1
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Martín-Villanueva S, Fernández-Pevida A, Kressler D, de la Cruz J. The Ubiquitin Moiety of Ubi1 Is Required for Productive Expression of Ribosomal Protein eL40 in Saccharomyces cerevisiae. Cells 2019; 8:cells8080850. [PMID: 31394841 PMCID: PMC6721733 DOI: 10.3390/cells8080850] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Revised: 08/02/2019] [Accepted: 08/06/2019] [Indexed: 01/01/2023] Open
Abstract
Ubiquitin is a highly conserved small eukaryotic protein. It is generated by proteolytic cleavage of precursor proteins in which it is fused either to itself, constituting a polyubiquitin precursor of head-to-tail monomers, or as a single N-terminal moiety to ribosomal proteins. Understanding the role of the ubiquitin fused to ribosomal proteins becomes relevant, as these proteins are practically invariably eS31 and eL40 in the different eukaryotes. Herein, we used the amenable yeast Saccharomyces cerevisiae to study whether ubiquitin facilitates the expression of the fused eL40 (Ubi1 and Ubi2 precursors) and eS31 (Ubi3 precursor) ribosomal proteins. We have analyzed the phenotypic effects of a genomic ubi1∆ub-HA ubi2∆ mutant, which expresses a ubiquitin-free HA-tagged eL40A protein as the sole source of cellular eL40. This mutant shows a severe slow-growth phenotype, which could be fully suppressed by increased dosage of the ubi1∆ub-HA allele, or partially by the replacement of ubiquitin by the ubiquitin-like Smt3 protein. While expression levels of eL40A-HA from ubi1∆ub-HA are low, eL40A is produced practically at normal levels from the Smt3-S-eL40A-HA precursor. Finally, we observed enhanced aggregation of eS31-HA when derived from a Ubi3∆ub-HA precursor and reduced aggregation of eL40A-HA when expressed from a Smt3-S-eL40A-HA precursor. We conclude that ubiquitin might serve as a cis-acting molecular chaperone that assists in the folding and synthesis of the fused eL40 and eS31 ribosomal proteins.
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Affiliation(s)
- Sara Martín-Villanueva
- Instituto de Biomedicina de Sevilla, Hospital Universitario Virgen del Rocio/CSIC/Universidad de Sevilla, E-41013 Seville, Spain
- Departamento de Genética, Universidad de Sevilla, E-41012 Seville, Spain
| | - Antonio Fernández-Pevida
- Instituto de Biomedicina de Sevilla, Hospital Universitario Virgen del Rocio/CSIC/Universidad de Sevilla, E-41013 Seville, Spain
- Departamento de Genética, Universidad de Sevilla, E-41012 Seville, Spain
| | - Dieter Kressler
- Unit of Biochemistry, Department of Biology, University of Fribourg, CH-1700 Fribourg, Switzerland.
| | - Jesús de la Cruz
- Instituto de Biomedicina de Sevilla, Hospital Universitario Virgen del Rocio/CSIC/Universidad de Sevilla, E-41013 Seville, Spain.
- Departamento de Genética, Universidad de Sevilla, E-41012 Seville, Spain.
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2
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Turi Z, Lacey M, Mistrik M, Moudry P. Impaired ribosome biogenesis: mechanisms and relevance to cancer and aging. Aging (Albany NY) 2019; 11:2512-2540. [PMID: 31026227 PMCID: PMC6520011 DOI: 10.18632/aging.101922] [Citation(s) in RCA: 110] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Accepted: 04/04/2019] [Indexed: 02/06/2023]
Abstract
The biosynthesis of ribosomes is a complex process that requires the coordinated action of many factors and a huge energy investment from the cell. Ribosomes are essential for protein production, and thus for cellular survival, growth and proliferation. Ribosome biogenesis is initiated in the nucleolus and includes: the synthesis and processing of ribosomal RNAs, assembly of ribosomal proteins, transport to the cytoplasm and association of ribosomal subunits. The disruption of ribosome biogenesis at various steps, with either increased or decreased expression of different ribosomal components, can promote cell cycle arrest, senescence or apoptosis. Additionally, interference with ribosomal biogenesis is often associated with cancer, aging and age-related degenerative diseases. Here, we review current knowledge on impaired ribosome biogenesis, discuss the main factors involved in stress responses under such circumstances and focus on examples with clinical relevance.
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Affiliation(s)
- Zsofia Turi
- Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacky University, 779 00 Olomouc, Czech Republic
| | - Matthew Lacey
- Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacky University, 779 00 Olomouc, Czech Republic
| | - Martin Mistrik
- Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacky University, 779 00 Olomouc, Czech Republic
| | - Pavel Moudry
- Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacky University, 779 00 Olomouc, Czech Republic
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3
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Emmott E, Jovanovic M, Slavov N. Ribosome Stoichiometry: From Form to Function. Trends Biochem Sci 2019; 44:95-109. [PMID: 30473427 PMCID: PMC6340777 DOI: 10.1016/j.tibs.2018.10.009] [Citation(s) in RCA: 57] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Revised: 08/27/2018] [Accepted: 10/20/2018] [Indexed: 12/11/2022]
Abstract
The existence of eukaryotic ribosomes with distinct ribosomal protein (RP) stoichiometry and regulatory roles in protein synthesis has been speculated for over 60 years. Recent advances in mass spectrometry (MS) and high-throughput analysis have begun to identify and characterize distinct ribosome stoichiometry in yeast and mammalian systems. In addition to RP stoichiometry, ribosomes host a vast array of protein modifications, effectively expanding the number of human RPs from 80 to many thousands of distinct proteoforms. Is it possible that these proteoforms combine to function as a 'ribosome code' to tune protein synthesis? We outline the specific benefits that translational regulation by specialized ribosomes can offer and discuss the means and methodologies available to correlate and characterize RP stoichiometry with function. We highlight previous research with a focus on formulating hypotheses that can guide future experiments and crack the ribosome code.
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Affiliation(s)
- Edward Emmott
- Department of Bioengineering, Northeastern University, Boston, MA, USA
| | - Marko Jovanovic
- Department of Biological Sciences, Columbia University, New York, NY, USA
| | - Nikolai Slavov
- Department of Bioengineering, Northeastern University, Boston, MA, USA; Department of Biology, Northeastern University, Boston, MA, USA.
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4
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Eisenberg AR, Higdon A, Keskin A, Hodapp S, Jovanovic M, Brar GA. Precise Post-translational Tuning Occurs for Most Protein Complex Components during Meiosis. Cell Rep 2018; 25:3603-3617.e2. [PMID: 30590036 PMCID: PMC6328264 DOI: 10.1016/j.celrep.2018.12.008] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2018] [Revised: 11/27/2018] [Accepted: 11/29/2018] [Indexed: 12/20/2022] Open
Abstract
Protein degradation is known to be a key component of expression regulation for individual genes, but its global impact on gene expression has been difficult to determine. We analyzed a parallel gene expression dataset of yeast meiotic differentiation, identifying instances of coordinated protein-level decreases to identify new cases of regulated meiotic protein degradation, including of ribosomes and targets of the meiosis-specific anaphase-promoting complex adaptor Ama1. Comparison of protein and translation measurements over time also revealed that, although meiotic cells are capable of synthesizing protein complex members at precisely matched levels, they typically do not. Instead, the members of most protein complexes are synthesized imprecisely, but their protein levels are matched, indicating that wild-type eukaryotic cells routinely use post-translational adjustment of protein complex partner levels to achieve proper stoichiometry. Outlier cases, in which specific complex components show divergent protein-level trends, suggest timed regulation of these complexes.
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Affiliation(s)
- Amy Rose Eisenberg
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Andrea Higdon
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Abdurrahman Keskin
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
| | - Stefanie Hodapp
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
| | - Marko Jovanovic
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
| | - Gloria Ann Brar
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA.
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5
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Cheng Z, Mugler CF, Keskin A, Hodapp S, Chan LYL, Weis K, Mertins P, Regev A, Jovanovic M, Brar GA. Small and Large Ribosomal Subunit Deficiencies Lead to Distinct Gene Expression Signatures that Reflect Cellular Growth Rate. Mol Cell 2018; 73:36-47.e10. [PMID: 30503772 DOI: 10.1016/j.molcel.2018.10.032] [Citation(s) in RCA: 73] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Revised: 09/04/2018] [Accepted: 10/18/2018] [Indexed: 01/13/2023]
Abstract
Levels of the ribosome, the conserved molecular machine that mediates translation, are tightly linked to cellular growth rate. In humans, ribosomopathies are diseases associated with cell-type-specific pathologies and reduced ribosomal protein (RP) levels. Because gene expression defects resulting from ribosome deficiency have not yet been experimentally defined, we systematically probed mRNA, translation, and protein signatures that were either unlinked from or linked to cellular growth rate in RP-deficient yeast cells. Ribosome deficiency was associated with altered translation of gene subclasses, and profound general secondary effects of RP loss on the spectrum of cellular mRNAs were seen. Among these effects, growth-defective 60S mutants increased synthesis of proteins involved in proteasome-mediated degradation, whereas 40S mutants accumulated mature 60S subunits and increased translation of ribosome biogenesis genes. These distinct signatures of protein synthesis suggest intriguing and currently mysterious differences in the cellular consequences of deficiency for small and large ribosomal subunits.
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MESH Headings
- Cell Proliferation
- Gene Expression Regulation, Fungal
- Mutation
- Protein Processing, Post-Translational
- RNA, Fungal/genetics
- RNA, Fungal/metabolism
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- Ribosomal Proteins/genetics
- Ribosomal Proteins/metabolism
- Ribosome Subunits, Large, Eukaryotic/genetics
- Ribosome Subunits, Large, Eukaryotic/metabolism
- Ribosome Subunits, Small, Eukaryotic/genetics
- Ribosome Subunits, Small, Eukaryotic/metabolism
- Saccharomyces cerevisiae/genetics
- Saccharomyces cerevisiae/growth & development
- Saccharomyces cerevisiae/metabolism
- Saccharomyces cerevisiae Proteins/genetics
- Saccharomyces cerevisiae Proteins/metabolism
- Time Factors
- Transcriptome
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Affiliation(s)
- Ze Cheng
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Christopher Frederick Mugler
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA; Department of Biology, Institute of Biochemistry, ETH, 8093 Zurich, Switzerland
| | - Abdurrahman Keskin
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
| | - Stefanie Hodapp
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
| | - Leon Yen-Lee Chan
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA; Department of Biology, Institute of Biochemistry, ETH, 8093 Zurich, Switzerland
| | - Karsten Weis
- Department of Biology, Institute of Biochemistry, ETH, 8093 Zurich, Switzerland
| | - Philipp Mertins
- Broad Institute of Harvard and MIT, Cambridge, MA 02139, USA
| | - Aviv Regev
- Broad Institute of Harvard and MIT, Cambridge, MA 02139, USA
| | - Marko Jovanovic
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
| | - Gloria Ann Brar
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA.
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Abstract
The billions of proteins inside a eukaryotic cell are organized among dozens of sub-cellular compartments, within which they are further organized into protein complexes. The maintenance of both levels of organization is crucial for normal cellular function. Newly made proteins that fail to be segregated to the correct compartment or assembled into the appropriate complex are defined as orphans. In this review, we discuss the challenges faced by a cell of minimizing orphaned proteins, the quality control systems that recognize orphans, and the consequences of excess orphans for protein homeostasis and disease.
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7
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Molon M, Panek A, Molestak E, Skoneczny M, Tchorzewski M, Wnuk M. Daughters of the budding yeast from old mothers have shorter replicative lifespans but not total lifespans. Are DNA damage and rDNA instability the factors that determine longevity? Cell Cycle 2018; 17:1173-1187. [PMID: 29895191 DOI: 10.1080/15384101.2018.1464846] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Although a lot of effort has been put into the search for factors responsible for aging in yeast mother cells, our knowledge of cellular changes in daughter cells originating from old mothers is still very limited. It has been shown that an old mother is not able to compensate for all negative changes within its cell and therefore transfers them to the bud. In this paper, we show for the first time that daughter cells of an old mother have a reset lifespan expressed in units of time despite drastic reduction of their budding lifespan, which suggests that a single yeast cell has a fixed programmed longevity regardless of the time point at which it was originated. Moreover, in our study we found that longevity parameters are not correlated with the rDNA level, DNA damage, chromosome structure or aging parameters (budding lifespan and total lifespan).
