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

The DNA sequence UAST (TCGTTTTGTACGTTTTTCA) was found to mediate transcription of yeast ribosomal protein gene TCM1. 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 CYC1 gene lacking its transcriptional activation region, and diminished transcription following nucleotide alterations in UAST. UAST bound in vitro to a protein denoted TAF (TCM1 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 TCM1 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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Association of RAP1 binding sites with stringent control of ribosomal protein gene transcription in Saccharomyces cerevisiae

Molecular and Cellular Biology ◽

10.1128/mcb.11.5.2723-2735.1991 ◽

1991 ◽

Vol 11 (5) ◽

pp. 2723-2735 ◽

Cited By ~ 1

Author(s):

C M Moehle ◽

A G Hinnebusch

Keyword(s):

Gene Expression ◽

Saccharomyces Cerevisiae ◽

Amino Acid ◽

Ribosomal Protein ◽

Binding Sites ◽

Protein Gene ◽

Ribosomal Protein Gene ◽

Ribosomal Protein Genes ◽

Biosynthetic Genes ◽

Stringent Control

An amino acid limitation in bacteria elicits a global response, called stringent control, that leads to reduced synthesis of rRNA and ribosomal proteins and increased expression of amino acid biosynthetic operons. We have used the antimetabolite 3-amino-1,2,4-triazole to cause histidine limitation as a means to elicit the stringent response in the yeast Saccharomyces cerevisiae. Fusions of the yeast ribosomal protein genes RPL16A, CRY1, RPS16A, and RPL25 with the Escherichia coli lacZ gene were used to show that the expression of these genes is reduced by a factor of 2 to 5 during histidine-limited exponential growth and that this regulation occurs at the level of transcription. Stringent regulation of the four yeast ribosomal protein genes was shown to be associated with a nucleotide sequence, known as the UASrpg (upstream activating sequence for ribosomal protein genes), that binds the transcriptional regulatory protein RAP1. The RAP1 binding sites also appeared to mediate the greater ribosomal protein gene expression observed in cells growing exponentially than in cells in stationary phase. Although expression of the ribosomal protein genes was reduced in response to histidine limitation, the level of RAP1 DNA-binding activity in cell extracts was unaffected. Yeast strains bearing a mutation in any one of the genes GCN1 to GCN4 are defective in derepression of amino acid biosynthetic genes in 10 different pathways under conditions of histidine limitation. These Gcn- mutants showed wild-type regulation of ribosomal protein gene expression, which suggests that separate regulatory pathways exist in S. cerevisiae for the derepression of amino acid biosynthetic genes and the repression of ribosomal protein genes in response to amino acid starvation.

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Ribosomal protein gene deletions in Diamond-Blackfan anemia

Blood ◽

10.1182/blood-2011-08-375170 ◽

2011 ◽

Vol 118 (26) ◽

pp. 6943-6951 ◽

Cited By ~ 87

Author(s):

Jason E. Farrar ◽

Adrianna Vlachos ◽

Eva Atsidaftos ◽

Hannah Carlson-Donohoe ◽

Thomas C. Markello ◽

...

Keyword(s):

