1
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Wu H, He B, Chen B, Liu A. Toxicity of polyvinyl chloride microplastics on Brassica rapa. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2023; 336:122435. [PMID: 37625773 DOI: 10.1016/j.envpol.2023.122435] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Revised: 08/16/2023] [Accepted: 08/21/2023] [Indexed: 08/27/2023]
Abstract
Microplastics (MPs) can pose high risk to living organisms due to their very small sizes. This study selected polyvinyl chloride MPs (PVC-MPs) which experienced up to 1000 h UV light radiation to investigate the influence of PVC-MPs on Brassica rapa growth. The outcomes showed the presence of PVC-MPs inhibited the plants' growth. The stem length, root length, fresh weight and dry weight of plants exposed to PVC-MPs after 30 days reduced by 45.9%, 35.2%, 26.1% and 5.2%, respectively. The chlorophyll, soluble sugar, malondialdehyde (MDA) and catalase (CAT) concentrations for plants exposed to PVC-MPs after 30 days increased by 25.9%, 135.7%, 88.7% and 47.1% respectively. It was also observed that PVC-MPs blocked the plants' leaf stomata and even entered plants' bodies. This might lead to PVC-MPs movement within the plants and influence plants' growth. The transcriptomic analysis results indicated that exposure to PVC-MPs up-regulated metabolic pathway of plant hormone signal transduction of the plants and down-regulated pathway network of ribosome. However, the research outcomes also showed that the PVC-MPs' locations in soil (located at the upper layers or at lower layers) and the UV light radiation time did not exert significantly different influences on inhibiting plants' growth. This can be attributed to PVC-MPs' small sizes and not much decomposition under light radiation. These imply that longer light radiation time and different particle sizes should be included into future research in order to further explore photodegraded MPs' toxicity effects on plants.
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Affiliation(s)
- Hao Wu
- College of Chemistry and Environmental Engineering, Shenzhen University, Shenzhen, 518060, China
| | - Beibei He
- College of Chemistry and Environmental Engineering, Shenzhen University, Shenzhen, 518060, China
| | - Bocheng Chen
- College of Chemistry and Environmental Engineering, Shenzhen University, Shenzhen, 518060, China
| | - An Liu
- College of Chemistry and Environmental Engineering, Shenzhen University, Shenzhen, 518060, China.
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2
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Garcia EL. Allele-specific alternative splicing of Drosophila Ribosomal protein S21 suppresses a lethal mutation in the Phosphorylated adaptor for RNA export ( Phax) gene. G3 GENES|GENOMES|GENETICS 2022; 12:6654594. [PMID: 35920767 PMCID: PMC9434302 DOI: 10.1093/g3journal/jkac195] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Accepted: 07/27/2022] [Indexed: 11/15/2022]
Abstract
Genetic disruptions to the biogenesis of spliceosomal small-nuclear ribonucleoproteins in Drosophila cause wide-spread alternative splicing changes, including changes to the splicing of pre-mRNA for Ribosomal protein S21 (RpS21). Using a transposon mutant for the Phosphorylated adaptor for RNA export (Phax) gene, we demonstrate that changes in the splicing of RpS21 transcripts have a strong influence on the developmental progression of PhaxSH/SH mutants. Different alleles of the Drosophila RpS21 gene are circulating in common laboratory strains and cell lines. These alleles exhibit differences in RpS21 intron retention and splicing efficiency. Differences in the splicing of RpS21 transcripts account for prior conflicting observations of the phenotypic severity of PhaxSH/SH mutant stocks. The alleles uncover a strong splicing enhancer in RpS21 transcripts that can fully suppress the larval lethality and partially suppress the pupal lethality exhibited by PhaxSH/SH mutant lines. In the absence of the splicing enhancer, the splicing of RpS21 transcripts can be modulated in trans by the SR-rich B52 splicing factor. As PhaxSH/SH mutants exhibit wide-spread splicing changes in transcripts for other genes, findings here establish the importance of a single alternative splicing event, RpS21 splicing or intron retention, to the developmental progression of Drosophila.
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Affiliation(s)
- Eric L Garcia
- Department of Microbiology, Immunology and Molecular Genetics, University of Kentucky College of Medicine , Lexington, KY 40536, USA
- Department of Biology, University of Kentucky , Lexington, KY 40506, USA
- Integrative Program for Biological and Genome Sciences, University of North Carolina at Chapel Hill , Chapel Hill, NC 27599, USA
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3
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Reza AMMT, Yuan YG. microRNAs Mediated Regulation of the Ribosomal Proteins and its Consequences on the Global Translation of Proteins. Cells 2021; 10:110. [PMID: 33435549 PMCID: PMC7827472 DOI: 10.3390/cells10010110] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2020] [Accepted: 12/14/2020] [Indexed: 12/23/2022] Open
Abstract
Ribosomal proteins (RPs) are mostly derived from the energy-consuming enzyme families such as ATP-dependent RNA helicases, AAA-ATPases, GTPases and kinases, and are important structural components of the ribosome, which is a supramolecular ribonucleoprotein complex, composed of Ribosomal RNA (rRNA) and RPs, coordinates the translation and synthesis of proteins with the help of transfer RNA (tRNA) and other factors. Not all RPs are indispensable; in other words, the ribosome could be functional and could continue the translation of proteins instead of lacking in some of the RPs. However, the lack of many RPs could result in severe defects in the biogenesis of ribosomes, which could directly influence the overall translation processes and global expression of the proteins leading to the emergence of different diseases including cancer. While microRNAs (miRNAs) are small non-coding RNAs and one of the potent regulators of the post-transcriptional gene expression, miRNAs regulate gene expression by targeting the 3' untranslated region and/or coding region of the messenger RNAs (mRNAs), and by interacting with the 5' untranslated region, and eventually finetune the expression of approximately one-third of all mammalian genes. Herein, we highlighted the significance of miRNAs mediated regulation of RPs coding mRNAs in the global protein translation.