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Affiliation(s)
- Mateusz Molon
- a Department of Biochemistry and Cell Biology , University of Rzeszow , Rzeszow , Poland
| | - Anita Panek
- b Department of Genetics , University of Rzeszow , Rzeszow , Poland
| | - Eliza Molestak
- c Department of Molecular Biology , Maria Curie-Sklodowska University , Lublin , Poland
| | - Marek Skoneczny
- d Department of Genetics , Institute of Biochemistry and Biophysics, Polish Academy of Sciences , Warsaw , Poland
| | - Marek Tchorzewski
- c Department of Molecular Biology , Maria Curie-Sklodowska University , Lublin , Poland
| | - Maciej Wnuk
- b Department of Genetics , University of Rzeszow , Rzeszow , Poland
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8
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Kale A, Ji Z, Kiparaki M, Blanco J, Rimesso G, Flibotte S, Baker NE. Ribosomal Protein S12e Has a Distinct Function in Cell Competition. Dev Cell 2018; 44:42-55.e4. [PMID: 29316439 DOI: 10.1016/j.devcel.2017.12.007] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2016] [Revised: 08/03/2017] [Accepted: 12/04/2017] [Indexed: 10/18/2022]
Abstract
Wild-type Drosophila cells can remove cells heterozygous for ribosomal protein mutations (known as "Minute" mutant cells) from genetic mosaics, a process termed cell competition. The ribosomal protein S12 was unusual because cells heterozygous for rpS12 mutations were not competed by wild-type, and a viable missense mutation in rpS12 protected Minute cells from cell competition with wild-type cells. Furthermore, cells with Minute mutations were induced to compete with one another by altering the gene dose of rpS12, eliminating cells with more rpS12 than their neighbors. Thus RpS12 has a special function in cell competition that defines the competitiveness of cells. We propose that cell competition between wild-type and Minute cells is initiated by a signal of ribosomal protein haploinsufficiency mediated by RpS12. Since competition between cells expressing different levels of Myc did not require RpS12, other kinds of cell competition may be initiated differently.
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Affiliation(s)
- Abhijit Kale
- Department of Genetics, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, USA
| | - Zhejun Ji
- Department of Genetics, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, USA
| | - Marianthi Kiparaki
- Department of Genetics, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, USA
| | - Jorge Blanco
- Department of Genetics, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, USA
| | - Gerard Rimesso
- Department of Genetics, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, USA
| | - Stephane Flibotte
- Department of Zoology, University of British Columbia, Vancouver, BC, Canada
| | - Nicholas E Baker
- Department of Genetics, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, USA; Department of Developmental and Molecular Biology, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, USA; Department of Ophthalmology and Visual Sciences, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, USA.
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9
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Gasch AP, Yu FB, Hose J, Escalante LE, Place M, Bacher R, Kanbar J, Ciobanu D, Sandor L, Grigoriev IV, Kendziorski C, Quake SR, McClean MN. Single-cell RNA sequencing reveals intrinsic and extrinsic regulatory heterogeneity in yeast responding to stress. PLoS Biol 2017; 15:e2004050. [PMID: 29240790 PMCID: PMC5746276 DOI: 10.1371/journal.pbio.2004050] [Citation(s) in RCA: 87] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Revised: 12/28/2017] [Accepted: 11/17/2017] [Indexed: 02/01/2023] Open
Abstract
From bacteria to humans, individual cells within isogenic populations can show significant variation in stress tolerance, but the nature of this heterogeneity is not clear. To investigate this, we used single-cell RNA sequencing to quantify transcript heterogeneity in single Saccharomyces cerevisiae cells treated with and without salt stress to explore population variation and identify cellular covariates that influence the stress-responsive transcriptome. Leveraging the extensive knowledge of yeast transcriptional regulation, we uncovered significant regulatory variation in individual yeast cells, both before and after stress. We also discovered that a subset of cells appears to decouple expression of ribosomal protein genes from the environmental stress response in a manner partly correlated with the cell cycle but unrelated to the yeast ultradian metabolic cycle. Live-cell imaging of cells expressing pairs of fluorescent regulators, including the transcription factor Msn2 with Dot6, Sfp1, or MAP kinase Hog1, revealed both coordinated and decoupled nucleocytoplasmic shuttling. Together with transcriptomic analysis, our results suggest that cells maintain a cellular filter against decoupled bursts of transcription factor activation but mount a stress response upon coordinated regulation, even in a subset of unstressed cells. Genetically identical cells growing in the same environment can vary in their cellular state and behavior. Such heterogeneity may explain why some cells in an isogenic population can survive sudden severe environmental stress whereas other cells succumb. Cell-to-cell variation in gene expression has been linked to variable stress survival, but how and why transcript levels vary across the transcriptome in single cells is only beginning to emerge. Here, we used single-cell RNA sequencing (scRNA-seq) to measure cell-to-cell heterogeneity in the transcriptome of budding yeast (Saccharomyces cerevisiae). We find surprising patterns of variation across known sets of transcription factor targets, indicating that cells vary in their transcriptome profile both before and after stress exposure. scRNA-seq analysis combined with live-cell imaging of transcription factor activation dynamics revealed some cells in which the stress response was coordinately activated and other cells in which the traditional response was decoupled, suggesting unrecognized regulatory nuances that expand our understanding of stress response and survival.
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Affiliation(s)
- Audrey P. Gasch
- Laboratory of Genetics, University of Wisconsin–Madison, Madison, Wisconsin, United States of America
- Great Lakes Bioenergy Research Center, University of Wisconsin–Madison, Madison, Wisconsin, United States of America
- * E-mail:
| | - Feiqiao Brian Yu
- Department of Bioengineering, Stanford University, Stanford, California, United States of America
| | - James Hose
- Laboratory of Genetics, University of Wisconsin–Madison, Madison, Wisconsin, United States of America
| | - Leah E. Escalante
- Laboratory of Genetics, University of Wisconsin–Madison, Madison, Wisconsin, United States of America
| | - Mike Place
- Great Lakes Bioenergy Research Center, University of Wisconsin–Madison, Madison, Wisconsin, United States of America
| | - Rhonda Bacher
- Department of Biostatistics and Medical Informatics, University of Wisconsin–Madison, Madison, Wisconsin, United States of America
| | - Jad Kanbar
- Department of Bioengineering, Stanford University, Stanford, California, United States of America
| | - Doina Ciobanu
- Department of Energy Joint Genome Institute, Walnut Creek, California, United States of America
| | - Laura Sandor
- Department of Energy Joint Genome Institute, Walnut Creek, California, United States of America
| | - Igor V. Grigoriev
- Department of Energy Joint Genome Institute, Walnut Creek, California, United States of America
| | - Christina Kendziorski
- Department of Biostatistics and Medical Informatics, University of Wisconsin–Madison, Madison, Wisconsin, United States of America
| | - Stephen R. Quake
- Department of Bioengineering, Stanford University, Stanford, California, United States of America
- Chan Zuckerberg Biohub, San Francisco, California, United States of America
| | - Megan N. McClean
- Department of Biomedical Engineering, University of Wisconsin–Madison, Madison, Wisconsin, United States of America
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10
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de la Cruz J, Gómez-Herreros F, Rodríguez-Galán O, Begley V, de la Cruz Muñoz-Centeno M, Chávez S. Feedback regulation of ribosome assembly. Curr Genet 2017; 64:393-404. [PMID: 29022131 DOI: 10.1007/s00294-017-0764-x] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2017] [Revised: 10/06/2017] [Accepted: 10/07/2017] [Indexed: 12/12/2022]
Abstract
Ribosome biogenesis is a crucial process for growth and constitutes the major consumer of cellular resources. This pathway is subjected to very stringent regulation to ensure correct ribosome manufacture with a wide variety of environmental and metabolic changes, and intracellular insults. Here we summarise our current knowledge on the regulation of ribosome biogenesis in Saccharomyces cerevisiae by particularly focusing on the feedback mechanisms that maintain ribosome homeostasis. Ribosome biogenesis in yeast is controlled mainly at the level of the production of both pre-rRNAs and ribosomal proteins through the transcriptional and post-transcriptional control of the TORC1 and protein kinase A signalling pathways. Pre-rRNA processing can occur before or after the 35S pre-rRNA transcript is completed; the switch between these two alternatives is regulated by growth conditions. The expression of both ribosomal proteins and the large family of transacting factors involved in ribosome biogenesis is co-regulated. Recently, it has been shown that the synthesis of rRNA and ribosomal proteins, but not of trans-factors, is coupled. Thus the so-called CURI complex sequesters specific transcription factor Ifh1 to repress ribosomal protein genes when rRNA transcription is impaired. We recently found that an analogue system should operate to control the expression of transacting factor genes in response to actual ribosome assembly performance. Regulation of ribosome biogenesis manages situations of imbalanced ribosome production or misassembled ribosomal precursors and subunits, which have been closely linked to distinct human diseases.
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Affiliation(s)
- Jesús de la Cruz
- Instituto de Biomedicina de Sevilla (IBiS), Hospital Virgen del Rocío-CSIC, Universidad de Sevilla, Seville, Spain. .,Departamento de Genética, Universidad de Sevilla, Seville, Spain.
| | - Fernando Gómez-Herreros
- Instituto de Biomedicina de Sevilla (IBiS), Hospital Virgen del Rocío-CSIC, Universidad de Sevilla, Seville, Spain.,Departamento de Genética, Universidad de Sevilla, Seville, Spain
| | - Olga Rodríguez-Galán
- Instituto de Biomedicina de Sevilla (IBiS), Hospital Virgen del Rocío-CSIC, Universidad de Sevilla, Seville, Spain.,Departamento de Genética, Universidad de Sevilla, Seville, Spain
| | - Victoria Begley
- Instituto de Biomedicina de Sevilla (IBiS), Hospital Virgen del Rocío-CSIC, Universidad de Sevilla, Seville, Spain.,Departamento de Genética, Universidad de Sevilla, Seville, Spain
| | - María de la Cruz Muñoz-Centeno
- Instituto de Biomedicina de Sevilla (IBiS), Hospital Virgen del Rocío-CSIC, Universidad de Sevilla, Seville, Spain.,Departamento de Genética, Universidad de Sevilla, Seville, Spain
| | - Sebastián Chávez
- Instituto de Biomedicina de Sevilla (IBiS), Hospital Virgen del Rocío-CSIC, Universidad de Sevilla, Seville, Spain. .,Departamento de Genética, Universidad de Sevilla, Seville, Spain.
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11
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Fan H, Li J, Jia Y, Wu J, Yuan L, Li M, Wei J, Xu B. Silencing of Ribosomal Protein L34 (RPL34) Inhibits the Proliferation and Invasion of Esophageal Cancer Cells. Oncol Res 2017; 25:1061-1068. [PMID: 28109079 PMCID: PMC7840969 DOI: 10.3727/096504016x14830466773541] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Ribosomal protein L34 (RPL34) belongs to the L34E family of ribosomal proteins and contains a zinc finger motif. Aberrant expression of RPL34 has been reported in several human malignancies. However, the precise role and potential underlying mechanisms of RPL34 in human esophageal cancer remain largely unknown. Thus, the objective of this study was to investigate the role of RPL34 in esophageal cancer progression. Our results showed that the expression of RPL34 at both the mRNA and protein levels was frequently upregulated in esophageal cancer cell lines. Knockdown of RPL34 efficiently inhibited esophageal cancer cell proliferation, migration, and invasion in vitro. Mechanistically, knockdown of RPL34 significantly downregulated the protein expression level of p-PI3K and p-Akt in esophageal cancer cells. Finally, knockdown of RPL34 attenuated tumor growth in nude mice. In conclusion, our study revealed that RPL34 functions as an oncogene that modulates the proliferation and metastasis of esophageal cancer cells, in part, by the inactivation of the PI3K/Akt signaling pathway. Thus, these findings suggest that RPL34 may serve as a potential therapeutic target for the treatment of esophageal cancer.
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12
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Sung MK, Porras-Yakushi TR, Reitsma JM, Huber FM, Sweredoski MJ, Hoelz A, Hess S, Deshaies RJ. A conserved quality-control pathway that mediates degradation of unassembled ribosomal proteins. eLife 2016; 5. [PMID: 27552055 PMCID: PMC5026473 DOI: 10.7554/elife.19105] [Citation(s) in RCA: 133] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2016] [Accepted: 08/19/2016] [Indexed: 12/17/2022] Open
Abstract
Overproduced yeast ribosomal protein (RP) Rpl26 fails to assemble into ribosomes and is degraded in the nucleus/nucleolus by a ubiquitin-proteasome system quality control pathway comprising the E2 enzymes Ubc4/Ubc5 and the ubiquitin ligase Tom1. tom1 cells show reduced ubiquitination of multiple RPs, exceptional accumulation of detergent-insoluble proteins including multiple RPs, and hypersensitivity to imbalances in production of RPs and rRNA, indicative of a profound perturbation to proteostasis. Tom1 directly ubiquitinates unassembled RPs primarily via residues that are concealed in mature ribosomes. Together, these data point to an important role for Tom1 in normal physiology and prompt us to refer to this pathway as ERISQ, for excess ribosomal protein quality control. A similar pathway, mediated by the Tom1 homolog Huwe1, restricts accumulation of overexpressed hRpl26 in human cells. We propose that ERISQ is a key element of the quality control machinery that sustains protein homeostasis and cellular fitness in eukaryotes.
