scholarly journals Intronic non-coding RNAs within ribosomal protein coding genes can regulate biogenesis of yeast ribosome

2018 ◽  
Author(s):  
Akshara Pande ◽  
Rani Sharma ◽  
Bharat Ravi Iyengar ◽  
Vinod Scaria ◽  
Beena Pillai ◽  
...  
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Ribosomal Protein ◽  
Small Rnas ◽  
Ribosomal Proteins ◽  
Ribosome Biogenesis ◽  
Rdna Locus ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
Protein Components ◽  
Retained Introns

AbstractThe genome of the budding yeast (Saccharomyces cerevisiae) has selectively retained introns in ribosomal protein coding genes. The function of these introns has remained elusive in spite of experimental evidence that they are required for the fitness of yeast. Here, we computationally predict novel small RNAs that arise from the intronic regions of ribosomal protein (RP) coding genes in Saccharomyces cerevisiae. Further, we experimentally validated the presence of seven intronic small RNAs (isRNAs). Computational predictions suggest that these isRNAs potentially bind to the ribosomal DNA (rDNA) locus or the corresponding rRNAs. Several isRNA candidates can also interact with transcripts of transcription factors and small nucleolar RNAs (snoRNAs) involved in the regulation of rRNA expression. We propose that the isRNAs derived from intronic regions of ribosomal protein coding genes may regulate the biogenesis of the ribosome through a feed-forward loop, ensuring the coordinated regulation of the RNA and protein components of the ribosomal machinery. Ribosome biogenesis and activity are fine-tuned to the conditions in the cell by integrating nutritional signals, stress response and growth to ensure optimal fitness. The enigmatic introns of ribosomal proteins may prove to be a novel and vital link in this regulatory balancing act.

scholarly journals Tsr4 Is a Cytoplasmic Chaperone for the Ribosomal Protein Rps2 in Saccharomyces cerevisiae

2019 ◽  
Vol 39 (17) ◽  
Author(s):  
Joshua J. Black ◽  
Sharmishtha Musalgaonkar ◽  
Arlen W. Johnson
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Ribosomal Protein ◽  
Unknown Function ◽  
Ribosomal Proteins ◽  
Ribosome Biogenesis ◽  
Eukaryotic Ribosome ◽  
Intrinsically Disordered ◽  
Intrinsically Disordered Regions ◽  
Nonspecific Interactions ◽  
Disordered Regions

ABSTRACT Eukaryotic ribosome biogenesis requires the action of approximately 200 trans-acting factors and the incorporation of 79 ribosomal proteins (RPs). The delivery of RPs to preribosomes is a major challenge for the cell because RPs are often highly basic and contain intrinsically disordered regions prone to nonspecific interactions and aggregation. To counteract this, eukaryotes developed dedicated chaperones for certain RPs that promote their solubility and expression, often by binding eukaryote-specific extensions of the RPs. Rps2 (uS5) is a universally conserved RP that assembles into nuclear pre-40S subunits. However, a chaperone for Rps2 had not been identified. Our laboratory previously characterized Tsr4 as a 40S biogenesis factor of unknown function. Here, we report that Tsr4 cotranslationally associates with Rps2. Rps2 harbors a eukaryote-specific N-terminal extension that is critical for its interaction with Tsr4. Moreover, Tsr4 perturbation resulted in decreased Rps2 levels and phenocopied Rps2 depletion. Despite Rps2 joining nuclear pre-40S particles, Tsr4 appears to be restricted to the cytoplasm. Thus, we conclude that Tsr4 is a cytoplasmic chaperone dedicated to Rps2.

scholarly journals Tsr4 is a cytoplasmic chaperone for the ribosomal protein Rps2 in Saccharomyces cerevisiae

2019 ◽  
Author(s):  
Joshua J. Black ◽  
Sharmishtha Musalgaonkar ◽  
Arlen W. Johnson
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Ribosomal Protein ◽  
Unknown Function ◽  
Ribosomal Proteins ◽  
Ribosome Biogenesis ◽  
Eukaryotic Ribosome ◽  
Intrinsically Disordered ◽  
Intrinsically Disordered Regions ◽  
Nonspecific Interactions ◽  
Disordered Regions