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Affiliation(s)
- Abu Musa Md Talimur Reza
- Jiangsu Co-Innovation Center of Prevention and Control of Important Animal Infectious Diseases and Zoonoses, College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China;
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5a, 02-106 Warsaw, Poland
| | - Yu-Guo Yuan
- Jiangsu Co-Innovation Center of Prevention and Control of Important Animal Infectious Diseases and Zoonoses, College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China;
- Jiangsu Key Laboratory of Zoonosis/Joint International Research Laboratory of Agriculture and Agri-Product Safety, The Ministry of Education of China, Yangzhou University, Yangzhou 225009, China
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4
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Martín-Villanueva S, Fernández-Fernández J, Rodríguez-Galán O, Fernández-Boraita J, Villalobo E, de La Cruz J. Role of the 40S beak ribosomal protein eS12 in ribosome biogenesis and function in Saccharomyces cerevisiae. RNA Biol 2020; 17:1261-1276. [PMID: 32408794 DOI: 10.1080/15476286.2020.1767951] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022] Open
Abstract
In eukaryotes, the beak structure of 40S subunits is formed by the protrusion of the 18S rRNA helix 33 and three ribosomal proteins: eS10, eS12 and eS31. The exact role of these proteins in ribosome biogenesis is not well understood. While eS10 is an essential protein encoded by two paralogous genes in Saccharomyces cerevisiae, eS12 and eS31 are not essential proteins encoded by the single-copy genes RPS12 and UBI3, respectively. Here, we have analysed the contribution of yeast eS12 to ribosome biogenesis and compared it with that of eS31. Polysome analysis reveals that deletion of either RPS12 or UBI3 results in equivalent 40S deficits. Analysis of pre-rRNA processing indicates that eS12, akin to eS31, is required for efficient processing of 20S pre-rRNA to mature 18S rRNA. Moreover, we show that the 20S pre-rRNA accumulates within cytoplasmic pre-40S particles, as deduced from FISH experiments and the lack of nuclear retention of 40S subunit reporter proteins, in rps12∆ and ubi3∆ cells. However, these particles containing 20S pre-rRNA are not efficiently incorporated into polyribosomes. We also provide evidence for a genetic interaction between eS12 or eS31 and the late-acting 40S assembly factors Enp1 and Ltv1, which appears not to be linked to the dynamics of their association with or release from pre-40S particles in the absence of either eS12 or eS31. Finally, we show that eS12- and eS31-deficient ribosomes exhibit increased levels of translational misreading. Altogether, our data highlight distinct important roles of the beak region during ribosome assembly and function.
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Affiliation(s)
- Sara Martín-Villanueva
- Departamento de Genética, Facultad de Biología, Universidad de Sevilla , Seville, Spain.,Instituto de Biomedicina de Sevilla, Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla , Seville, Spain
| | - José Fernández-Fernández
- Departamento de Genética, Facultad de Biología, Universidad de Sevilla , Seville, Spain.,Instituto de Biomedicina de Sevilla, Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla , Seville, Spain
| | - Olga Rodríguez-Galán
- Departamento de Genética, Facultad de Biología, Universidad de Sevilla , Seville, Spain.,Instituto de Biomedicina de Sevilla, Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla , Seville, Spain
| | - Julia Fernández-Boraita
- Departamento de Genética, Facultad de Biología, Universidad de Sevilla , Seville, Spain.,Instituto de Biomedicina de Sevilla, Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla , Seville, Spain
| | - Eduardo Villalobo
- Instituto de Biomedicina de Sevilla, Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla , Seville, Spain.,Departamento de Microbiología, Facultad de Biología, Universidad de Sevilla , Seville, Spain
| | - Jesús de La Cruz
- Departamento de Genética, Facultad de Biología, Universidad de Sevilla , Seville, Spain.,Instituto de Biomedicina de Sevilla, Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla , Seville, Spain
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5
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Hu Y, Ranganathan M, Shu C, Liang X, Ganesh S, Osafo-Addo A, Yan C, Zhang X, Aouizerat BE, Krystal JH, D'Souza DC, Xu K. Single-cell Transcriptome Mapping Identifies Common and Cell-type Specific Genes Affected by Acute Delta9-tetrahydrocannabinol in Humans. Sci Rep 2020; 10:3450. [PMID: 32103029 PMCID: PMC7044203 DOI: 10.1038/s41598-020-59827-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Accepted: 02/03/2020] [Indexed: 01/02/2023] Open
Abstract
Delta-9-tetrahydrocannabinol (THC) is known to modulate immune response in peripheral blood cells. The mechanisms of THC's effects on gene expression in human immune cells remains poorly understood. Combining a within-subject design with single cell transcriptome mapping, we report that THC acutely alters gene expression in 15,973 blood cells. We identified 294 transcriptome-wide significant genes among eight cell types including 69 common genes and 225 cell-type-specific genes affected by THC administration, including those genes involving in immune response, cytokine production, cell proliferation and apoptosis. We revealed distinct transcriptomic sub-clusters affected by THC in major immune cell types where THC perturbed cell-type-specific intracellular gene expression correlations. Gene set enrichment analysis further supports the findings of THC's common and cell-type-specific effects on immune response and cell toxicity. This comprehensive single-cell transcriptomic profiling provides important insights into THC's acute effects on immune function that may have important medical implications.
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Affiliation(s)
- Ying Hu
- Center for Biomedical Information and Information Technology, National Cancer Institute, Rockville, MD, 20850, USA
| | - Mohini Ranganathan
- Department of Psychiatry, Yale School of Medicine, 300 George street, Suite 901, New Haven, CT, 06511, USA
- Connecticut Veteran Healthcare System, West Haven, CT, 06516, USA
| | - Chang Shu
- Department of Psychiatry, Yale School of Medicine, 300 George street, Suite 901, New Haven, CT, 06511, USA
- Connecticut Veteran Healthcare System, West Haven, CT, 06516, USA
| | - Xiaoyu Liang
- Department of Psychiatry, Yale School of Medicine, 300 George street, Suite 901, New Haven, CT, 06511, USA
- Connecticut Veteran Healthcare System, West Haven, CT, 06516, USA
| | - Suhas Ganesh
- Department of Psychiatry, Yale School of Medicine, 300 George street, Suite 901, New Haven, CT, 06511, USA
- Connecticut Veteran Healthcare System, West Haven, CT, 06516, USA
| | - Awo Osafo-Addo
- Department of Psychiatry, Yale School of Medicine, 300 George street, Suite 901, New Haven, CT, 06511, USA
- Connecticut Veteran Healthcare System, West Haven, CT, 06516, USA
| | - Chunhua Yan
- Center for Biomedical Information and Information Technology, National Cancer Institute, Rockville, MD, 20850, USA
| | - Xinyu Zhang
- Department of Psychiatry, Yale School of Medicine, 300 George street, Suite 901, New Haven, CT, 06511, USA
- Connecticut Veteran Healthcare System, West Haven, CT, 06516, USA
| | - Bradley E Aouizerat
- Bluestone Center for Clinical Research, College of Dentistry, New York University, New York, NY, 10010, USA
- Department of Oral and Maxillofacial Surgery, College of Dentistry, New York University, New York, NY, 10010, USA
| | - John H Krystal
- Department of Psychiatry, Yale School of Medicine, 300 George street, Suite 901, New Haven, CT, 06511, USA
- Connecticut Veteran Healthcare System, West Haven, CT, 06516, USA
| | - Deepak C D'Souza
- Department of Psychiatry, Yale School of Medicine, 300 George street, Suite 901, New Haven, CT, 06511, USA
- Connecticut Veteran Healthcare System, West Haven, CT, 06516, USA
| | - Ke Xu
- Department of Psychiatry, Yale School of Medicine, 300 George street, Suite 901, New Haven, CT, 06511, USA.