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Affiliation(s)
- Min-Kyung Sung
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, United States
| | - Tanya R Porras-Yakushi
- Proteome Exploration Laboratory, Division of Biology and Biological Engineering, Beckman Institue, California Institute of Technology, Pasadena, United States
| | - Justin M Reitsma
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, United States
| | - Ferdinand M Huber
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, United States
| | - Michael J Sweredoski
- Proteome Exploration Laboratory, Division of Biology and Biological Engineering, Beckman Institue, California Institute of Technology, Pasadena, United States
| | - André Hoelz
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, United States
| | - Sonja Hess
- Proteome Exploration Laboratory, Division of Biology and Biological Engineering, Beckman Institue, California Institute of Technology, Pasadena, United States
| | - Raymond J Deshaies
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, United States.,Howard Hughes Medical Institute, California Institute of Technology, Pasadena, United States
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13
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Fernández-Pevida A, Martín-Villanueva S, Murat G, Lacombe T, Kressler D, de la Cruz J. The eukaryote-specific N-terminal extension of ribosomal protein S31 contributes to the assembly and function of 40S ribosomal subunits. Nucleic Acids Res 2016; 44:7777-91. [PMID: 27422873 PMCID: PMC5027506 DOI: 10.1093/nar/gkw641] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2016] [Accepted: 07/07/2016] [Indexed: 11/12/2022] Open
Abstract
The archaea-/eukaryote-specific 40S-ribosomal-subunit protein S31 is expressed as an ubiquitin fusion protein in eukaryotes and consists of a conserved body and a eukaryote-specific N-terminal extension. In yeast, S31 is a practically essential protein, which is required for cytoplasmic 20S pre-rRNA maturation. Here, we have studied the role of the N-terminal extension of the yeast S31 protein. We show that deletion of this extension partially impairs cell growth and 40S subunit biogenesis and confers hypersensitivity to aminoglycoside antibiotics. Moreover, the extension harbours a nuclear localization signal that promotes active nuclear import of S31, which associates with pre-ribosomal particles in the nucleus. In the absence of the extension, truncated S31 inefficiently assembles into pre-40S particles and two subpopulations of mature small subunits, one lacking and another one containing truncated S31, can be identified. Plasmid-driven overexpression of truncated S31 partially suppresses the growth and ribosome biogenesis defects but, conversely, slightly enhances the hypersensitivity to aminoglycosides. Altogether, these results indicate that the N-terminal extension facilitates the assembly of S31 into pre-40S particles and contributes to the optimal translational activity of mature 40S subunits but has only a minor role in cytoplasmic cleavage of 20S pre-rRNA at site D.
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Affiliation(s)
- Antonio Fernández-Pevida
- Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla, Avda. Manuel Siurot, s/n; E-41013 Seville, Spain Departamento de Genética, Universidad de Sevilla, Seville, Spain
| | - Sara Martín-Villanueva
- Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla, Avda. Manuel Siurot, s/n; E-41013 Seville, Spain Departamento de Genética, Universidad de Sevilla, Seville, Spain
| | - Guillaume Murat
- Unit of Biochemistry, Department of Biology, University of Fribourg, Chemin du Musée 10, CH-1700 Fribourg, Switzerland
| | - Thierry Lacombe
- Department of Microbiology and Molecular Medicine, Centre Médical Universitaire, University of Geneva, Geneva, Switzerland
| | - Dieter Kressler
- Unit of Biochemistry, Department of Biology, University of Fribourg, Chemin du Musée 10, CH-1700 Fribourg, Switzerland
| | - Jesús de la Cruz
- Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla, Avda. Manuel Siurot, s/n; E-41013 Seville, Spain Departamento de Genética, Universidad de Sevilla, Seville, Spain
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14
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Sung MK, Reitsma JM, Sweredoski MJ, Hess S, Deshaies RJ. Ribosomal proteins produced in excess are degraded by the ubiquitin-proteasome system. Mol Biol Cell 2016; 27:2642-52. [PMID: 27385339 PMCID: PMC5007085 DOI: 10.1091/mbc.e16-05-0290] [Citation(s) in RCA: 84] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2016] [Accepted: 06/30/2016] [Indexed: 01/08/2023] Open
Abstract
Overexpression of ribosomal proteins in yeast is prevented by ubiquitination of unassembled ribosomal proteins in the nucleus and/or nucleolus followed by proteasome-dependent degradation. Brief inhibition of proteasome causes strong accumulation of multiple ribosomal proteins in an insoluble fraction, suggesting that this is a general phenomenon. Ribosome assembly is an essential process that consumes prodigious quantities of cellular resources. Ribosomal proteins cannot be overproduced in Saccharomyces cerevisiae because the excess proteins are rapidly degraded. However, the responsible quality control (QC) mechanisms remain poorly characterized. Here we demonstrate that overexpression of multiple proteins of the small and large yeast ribosomal subunits is suppressed. Rpl26 overexpressed from a plasmid can be detected in the nucleolus and nucleoplasm, but it largely fails to assemble into ribosomes and is rapidly degraded. However, if the endogenous RPL26 loci are deleted, plasmid-encoded Rpl26 assembles into ribosomes and localizes to the cytosol. Chemical and genetic perturbation studies indicate that overexpressed ribosomal proteins are degraded by the ubiquitin–proteasome system and not by autophagy. Inhibition of the proteasome led to accumulation of multiple endogenous ribosomal proteins in insoluble aggregates, consistent with the operation of this QC mechanism in the absence of ribosomal protein overexpression. Our studies reveal that ribosomal proteins that fail to assemble into ribosomes are rapidly distinguished from their assembled counterparts and ubiquitinated and degraded within the nuclear compartment.
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Affiliation(s)
- Min-Kyung Sung
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125
| | - Justin M Reitsma
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125
| | - Michael J Sweredoski
- Proteome Exploration Laboratory, Division of Biology and Biological Engineering, Beckman Institute, California Institute of Technology, Pasadena, CA 91125
| | - Sonja Hess
- Proteome Exploration Laboratory, Division of Biology and Biological Engineering, Beckman Institute, California Institute of Technology, Pasadena, CA 91125
| | - Raymond J Deshaies
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125 Howard Hughes Medical Institute, California Institute of Technology, Pasadena, CA 91125
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15
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Gerhardt C, Leu T, Lier JM, Rüther U. The cilia-regulated proteasome and its role in the development of ciliopathies and cancer. Cilia 2016; 5:14. [PMID: 27293550 PMCID: PMC4901515 DOI: 10.1186/s13630-016-0035-3] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Accepted: 02/29/2016] [Indexed: 12/21/2022] Open
Abstract
The primary cilium is an essential structure for the mediation of numerous signaling pathways involved in the coordination and regulation of cellular processes essential for the development and maintenance of health. Consequently, ciliary dysfunction results in severe human diseases called ciliopathies. Since many of the cilia-mediated signaling pathways are oncogenic pathways, cilia are linked to cancer. Recent studies demonstrate the existence of a cilia-regulated proteasome and that this proteasome is involved in cancer development via the progression of oncogenic, cilia-mediated signaling. This review article investigates the association between primary cilia and cancer with particular emphasis on the role of the cilia-regulated proteasome.
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Affiliation(s)
- Christoph Gerhardt
- Institute for Animal Developmental and Molecular Biology, Heinrich-Heine University Düsseldorf, 40225 Düsseldorf, Germany
| | - Tristan Leu
- Institute for Animal Developmental and Molecular Biology, Heinrich-Heine University Düsseldorf, 40225 Düsseldorf, Germany
| | - Johanna Maria Lier
- Institute for Animal Developmental and Molecular Biology, Heinrich-Heine University Düsseldorf, 40225 Düsseldorf, Germany
| | - Ulrich Rüther
- Institute for Animal Developmental and Molecular Biology, Heinrich-Heine University Düsseldorf, 40225 Düsseldorf, Germany
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16
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Gasch AP, Hose J, Newton MA, Sardi M, Yong M, Wang Z. Further support for aneuploidy tolerance in wild yeast and effects of dosage compensation on gene copy-number evolution. eLife 2016; 5:e14409. [PMID: 26949252 PMCID: PMC4798956 DOI: 10.7554/elife.14409] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2016] [Accepted: 02/26/2016] [Indexed: 12/19/2022] Open
Abstract
In our prior work by Hose et al., we performed a genome-sequencing survey and reported that aneuploidy was frequently observed in wild strains of S. cerevisiae. We also profiled transcriptome abundance in naturally aneuploid isolates compared to isogenic euploid controls and found that 10–30% of amplified genes, depending on the strain and affected chromosome, show lower-than-expected expression compared to gene copy number. In Hose et al., we argued that this gene group is enriched for genes subject to one or more modes of dosage compensation, where mRNA abundance is decreased in response to higher dosage of that gene. A recent manuscript by Torres et al. refutes our prior work. Here, we provide a response to Torres et al., along with additional analysis and controls to support our original conclusions. We maintain that aneuploidy is well tolerated in the wild strains of S. cerevisiae that we studied and that the group of genes enriched for those subject to dosage compensation show unique evolutionary signatures. DOI:http://dx.doi.org/10.7554/eLife.14409.001 Cells package their DNA into structures called chromosomes. Sometimes when a cell divides, it fails to allocate the right number of chromosomes to each new cell and so they end up with too many or too few chromosomes. The extra copies of the genes on an additional chromosome can be harmful to the cells, because the levels of the proteins encoded by those genes may rise abnormally. Some organisms counteract the harmful effect of having additional chromosomes through a process called dosage compensation. Proteins are produced using genetic information via two steps: first a gene’s DNA sequence is copied into a molecule of RNA, which is then translated into a protein. Dosage compensation can inactivate single genes or whole chromosomes via various means to ensure that the levels of RNA expressed remain normal, even in the presence of extra genes. In 2015, researchers from the University of Wisconsin-Madison reported that dosage compensation occurs in wild strains of budding yeast and effectively protects against the harmful effects of having extra chromosomes. However, these findings conflicted with earlier studies of laboratory strains of this yeast, and earlier in 2016, other researchers re-analysed the previous study’s data and challenged its findings. Now, Gasch et al. – who conducted the work reported in 2015 – provide additional controls and computational experiments that support their original analysis. The latest analysis confirmed that the genes identified in the first study are indeed commonly duplicated in wild yeast populations, yet the expression of these genes remains controlled. This is consistent with a model of dosage compensation, for at least some of duplicated genes. Gasch et al. believe that part of the difference in interpretation of the data relates to perspective. The challenging researchers tested to see if there was a mechanism of dosage compensation that acted across entire chromosomes, which is known to occur in the case of sex chromosomes in mammals. Gasch et al. on the other hand took a different approach and looked to identify effects at the level of individual genes. Together, the analyses show that, while there is no evidence for a widespread mechanism, the expression of a select set of genes in wild yeast is consistent with gene-specific dosage compensation. Future work will now undoubtedly test the mechanisms behind the gene-specific effects, and explore why wild yeast strains are more tolerant to extra chromosomes than laboratory strains. DOI:http://dx.doi.org/10.7554/eLife.14409.002
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Affiliation(s)
- Audrey P Gasch
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, United States.,Genome Center of Wisconsin, University of Wisconsin-Madison, Madison, United States
| | - James Hose
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, United States
| | - Michael A Newton
- Genome Center of Wisconsin, University of Wisconsin-Madison, Madison, United States.,Department of Statistics, University of Wisconsin-Madison, Madison, United States
| | - Maria Sardi
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, United States
| | - Mun Yong
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, United States
| | - Zhishi Wang
- Department of Statistics, University of Wisconsin-Madison, Madison, United States
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17
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Rußmayer H, Buchetics M, Gruber C, Valli M, Grillitsch K, Modarres G, Guerrasio R, Klavins K, Neubauer S, Drexler H, Steiger M, Troyer C, Al Chalabi A, Krebiehl G, Sonntag D, Zellnig G, Daum G, Graf AB, Altmann F, Koellensperger G, Hann S, Sauer M, Mattanovich D, Gasser B. Systems-level organization of yeast methylotrophic lifestyle. BMC Biol 2015; 13:80. [PMID: 26400155 PMCID: PMC4580311 DOI: 10.1186/s12915-015-0186-5] [Citation(s) in RCA: 93] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2015] [Accepted: 09/03/2015] [Indexed: 12/20/2022] Open