Ribosomal Protein ◽

Ribosomal Proteins ◽

Protein Gene ◽

Single Nucleotide Polymorphism Array ◽

Ribosomal Protein Gene ◽

Small Subunit ◽

Ribosomal Protein Genes ◽

Gene Deletions ◽

Diamond Blackfan Anemia ◽

Genome Wide

Abstract Diamond-Blackfan anemia (DBA) is a congenital BM failure syndrome characterized by hypoproliferative anemia, associated physical abnormalities, and a predisposition to cancer. Perturbations of the ribosome appear to be critically important in DBA; alterations in 9 different ribosomal protein genes have been identified in multiple unrelated families, along with rarer abnormalities of additional ribosomal proteins. However, at present, only 50% to 60% of patients have an identifiable genetic lesion by ribosomal protein gene sequencing. Using genome-wide single-nucleotide polymorphism array to evaluate for regions of recurrent copy variation, we identified deletions at known DBA-related ribosomal protein gene loci in 17% (9 of 51) of patients without an identifiable mutation, including RPS19, RPS17, RPS26, and RPL35A. No recurrent regions of copy variation at novel loci were identified. Because RPS17 is a duplicated gene with 4 copies in a diploid genome, we demonstrate haploinsufficient RPS17 expression and a small subunit ribosomal RNA processing abnormality in patients harboring RPS17 deletions. Finally, we report the novel identification of variable mosaic loss involving known DBA gene regions in 3 patients from 2 kindreds. These data suggest that ribosomal protein gene deletion is more common than previously suspected and should be considered a component of the initial genetic evaluation in cases of suspected DBA.

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A memory of eS25 loss drives resistance phenotypes

Nucleic Acids Research ◽

10.1093/nar/gkaa444 ◽

2020 ◽

Author(s):

Alex G Johnson ◽

Ryan A Flynn ◽

Christopher P Lapointe ◽

Yaw Shin Ooi ◽

Michael L Zhao ◽

...

Keyword(s):

Ribosomal Protein ◽

Translational Control ◽

Ribosomal Proteins ◽

Ribosomal Protein Gene ◽

Human Cell Line ◽

Cellular Protein ◽

Ribosomal Protein Genes ◽

Genomic Locus ◽

Cellular Phenotypes

Abstract In order to maintain cellular protein homeostasis, ribosomes are safeguarded against dysregulation by myriad processes. Remarkably, many cell types can withstand genetic lesions of certain ribosomal protein genes, some of which are linked to diverse cellular phenotypes and human disease. Yet the direct and indirect consequences from these lesions are poorly understood. To address this knowledge gap, we studied in vitro and cellular consequences that follow genetic knockout of the ribosomal proteins RPS25 or RACK1 in a human cell line, as both proteins are implicated in direct translational control. Prompted by the unexpected detection of an off-target ribosome alteration in the RPS25 knockout, we closely interrogated cellular phenotypes. We found that multiple RPS25 knockout clones display viral- and toxin-resistance phenotypes that cannot be rescued by functional cDNA expression, suggesting that RPS25 loss elicits a cell state transition. We characterized this state and found that it underlies pleiotropic phenotypes and has a common rewiring of gene expression. Rescuing RPS25 expression by genomic locus repair failed to correct for the phenotypic and expression hysteresis. Our findings illustrate how the elasticity of cells to a ribosome perturbation can drive specific phenotypic outcomes that are indirectly linked to translation and suggests caution in the interpretation of ribosomal protein gene mutation data.

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Eaf1p Is Required for Recruitment of NuA4 in Targeting TFIID to the Promoters of the Ribosomal Protein Genes for Transcriptional InitiationIn Vivo

Molecular and Cellular Biology ◽

10.1128/mcb.01524-14 ◽

2015 ◽

Vol 35 (17) ◽

pp. 2947-2964 ◽

Cited By ~ 16

Author(s):

Bhawana Uprety ◽

Rwik Sen ◽

Sukesh R. Bhaumik

Keyword(s):