- Connecticut Veteran Healthcare System, West Haven, CT, 06516, USA.
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6
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Pilla SP, Bahadur RP. Residue conservation elucidates the evolution of r-proteins in ribosomal assembly and function. Int J Biol Macromol 2019; 140:323-329. [PMID: 31421176 DOI: 10.1016/j.ijbiomac.2019.08.127] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2019] [Revised: 08/14/2019] [Accepted: 08/14/2019] [Indexed: 02/08/2023]
Abstract
Ribosomes are the translational machineries having two unequal subunits, small subunit (SSU) and large subunit (LSU) across all the domains of life. Origin and evolution of ribosome are encoded in its structure, and the core of the ribosome is highly conserved. Here, we have used Shannon entropy to analyze the evolution of ribosomal proteins (r-proteins) across the three domains of life. Moreover, we have analyzed the residue conservation at protein-protein (PP) and protein-RNA (PR) interfaces in SSU and LSU. Furthermore, we have studied the evolution of early, intermediate and late binding r-proteins. We show that the r-proteins of Thermus thermophilus are better conserved during the evolution. Furthermore, we find the late binders are better conserved than the early and the intermediate binders. The residues at the interior of the r-proteins are the most conserved followed by those at the interface and the solvent accessible surface. Additionally, we show that the residues at the PP interfaces are better conserved than those at the PR interfaces. However, between PR and PP interfaces, the multi-interface residues at the former are better conserved than those at the latter ones. Our findings may provide insights into the evolution of r-proteins in ribosomal assembly and function.
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Affiliation(s)
- Smita P Pilla
- Computational Structural Biology Laboratory, Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur 721302, India
| | - Ranjit Prasad Bahadur
- Computational Structural Biology Laboratory, Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur 721302, India.
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7
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Linnemann J, Pöll G, Jakob S, Ferreira-Cerca S, Griesenbeck J, Tschochner H, Milkereit P. Impact of two neighbouring ribosomal protein clusters on biogenesis factor binding and assembly of yeast late small ribosomal subunit precursors. PLoS One 2019; 14:e0203415. [PMID: 30653518 PMCID: PMC6336269 DOI: 10.1371/journal.pone.0203415] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Accepted: 01/01/2019] [Indexed: 11/25/2022] Open
Abstract
Many of the small ribosomal subunit proteins are required for the stabilisation of late small ribosomal subunit (SSU) precursors and for final SSU rRNA processing in S. cerevisiae. Among them are ribosomal proteins (r-proteins) which form a protein cluster around rpS0 (uS2) at the "neck" of the SSU (S0-cluster) and others forming a nearby protein cluster around rpS3 (uS3) at the SSU "beak". Here we applied semi-quantitative proteomics together with complementary biochemical approaches to study how incomplete assembly of these two r-protein clusters affects binding and release of SSU maturation factors and assembly of other r-proteins in late SSU precursors in S. cerevisiae. For each of the two clusters specific impairment of the local r-protein assembly state was observed in Rio2 associated SSU precursors. Besides, cluster-specific effects on the association of biogenesis factors were detected. These suggested a role of S0-cluster formation for the efficient release of the two nuclear export factors Rrp12 and Slx9 from SSU precursors and for the correct incorporation of the late acting biogenesis factor Rio2. Based on our and on previous results we propose the existence of at least two different r-protein assembly checkpoints during late SSU maturation in S. cerevisiae. We discuss in the light of recent SSU precursor structure models how r-protein assembly states might be sensed by biogenesis factors at the S0-cluster checkpoint.
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Affiliation(s)
- Jan Linnemann
- Lehrstuhl für Biochemie III, Universität Regensburg, Regensburg, Germany
| | - Gisela Pöll
- Lehrstuhl für Biochemie III, Universität Regensburg, Regensburg, Germany
| | - Steffen Jakob
- Lehrstuhl für Biochemie III, Universität Regensburg, Regensburg, Germany
| | | | - Joachim Griesenbeck
- Lehrstuhl für Biochemie III, Universität Regensburg, Regensburg, Germany
- * E-mail: (JG); (HT); (PM)
| | - Herbert Tschochner
- Lehrstuhl für Biochemie III, Universität Regensburg, Regensburg, Germany
- * E-mail: (JG); (HT); (PM)
| | - Philipp Milkereit
- Lehrstuhl für Biochemie III, Universität Regensburg, Regensburg, Germany
- * E-mail: (JG); (HT); (PM)
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8
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Hansji H, Leung EY, Baguley BC, Finlay GJ, Cameron-Smith D, Figueiredo VC, Askarian-Amiri ME. ZFAS1: a long noncoding RNA associated with ribosomes in breast cancer cells. Biol Direct 2016; 11:62. [PMID: 27871336 PMCID: PMC5117590 DOI: 10.1186/s13062-016-0165-y] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2016] [Accepted: 11/11/2016] [Indexed: 12/20/2022] Open
Abstract
Background Most of the eukaryotic genome is transcribed, yielding a complex network of transcripts including thousands of lncRNAs that generally lack protein coding potential. However, only a small percentage of these molecules has been functionally characterised, and discoveries of specific functions demonstrate layers of complexity. A large percentage of lncRNAs is located in the cytoplasm, associated with ribosomes but the function of the majority of these transcripts is unclear. The current study analyses putative mechanisms of action of the lncRNA species member ZFAS1 that was initially discovered by microarray analysis of murine tissues undergoing mammary gland development. As developmental genes are often deregulated in cancer, here we have studied its function in breast cancer cell lines. Results Using human breast cancer cell lines, ZFAS1 was found to be expressed in all cell lines tested, albeit at different levels of abundance. Following subcellular fractionation, human ZFAS1 was found in both nucleus and cytoplasm (as is the mouse orthologue) in an isoform-independent manner. Sucrose gradients based on velocity sedimentation were utilised to separate the different components of total cell lysate, and surprisingly ZFAS1 was primarily co-localised with light polysomes. Further investigation into ribosome association through subunit dissociation studies showed that ZFAS1 was predominantly associated with the 40S small ribosomal subunit. The expression levels of ZFAS1 and of mRNAs encoding several ribosomal proteins that have roles in ribosome assembly, production and maturation were tightly correlated. ZFAS1 knockdown significantly reduced RPS6 phosphorylation. Conclusion A large number of lncRNAs associate with ribosomes but the function of the majority of these lncRNAs has not been elucidated. The association of the lncRNA ZFAS1 with a subpopulation of ribosomes and the correlation with expression of mRNAs for ribosomal proteins suggest a ribosome-interacting mechanism pertaining to their assembly or biosynthetic activity. ZFAS1 may represent a new class of lncRNAs which associates with ribosomes to regulate their function. Reviewers This article was reviewed by Christine Vande Velde, Nicola Aceto and Haruhiko Siomi. Electronic supplementary material The online version of this article (doi:10.1186/s13062-016-0165-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Herah Hansji
- Auckland Cancer Society Research Centre, University of Auckland, 85 Park Rd, Grafton, Auckland, 1023, New Zealand.,Department of Molecular Medicine and Pathology, University of Auckland, 85 Park Rd, Grafton, Auckland, 1023, New Zealand
| | - Euphemia Y Leung
- Auckland Cancer Society Research Centre, University of Auckland, 85 Park Rd, Grafton, Auckland, 1023, New Zealand.,Department of Molecular Medicine and Pathology, University of Auckland, 85 Park Rd, Grafton, Auckland, 1023, New Zealand
| | - Bruce C Baguley
- Auckland Cancer Society Research Centre, University of Auckland, 85 Park Rd, Grafton, Auckland, 1023, New Zealand
| | - Graeme J Finlay
- Auckland Cancer Society Research Centre, University of Auckland, 85 Park Rd, Grafton, Auckland, 1023, New Zealand.,Department of Molecular Medicine and Pathology, University of Auckland, 85 Park Rd, Grafton, Auckland, 1023, New Zealand
| | - David Cameron-Smith
- The Liggins Institute, University of Auckland, 85 Park Rd, Grafton, Auckland, 1023, New Zealand
| | - Vandre C Figueiredo
- The Liggins Institute, University of Auckland, 85 Park Rd, Grafton, Auckland, 1023, New Zealand
| | - Marjan E Askarian-Amiri
- Auckland Cancer Society Research Centre, University of Auckland, 85 Park Rd, Grafton, Auckland, 1023, New Zealand. .,Department of Molecular Medicine and Pathology, University of Auckland, 85 Park Rd, Grafton, Auckland, 1023, New Zealand.