Abstract
Background Some yeasts have evolved a methylotrophic lifestyle enabling them to utilize the single carbon compound methanol as a carbon and energy source. Among them, Pichia pastoris (syn. Komagataella sp.) is frequently used for the production of heterologous proteins and also serves as a model organism for organelle research. Our current knowledge of methylotrophic lifestyle mainly derives from sophisticated biochemical studies which identified many key methanol utilization enzymes such as alcohol oxidase and dihydroxyacetone synthase and their localization to the peroxisomes. C1 assimilation is supposed to involve the pentose phosphate pathway, but details of these reactions are not known to date. Results In this work we analyzed the regulation patterns of 5,354 genes, 575 proteins, 141 metabolites, and fluxes through 39 reactions of P. pastoris comparing growth on glucose and on a methanol/glycerol mixed medium, respectively. Contrary to previous assumptions, we found that the entire methanol assimilation pathway is localized to peroxisomes rather than employing part of the cytosolic pentose phosphate pathway for xylulose-5-phosphate regeneration. For this purpose, P. pastoris (and presumably also other methylotrophic yeasts) have evolved a duplicated methanol inducible enzyme set targeted to peroxisomes. This compartmentalized cyclic C1 assimilation process termed xylose-monophosphate cycle resembles the principle of the Calvin cycle and uses sedoheptulose-1,7-bisphosphate as intermediate. The strong induction of alcohol oxidase, dihydroxyacetone synthase, formaldehyde and formate dehydrogenase, and catalase leads to high demand of their cofactors riboflavin, thiamine, nicotinamide, and heme, respectively, which is reflected in strong up-regulation of the respective synthesis pathways on methanol. Methanol-grown cells have a higher protein but lower free amino acid content, which can be attributed to the high drain towards methanol metabolic enzymes and their cofactors. In context with up-regulation of many amino acid biosynthesis genes or proteins, this visualizes an increased flux towards amino acid and protein synthesis which is reflected also in increased levels of transcripts and/or proteins related to ribosome biogenesis and translation. Conclusions Taken together, our work illustrates how concerted interpretation of multiple levels of systems biology data can contribute to elucidation of yet unknown cellular pathways and revolutionize our understanding of cellular biology. Electronic supplementary material The online version of this article (doi:10.1186/s12915-015-0186-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Hannes Rußmayer
- Department of Biotechnology, BOKU - University of Natural Resources and Life Sciences Vienna, Muthgasse 18, 1190, Vienna, Austria.,Austrian Centre of Industrial Biotechnology, A-1190, Vienna, Austria
| | - Markus Buchetics
- Department of Biotechnology, BOKU - University of Natural Resources and Life Sciences Vienna, Muthgasse 18, 1190, Vienna, Austria.,Austrian Centre of Industrial Biotechnology, A-1190, Vienna, Austria
| | - Clemens Gruber
- Austrian Centre of Industrial Biotechnology, A-1190, Vienna, Austria.,Department of Chemistry, BOKU - University of Natural Resources and Life Sciences Vienna, A-1190 Vienna, Austria
| | - Minoska Valli
- Department of Biotechnology, BOKU - University of Natural Resources and Life Sciences Vienna, Muthgasse 18, 1190, Vienna, Austria.,Austrian Centre of Industrial Biotechnology, A-1190, Vienna, Austria
| | - Karlheinz Grillitsch
- Institute of Biochemistry, Graz University of Technology, A-8010 Graz, Austria.,Austrian Centre of Industrial Biotechnology, A-8010 Graz, Austria
| | - Gerda Modarres
- Austrian Centre of Industrial Biotechnology, A-1190, Vienna, Austria.,School of Bioengineering, University of Applied Sciences FH Campus, A-1190 Vienna, Austria
| | - Raffaele Guerrasio
- Austrian Centre of Industrial Biotechnology, A-1190, Vienna, Austria.,Department of Chemistry, BOKU - University of Natural Resources and Life Sciences Vienna, A-1190 Vienna, Austria.,Present addresses: Sandoz GmbH, A-6250 Kundl, Austria
| | - Kristaps Klavins
- Austrian Centre of Industrial Biotechnology, A-1190, Vienna, Austria.,Department of Chemistry, BOKU - University of Natural Resources and Life Sciences Vienna, A-1190 Vienna, Austria.,Present addresses: BIOCRATES Life Sciences AG, A-6020 Innsbruck, Austria
| | - Stefan Neubauer
- Austrian Centre of Industrial Biotechnology, A-1190, Vienna, Austria.,Department of Chemistry, BOKU - University of Natural Resources and Life Sciences Vienna, A-1190 Vienna, Austria.,University of Tübingen, D-72076 Tübingen, Germany
| | - Hedda Drexler
- Austrian Centre of Industrial Biotechnology, A-1190, Vienna, Austria.,Department of Chemistry, BOKU - University of Natural Resources and Life Sciences Vienna, A-1190 Vienna, Austria
| | - Matthias Steiger
- Department of Biotechnology, BOKU - University of Natural Resources and Life Sciences Vienna, Muthgasse 18, 1190, Vienna, Austria.,Austrian Centre of Industrial Biotechnology, A-1190, Vienna, Austria
| | - Christina Troyer
- Austrian Centre of Industrial Biotechnology, A-1190, Vienna, Austria.,Department of Chemistry, BOKU - University of Natural Resources and Life Sciences Vienna, A-1190 Vienna, Austria
| | | | | | | | - Günther Zellnig
- Institute of Plant Sciences, NAWI Graz, University of Graz, A-8010 Graz, Austria
| | - Günther Daum
- Institute of Biochemistry, Graz University of Technology, A-8010 Graz, Austria.,Austrian Centre of Industrial Biotechnology, A-8010 Graz, Austria
| | - Alexandra B Graf
- Austrian Centre of Industrial Biotechnology, A-1190, Vienna, Austria.,Austrian Centre of Industrial Biotechnology, A-8010 Graz, Austria
| | - Friedrich Altmann
- Austrian Centre of Industrial Biotechnology, A-1190, Vienna, Austria.,Department of Chemistry, BOKU - University of Natural Resources and Life Sciences Vienna, A-1190 Vienna, Austria
| | | | - Stephan Hann
- Austrian Centre of Industrial Biotechnology, A-1190, Vienna, Austria.,Department of Chemistry, BOKU - University of Natural Resources and Life Sciences Vienna, A-1190 Vienna, Austria
| | - Michael Sauer
- Department of Biotechnology, BOKU - University of Natural Resources and Life Sciences Vienna, Muthgasse 18, 1190, Vienna, Austria.,Austrian Centre of Industrial Biotechnology, A-1190, Vienna, Austria
| | - Diethard Mattanovich
- Department of Biotechnology, BOKU - University of Natural Resources and Life Sciences Vienna, Muthgasse 18, 1190, Vienna, Austria. .,Austrian Centre of Industrial Biotechnology, A-1190, Vienna, Austria.
| | - Brigitte Gasser
- Department of Biotechnology, BOKU - University of Natural Resources and Life Sciences Vienna, Muthgasse 18, 1190, Vienna, Austria.,Austrian Centre of Industrial Biotechnology, A-1190, Vienna, Austria
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18
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Liu H, Liang S, Yang X, Ji Z, Zhao W, Ye X, Rui J. RNAi-mediated RPL34 knockdown suppresses the growth of human gastric cancer cells. Oncol Rep 2015; 34:2267-72. [PMID: 26323242 PMCID: PMC4583519 DOI: 10.3892/or.2015.4219] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2015] [Accepted: 08/07/2015] [Indexed: 01/23/2023] Open
Abstract
An increasing body of evidence suggests that ribosomal proteins may have ribosome-independent functions and may be involved in various physiological and pathological processes. To examine the role of ribosomal protein L34 (RPL34) in cancer transformation, we assessed its expression in gastric cancer cell lines and found it highly expressed. We further used lentivirus-mediated small interfering RNAs (siRNAs) to knockdown RPL34 expression in the human gastric cancer cell line SGC-7901. RNA interference (RNAi)-mediated inhibition of RPL34 expression in SGC-7901 cells significantly suppressed cell proliferation, increased apoptosis and arrested cells in the S phase. The results of the present study suggest that RPL34 plays a critical role in cell proliferation, cell cycle distribution and apoptosis of human malignant gastric cells.
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Affiliation(s)
- Hui Liu
- Department of Oncology, Wannan Medical College, Wuhu, Anhui 241001, P.R. China
| | - Shaohua Liang
- Department of Oncology, Wannan Medical College, Wuhu, Anhui 241001, P.R. China
| | - Xi Yang
- Department of Oncology, Wannan Medical College, Wuhu, Anhui 241001, P.R. China
| | - Zhaoning Ji
- Department of Medical Oncology, Yijishan Hospital of Wannan Medical College, Wuhu, Anhui 241001, P.R. China
| | - Wenying Zhao
- Department of Medical Oncology, Yijishan Hospital of Wannan Medical College, Wuhu, Anhui 241001, P.R. China
| | - Xiaobing Ye
- Department of Medical Oncology, Yijishan Hospital of Wannan Medical College, Wuhu, Anhui 241001, P.R. China
| | - Jing Rui
- Department of Medical Oncology, Yijishan Hospital of Wannan Medical College, Wuhu, Anhui 241001, P.R. China
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19
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Kim TH, Leslie P, Zhang Y. Ribosomal proteins as unrevealed caretakers for cellular stress and genomic instability. Oncotarget 2015; 5:860-71. [PMID: 24658219 PMCID: PMC4011588 DOI: 10.18632/oncotarget.1784] [Citation(s) in RCA: 67] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Ribosomal proteins (RPs) have gained much attention for their extraribosomal functions particularly with respect to p53 regulation. To date, about fourteen RPs have shown to bind to MDM2 and regulate p53. Upon binding to MDM2, the RPs suppress MDM2 E3 ubiquitin ligase activity resulting in the stabilization and activation of p53. Of the RPs that bind to MDM2, RPL5 and RPL11 are the most studied and RPL11 appears to have the most significant role in p53 regulation. Considering that more than 17% of RP species have been shown to interact with MDM2, one of the questions remains unresolved is why so many RPs bind MDM2 and modulate p53. Genes encoding RPs are widely dispersed on different chromosomes in both mice and humans. As components of ribosome, RP expression is tightly regulated to meet the appropriate stoichiometric ratio between RPs and rRNAs. Once genomic instability (e.g. aneuploidy) occurs, transcriptional and translational changes due to change of DNA copy number can result in an imbalance in the expression of RPs including those that bind to MDM2. Such an imbalance in RP expression could lead to failure to assemble functional ribosomes resulting in ribosomal stress. We propose that RPs have evolved ability to regulate MDM2 in response to genomic instability as an additional layer of p53 regulation. Full understanding of the biological roles of RPs could potentially establish RPs as a novel class of therapeutic targets in human diseases such as cancer.
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Affiliation(s)
- Tae-Hyung Kim
- Department of Radiation Oncology, University of North Carolina, Chapel Hill, NC, USA
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20
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Abstract
Genomic alterations may make cancer cells more dependent than normal cells on mechanisms of proteostasis, including protein folding and degradation. This proposition is the basis for the clinical use of proteasome inhibitors to treat multiple myeloma and mantle cell lymphoma. However, proteasome inhibitors have not proved effective in treating other cancers, and this has called into question the general applicability of this approach. Here, I consider possible explanations for this apparently limited applicability, and discuss whether inhibiting other broadly acting components of the ubiquitin-proteasome system - including ubiquitin-activating enzyme and the AAA-ATPase p97/VCP - might be more generally effective in cancer therapy.
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Affiliation(s)
- Raymond J Deshaies
- Division of Biology and Biological Engineering and Howard Hughes Medical Institute, California Institute of Technology, Pasadena 91107, CA, USA.
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21
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Depuydt G, Xie F, Petyuk VA, Shanmugam N, Smolders A, Dhondt I, Brewer HM, Camp DG, Smith RD, Braeckman BP. Reduced insulin/insulin-like growth factor-1 signaling and dietary restriction inhibit translation but preserve muscle mass in Caenorhabditis elegans. Mol Cell Proteomics 2013; 12:3624-39. [PMID: 24002365 PMCID: PMC3861712 DOI: 10.1074/mcp.m113.027383] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Reduced signaling through the C. elegans insulin/insulin-like growth factor-1-like tyrosine kinase receptor daf-2 and dietary restriction via bacterial dilution are two well-characterized lifespan-extending interventions that operate in parallel or through (partially) independent mechanisms. Using accurate mass and time tag LC-MS/MS quantitative proteomics, we detected that the abundance of a large number of ribosomal subunits is decreased in response to dietary restriction, as well as in the daf-2(e1370) insulin/insulin-like growth factor-1-receptor mutant. In addition, general protein synthesis levels in these long-lived worms are repressed. Surprisingly, ribosomal transcript levels were not correlated to actual protein abundance, suggesting that post-transcriptional regulation determines ribosome content. Proteomics also revealed the increased presence of many structural muscle cell components in long-lived worms, which appeared to result from the prioritized preservation of muscle cell volume in nutrient-poor conditions or low insulin-like signaling. Activation of DAF-16, but not diet restriction, stimulates mRNA expression of muscle-related genes to prevent muscle atrophy. Important daf-2-specific proteome changes include overexpression of aerobic metabolism enzymes and general activation of stress-responsive and immune defense systems, whereas the increased abundance of many protein subunits of the proteasome core complex is a dietary-restriction-specific characteristic.
