TCMI activation factor); TAF was concluded to be a transcriptional activator protein because nucleotide alterations in UAST that diminished transcription in vivo also diminished TAF binding in vitro. The sequence of UAST bore no obvious resemblance to UASrpg, the principal cis-acting element common to most yeast ribosomal protein genes. Likewise, TAF was distinguished from the UASrpg-binding protein TUF, since (i) TAF and TUF were chromatographically separable, (ii) binding of either TAF or TUF to its corresponding UAS was unaffected by an excess of UASrpg or UAST DNA, respectively, and (iii) photochemical cross-linking experiments showed that TAF was a protein of 147 kilodaltons (kDa), while TUF was detected as an approximately 120-kDa polypeptide, consistent with its known size. Cross-linking experiments also revealed that both UAST and UASrPg bound a second heretofore unobserved 82-kDa protein; binding of this additional protein appeared to require binding of TAF or TUF. On the basis of the biochemical characterization of TAF and a lack of sequence similarity between UAST and UASrpg, we suggest that transcription of TCMI is mediated by a cis-acting sequence and at least one trans-acting factor different from the elements which promote transcription of most other ribosomal protein genes. A second trans-acting factor may be shared by TCM1 and other ribosomal protein genes; this factor could mediate coordinate regulation of these genes.

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“…DNA containing the Saccharomyces cerevisiae RP28 gene (43) was generated by PCR amplification of the genomic sequences with oligonucleotides ZL14 and ZL15. The PCR-amplified DNA was digested with EcoRI and XbaI and cloned into plasmid YEp357 (46) to construct plasmid pZL106, containing an RP28-lacZ gene fusion.…”

Section: Methodsmentioning

confidence: 99%

Feedback Inhibition of the Yeast Ribosomal Protein Gene CRY2 Is Mediated by the Nucleotide Sequence and Secondary Structure of CRY2 Pre-mRNA

Paulovich

Woolford

1995

Molecular and Cellular Biology

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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-⌬ 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.The expression of ribosomal genes is coordinately regulated so that equimolar amounts of rRNAs and ribosomal proteins accumulate for assembly into ribosomes. The rate of synthesis of ribosomal molecules is also tightly coordinated with the physiological state of cells (reviewed in references 72 and 73). Coordinate synthesis of yeast ribosomal proteins is controlled primarily at the level of transcription of their genes through one of two common upstream activating sequences, UAS RPG or UAS T (reviewed in references 72 and 73). Posttranscriptional controls provide mechanisms for fine-tuning the expression of individual ribosomal protein (rp) genes (1,7,14,41,50,53,64,69).Balanced accumulation of ribosomal proteins in Escherichia coli results from feedback regulation of their expression (reviewed in references 47 and 48). Certain E. coli ribosomal proteins, when synthesized in excess of the rRNAs to which they bind in the assembling ribosome, repress expression of their own operons. Four eukaryotic rp genes have also been found to be autogenously regulated. Yeast ribosomal protein L32 binds to a structure comprising the 5Ј exon and the first few nucleotides of the intron of RPL32 pre-mRNA and blocks its splicing (15, 67). L32 also regulates the translation of its own mRNA through a similar secondary structure formed in the 5Ј end of the mature mRNA (8). Expression of the yeast rp gene RPL2 is autogenously controlled at the level of mRNA accumulation (53). The Xenopus laevis gene that encod...

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Structure and organization of two linked ribosomal protein genes in yeast

Cited by 75 publications

References 34 publications

Saccharomyces cerevisiae coordinates accumulation of yeast ribosomal proteins by modulating mRNA splicing, translational initiation, and protein turnover.

Saccharomyces cerevisiae coordinates accumulation of yeast ribosomal proteins by modulating mRNA splicing, translational initiation, and protein turnover.

Constitutive transcription of yeast ribosomal protein gene TCM1 is promoted by uncommon cis- and trans-acting elements.

Feedback Inhibition of the Yeast Ribosomal Protein Gene CRY2 Is Mediated by the Nucleotide Sequence and Secondary Structure of CRY2 Pre-mRNA

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