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9
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Ribosomal Protein Rps26 Influences 80S Ribosome Assembly in Saccharomyces cerevisiae. mSphere 2016; 1:mSphere00109-15. [PMID: 27303706 PMCID: PMC4863615 DOI: 10.1128/msphere.00109-15] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2015] [Accepted: 02/04/2016] [Indexed: 11/20/2022] Open
Abstract
Rps26 is an essential protein of the eukaryotic small ribosomal subunit. Previous experiments demonstrated an interaction between the eukaryote-specific Y62–K70 segment of Rps26 and the 5′ untranslated region of mRNA. The data suggested a specific role of the Y62–K70 motif during translation initiation. Here, we report that single-site substitutions within the Y62–K70 peptide did not affect the growth of engineered yeast strains, arguing against its having a critical role during translation initiation via specific interactions with the 5′ untranslated region of mRNA molecules. Only the simultaneous replacement of five conserved residues within the Y62–K70 fragment or the replacement of the yeast protein with the human homolog resulted in growth defects and caused significant changes in polysome profiles. The results expand our knowledge of ribosomal protein function and suggest a role of Rps26 during ribosome assembly in yeast. The eukaryotic ribosome consists of a small (40S) and a large (60S) subunit. Rps26 is one of the essential ribosomal proteins of the 40S subunit and is encoded by two almost identical genes, RPS26a and RPS26b. Previous studies demonstrated that Rps26 interacts with the 5′ untranslated region of mRNA via the eukaryote-specific 62-YXXPKXYXK-70 (Y62–K70) motif. Those observations suggested that this peptide within Rps26 might play an important and specific role during translation initiation. By using alanine-scanning mutagenesis and engineered strains of the yeast Saccharomyces cerevisiae, we found that single amino acid substitutions within the Y62–K70 motif of Rps26 did not affect the in vivo function of the protein. In contrast, complete deletion of the Y62–K70 segment was lethal. The simultaneous replacement of five conserved residues within the Y62–K70 segment by alanines resulted in growth defects under stress conditions and produced distinct changes in polysome profiles that were indicative of the accumulation of free 60S subunits. Human Rps26 (Rps26-Hs), which displays significant homology with yeast Rps26, supported the growth of an S. cerevisiae Δrps26a Δrps26b strain. However, the Δrps26a Δrps26b double deletion strain expressing Rps26-Hs displayed substantial growth defects and an altered ratio of 40S/60S ribosomal subunits. The combined data strongly suggest that the eukaryote-specific motif within Rps26 does not play a specific role in translation initiation. Rather, the data indicate that Rps26 as a whole is necessary for proper assembly of the 40S subunit and the 80S ribosome in yeast. IMPORTANCE Rps26 is an essential protein of the eukaryotic small ribosomal subunit. Previous experiments demonstrated an interaction between the eukaryote-specific Y62–K70 segment of Rps26 and the 5′ untranslated region of mRNA. The data suggested a specific role of the Y62–K70 motif during translation initiation. Here, we report that single-site substitutions within the Y62–K70 peptide did not affect the growth of engineered yeast strains, arguing against its having a critical role during translation initiation via specific interactions with the 5′ untranslated region of mRNA molecules. Only the simultaneous replacement of five conserved residues within the Y62–K70 fragment or the replacement of the yeast protein with the human homolog resulted in growth defects and caused significant changes in polysome profiles. The results expand our knowledge of ribosomal protein function and suggest a role of Rps26 during ribosome assembly in yeast.
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10
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Wang S, You Z, Feng M, Che J, Zhang Y, Qian Q, Komatsu S, Zhong B. Analyses of the Molecular Mechanisms Associated with Silk Production in Silkworm by iTRAQ-Based Proteomics and RNA-Sequencing-Based Transcriptomics. J Proteome Res 2015; 15:15-28. [DOI: 10.1021/acs.jproteome.5b00821] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Shaohua Wang
- College
of Animal Sciences, Zhejiang University, Hangzhou 310058, PR China
| | - Zhengying You
- College
of Animal Sciences, Zhejiang University, Hangzhou 310058, PR China
| | - Mao Feng
- Institute
of Apicultural Research/Key Laboratory of Pollinating Insect Biology,
Ministry of Agriculture, Chinese Academy of Agricultural Science, Beijing 100093, China
| | - Jiaqian Che
- College
of Animal Sciences, Zhejiang University, Hangzhou 310058, PR China
| | - Yuyu Zhang
- College
of Animal Sciences, Zhejiang University, Hangzhou 310058, PR China
| | - Qiujie Qian
- College
of Animal Sciences, Zhejiang University, Hangzhou 310058, PR China
| | - Setsuko Komatsu
- National Institute of Crop Science, NARO, Tsukuba 305-8518, Japan
| | - Boxiong Zhong
- College
of Animal Sciences, Zhejiang University, Hangzhou 310058, PR China
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11
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Abstract
The proteome of cells is synthesized by ribosomes, complex ribonucleoproteins that in eukaryotes contain 79-80 proteins and four ribosomal RNAs (rRNAs) more than 5,400 nucleotides long. How these molecules assemble together and how their assembly is regulated in concert with the growth and proliferation of cells remain important unanswered questions. Here, we review recently emerging principles to understand how eukaryotic ribosomal proteins drive ribosome assembly in vivo. Most ribosomal proteins assemble with rRNA cotranscriptionally; their association with nascent particles is strengthened as assembly proceeds. Each subunit is assembled hierarchically by sequential stabilization of their subdomains. The active sites of both subunits are constructed last, perhaps to prevent premature engagement of immature ribosomes with active subunits. Late-assembly intermediates undergo quality-control checks for proper function. Mutations in ribosomal proteins that affect mostly late steps lead to ribosomopathies, diseases that include a spectrum of cell type-specific disorders that often transition from hypoproliferative to hyperproliferative growth.