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Affiliation(s)
- Geert Depuydt
- Biology Department, Ghent University, Proeftuinstraat 86 N1, B-9000 Ghent, Belgium
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22
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Golomb L, Bublik DR, Wilder S, Nevo R, Kiss V, Grabusic K, Oren M. Importin 7 and exportin 1 link c-Myc and p53 to regulation of ribosomal biogenesis. Mol Cell 2012; 45:222-32. [PMID: 22284678 PMCID: PMC3270374 DOI: 10.1016/j.molcel.2011.11.022] [Citation(s) in RCA: 93] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2011] [Revised: 07/13/2011] [Accepted: 11/04/2011] [Indexed: 11/22/2022]
Abstract
Members of the β-karyopherin family mediate nuclear import of ribosomal proteins and export of ribosomal subunits, both required for ribosome biogenesis. We report that transcription of the β-karyopherin genes importin 7 (IPO7) and exportin 1 (XPO1), and several additional nuclear import receptors, is regulated positively by c-Myc and negatively by p53. Partial IPO7 depletion triggers p53 activation and p53-dependent growth arrest. Activation of p53 by IPO7 knockdown has distinct features of ribosomal biogenesis stress, with increased binding of Mdm2 to ribosomal proteins L5 and L11 (RPL5 and RPL11). Furthermore, p53 activation is dependent on RPL5 and RPL11. Of note, IPO7 and XPO1 are frequently overexpressed in cancer. Altogether, we propose that c-Myc and p53 counter each other in the regulation of elements within the nuclear transport machinery, thereby exerting opposing effects on the rate of ribosome biogenesis. Perturbation of this balance may play a significant role in promoting cancer.
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Affiliation(s)
- Lior Golomb
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Debora Rosa Bublik
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Sylvia Wilder
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Reinat Nevo
- Department of Biological Chemistry, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Vladimir Kiss
- Department of Biological Chemistry, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Kristina Grabusic
- Department of Molecular medicine and Biotechnology, University of Rijeka, School of Medicine, Rijeka 51000, Croatia
| | - Moshe Oren
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot 76100, Israel
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23
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Sheltzer JM, Amon A. The aneuploidy paradox: costs and benefits of an incorrect karyotype. Trends Genet 2011; 27:446-53. [PMID: 21872963 DOI: 10.1016/j.tig.2011.07.003] [Citation(s) in RCA: 167] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2011] [Revised: 07/21/2011] [Accepted: 07/26/2011] [Indexed: 01/09/2023]
Abstract
Aneuploidy has a paradoxical effect on cell proliferation. In all normal cells analyzed to date, aneuploidy has been found to decrease the rate of cell proliferation. Yet, aneuploidy is also a hallmark of cancer, a disease of enhanced proliferative capacity, and aneuploid cells are frequently recovered following the experimental evolution of microorganisms. Thus, in certain contexts, aneuploidy might also have growth-advantageous properties. New models of aneuploidy and chromosomal instability have shed light on the diverse effects that karyotypic imbalances have on cellular phenotypes, and suggest novel ways of understanding the role of aneuploidy in development and disease.
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Affiliation(s)
- Jason M Sheltzer
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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Lee MV, Topper SE, Hubler SL, Hose J, Wenger CD, Coon JJ, Gasch AP. A dynamic model of proteome changes reveals new roles for transcript alteration in yeast. Mol Syst Biol 2011; 7:514. [PMID: 21772262 PMCID: PMC3159980 DOI: 10.1038/msb.2011.48] [Citation(s) in RCA: 218] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2010] [Accepted: 06/15/2011] [Indexed: 12/20/2022] Open
Abstract
By characterizing dynamic changes in yeast protein abundance following osmotic shock, this study shows that the correlation between protein and mRNA differs for transcripts that increase versus decrease in abundance, and reveals physiological reasons for these differences. The correlation between protein and mRNA change is very high at transcripts that increase in abundance, but negligible at reduced transcripts following NaCl shock. Modeling and experimental data suggest that reducing levels of high-abundance transcripts helps to direct translational machinery to newly made transcripts. The transient burst of transcript increase serves to accelerate changes in protein abundance. Post-transcriptional regulation of protein abundance is pervasive, although most of the variance in protein change is explained by changes in mRNA abundance.
Natural microenvironments change rapidly, and living creatures must respond quickly and efficiently to thrive within this flux. At all cellular levels—signaling, transcription, translation, metabolism, cell growth, and division—the response is dynamic and coordinated. Some aspects of this response, such as dynamic changes of the transcriptome, are well understood. But other aspects, like the response of the proteome, have remained obscured primarily because of previous limitations in technology. Without coordinated time-course data, it has remained impossible to correctly characterize the correlations and dependencies between these two essential levels of cell biology. This work presents an extended picture of the coordinated response of the transcriptome and proteome as cells respond to an abrupt environmental change. To assay proteomic dynamics, we developed a strategy for large-scale, multiplexed quantitation using isobaric tags and high mass accuracy mass spectrometry. This sensitive yet efficient platform allows for the expedient collection of quantitative time-course proteomic data at six time points, sufficiently reproducible to permit meaningful interpretation of variation across biological replicates. Time-course transcriptome data were generated from paired biological samples, allowing us to examine the relationships between changes in mRNA and protein for each gene in terms of direction and intensity, as well as the characteristics of the temporal profiles for each gene. It was immediately obvious that a single measure of correlation across the entire data set was a meaningless metric. We therefore analyzed relationships between mRNA and protein for different subsets of data. In response to osmotic shock, hundreds of transcripts are highly induced, and their temporal pattern reveals a transient peak of maximal induction, which resolves into a new elevated level as cells acclimate (Figure 2). For this group of genes, there is extremely high correlation between peak mRNA change and protein change (R2∼0.8). But the dynamics of the molecules differ: while mRNA levels transiently overshoot their final levels, proteins gradually rise in abundance toward their new, elevated state. We observed, however, that a measure of efficiency connects the two profiles. The time it takes for a protein to acclimate to its new state correlates with the magnitude of the excess mRNA induction. Thus, the cell imparts an urgency to protein induction by transiently producing excess transcript. The most surprising result, however, involves transcripts that decrease in abundance. In response to osmotic shock, the cell transiently reduces over 600 transcripts, many of which are among the most highly expressed in unstressed cells. But protein levels for these genes remain, for the most part, almost completely unchanged. The stark absence of protein repression is independent of basal protein abundance, independent of reported protein half-lives, reproducible across biological replicates, and validated by quantitative western blots. Furthermore, since we do detect a handful of proteins whose abundance is significantly reduced, our technology is capable of identifying protein loss. Thus, we conclude that transcript reduction serves another purpose besides reducing protein levels. To explore alternate interpretations of the consequence of transcriptional repression, we devised a mass-action kinetic model, which describes protein changes based on mRNA dynamics in the context of transient changes in the rates of cell division. The model successfully recapitulated the observed data, allowing us to alter modeling parameters to test various hypotheses. In response to osmotic shock, overall rates of translation temporarily decrease and cell growth transiently arrests before resuming at a slower rate. We reasoned that mRNA reduction might lower the rate of new protein synthesis, but that retarded production is balanced by reduced cell division. We explored both aspects of this logic with our model. As expected, removing cell division from our model led to a calculated decrease of protein levels, indicating that reduced growth is necessary for maintaining protein levels. However, when we computationally held mRNA levels stable and calculated protein levels in the absence of mRNA repression, we did not find the expected increase in protein abundance. We then considered the possibility that one function of the regulated repression of these highly abundant transcripts was to liberate proteins essential for translation, such as ribosomes or translation initiation factors. To explore this, we examined a mutant lacking the Dot6p/Tod6p transcriptional repressors, which fails to properly repress ∼250 genes in response to osmotic shock. In the wild type, the mRNA for a Dot6p/Tod6p target (ARX1) decreased seven-fold, and the remaining transcript was generally unassociated with poly-ribosomes. In the mutant, however, the mRNA levels were reduced only two-fold, while the remaining transcript continued to bind ribosomes. Therefore, failure to reduce transcript levels led to a persistent association with poly-ribosomes, thereby consuming translational machinery. Our hypothesis is, therefore, that widespread changes in the transcriptome promote efficient translation of new proteins. Transcript increase serves to increase abundance of the encoded proteins, while reduction of some of the most abundant and highly translated mRNAs supports this project by liberating translational capacity. While it is not clear what factors are the limiting elements, it is clear that a full picture of cellular biology requires exploring the dynamics of the cellular response. The transcriptome and proteome change dynamically as cells respond to environmental stress; however, prior proteomic studies reported poor correlation between mRNA and protein, rendering their relationships unclear. To address this, we combined high mass accuracy mass spectrometry with isobaric tagging to quantify dynamic changes in ∼2500 Saccharomyces cerevisiae proteins, in biological triplicate and with paired mRNA samples, as cells acclimated to high osmolarity. Surprisingly, while transcript induction correlated extremely well with protein increase, transcript reduction produced little to no change in the corresponding proteins. We constructed a mathematical model of dynamic protein changes and propose that the lack of protein reduction is explained by cell-division arrest, while transcript reduction supports redistribution of translational machinery. Furthermore, the transient ‘burst' of mRNA induction after stress serves to accelerate change in the corresponding protein levels. We identified several classes of post-transcriptional regulation, but show that most of the variance in protein changes is explained by mRNA. Our results present a picture of the coordinated physiological responses at the levels of mRNA, protein, protein-synthetic capacity, and cellular growth.
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Affiliation(s)
- M Violet Lee
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, USA
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Why Dom34 stimulates growth of cells with defects of 40S ribosomal subunit biosynthesis. Mol Cell Biol 2010; 30:5562-71. [PMID: 20876302 DOI: 10.1128/mcb.00618-10] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A set of genome-wide screens for proteins whose absence exacerbates growth defects due to pseudo-haploinsufficiency of ribosomal proteins in Saccharomyces cerevisiae identified Dom34 as being particularly important for cell growth when there is a deficit of 40S ribosomal subunits. In contrast, strains with a deficit of 60S ribosomal proteins were largely insensitive to the loss of Dom34. The slow growth of cells lacking Dom34 and haploinsufficient for a protein of the 40S subunit is caused by a severe shortage of 40S subunits available for translation initiation due to a combination of three effects: (i) the natural deficiency of 40S subunits due to defective synthesis, (ii) the sequestration of 40S subunits due to the large accumulation of free 60S subunits, and (iii) the accumulation of ribosomes "stuck" in a distinct 80S form, insensitive to the Mg(2+) concentration, and at least temporarily unavailable for further translation. Our data suggest that these stuck ribosomes have neither mRNA nor tRNA. We postulate, based on our results and on previously published work, that the stuck ribosomes arise because of the lack of Dom34, which normally resolves a ribosome stalled due to insufficient tRNAs, to structural problems with its mRNA, or to a defect in the ribosome itself.
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Nomura M. Switching from prokaryotic molecular biology to eukaryotic molecular biology. J Biol Chem 2009; 284:9625-35. [PMID: 19074426 DOI: 10.1074/jbc.x800014200] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Affiliation(s)
- Masayasu Nomura
- Department of Biological Chemistry, University of California, Irvine, California 92697-1700, USA.
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Marygold SJ, Roote J, Reuter G, Lambertsson A, Ashburner M, Millburn GH, Harrison PM, Yu Z, Kenmochi N, Kaufman TC, Leevers SJ, Cook KR. The ribosomal protein genes and Minute loci of Drosophila melanogaster. Genome Biol 2008; 8:R216. [PMID: 17927810 PMCID: PMC2246290 DOI: 10.1186/gb-2007-8-10-r216] [Citation(s) in RCA: 280] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2007] [Revised: 10/10/2007] [Accepted: 10/10/2007] [Indexed: 02/07/2023] Open
Abstract
A combined bioinformatic and genetic approach was used to conduct a systematic analysis of the relationship between ribosomal protein genes and Minute loci in Drosophila melanogaster, allowing the identification of 64 Minute loci corresponding to ribosomal genes. Background Mutations in genes encoding ribosomal proteins (RPs) have been shown to cause an array of cellular and developmental defects in a variety of organisms. In Drosophila melanogaster, disruption of RP genes can result in the 'Minute' syndrome of dominant, haploinsufficient phenotypes, which include prolonged development, short and thin bristles, and poor fertility and viability. While more than 50 Minute loci have been defined genetically, only 15 have so far been characterized molecularly and shown to correspond to RP genes. Results We combined bioinformatic and genetic approaches to conduct a systematic analysis of the relationship between RP genes and Minute loci. First, we identified 88 genes encoding 79 different cytoplasmic RPs (CRPs) and 75 genes encoding distinct mitochondrial RPs (MRPs). Interestingly, nine CRP genes are present as duplicates and, while all appear to be functional, one member of each gene pair has relatively limited expression. Next, we defined 65 discrete Minute loci by genetic criteria. Of these, 64 correspond to, or very likely correspond to, CRP genes; the single non-CRP-encoding Minute gene encodes a translation initiation factor subunit. Significantly, MRP genes and more than 20 CRP genes do not correspond to Minute loci. Conclusion This work answers a longstanding question about the molecular nature of Minute loci and suggests that Minute phenotypes arise from suboptimal protein synthesis resulting from reduced levels of cytoribosomes. Furthermore, by identifying the majority of haplolethal and haplosterile loci at the molecular level, our data will directly benefit efforts to attain complete deletion coverage of the D. melanogaster genome.