AbstractEukaryotic ribosome biogenesis requires the action of approximately 200 trans-acting factors and the incorporation of 79 ribosomal proteins (RPs). The delivery of RPs to pre-ribosomes is a major challenge for the cell because RPs are often highly basic and contain intrinsically disordered regions prone to nonspecific interactions and aggregation. To counteract this, eukaryotes developed dedicated chaperones for certain RPs that promote their solubility and expression, often by binding eukaryotic-specific extensions of the RPs. Rps2 (uS5) is a universally conserved RP that assembles into nuclear pre-40S subunits. However, a chaperone for Rps2 had not been identified. Our lab previously characterized Tsr4 as a 40S biogenesis factor of unknown function. Here, we report that Tsr4 co-translationally associates with Rps2. Rps2 harbors a eukaryotic-specific N-terminal extension that was critical for its interaction with Tsr4. Moreover, Tsr4 perturbation resulted in decreased Rps2 levels and phenocopied Rps2 depletion. Despite Rps2 joining nuclear pre-40S particles, Tsr4 appeared to be restricted to the cytoplasmic. Thus, we conclude that Tsr4 is a cytoplasmic chaperone dedicated to Rps2.

scholarly journals Analysis of thepdx-1(snz-1/sno-1) Region of theNeurospora crassaGenome: Correlation of Pyridoxine-Requiring Phenotypes With Mutations in Two Structural Genes

Genetics ◽  
2001 ◽  
Vol 157 (3) ◽  
pp. 1067-1075 ◽  
Author(s):  
Laura E Bean ◽  
William H Dvorachek ◽  
Edward L Braun ◽  
Allison Errett ◽  
Gregory S Saenz ◽  
...  
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Stationary Phase ◽  
Neurospora Crassa ◽  
Vitamin B6 ◽  
Structural Genes ◽  
Protein Coding ◽  
Previous Conclusion ◽  
Protein Coding Genes ◽  
Shared Function ◽  
High Gene

AbstractWe report the analysis of a 36-kbp region of the Neurospora crassa genome, which contains homologs of two closely linked stationary phase genes, SNZ1 and SNO1, from Saccharomyces cerevisiae. Homologs of SNZ1 encode extremely highly conserved proteins that have been implicated in pyridoxine (vitamin B6) metabolism in the filamentous fungi Cercospora nicotianae and in Aspergillus nidulans. In N. crassa, SNZ and SNO homologs map to the region occupied by pdx-1 (pyridoxine requiring), a gene that has been known for several decades, but which was not sequenced previously. In this study, pyridoxine-requiring mutants of N. crassa were found to possess mutations that disrupt conserved regions in either the SNZ or SNO homolog. Previously, nearly all of these mutants were classified as pdx-1. However, one mutant with a disrupted SNO homolog was at one time designated pdx-2. It now appears appropriate to reserve the pdx-1 designation for the N. crassa SNZ homolog and pdx-2 for the SNO homolog. We further report annotation of the entire 36,030-bp region, which contains at least 12 protein coding genes, supporting a previous conclusion of high gene densities (12,000-13,000 total genes) for N. crassa. Among genes in this region other than SNZ and SNO homologs, there was no evidence of shared function. Four of the genes in this region appear to have been lost from the S. cerevisiae lineage.