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Affiliation(s)
- Jesus de la Cruz
- Instituto de Biomedicina de Sevilla, Hospital Universitario Virgen del Rocio/CSIC/Universidad de Sevilla, E-41013 Sevilla, Spain
- Departamento de Genetica, Universidad de Sevilla, E-41013 Sevilla, Spain
| | - Katrin Karbstein
- Department of Cancer Biology, The Scripps Research Institute, Jupiter, Florida 33458
| | - John L Woolford
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213
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12
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DiGiacomo V, Meruelo D. Looking into laminin receptor: critical discussion regarding the non-integrin 37/67-kDa laminin receptor/RPSA protein. Biol Rev Camb Philos Soc 2015; 91:288-310. [PMID: 25630983 DOI: 10.1111/brv.12170] [Citation(s) in RCA: 94] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2013] [Revised: 12/04/2014] [Accepted: 12/08/2014] [Indexed: 02/06/2023]
Abstract
The 37/67-kDa laminin receptor (LAMR/RPSA) was originally identified as a 67-kDa binding protein for laminin, an extracellular matrix glycoprotein that provides cellular adhesion to the basement membrane. LAMR has evolutionary origins, however, as a 37-kDa RPS2 family ribosomal component. Expressed in all domains of life, RPS2 proteins have been shown to have remarkably diverse physiological roles that vary across species. Contributing to laminin binding, ribosome biogenesis, cytoskeletal organization, and nuclear functions, this protein governs critical cellular processes including growth, survival, migration, protein synthesis, development, and differentiation. Unsurprisingly given its purview, LAMR has been associated with metastatic cancer, neurodegenerative disease and developmental abnormalities. Functioning in a receptor capacity, this protein also confers susceptibility to bacterial and viral infection. LAMR is clearly a molecule of consequence in human disease, directly mediating pathological events that make it a prime target for therapeutic interventions. Despite decades of research, there are still a large number of open questions regarding the cellular biology of LAMR, the nature of its ability to bind laminin, the function of its intrinsically disordered C-terminal region and its conversion from 37 to 67 kDa. This review attempts to convey an in-depth description of the complexity surrounding this multifaceted protein across functional, structural and pathological aspects.
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Affiliation(s)
- Vincent DiGiacomo
- Department of Pathology, New York University School of Medicine, 180 Varick Street, New York, NY 10014, U.S.A
| | - Daniel Meruelo
- Department of Pathology, New York University School of Medicine, 180 Varick Street, New York, NY 10014, U.S.A.,NYU Cancer Institute, 550 First Avenue, New York, NY 10016, U.S.A.,NYU Gene Therapy Center, 550 First Avenue, New York, NY 10016, U.S.A
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13
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Venticinque L, Meruelo D. Comprehensive proteomic analysis of nonintegrin laminin receptor interacting proteins. J Proteome Res 2012; 11:4863-72. [PMID: 22909348 PMCID: PMC3495180 DOI: 10.1021/pr300307h] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Human nonintegrin laminin receptor is a multifunctional protein acting as an integral component of the ribosome and a cell surface receptor for laminin-1. The laminin receptor is overexpressed in several human cancers and is also the cell surface receptor for several viruses and pathogenic prion proteins, making it a pathologically significant protein. This study focused on the proteomic characterization of laminin receptor interacting proteins from Mus musculus. The use of affinity chromatography with immobilized recombinant laminin receptor coupled with mass spectrometry analysis identified 45 proteins with high confidence. Following validation through coimmunoprecipitation, the proteins were classified based on predicted function into ribosomal, RNA processing, signal transduction/metabolism, protein processing, cytoskeleton/cell anchorage, DNA/chromatin, and unknown functions. A significant portion of the identified proteins is related to functions or localizations previously described for laminin receptor. This work represents a comprehensive proteomic approach to studying laminin receptor and provides an essential stepping stone to a better mechanistic understanding of this protein's diverse functions.
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Affiliation(s)
- Lisa Venticinque
- Gene Therapy Center, Cancer Institute and Department of Pathology, New York University School of Medicine, 550 First Avenue, New York, NY 10016
| | - Daniel Meruelo
- Gene Therapy Center, Cancer Institute and Department of Pathology, New York University School of Medicine, 550 First Avenue, New York, NY 10016
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14
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Abstract
Despite the fact that ribosomal proteins are the constituents of an organelle that is present in every cell, they show a surprising level of regulation, and several of them have also been shown to have other extra-ribosomal functions, such in replication, transcription, splicing or even ageing. This review provides a comprehensive summary of these important aspects.
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Affiliation(s)
- Rital B Bhavsar
- Department of Biology, University of Dayton, OH 45469-2320, USA
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15
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O'Donohue MF, Choesmel V, Faubladier M, Fichant G, Gleizes PE. Functional dichotomy of ribosomal proteins during the synthesis of mammalian 40S ribosomal subunits. ACTA ACUST UNITED AC 2010; 190:853-66. [PMID: 20819938 PMCID: PMC2935573 DOI: 10.1083/jcb.201005117] [Citation(s) in RCA: 157] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Subsets of 40S ribosomal subunits are required for initiating rRNA processing, rRNA maturation, and nuclear export. Our knowledge of the functions of metazoan ribosomal proteins in ribosome synthesis remains fragmentary. Using siRNAs, we show that knockdown of 31 of the 32 ribosomal proteins of the human 40S subunit (ribosomal protein of the small subunit [RPS]) strongly affects pre–ribosomal RNA (rRNA) processing, which often correlates with nucleolar chromatin disorganization. 16 RPSs are strictly required for initiating processing of the sequences flanking the 18S rRNA in the pre-rRNA except at the metazoan-specific early cleavage site. The remaining 16 proteins are necessary for progression of the nuclear and cytoplasmic maturation steps and for nuclear export. Distribution of these two subsets of RPSs in the 40S subunit structure argues for a tight dependence of pre-rRNA processing initiation on the folding of both the body and the head of the forming subunit. Interestingly, the functional dichotomy of RPS proteins reported in this study is correlated with the mutation frequency of RPS genes in Diamond-Blackfan anemia.