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Affiliation(s)
- Steven J Marygold
- Growth Regulation Laboratory, Cancer Research UK London Research Institute, Lincoln's Inn Fields, London WC2A 3PX, UK.
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Steffen KK, MacKay VL, Kerr EO, Tsuchiya M, Hu D, Fox LA, Dang N, Johnston ED, Oakes JA, Tchao BN, Pak DN, Fields S, Kennedy BK, Kaeberlein M. Yeast life span extension by depletion of 60s ribosomal subunits is mediated by Gcn4. Cell 2008; 133:292-302. [PMID: 18423200 DOI: 10.1016/j.cell.2008.02.037] [Citation(s) in RCA: 367] [Impact Index Per Article: 22.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2006] [Revised: 12/27/2007] [Accepted: 02/06/2008] [Indexed: 11/27/2022]
Abstract
In nearly every organism studied, reduced caloric intake extends life span. In yeast, span extension from dietary restriction is thought to be mediated by the highly conserved, nutrient-responsive target of rapamycin (TOR), protein kinase A (PKA), and Sch9 kinases. These kinases coordinately regulate various cellular processes including stress responses, protein turnover, cell growth, and ribosome biogenesis. Here we show that a specific reduction of 60S ribosomal subunit levels slows aging in yeast. Deletion of genes encoding 60S subunit proteins or processing factors or treatment with a small molecule, which all inhibit 60S subunit biogenesis, are each sufficient to significantly increase replicative life span. One mechanism by which reduced 60S subunit levels leads to life span extension is through induction of Gcn4, a nutrient-responsive transcription factor. Genetic epistasis analyses suggest that dietary restriction, reduced 60S subunit abundance, and Gcn4 activation extend yeast life span by similar mechanisms.
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Affiliation(s)
- Kristan K Steffen
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
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Malygin AA, Parakhnevitch NM, Ivanov AV, Eperon IC, Karpova GG. Human ribosomal protein S13 regulates expression of its own gene at the splicing step by a feedback mechanism. Nucleic Acids Res 2007; 35:6414-23. [PMID: 17881366 PMCID: PMC2095825 DOI: 10.1093/nar/gkm701] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2006] [Revised: 08/22/2007] [Accepted: 08/22/2007] [Indexed: 12/14/2022] Open
Abstract
The expression of ribosomal protein (rp) genes is regulated at multiple levels. In yeast, two genes are autoregulated by feedback effects of the protein on pre-mRNA splicing. Here, we have investigated whether similar mechanisms occur in eukaryotes with more complicated and highly regulated splicing patterns. Comparisons of the sequences of ribosomal protein S13 gene (RPS13) among mammals and birds revealed that intron 1 is more conserved than the other introns. Transfection of HEK 293 cells with a minigene-expressing ribosomal protein S13 showed that the presence of intron 1 reduced expression by a factor of four. Ribosomal protein S13 was found to inhibit excision of intron 1 from rpS13 pre-mRNA fragment in vitro. This protein was shown to be able to specifically bind the fragment and to confer protection against ribonuclease cleavage at sequences near the 5' and 3' splice sites. The results suggest that overproduction of rpS13 in mammalian cells interferes with splicing of its own pre-mRNA by a feedback mechanism.
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Affiliation(s)
- Alexey A. Malygin
- Institute for Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090, Russia and Biochemistry Department, University of Leicester, Leicester, UK
| | - Natalia M. Parakhnevitch
- Institute for Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090, Russia and Biochemistry Department, University of Leicester, Leicester, UK
| | - Anton V. Ivanov
- Institute for Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090, Russia and Biochemistry Department, University of Leicester, Leicester, UK
| | - Ian C. Eperon
- Institute for Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090, Russia and Biochemistry Department, University of Leicester, Leicester, UK
| | - Galina G. Karpova
- Institute for Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090, Russia and Biochemistry Department, University of Leicester, Leicester, UK
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Lam YW, Lamond AI, Mann M, Andersen JS. Analysis of nucleolar protein dynamics reveals the nuclear degradation of ribosomal proteins. Curr Biol 2007; 17:749-60. [PMID: 17446074 PMCID: PMC1885954 DOI: 10.1016/j.cub.2007.03.064] [Citation(s) in RCA: 279] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2007] [Revised: 02/28/2007] [Accepted: 03/14/2007] [Indexed: 11/21/2022]
Abstract
Background The nucleolus is a subnuclear organelle in which rRNAs are transcribed, processed, and assembled with ribosomal proteins into ribosome subunits. Mass spectrometry combined with pulsed incorporation of stable isotopes of arginine and lysine was used to perform a quantitative and unbiased global analysis of the rates at which newly synthesized, endogenous proteins appear within mammalian nucleoli. Results Newly synthesized ribosomal proteins accumulated in nucleoli more quickly than other nucleolar components. Studies involving time-lapse fluorescence microscopy of stable HeLa cell lines expressing fluorescent-protein-tagged nucleolar factors also showed that ribosomal proteins accumulate more quickly than other components. Photobleaching and mass-spectrometry experiments suggest that only a subset of newly synthesized ribosomal proteins are assembled into ribosomes and exported to the cytoplasm. Inhibition of the proteasome caused an accumulation of ribosomal proteins in the nucleus but not in the cytoplasm. Inhibition of rRNA transcription prior to proteasomal inhibition further increased the accumulation of ribosomal proteins in the nucleoplasm. Conclusions Ribosomal proteins are expressed at high levels beyond that required for the typical rate of ribosome-subunit production and accumulate in the nucleolus more quickly than all other nucleolar components. This is balanced by continual degradation of unassembled ribosomal proteins in the nucleoplasm, thereby providing a mechanism for mammalian cells to ensure that ribosomal protein levels are never rate limiting for the efficient assembly of ribosome subunits. The dual time-lapse strategy used in this study, combining proteomics and imaging, provides a powerful approach for the quantitative analysis of the flux of newly synthesized proteins through a cell organelle.
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Affiliation(s)
- Yun Wah Lam
- Division of Gene Regulation and Expression, Wellcome Trust Biocentre, College of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, United Kingdom
| | - Angus I. Lamond
- Division of Gene Regulation and Expression, Wellcome Trust Biocentre, College of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, United Kingdom
- Corresponding author
| | - Matthias Mann
- Proteomics and Signal Transduction, Max Planck Institute for Biochemistry, Am Klopferspitz 18, D-82152 Martinsried, Germany
| | - Jens S. Andersen
- Center for Experimental BioInformatics, University of Southern Denmark, Campusvej 55, DK-5230 Odense, Denmark
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31
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Juneau K, Palm C, Miranda M, Davis RW. High-density yeast-tiling array reveals previously undiscovered introns and extensive regulation of meiotic splicing. Proc Natl Acad Sci U S A 2007; 104:1522-7. [PMID: 17244705 PMCID: PMC1780280 DOI: 10.1073/pnas.0610354104] [Citation(s) in RCA: 106] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Revised: 11/06/2006] [Indexed: 02/03/2023] Open
Abstract
Knowing gene structure is vital to understanding gene function, and accurate genome annotation is essential for understanding cellular function. To this end, we have developed a genome-wide assay for mapping introns in Saccharomyces cerevisiae. Using high-density tiling arrays, we compared wild-type yeast to a mutant deficient for intron degradation. Our method identified 76% of the known introns, confirmed 18 previously predicted introns, and revealed 9 formerly undiscovered introns. Furthermore, we discovered that all 13 meiosis-specific intronic yeast genes undergo regulated splicing, which provides posttranscriptional regulation of the genes involved in yeast cell differentiation. Moreover, we found that approximately 16% of intronic genes in yeast are incompletely spliced during exponential growth in rich medium, which suggests that meiosis is not the only biological process regulated by splicing. Our tiling-array assay provides a snapshot of the spliced transcriptome in yeast. This robust methodology can be used to explore environmentally distinct splicing responses and should be readily adaptable to the study of other organisms, including humans.
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Affiliation(s)
- Kara Juneau
- *Department of Biochemistry, Stanford University School of Medicine, Stanford, CA 94305; and
- Stanford Genome Technology Center, Stanford University, Palo Alto, CA 94304
| | - Curtis Palm
- Stanford Genome Technology Center, Stanford University, Palo Alto, CA 94304
| | - Molly Miranda
- Stanford Genome Technology Center, Stanford University, Palo Alto, CA 94304
| | - Ronald W. Davis
- *Department of Biochemistry, Stanford University School of Medicine, Stanford, CA 94305; and
- Stanford Genome Technology Center, Stanford University, Palo Alto, CA 94304
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Mandal AK, Lee P, Chen JA, Nillegoda N, Heller A, DiStasio S, Oen H, Victor J, Nair DM, Brodsky JL, Caplan AJ. Cdc37 has distinct roles in protein kinase quality control that protect nascent chains from degradation and promote posttranslational maturation. ACTA ACUST UNITED AC 2007; 176:319-28. [PMID: 17242065 PMCID: PMC1857360 DOI: 10.1083/jcb.200604106] [Citation(s) in RCA: 79] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
Abstract
Cdc37 is a molecular chaperone that functions with Hsp90 to promote protein kinase folding. Analysis of 65 Saccharomyces cerevisiae protein kinases (∼50% of the kinome) in a cdc37 mutant strain showed that 51 had decreased abundance compared with levels in the wild-type strain. Several lipid kinases also accumulated in reduced amounts in the cdc37 mutant strain. Results from our pulse-labeling studies showed that Cdc37 protects nascent kinase chains from rapid degradation shortly after synthesis. This degradation phenotype was suppressed when cdc37 mutant cells were grown at reduced temperatures, although this did not lead to a full restoration of kinase activity. We propose that Cdc37 functions at distinct steps in kinase biogenesis that involves protecting nascent chains from rapid degradation followed by its folding function in association with Hsp90. Our studies demonstrate that Cdc37 has a general role in kinome biogenesis.
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Affiliation(s)
- Atin K Mandal
- Department of Pharmacology and Biological Chemistry, Mount Sinai School of Medicine, New York, NY 10029, USA
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Bachand F, Lackner DH, Bähler J, Silver PA. Autoregulation of ribosome biosynthesis by a translational response in fission yeast. Mol Cell Biol 2006; 26:1731-42. [PMID: 16478994 PMCID: PMC1430238 DOI: 10.1128/mcb.26.5.1731-1742.2006] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2005] [Revised: 08/29/2005] [Accepted: 12/05/2005] [Indexed: 11/20/2022] Open
Abstract
Maintaining the appropriate balance between the small and large ribosomal subunits is critical for translation and cell growth. We previously identified the 40S ribosomal protein S2 (rpS2) as a substrate of the protein arginine methyltransferase 3 (RMT3) and reported a misregulation of the 40S/60S ratio in rmt3 deletion mutants of Schizosaccharomyces pombe. For this study, using DNA microarrays, we have investigated the genome-wide biological response of rmt3-null cells to this ribosomal subunit imbalance. Whereas little change was observed at the transcriptional level, a number of genes showed significant alterations in their polysomal-to-monosomal ratios in rmt3Delta mutants. Importantly, nearly all of the 40S ribosomal protein-encoding mRNAs showed increased ribosome density in rmt3 disruptants. Sucrose gradient analysis also revealed that the ribosomal subunit imbalance detected in rmt3-null cells is due to a deficit in small-subunit levels and can be rescued by rpS2 overexpression. Our results indicate that rmt3-null fission yeast compensate for the reduced levels of small ribosomal subunits by increasing the ribosome density, and likely the translation efficiency, of 40S ribosomal protein-encoding mRNAs. Our findings support the existence of autoregulatory mechanisms that control ribosome biosynthesis and translation as an important layer of gene regulation.
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Affiliation(s)
- François Bachand
- Department of Biochemistry, Université de Sherbrooke, Sherbrooke, Québec, Canada.
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Steigele S, Nieselt K. Open reading frames provide a rich pool of potential natural antisense transcripts in fungal genomes. Nucleic Acids Res 2005; 33:5034-44. [PMID: 16147987 PMCID: PMC1201330 DOI: 10.1093/nar/gki804] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2005] [Revised: 08/15/2005] [Accepted: 08/15/2005] [Indexed: 12/28/2022] Open
Abstract
Natural antisense transcripts are reported from all kingdoms of life and several recent reports of genomewide screens indicate that they are widely distributed. These transcripts seem to be involved in various biological functions and may govern the expression of their respective sense partner. Very little, however, is known about the degree of evolutionary conservation of antisense transcripts. Furthermore, none of the earlier analyses has studied whether antisense relationships are solely dual or involved in more complex relationships. Here we present a systematic screen for cis- and trans-located antisense transcripts based on open reading frames (ORFs) from five fungal species. The relative number of ORFs involved in antisense relationships varies greatly between the five species. In addition, other significant differences are found between the species, such as the mean length of the antisense region. The majority of trans-located antisense transcripts is found to be involved in complex relationships, resulting in highly connected networks. The analysis of the degree of evolutionary conservation of antisense transcripts shows that most antisense transcripts have no ortholog in any other species. An annotation of antisense transcripts based on Gene Ontology directs to common terms and shows that proteins of genes involved in antisense relationships preferentially localize to the nucleus with common functions in the regulation or maintenance of nucleic acids.