Mutation in genes coding for glucose-induced degradation-deficient protein contribute to high malate production in yeast strains No. 28 and No. 77 used for industrial brewing of sake

2021 ◽  
Author(s):  
Hiroaki Negoro ◽  
Atsushi Kotaka ◽  
Hiroki Ishida
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Organic Acids ◽  
Nonsense Mutation ◽  
Yeast Strain ◽  
Homozygous Mutation ◽  
Alcohol Fermentation ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
Yeast Strains

ABSTRACT Saccharomyces cerevisiae produces organic acids including malate during alcohol fermentation. Since malate contributes to the pleasant flavor of sake, high-malate-producing yeast strain No. 28 and No. 77 have been developed by the Brewing Society of Japan. In this study, the genes responsible for the high malate phenotype in these strains were investigated. We had found previously that the deletion of components of the glucose induced degradation-deficient (GID) complex led to high malate production in yeast. Upon examining GID protein-coding genes in yeast strain No. 28 and No. 77, a nonsense homozygous mutation of GID4 in strain No. 28, and of GID2 in strain No. 77, were identified as the cause of high malate production. Furthermore, complementary tests of these mutations indicated that the heterozygous nonsense mutation in GID2 was recessive. In contrast, the heterozygous nonsense mutation in GID4 was considered semi-dominant.

Mild temperature shock alters the transcription of a discrete class of Saccharomyces cerevisiae genes

1983 ◽  
Vol 3 (3) ◽  
pp. 457-465
Author(s):  
C H Kim ◽  
J R Warner
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Ribosomal Protein ◽  
Ribosomal Proteins ◽  
Temperature Shift ◽  
Restrictive Temperature ◽  
Ribosomal Protein Genes ◽  
Wild Type ◽  
Temperature Shock ◽  
Mild Temperature ◽  
Mutant Cells

In Saccharomyces cerevisiae the synthesis of ribosomal proteins declines temporarily after a culture has been subjected to a mild temperature shock, i.e., a shift from 23 to 36 degrees C, each of which support growth. Using cloned genes for several S. cerevisiae ribosomal proteins, we found that the changes in the synthesis of ribosomal proteins parallel the changes in the concentration of mRNA of each. The disappearance and reappearance of the mRNA is due to a brief but severe inhibition of the transcription of each of the ribosomal protein genes, although the total transcription of mRNA in the cells is relatively unaffected by the temperature shock. The precisely coordinated response of these genes, which are scattered throughout the genome, suggests that either they or the enzyme which transcribes them has unique properties. In certain S. cerevisiae mutants, the synthesis of ribosomal proteins never recovers from a temperature shift. Yet both the decline and the resumption of transcription of these genes during the 30 min after the temperature shift are indistinguishable from those in wild-type cells. The failure of the mutant cells to grow at the restrictive temperature appears to be due to their inability to process the RNA transcribed from genes which have introns (Rosbash et al., Cell 24:679-686, 1981), a large proportion of which appear to be ribosomal protein genes.

Biogenic mechanisms and utilization of small RNAs derived from human protein-coding genes

2011 ◽  
Vol 18 (9) ◽  
pp. 1075-1082 ◽  
Author(s):  
Eivind Valen ◽  
Pascal Preker ◽  
Peter Refsing Andersen ◽  
Xiaobei Zhao ◽  
Yun Chen ◽  
...  
Keyword(s):  
Small Rnas ◽  
Human Protein ◽  
Protein Coding ◽  
Protein Coding Genes

scholarly journals Proteotoxicity from aberrant ribosome biogenesis compromises cell fitness

eLife ◽  
2019 ◽  
Vol 8 ◽  
Author(s):  
Blake W Tye ◽  
Nicoletta Commins ◽  
Lillia V Ryazanova ◽  
Martin Wühr ◽  
Michael Springer ◽  
...  
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Ribosomal Proteins ◽  
Ribosome Biogenesis ◽  
Ribosome Assembly ◽  
Maximal Growth ◽  
Proliferating Cells ◽  
Cellular Processes ◽  
Direct Contribution ◽  
The Face ◽  
Cellular Phenotypes