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Affiliation(s)
- Marie-Françoise O'Donohue
- Laboratoire de Biologie Moléculaire des Eucaryotes, Université de Toulouse-UPS and Centre National de La Recherche Scientifique, F-31000 Toulouse, France
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16
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Babiano R, de la Cruz J. Ribosomal protein L35 is required for 27SB pre-rRNA processing in Saccharomyces cerevisiae. Nucleic Acids Res 2010; 38:5177-92. [PMID: 20392820 PMCID: PMC2926614 DOI: 10.1093/nar/gkq260] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2009] [Revised: 03/19/2010] [Accepted: 03/29/2010] [Indexed: 11/12/2022] Open
Abstract
Ribosome synthesis involves the concomitance of pre-rRNA processing and ribosomal protein assembly. In eukaryotes, this is a complex process that requires the participation of specific sequences and structures within the pre-rRNAs, at least 200 trans-acting factors and the ribosomal proteins. There is little information on the function of individual 60S ribosomal proteins in ribosome synthesis. Herein, we have analysed the contribution of ribosomal protein L35 in ribosome biogenesis. In vivo depletion of L35 results in a deficit in 60S ribosomal subunits and the appearance of half-mer polysomes. Pulse-chase, northern hybridization and primer extension analyses show that processing of the 27SB to 7S pre-rRNAs is strongly delayed upon L35 depletion. Most likely as a consequence of this, release of pre-60S ribosomal particles from the nucleolus to the nucleoplasm is also blocked. Deletion of RPL35A leads to similar although less pronounced phenotypes. Moreover, we show that L35 assembles in the nucleolus and binds to early pre-60S ribosomal particles. Finally, flow cytometry analysis indicated that L35-depleted cells mildly delay the G1 phase of the cell cycle. We conclude that L35 assembly is a prerequisite for the efficient cleavage of the internal transcribed spacer 2 at site C(2).
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Affiliation(s)
| | - Jesús de la Cruz
- Departamento de Genética, Universidad de Sevilla, Sevilla, Spain
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17
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Lee SC, Weiss LM, Heitman J. Generation of genetic diversity in microsporidia via sexual reproduction and horizontal gene transfer. Commun Integr Biol 2010; 2:414-7. [PMID: 19907704 DOI: 10.4161/cib.2.5.8846] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2009] [Accepted: 04/27/2009] [Indexed: 01/06/2023] Open
Abstract
Microsporidia are obligate intracellular pathogens mainly infecting both vertebrate and invertebrate hosts. The group comprises approximately 150 genera with 1,200 species. Due to sequence divergence phylogenic reconstructions that are solely based on DNA sequence have been unprecise for these pathogens. Our previous study identified that three microsporidian genomes contained a putative sex-related locus similar to that of zygomycetes. In a comparison of genome architecture of the microsporidia to other fungi, Rhizopus oryzae, a zygomycete fungus, shared more common gene clusters with Encephalitozoon cuniculi, a microsporidian. This provides evidence supporting the hypothesis that microsporidia and zygomycete fungi may share a more recent common ancestor than other fungal lineages. Genetic recombination is an important outcome of sexual development. We describe genetic markers which will enable tests of whether sex occurs within E. cuniculi populations by analyzing tandem repeat DNA regions in three different isolates. Taken together, the phylogenetic relationship of microsporidia to fungi and the presence of a sex-related locus in their genomes suggest the microsporidia may have an extant sexual cycle. In addition, we describe recently reported evidence of horizontal gene transfer from Chlamydia to the E. cuniculi genome and show that these two obligate intracellular pathogens can infect the same host cells.
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Affiliation(s)
- Soo Chan Lee
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710, USA
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18
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Granneman S, Petfalski E, Swiatkowska A, Tollervey D. Cracking pre-40S ribosomal subunit structure by systematic analyses of RNA-protein cross-linking. EMBO J 2010; 29:2026-36. [PMID: 20453830 PMCID: PMC2892368 DOI: 10.1038/emboj.2010.86] [Citation(s) in RCA: 114] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2009] [Accepted: 04/14/2010] [Indexed: 12/21/2022] Open
Abstract
Understanding of eukaryotic ribosome synthesis has been slowed by a lack of structural data for the pre-ribosomal particles. We report rRNA-binding sites for six late-acting 40S ribosome synthesis factors, three of which cluster around the 3' end of the 18S rRNA in model 3D structures. Enp1 and Ltv1 were previously implicated in 'beak' structure formation during 40S maturation--and their binding sites indicate direct functions. The kinase Rio2, putative GTPase Tsr1 and dimethylase Dim1 bind sequences involved in tRNA interactions and mRNA decoding, indicating that their presence is incompatible with translation. The Dim1- and Tsr1-binding sites overlap with those of homologous Escherichia coli proteins, revealing conservation in assembly pathways. The primary binding sites for the 18S 3'-endonuclease Nob1 are distinct from its cleavage site and were unaltered by mutation of the catalytic PIN domain. Structure probing indicated that at steady state the cleavage site is likely unbound by Nob1 and flexible in the pre-rRNA. Nob1 binds before pre-rRNA cleavage, and we conclude that structural reorganization is needed to bring together the catalytic PIN domain and its target.
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Affiliation(s)
- Sander Granneman
- Wellcome Trust Centre for Cell Biology, University of Edinburgh, Edinburgh, Scotland, UK
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19
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Neueder A, Jakob S, Pöll G, Linnemann J, Deutzmann R, Tschochner H, Milkereit P. A local role for the small ribosomal subunit primary binder rpS5 in final 18S rRNA processing in yeast. PLoS One 2010; 5:e10194. [PMID: 20419091 PMCID: PMC2856670 DOI: 10.1371/journal.pone.0010194] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2010] [Accepted: 03/28/2010] [Indexed: 11/18/2022] Open
Abstract
In vivo depletion of the yeast small ribosomal subunit (SSU) protein S5 (rpS5) leads to nuclear degradation of nascent SSUs and to a perturbed global assembly state of the SSU head domain. Here, we report that rpS5 plays an additional local role at the head/platform interface in efficient SSU maturation. We find that yeast small ribosomal subunits which incorporated an rpS5 variant lacking the seven C-terminal amino acids have a largely assembled head domain and are exported to the cytoplasm. On the other hand, 3' processing of 18S rRNA precursors is inhibited in these ribosomal particles, although they associate with the putative endonuclease Nob1p and other late acting 40S biogenesis factors. We suggest that the SSU head component rpS5 and platform components as rpS14 are crucial constituents of a highly defined spatial arrangement in the head-platform interface of nascent SSUs, which is required for efficient processing of the therein predicted SSU rRNA 3' end. Positioning of rpS5 in nascent SSUs, including its relative orientation towards platform components in the head-platform cleft, will depend on the general assembly and folding state of the head domain. Therefore, the suggested model can explain 18S precursor rRNA 3' processing phenotypes observed in many eukaryotic SSU head assembly mutants.