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MESH Headings
- Evolution, Molecular
- Genome, Fungal
- Genomics
- Models, Genetic
- Open Reading Frames
- RNA, Antisense/chemistry
- RNA, Antisense/classification
- RNA, Antisense/genetics
- RNA, Fungal/chemistry
- RNA, Fungal/classification
- RNA, Fungal/genetics
- Transcription, Genetic
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Affiliation(s)
- Stephan Steigele
- Wilhelm-Schickard-Institut f. Informatik, ZBIT–Center for Bioinformatics, Tübingen, University of TübingenGermany
| | - Kay Nieselt
- Wilhelm-Schickard-Institut f. Informatik, ZBIT–Center for Bioinformatics, Tübingen, University of TübingenGermany
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35
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Plafker SM, Macara IG. Ribosomal protein L12 uses a distinct nuclear import pathway mediated by importin 11. Mol Cell Biol 2002; 22:1266-75. [PMID: 11809816 PMCID: PMC134630 DOI: 10.1128/mcb.22.4.1266-1275.2002] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2001] [Revised: 07/25/2001] [Accepted: 11/19/2001] [Indexed: 11/20/2022] Open
Abstract
Ribosome biogenesis requires the nuclear translocation of ribosomal proteins from their site of synthesis in the cytoplasm to the nucleus. Analyses of the import mechanisms have revealed that most ribosomal proteins can be delivered to the nucleus by multiple transport receptors (karyopherins or importins). We now provide evidence that ribosomal protein L12 (rpL12) is distinguished from the bulk of ribosomal proteins because it accesses the importin 11 pathway as a major route into the nucleus. rpL12 specifically and directly interacted with importin 11 in vitro and in vivo. Both rpL12 binding to and import by importin 11 were inhibited by another importin 11 substrate, UbcM2, indicating that these two cargoes may bind overlapping sites on the transport receptor. In contrast, the import of rpL23a, a ribosomal protein that uses the general ribosomal protein import system, was not competed by UbcM2, and in an in vitro binding assay, importin 11 did not bind to the nuclear localization signal of rpL23a. Furthermore, in a transient transfection assay, the nuclear accumulation of rpL12 was increased by coexpressed importin 11, but not by other importins. These data are consistent with importin 11 being a mediator of rpL12 nuclear import. Taken together, these results indicate that rpL12 uses a distinct nuclear import pathway that may contribute to a mechanism for regulating ribosome synthesis and/or maturation.
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Affiliation(s)
- Scott M Plafker
- Center for Cell Signaling and Department of Pharmacology, University of Virginia, Charlottesville, Virginia 22908, USA.
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36
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Bonner JJ, Carlson T, Fackenthal DL, Paddock D, Storey K, Lea K. Complex regulation of the yeast heat shock transcription factor. Mol Biol Cell 2000; 11:1739-51. [PMID: 10793148 PMCID: PMC14880 DOI: 10.1091/mbc.11.5.1739] [Citation(s) in RCA: 42] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
The yeast heat shock transcription factor (HSF) is regulated by posttranslational modification. Heat and superoxide can induce the conformational change associated with the heat shock response. Interaction between HSF and the chaperone hsp70 is also thought to play a role in HSF regulation. Here, we show that the Ssb1/2p member of the hsp70 family can form a stable, ATP-sensitive complex with HSF-a surprising finding because Ssb1/2p is not induced by heat shock. Phosphorylation and the assembly of HSF into larger, ATP-sensitive complexes both occur when HSF activity decreases, whether during adaptation to a raised temperature or during growth at low glucose concentrations. These larger HSF complexes also form during recovery from heat shock. However, if HSF is assembled into ATP-sensitive complexes (during growth at a low glucose concentration), heat shock does not stimulate the dissociation of the complexes. Nor does induction of the conformational change induce their dissociation. Modulation of the in vivo concentrations of the SSA and SSB proteins by deletion or overexpression affects HSF activity in a manner that is consistent with these findings and suggests the model that the SSA and SSB proteins perform distinct roles in the regulation of HSF activity.
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Affiliation(s)
- J J Bonner
- Department of Biology, Indiana University, Bloomington, Indiana 47405-3700, USA.
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37
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Nomura M. Regulation of ribosome biosynthesis in Escherichia coli and Saccharomyces cerevisiae: diversity and common principles. J Bacteriol 1999; 181:6857-64. [PMID: 10559149 PMCID: PMC94158 DOI: 10.1128/jb.181.22.6857-6864.1999] [Citation(s) in RCA: 120] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Affiliation(s)
- M Nomura
- Department of Biological Chemistry, University of California, Irvine, Irvine, California 92697-1700, USA.
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38
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Fewell SW, Woolford JL. Ribosomal protein S14 of Saccharomyces cerevisiae regulates its expression by binding to RPS14B pre-mRNA and to 18S rRNA. Mol Cell Biol 1999; 19:826-34. [PMID: 9858605 PMCID: PMC83939 DOI: 10.1128/mcb.19.1.826] [Citation(s) in RCA: 111] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/1998] [Accepted: 09/24/1998] [Indexed: 11/20/2022] Open
Abstract
Production of ribosomal protein S14 in Saccharomyces cerevisiae is coordinated with the rate of ribosome assembly by a feedback mechanism that represses expression of RPS14B. Three-hybrid assays in vivo and filter binding assays in vitro demonstrate that rpS14 directly binds to an RNA stem-loop structure in RPS14B pre-mRNA that is necessary for RPS14B regulation. Moreover, rpS14 binds to a conserved helix in 18S rRNA with approximately five- to sixfold-greater affinity. These results support the model that RPS14B regulation is mediated by direct binding of rpS14 either to its pre-mRNA or to rRNA. Investigation of these interactions with the three-hybrid system reveals two regions of rpS14 that are involved in RNA recognition. D52G and E55G mutations in rpS14 alter the specificity of rpS14 for RNA, as indicated by increased affinity for RPS14B RNA but reduced affinity for the rRNA target. Deletion of the C terminus of rpS14, where multiple antibiotic resistance mutations map, prevents binding of rpS14 to RNA and production of functional 40S subunits. The emetine-resistant protein, rpS14-EmRR, which contains two mutations near the C terminus of rpS14, does not bind either RNA target in the three-hybrid or in vitro assays. This is the first direct demonstration that an antibiotic resistance mutation alters binding of an r protein to rRNA and is consistent with the hypothesis that antibiotic resistance mutations can result from local alterations in rRNA structure.
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Affiliation(s)
- S W Fewell
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, USA
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Vilardell J, Warner JR. Ribosomal protein L32 of Saccharomyces cerevisiae influences both the splicing of its own transcript and the processing of rRNA. Mol Cell Biol 1997; 17:1959-65. [PMID: 9121443 PMCID: PMC232042 DOI: 10.1128/mcb.17.4.1959] [Citation(s) in RCA: 117] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Ribosomal protein L32 of Saccharomyces cerevisiae binds to and regulates the splicing and the translation of the transcript of its own gene. Selecting for mutants deficient in the regulation of splicing, we have identified a mutant form of L32 that no longer binds to the transcript of RPL32 and therefore does not regulate its splicing. The mutation is the deletion of an isoleucine residue from a highly conserved hydrophobic domain near the middle of L32. The mutant protein supports growth, at a reduced rate, and is found at normal levels in mature ribosomes. However, in cells homozygous for the mutant gene, the rate of processing of the ribosomal RNA component of the 60S ribosomal subunit is severely reduced, leading to an insufficiency of 60S subunits. L32 must be considered a remarkable protein. Composed of only 104 amino acids, it appears to interact with three distinct RNA molecules to influence three different elements of RNA processing and function in three different locations of the cell: the processing of pre-rRNA in the nucleolus, the splicing of the RPL32 transcript in the nucleus, and the translation of the spliced RPL32 mRNA in the cytoplasm.
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Affiliation(s)
- J Vilardell
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, New York 10461, USA
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40
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Cujec TP, Tyler BM. Nutritional and growth control of ribosomal protein mRNA and rRNA in Neurospora crassa. Nucleic Acids Res 1996; 24:943-50. [PMID: 8600464 PMCID: PMC145710 DOI: 10.1093/nar/24.5.943] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
The effects of changing growth rates on the levels of 40S pre-rRNA and two r-protein mRNAs were examined to gain insight into the coordinate transcriptional regulation of ribosomal genes in the ascomycete fungus Neurospora crassa. Growth rates were varied either by altering carbon nutritional conditions, or by subjecting the isolates to inositol-limiting conditions. During carbon up- or down-shifts, r-protein mRNA levels were stoichiometrically coordinated. Changes in 40S pre-rRNA levels paralleled those of the r-protein mRNAs but in a non-stoichiometric manner. Comparison of crp-2 mRNA levels with those of a crp-2::qa-2 fusion gene indicated no major effect from changes in crp-2 mRNA stability. Crp-2 promoter mutagenesis experiments revealed that two elements of the crp-2 promoter, -95 to -83 bp (Dde box) and -74 to -66 bp (CG repeat) important for transcription under constant growth conditions, are also critical for transcriptional regulation by a carbon source. Ribosomal protein mRNA and rRNA levels were unaffected by changes in growth rates when the cultures were grown under inositol-limiting conditions, suggesting that, under these conditions, transcription of the ribosomal genes in N.crassa was regulated independently of growth rate.
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Affiliation(s)
- T P Cujec
- Department of Plant Pathology, University of California, Davis 95616, USA
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41
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Li B, Vilardell J, Warner JR. An RNA structure involved in feedback regulation of splicing and of translation is critical for biological fitness. Proc Natl Acad Sci U S A 1996; 93:1596-600. [PMID: 8643676 PMCID: PMC39987 DOI: 10.1073/pnas.93.4.1596] [Citation(s) in RCA: 75] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
While studies of the regulation of gene expression have generally concerned qualitative changes in the selection or the level of expression of a gene, much of the regulation that occurs within a cell involves the continuous subtle optimization of the levels of proteins used in macromolecular complexes. An example is the biosynthesis of the ribosome, in which equimolar amounts of nearly 80 ribosomal proteins must be supplied by the cytoplasm to the nucleolus. We have found that the transcript of one of the ribosomal protein genes of Saccharomyces cerevisiae, RPL32, participates in such fine tuning. Sequences from exon I of the RPL32 transcript interact with nucleotides from the intron to form a structure that binds L32 to regulate splicing. In the spliced transcript, the same sequences interact with nucleotides from exon II to form a structure that binds L32 to regulate translation, thus providing two levels of autoregulation. We now show, by using a sensitive cocultivation assay, that these RNA structures and their interaction with L32 play a role in the fitness of the cell. The change of a single nucleotide within the 5' leader of the RPL32 transcript, which abolishes the site for L32 binding, leads to detectably slower growth and to eventual loss of the mutant strain from the culture. Experiments designed to assess independently the regulation of splicing and the regulation of translation are presented. These observations demonstrate that, in evolutionary terms, subtle regulatory compensations can be critical. The change in structure of an RNA, due to alteration of just one noncoding nucleotide, can spell the difference between biological success and failure.
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Affiliation(s)
- B Li
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, NY 10461, USA
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42
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Kondo K, Saito T, Kajiwara S, Takagi M, Misawa N. A transformation system for the yeast Candida utilis: use of a modified endogenous ribosomal protein gene as a drug-resistant marker and ribosomal DNA as an integration target for vector DNA. J Bacteriol 1995; 177:7171-7. [PMID: 8522525 PMCID: PMC177597 DOI: 10.1128/jb.177.24.7171-7177.1995] [Citation(s) in RCA: 51] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
We have developed a transformation system for the yeast Candida utilis. A novel strategy was applied to construct the transformation system, since auxotrophic mutants which could be used as hosts for transformation are not available. A gene encoding the ribosomal protein L41 was cloned from C. utilis, which is sensitive to cycloheximide, and used as a marker gene conferring cycloheximide resistance after modification of its amino acid sequence. The marker gene was constructed by substitution of the proline codon at position 56 with the glutamine codon by in vitro mutagenesis, as it had been reported previously that the 56th amino acid residue of L41 is responsible for the cycloheximide sensitivity of various organisms (S. Kawai, S. Murao, M. Mochizuki, I. Shibuya, K. Yano, and M. Takagi, J. Bacteriol. 174:254-262 1992). The ribosomal DNA (i.e., DNA coding for rRNA) of C. utilis was also cloned and used as a multiple-copy target for the integration of vector DNA into the genome, which resulted in a high transformation efficiency. Transformants were obtained by electroporation with a maximum efficiency of approximately 1,400 transformants per 1 microgram of linearized DNA carrying the gene for cycloheximide resistance and part of the ribosomal DNA. No transformants were obtained with intact plasmids. Multiple copies of the linearized plasmid were integrated into the host chromosome by homologous recombination. Southern analysis of the transformants in which vector DNA was integrated at the L41 gene locus indicated that there are two copies of gene for the L41 protein per cell, suggesting that C. utilis is diploid. Transformants were obtained from a variety of C. utilis strains, indicating that this method is applicable to the transformation of other C. utilis strains, even though there is significant heterogeneity in chromosomal karyotypes among these strains.