Ribosomal Protein ◽

Ribosome Biogenesis ◽

Protein Gene ◽

Ribosomal Protein Gene ◽

Ribosomal Protein Genes ◽

Transcriptional Initiation ◽

Independent Form ◽

Dependent Form ◽

Histone Acetyltransferase Activity

NuA4 (nucleosome acetyltransferase of H4) promotes transcriptional initiation of TFIID (a complex of TBP and TBP-associated factors [TAFs])-dependent ribosomal protein genes involved in ribosome biogenesis. However, it is not clearly understood how NuA4 regulates the transcription of ribosomal protein genes. Here, we show that NuA4 is recruited to the promoters of ribosomal protein genes, such asRPS5,RPL2B, andRPS11B, for TFIID recruitment to initiate transcription, and the recruitment of NuA4 to these promoters is impaired in the absence of its Eaf1p component. Intriguingly, impaired NuA4 recruitment in aΔeaf1strain depletes recruitment of TFIID (a TAF-dependent form of TBP) but not the TAF-independent form of TBP to the promoters of ribosomal protein genes. However, in the absence of NuA4, SAGA (Spt-Ada-Gcn5-acetyltransferase) is involved in targeting the TAF-independent form of TBP to the promoters of ribosomal protein genes for transcriptional initiation. Thus, NuA4 plays an important role in targeting TFIID to the promoters of ribosomal protein genes for transcriptional initiationin vivo. Such a function is mediated via its targeted histone acetyltransferase activity. In the absence of NuA4, ribosomal protein genes lose TFIID dependency and become SAGA dependent for transcriptional initiation. Collectively, these results provide significant insights into the regulation of ribosomal protein gene expression and, hence, ribosome biogenesis and functions.

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Lack of introns in the ribosomal protein gene S14 of trypanosomes

Molecular and Cellular Biology ◽

10.1128/mcb.10.6.3284-3288.1990 ◽

1990 ◽

Vol 10 (6) ◽

pp. 3284-3288

Author(s):

D Perelman ◽

J C Boothroyd

Keyword(s):

Ribosomal Protein ◽

Protein Gene ◽

Ribosomal Protein Gene ◽

Ribosomal Protein Genes

Introns are almost always present in ribosomal protein genes, even in organisms in which introns are rare. Although trans spliced, the trypanosome ribosomal protein gene S14 apparently does not have cis introns, which supports the notion that such introns are absent in this organism.

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Association of RAP1 binding sites with stringent control of ribosomal protein gene transcription in Saccharomyces cerevisiae.

Molecular and Cellular Biology ◽

10.1128/mcb.11.5.2723 ◽

1991 ◽

Vol 11 (5) ◽

pp. 2723-2735 ◽

Cited By ~ 104

Author(s):

C M Moehle ◽

A G Hinnebusch

Keyword(s):

Gene Expression ◽

Saccharomyces Cerevisiae ◽

Amino Acid ◽

Ribosomal Protein ◽

Binding Sites ◽

Protein Gene ◽

Ribosomal Protein Gene ◽

Ribosomal Protein Genes ◽

Biosynthetic Genes ◽

Stringent Control

An amino acid limitation in bacteria elicits a global response, called stringent control, that leads to reduced synthesis of rRNA and ribosomal proteins and increased expression of amino acid biosynthetic operons. We have used the antimetabolite 3-amino-1,2,4-triazole to cause histidine limitation as a means to elicit the stringent response in the yeast Saccharomyces cerevisiae. Fusions of the yeast ribosomal protein genes RPL16A, CRY1, RPS16A, and RPL25 with the Escherichia coli lacZ gene were used to show that the expression of these genes is reduced by a factor of 2 to 5 during histidine-limited exponential growth and that this regulation occurs at the level of transcription. Stringent regulation of the four yeast ribosomal protein genes was shown to be associated with a nucleotide sequence, known as the UASrpg (upstream activating sequence for ribosomal protein genes), that binds the transcriptional regulatory protein RAP1. The RAP1 binding sites also appeared to mediate the greater ribosomal protein gene expression observed in cells growing exponentially than in cells in stationary phase. Although expression of the ribosomal protein genes was reduced in response to histidine limitation, the level of RAP1 DNA-binding activity in cell extracts was unaffected. Yeast strains bearing a mutation in any one of the genes GCN1 to GCN4 are defective in derepression of amino acid biosynthetic genes in 10 different pathways under conditions of histidine limitation. These Gcn- mutants showed wild-type regulation of ribosomal protein gene expression, which suggests that separate regulatory pathways exist in S. cerevisiae for the derepression of amino acid biosynthetic genes and the repression of ribosomal protein genes in response to amino acid starvation.