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Affiliation(s)
- Andreas Neueder
- Institut für Biochemie, Genetik und Mikrobiologie, University of Regensburg, Regensburg, Germany
| | - Steffen Jakob
- Institut für Biochemie, Genetik und Mikrobiologie, University of Regensburg, Regensburg, Germany
| | - Gisela Pöll
- Institut für Biochemie, Genetik und Mikrobiologie, University of Regensburg, Regensburg, Germany
| | - Jan Linnemann
- Institut für Biochemie, Genetik und Mikrobiologie, University of Regensburg, Regensburg, Germany
| | - Rainer Deutzmann
- Institut für Biochemie, Genetik und Mikrobiologie, University of Regensburg, Regensburg, Germany
| | - Herbert Tschochner
- Institut für Biochemie, Genetik und Mikrobiologie, University of Regensburg, Regensburg, Germany
| | - Philipp Milkereit
- Institut für Biochemie, Genetik und Mikrobiologie, University of Regensburg, Regensburg, Germany
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20
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Soudet J, Gélugne JP, Belhabich-Baumas K, Caizergues-Ferrer M, Mougin A. Immature small ribosomal subunits can engage in translation initiation in Saccharomyces cerevisiae. EMBO J 2009; 29:80-92. [PMID: 19893492 DOI: 10.1038/emboj.2009.307] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2009] [Accepted: 09/03/2009] [Indexed: 11/09/2022] Open
Abstract
It is generally assumed that, in Saccharomyces cerevisiae, immature 40S ribosomal subunits are not competent for translation initiation. Here, we show by different approaches that, in wild-type conditions, a portion of pre-40S particles (pre-SSU) associate with translating ribosomal complexes. When cytoplasmic 20S pre-rRNA processing is impaired, as in Rio1p- or Nob1p-depleted cells, a large part of pre-SSUs is associated with translating ribosomes complexes. Loading of pre-40S particles onto mRNAs presumably uses the canonical pathway as translation-initiation factors interact with 20S pre-rRNA. However, translation initiation is not required for 40S ribosomal subunit maturation. We also provide evidence suggesting that cytoplasmic 20S pre-rRNAs that associate with translating complexes are turned over by the no go decay (NGD) pathway, a process known to degrade mRNAs on which ribosomes are stalled. We propose that the cytoplasmic fate of 20S pre-rRNA is determined by the balance between pre-SSU processing kinetics and sensing of ribosome-like particles loaded onto mRNAs by the NGD machinery, which acts as an ultimate ribosome quality check point.
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Affiliation(s)
- Julien Soudet
- Laboratoire de Biologie Moléculaire Eucaryote, Université de Toulouse, Université Paul Sabatier, Toulouse, France
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21
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Perreault A, Bellemer C, Bachand F. Nuclear export competence of pre-40S subunits in fission yeast requires the ribosomal protein Rps2. Nucleic Acids Res 2008; 36:6132-42. [PMID: 18820293 PMCID: PMC2577348 DOI: 10.1093/nar/gkn625] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
Ribosome biogenesis is an evolutionarily conserved pathway that requires ribosomal and nonribosomal proteins. Here, we investigated the role of the ribosomal protein S2 (Rps2) in fission yeast ribosome synthesis. As for many budding yeast ribosomal proteins, Rps2 was essential for cell viability in fission yeast and the genetic depletion of Rps2 caused a complete inhibition of 40S ribosomal subunit production. The pattern of pre-rRNA processing upon depletion of Rps2 revealed a reduction of 27SA2 pre-rRNAs and the concomitant production of 21S rRNA precursors, consistent with a role for Rps2 in efficient cleavage at site A2 within the 32S pre-rRNA. Importantly, kinetics of pre-rRNA accumulation as determined by rRNA pulse-chases assays indicated that a small fraction of 35S precursors matured into 20S-containing particles, suggesting that most 40S precursors were rapidly degraded in the absence of Rps2. Analysis of steady-state RNA levels revealed that some pre-40S particles were produced in Rps2-depleted cells, but that these precursors were retained in the nucleolus. Our findings suggest a role for Rps2 in a mechanism that monitors pre-40S export competence.
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Affiliation(s)
- Audrey Perreault
- RNA Group, Department of Biochemistry, Université de Sherbrooke, Québec, Canada
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22
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Zemp I, Kutay U. Nuclear export and cytoplasmic maturation of ribosomal subunits. FEBS Lett 2007; 581:2783-93. [PMID: 17509569 DOI: 10.1016/j.febslet.2007.05.013] [Citation(s) in RCA: 137] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2007] [Accepted: 05/06/2007] [Indexed: 01/20/2023]
Abstract
Based on the characterization of ribosome precursor particles and associated trans-acting factors, a biogenesis pathway for the 40S and 60S subunits has emerged. After nuclear synthesis and assembly steps, pre-ribosomal subunits are exported through the nuclear pore complex in a Crm1- and RanGTP-dependent manner. Subsequent cytoplasmic biogenesis steps of pre-60S particles include the facilitated release of several non-ribosomal proteins, yielding fully functional 60S subunits. Cytoplasmic maturation of 40S subunit precursors includes rRNA dimethylation and pre-rRNA cleavage, allowing 40S subunits to achieve translation competence. We review current knowledge of nuclear export and cytoplasmic maturation of ribosomal subunits.
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Affiliation(s)
- Ivo Zemp
- Institute of Biochemistry, HPM F11.1, Schafmattstr. 18, ETH Zurich, 8093 Zurich, Switzerland
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23
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Decatur WA, Liang XH, Piekna-Przybylska D, Fournier MJ. Identifying effects of snoRNA-guided modifications on the synthesis and function of the yeast ribosome. Methods Enzymol 2007; 425:283-316. [PMID: 17673089 DOI: 10.1016/s0076-6879(07)25013-x] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The small nucleolar RNAs (snoRNAs) are associated with proteins in ribonucleoprotein complexes called snoRNPs ("snorps"). These complexes create modified nucleotides in preribosomal RNA and other RNAs and participate in nucleolytic cleavages of pre-rRNA. The various reactions occur in site-specific fashion, and the mature rRNAs are ultimately incorporated into cytoplasmic ribosomes. Most snoRNAs exist in two structural classes, and most members in each class are involved in nucleotide modification reactions. Guide snoRNAs in the "box C/D" class target methylation of the 2'-hydroxyl moiety, to form 2'-O-methylated nucleotides (Nm), whereas guide snoRNAs in the "box H/ACA" class target specific uridines for conversion to pseudouridine (Psi). The rRNA nucleotides modified in this manner are numerous, totaling approximately 100 in yeast and twice that number in humans. Although the chemistry of the modifications and the factors involved in their formation are largely explained, very little is known about the influence of the copious snoRNA-guided nucleotide modifications on rRNA activity and ribosome function. Among eukaryotic organisms the sites of rRNA modification and the corresponding guide snoRNAs have been best characterized in S. cerevisiae, making this a model organism for analyzing the consequences of modification. This chapter presents approaches to characterizing rRNA modification effects in yeast and includes strategies for evaluating a variety of specific rRNA functions. To aid in planning, a package of bioinformatics tools is described that enables investigators to correlate guide function with targeted ribosomal sites in several contexts. Genetic procedures are presented for depleting modifications at one or more rRNA sites, including ablation of all Nm or Psi modifications made by snoRNPs, and for introducing modifications at novel sites. Methods are also included for characterizing modification effects on cell growth, antibiotic sensitivity, rRNA processing, formation of various rRNP complexes, translation activity, and rRNA structure within the ribosome.