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Affiliation(s)
- K Kondo
- Central Laboratories for Key Technology, Kirin Brewery Co., Ltd., Kanagawa, Japan
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43
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Li Z, Paulovich AG, Woolford JL. Feedback inhibition of the yeast ribosomal protein gene CRY2 is mediated by the nucleotide sequence and secondary structure of CRY2 pre-mRNA. Mol Cell Biol 1995; 15:6454-64. [PMID: 7565797 PMCID: PMC230896 DOI: 10.1128/mcb.15.11.6454] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
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.
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Affiliation(s)
- Z Li
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, USA
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44
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Yun DF, Sherman F. Initiation of translation can occur only in a restricted region of the CYC1 mRNA of Saccharomyces cerevisiae. Mol Cell Biol 1995; 15:1021-33. [PMID: 7823918 PMCID: PMC232000 DOI: 10.1128/mcb.15.2.1021] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
The steady-state levels and half-lives of CYC1 mRNAs were estimated in a series of mutant strains of Saccharomyces cerevisiae containing (i) TAA nonsense codons, (ii) ATG initiator codons, or (iii) the sequence ATA ATG ACT TAA (denoted ATG-TAA) at various positions along the CYC1 gene, which encodes iso-1-cytochrome c. These mutational alterations were made in backgrounds lacking all internal in-frame and out-of-frame ATG triplets or containing only one ATG initiator codon at the normal position. The results revealed a "sensitive" region encompassing approximately the first half of the CYC1 mRNA, in which nonsense codons caused Upf1-dependent degradation. This result and the stability of CYC1 mRNAs lacking all ATG triplets, as well as other results, suggested that degradation occurs unless elements associated with this sensitive region are covered with 80S ribosomes, 40S ribosomal subunits, or ribonucleoprotein particle proteins. While elongation by 80S ribosomes could be prematurely terminated by TAA codons, the scanning of 40S ribosomal units could not be terminated solely by TAA codons but could be disrupted by the ATG-TAA sequence, which caused the formation and subsequent prompt release of 80S ribosomes. The ATG-TAA sequence caused degradation of the CYC1 mRNA only when it was in the region spanning nucleotide positions -27 to +37 but not in the remaining 3' distal region, suggesting that translation could initiate only in this restricted initiation region. CYC1 mRNA distribution on polyribosomes confirmed that only ATG codons within the initiation region were translated at high efficiency. This initiation region was not entirely dependent on the distance from the 5' cap site and was not obviously dependent on the short-range secondary structure but may simply reflect an open structural requirement for initiation of translation of the CYC1 mRNA.
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Affiliation(s)
- D F Yun
- Department of Biochemistry, University of Rochester School of Medicine and Dentistry, Rochester, New York 14642
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45
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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. [PMID: 8474444 DOI: 10.1128/mcb.13.5.2835] [Citation(s) in RCA: 61] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Ribosomal protein L1 from Saccharomyces cerevisiae binds 5S rRNA and can be released from intact 60S ribosomal subunits as an L1-5S ribonucleoprotein (RNP) particle. To understand the nature of the interaction between L1 and 5S rRNA and to assess the role of L1 in ribosome assembly and function, we cloned the RPL1 gene encoding L1. We have shown that RPL1 is an essential single-copy gene. A conditional null mutant in which the only copy of RPL1 is under control of the repressible GAL1 promoter was constructed. Depletion of L1 causes instability of newly synthesized 5S rRNA in vivo. Cells depleted of L1 no longer assemble 60S ribosomal subunits, indicating that L1 is required for assembly of stable 60S ribosomal subunits but not 40S ribosomal subunits. An L1-5S RNP particle not associated with ribosomal particles was detected by coimmunoprecipitation of L1 and 5S rRNA. This pool of L1-5S RNP remained stable even upon cessation of 60S ribosomal subunit assembly by depletion of another ribosomal protein, L16. Preliminary results suggest that transcription of RPL1 is not autogenously regulated by L1.
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46
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Deshmukh M, Tsay YF, Paulovich AG, Woolford JL. 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; 13:2835-45. [PMID: 8474444 PMCID: PMC359670 DOI: 10.1128/mcb.13.5.2835-2845.1993] [Citation(s) in RCA: 86] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
Ribosomal protein L1 from Saccharomyces cerevisiae binds 5S rRNA and can be released from intact 60S ribosomal subunits as an L1-5S ribonucleoprotein (RNP) particle. To understand the nature of the interaction between L1 and 5S rRNA and to assess the role of L1 in ribosome assembly and function, we cloned the RPL1 gene encoding L1. We have shown that RPL1 is an essential single-copy gene. A conditional null mutant in which the only copy of RPL1 is under control of the repressible GAL1 promoter was constructed. Depletion of L1 causes instability of newly synthesized 5S rRNA in vivo. Cells depleted of L1 no longer assemble 60S ribosomal subunits, indicating that L1 is required for assembly of stable 60S ribosomal subunits but not 40S ribosomal subunits. An L1-5S RNP particle not associated with ribosomal particles was detected by coimmunoprecipitation of L1 and 5S rRNA. This pool of L1-5S RNP remained stable even upon cessation of 60S ribosomal subunit assembly by depletion of another ribosomal protein, L16. Preliminary results suggest that transcription of RPL1 is not autogenously regulated by L1.
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Affiliation(s)
- M Deshmukh
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213-2683
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47
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Girard JP, Feliu J, Caizergues-Ferrer M, Lapeyre B. Study of multiple fibrillarin mRNAs reveals that 3' end formation in Schizosaccharomyces pombe is sensitive to cold shock. Nucleic Acids Res 1993; 21:1881-7. [PMID: 8493104 PMCID: PMC309428 DOI: 10.1093/nar/21.8.1881] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
Fibrillarin is a nucleolar protein which is associated with small nucleolar RNAs, and is required for pre-rRNA processing. We have cloned and characterized the gene encoding fibrillarin in the fission yeast Schizosaccharomyces pombe and we have followed its expression under various conditions. Fission yeast fibrillarin is a 305 amino-acid protein which appears to be highly conserved throughout evolution. In Xenopus, human or Saccharomyces cerevisiae, a single fibrillarin mRNA is detected while, in S. pombe a single copy gene encodes different mRNAs which differ at the 3' ends. Under normal growth conditions, two mRNAs of 1.1 and 1.35 kb are detected with the 1.1 kb being the most abundant. Both the total amount and relative abundance of these two mRNAs are strongly affected by exposure to low temperature, namely the 1.1 kb mRNA almost disappears while the 1.35 kb is less markedly diminished. A new species of 3.2 kb accumulates in the cell, which contains an unusually long 3' untranslated region of 2 kb. We have found that exposure of the cells to a cold shock has a profound effect on 3' end formation in S.pombe since the transcription of several other mRNAs is also capable of skipping the normal 3' end site to terminate at a further downstream site.
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MESH Headings
- Amino Acid Sequence
- Base Sequence
- Blotting, Northern
- Chromosomal Proteins, Non-Histone/genetics
- Cloning, Molecular
- Cold Temperature
- DNA, Fungal
- Gene Expression Regulation, Fungal
- Genes, Fungal
- Humans
- Molecular Sequence Data
- RNA Processing, Post-Transcriptional
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- Ribonucleoproteins/genetics
- Schizosaccharomyces/genetics
- Sequence Homology, Amino Acid
- Transcription, Genetic
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48
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Abstract
Meiosis in Saccharomyces cerevisiae requires the induction of a large number of genes whose mRNAs accumulate at specific times during meiotic development. This study addresses the role of mRNA stability in the regulation of meiosis-specific gene expression. Evidence is provided below demonstrating that the levels of meiotic mRNAs are exquisitely regulated by both transcriptional control and RNA turnover. The data show that (i) early meiotic transcripts are extremely unstable when expressed during either vegetative growth or sporulation, and (ii) transcriptional induction, rather than RNA turnover, is the predominant mechanism responsible for meiosis-specific transcript accumulation. When genes encoding the early meiotic mRNAs are fused to other promoters and expressed during vegetative growth, their mRNA half-lives, of under 3 min, are among the shortest known in S. cerevisiae. Since these mRNAs are only twofold more stable when expressed during sporulation, we conclude that developmental regulation of mRNA turnover can be eliminated as a major contributor to meiosis-specific mRNA accumulation. The rapid degradation of the early mRNAs at all stages of the yeast life cycle, however, suggests that a specific RNA degradation system operates to maintain very low basal levels of these transcripts during vegetative growth and after their transient transcriptional induction in meiosis. Studies to identify specific cis-acting elements required for the rapid degradation of early meiotic transcripts support this idea. A series of deletion derivatives of one early meiosis-specific gene, SPO13, indicate that its mRNA contains determinants, located within the coding region, which contribute to the high instability of this transcript. Translation is another component of the degradation mechanism since frameshift and nonsense mutations within the SPO13 mRNA stabilize the transcript.
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49
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Abstract
Meiosis in Saccharomyces cerevisiae requires the induction of a large number of genes whose mRNAs accumulate at specific times during meiotic development. This study addresses the role of mRNA stability in the regulation of meiosis-specific gene expression. Evidence is provided below demonstrating that the levels of meiotic mRNAs are exquisitely regulated by both transcriptional control and RNA turnover. The data show that (i) early meiotic transcripts are extremely unstable when expressed during either vegetative growth or sporulation, and (ii) transcriptional induction, rather than RNA turnover, is the predominant mechanism responsible for meiosis-specific transcript accumulation. When genes encoding the early meiotic mRNAs are fused to other promoters and expressed during vegetative growth, their mRNA half-lives, of under 3 min, are among the shortest known in S. cerevisiae. Since these mRNAs are only twofold more stable when expressed during sporulation, we conclude that developmental regulation of mRNA turnover can be eliminated as a major contributor to meiosis-specific mRNA accumulation. The rapid degradation of the early mRNAs at all stages of the yeast life cycle, however, suggests that a specific RNA degradation system operates to maintain very low basal levels of these transcripts during vegetative growth and after their transient transcriptional induction in meiosis. Studies to identify specific cis-acting elements required for the rapid degradation of early meiotic transcripts support this idea. A series of deletion derivatives of one early meiosis-specific gene, SPO13, indicate that its mRNA contains determinants, located within the coding region, which contribute to the high instability of this transcript. Translation is another component of the degradation mechanism since frameshift and nonsense mutations within the SPO13 mRNA stabilize the transcript.
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Affiliation(s)
- R T Surosky
- Department of Molecular Genetics and Cell Biology, University of Chicago, Illinois 60637
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50
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Shi YG, Tyler BM. Coordinate expression of ribosomal protein genes in Neurospora crassa and identification of conserved upstream sequences. Nucleic Acids Res 1991; 19:6511-7. [PMID: 1836561 PMCID: PMC329209 DOI: 10.1093/nar/19.23.6511] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
The relative levels of rRNAs and ribosomal proteins are coordinately regulated by growth rate and carbon nutrition in Neurospora crassa. However, little is known about the mechanisms involved. To investigate the transcriptional regulation of ribosomal protein genes in N. crassa, we cloned and sequenced a ribosomal protein gene (crp-3). The inferred crp-3 protein sequence shares 89% and 83% homology at its N-terminus with the yeast rp51 and the human S17 ribosomal proteins respectively. The crp-3 gene contains two introns, neither of which are conserved in position with the RP51 or the S17 genes. The crp-3 gene is present in a single copy and was mapped by RFLP analysis to the right arm of linkage group IV, near the cot-1 locus. Sequence comparisons of the upstream regions of the three sequenced crp genes revealed several common features. These include a 'Taq box' (consensus: ARTTYGACTT) at -39, a CG repeat (consensus: CCCRCCRRR) at -65, and a major transcription initiation site embedded in a purine rich region flanked by an upstream pyrimidine rich sequence. Using four N.crassa ribosomal protein genes as probes, we demonstrated that the levels of the four ribosomal protein mRNAs were closely coordinated during a nutritional downshift from sucrose to quinic acid.
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Affiliation(s)
- Y G Shi
- Department of Plant Pathology, University of California-Davis 95616
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