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Inefficient in vitro splicing of the regulatory intron of the L1 ribosomal protein gene of X.laevis depends on suboptimal splice site sequences

Biochemical and Biophysical Research Communications ◽

10.1016/0006-291x(92)90536-t ◽

1992 ◽

Vol 183 (2) ◽

pp. 680-687 ◽

Cited By ~ 2

Author(s):

Elisa Caffarelli ◽

Paola Fragapane ◽

Irene Bozzoni

Keyword(s):

Ribosomal Protein ◽

Splice Site ◽

Protein Gene ◽

Ribosomal Protein Gene ◽

In Vitro Splicing

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The Ribb-osome: Ribbon boosts ribosomal protein gene expression to coordinate organ form and function

10.1101/2021.10.27.466115 ◽

2021 ◽

Author(s):

Rajprasad Loganathan ◽

Daniel C Levings ◽

Ji Hoon Kim ◽

Michael B Wells ◽

Hannah Chiu ◽

...

Keyword(s):

Cell Growth ◽

Ribosomal Protein ◽

Regulatory Networks ◽

Protein Gene ◽

Ribosomal Protein Gene ◽

Embryonic Cell ◽

Transcriptional Regulatory Networks ◽

Form And Function ◽

And Function

Cell growth is well defined for the late (post-embryonic) stages of development, but evidence for early (embryonic) cell growth during post-mitotic morphogenesis is quite limited. Here, we identify early cell growth as a key characteristic of tubulogenesis in the Drosophila embryonic salivary gland (SG). A BTB/POZ domain nuclear factor, Ribbon (Rib), mediates this early cell growth. Rib binds the transcription start site of nearly every SG-expressed ribosomal protein gene (RPG) and is required for full expression of all RPGs tested. Rib binding to RPG promoters in vitro is weak and not sequence-specific, suggesting that specificity is achieved through cofactor interactions. Consistent with this hypothesis, we demonstrate the ability of Rib to physically interact with each of the three known contributors to RPG transcription. Surprisingly, Rib-dependent early cell growth in another tubular organ, the embryonic trachea, is not mediated by direct RPG transcription. These findings support a model of early cell growth sustained by transcriptional regulatory networks customized for organ form and function.

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Identification of the sequences responsible for the splicing phenotype of the regulatory intron of the L1 ribosomal protein gene of Xenopus laevis.

Molecular and Cellular Biology ◽

10.1128/mcb.12.3.1117 ◽

1992 ◽

Vol 12 (3) ◽

pp. 1117-1125 ◽

Cited By ~ 12

Author(s):

P Fragapane ◽

E Caffarelli ◽

M Lener ◽

S Prislei ◽

B Santoro ◽

...

Keyword(s):

Xenopus Laevis ◽

Ribosomal Protein ◽

Protein Gene ◽

Ribosomal Protein Gene ◽

Nuclear Extract ◽

Wild Type ◽

Hela Nuclear Extract ◽

Low Efficiency

Splicing of the regulated third intron of the L1 ribosomal protein gene of Xenopus laevis has been studied in vivo by oocyte microinjection of wild-type and mutant SP6 precursor RNAs and in vitro in the heterologous HeLa nuclear extract. We show that two different phenomena combine to produce the peculiar splicing phenotype of this intron. One, which can be defined constitutive, shows the same features in the two systems and leads to the accumulation of spliced mRNA, but in very small amounts. The low efficiency of splicing is due to the presence of a noncanonical 5' splice site which acts in conjunction with sequences present in the 3' portion of the intron. The second leads to the massive conversion of the pre-mRNA into site specific truncated molecules. This has the effect of decreasing the concentration of the pre-mRNA available for splicing. We show that this aberrant cleavage activity occurs only in the in vivo oocyte system and depends on the presence of an intact U1 RNA.

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