To achieve maximal growth, cells must manage a massive economy of ribosomal proteins (r-proteins) and RNAs (rRNAs) to produce thousands of ribosomes every minute. Although ribosomes are essential in all cells, natural disruptions to ribosome biogenesis lead to heterogeneous phenotypes. Here, we model these perturbations in Saccharomyces cerevisiae and show that challenges to ribosome biogenesis result in acute loss of proteostasis. Imbalances in the synthesis of r-proteins and rRNAs lead to the rapid aggregation of newly synthesized orphan r-proteins and compromise essential cellular processes, which cells alleviate by activating proteostasis genes. Exogenously bolstering the proteostasis network increases cellular fitness in the face of challenges to ribosome assembly, demonstrating the direct contribution of orphan r-proteins to cellular phenotypes. We propose that ribosome assembly is a key vulnerability of proteostasis maintenance in proliferating cells that may be compromised by diverse genetic, environmental, and xenobiotic perturbations that generate orphan r-proteins.

scholarly journals Ribosomal protein L30 is dispensable in the yeast Saccharomyces cerevisiae.

1990 ◽  
Vol 10 (10) ◽  
pp. 5235-5243 ◽  
Author(s):  
D M Baronas-Lowell ◽  
J R Warner
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Ribosomal Protein ◽  
Ribosomal Proteins ◽  
Wild Type ◽  
Diploid Strain ◽  
Chain Reaction ◽  
Yeast Saccharomyces Cerevisiae ◽  
Ribosomal Subunits ◽  
Strong Homology ◽  
Polymerase Chain

In the yeast Saccharomyces cerevisiae, L30 is one of many ribosomal proteins that is encoded by two functional genes. We have cloned and sequenced RPL30B, which shows strong homology to RPL30A. Use of mRNA as a template for a polymerase chain reaction demonstrated that RPL30B contains an intron in its 5' untranslated region. This intron has an unusual 5' splice site, C/GUAUGU. The genomic copies of RPL30A and RPL30B were disrupted by homologous recombination. Growth rates, primer extension, and two-dimensional ribosomal protein analyses of these disruption mutants suggested that RPL30A is responsible for the majority of L30 production. Surprisingly, meiosis of a diploid strain carrying one disrupted RPL30A and one disrupted RPL30B yielded four viable spores. Ribosomes from haploid cells carrying both disrupted genes had no detectable L30, yet such cells grew with a doubling time only 30% longer than that of wild-type cells. Furthermore, depletion of L30 did not alter the ratio of 60S to 40S ribosomal subunits, suggesting that there is no serious effect on the assembly of 60S subunits. Polysome profiles, however, suggest that the absence of L30 leads to the formation of stalled translation initiation complexes.

Ribosomal protein L30 is dispensable in the yeast Saccharomyces cerevisiae

1990 ◽  
Vol 10 (10) ◽  
pp. 5235-5243
Author(s):  
D M Baronas-Lowell ◽  
J R Warner
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Ribosomal Protein ◽  
Ribosomal Proteins ◽  
Wild Type ◽  
Diploid Strain ◽  
Chain Reaction ◽  
Yeast Saccharomyces Cerevisiae ◽  
Ribosomal Subunits ◽  
Strong Homology ◽  
Polymerase Chain

In the yeast Saccharomyces cerevisiae, L30 is one of many ribosomal proteins that is encoded by two functional genes. We have cloned and sequenced RPL30B, which shows strong homology to RPL30A. Use of mRNA as a template for a polymerase chain reaction demonstrated that RPL30B contains an intron in its 5' untranslated region. This intron has an unusual 5' splice site, C/GUAUGU. The genomic copies of RPL30A and RPL30B were disrupted by homologous recombination. Growth rates, primer extension, and two-dimensional ribosomal protein analyses of these disruption mutants suggested that RPL30A is responsible for the majority of L30 production. Surprisingly, meiosis of a diploid strain carrying one disrupted RPL30A and one disrupted RPL30B yielded four viable spores. Ribosomes from haploid cells carrying both disrupted genes had no detectable L30, yet such cells grew with a doubling time only 30% longer than that of wild-type cells. Furthermore, depletion of L30 did not alter the ratio of 60S to 40S ribosomal subunits, suggesting that there is no serious effect on the assembly of 60S subunits. Polysome profiles, however, suggest that the absence of L30 leads to the formation of stalled translation initiation complexes.

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