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Affiliation(s)
- Wayne A Decatur
- Department of Biochemistry and Molecular Biology, University of Massachusetts, Amherst, MA, USA
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24
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Chiocchetti A, Zhou J, Zhu H, Karl T, Haubenreisser O, Rinnerthaler M, Heeren G, Oender K, Bauer J, Hintner H, Breitenbach M, Breitenbach-Koller L. Ribosomal proteins Rpl10 and Rps6 are potent regulators of yeast replicative life span. Exp Gerontol 2006; 42:275-86. [PMID: 17174052 DOI: 10.1016/j.exger.2006.11.002] [Citation(s) in RCA: 90] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2006] [Revised: 10/27/2006] [Accepted: 11/07/2006] [Indexed: 11/17/2022]
Abstract
The yeast ribosome is composed of two subunits, the large 60S subunit (LSU) and the small 40S subunit (SSU) and harbors 78 ribosomal proteins (RPs), 59 of which are encoded by duplicate genes. Recently, deletions of the LSU paralogs RPL31A and RPL6B were found to increase significantly yeast replicative life span (RLS). RPs Rpl10 and Rps6 are known translational regulators. Here, we report that heterozygosity for rpl10Delta but not for rpl25Delta, both LSU single copy RP genes, increased RLS by 24%. Deletion of the SSU RPS6B paralog, but not of the RPS6A paralog increased replicative life span robustly by 45%, while deletion of both the SSU RPS18A, and RPS18B paralogs increased RLS moderately, but significantly by 15%. Altering the gene dosage of RPL10 reduced the translating ribosome population, whereas deletion of the RPS6A, RPS6B, RPS18A, and RPS18B paralogs produced a large shift in free ribosomal subunit stoichiometry. We observed a reduction in growth rate in all deletion strains and reduced cell size in the SSU RPS6B, RPS6A, and RPS18B deletion strains. Thus, reduction of gene dosage of RP genes belonging to both the 60S and the 40S subunit affect lifespan, possibly altering the aging process by modulation of translation.
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Affiliation(s)
- Andreas Chiocchetti
- Department of Cell Biology, University of Salzburg, Hellbrunnerstrasse 34, A-5020 Salzburg, Austria
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25
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Ferreira-Cerca S, Pöll G, Gleizes PE, Tschochner H, Milkereit P. Roles of eukaryotic ribosomal proteins in maturation and transport of pre-18S rRNA and ribosome function. Mol Cell 2006; 20:263-75. [PMID: 16246728 DOI: 10.1016/j.molcel.2005.09.005] [Citation(s) in RCA: 231] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2005] [Revised: 08/08/2005] [Accepted: 09/06/2005] [Indexed: 11/26/2022]
Abstract
Despite the rising knowledge about ribosome function and structure and how ribosomal subunits assemble in vitro in bacteria, the in vivo role of many ribosomal proteins remains obscure both in pro- and eukaryotes. Our systematic analysis of yeast ribosomal proteins (r-proteins) of the small subunit revealed that most eukaryotic r-proteins fulfill different roles in ribosome biogenesis, making them indispensable for growth. Different r-proteins control distinct steps of nuclear and cytoplasmic pre-18S rRNA processing and, thus, ensure that only properly assembled ribosomes become engaged in translation. Comparative analysis of dynamic and steady-state maturation assays revealed that several r-proteins are required for efficient nuclear export of pre-18S rRNA, suggesting that they form an interaction platform with the export machinery. In contrast, the presence of other r-proteins is mainly required before nuclear export is initiated. Our studies draw a correlation between the in vitro assembly, structural localization, and in vivo function of r-proteins.
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Affiliation(s)
- Sébastien Ferreira-Cerca
- Institut für Biochemie, Genetik und Mikrobiologie, Universität Regensburg, Universitätsstr 31, 93053 Regensburg, Germany
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26
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Léger-Silvestre I, Caffrey JM, Dawaliby R, Alvarez-Arias DA, Gas N, Bertolone SJ, Gleizes PE, Ellis SR. Specific Role for Yeast Homologs of the Diamond Blackfan Anemia-associated Rps19 Protein in Ribosome Synthesis. J Biol Chem 2005; 280:38177-85. [PMID: 16159874 DOI: 10.1074/jbc.m506916200] [Citation(s) in RCA: 99] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Approximately 25% of cases of Diamond Blackfan anemia, a severe hypoplastic anemia, are linked to heterozygous mutations in the gene encoding ribosomal protein S19 that result in haploinsufficiency for this protein. Here we show that deletion of either of the two genes encoding Rps19 in yeast severely affects the production of 40 S ribosomal subunits. Rps19 is an essential protein that is strictly required for maturation of the 3'-end of 18 S rRNA. Depletion of Rps19 results in the accumulation of aberrant pre-40 S particles retained in the nucleus that fail to associate with pre-ribosomal factors involved in late maturation steps, including Enp1, Tsr1, and Rio2. When introduced in yeast Rps19, amino acid substitutions found in Diamond Blackfan anemia patients induce defects in the processing of the pre-rRNA similar to those observed in cells under-expressing Rps19. These results uncover a pivotal role of Rps19 in the assembly and maturation of the pre-40 S particles and demonstrate for the first time the effect of Diamond Blackfan anemia-associated mutations on the function of Rps19, strongly connecting the pathology to ribosome biogenesis.
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Affiliation(s)
- Isabelle Léger-Silvestre
- Laboratoire de Biologie Moléculaire des Eucaryotes (UMR5099) and Institut d'Exploration Fonctionnelle des Génomes (IFR109), CNRS and Université Paul Sabatier, 118 route de Narbonne, 31062 Toulouse, France
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27
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Borovjagin AV, Gerbi SA. An evolutionary intra-molecular shift in the preferred U3 snoRNA binding site on pre-ribosomal RNA. Nucleic Acids Res 2005; 33:4995-5005. [PMID: 16147982 PMCID: PMC1199564 DOI: 10.1093/nar/gki815] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
Abstract
Correct docking of U3 small nucleolar RNA (snoRNA) on pre-ribosomal RNA (pre-rRNA) is essential for rRNA processing to produce 18S rRNA. In this report, we have used Xenopus oocytes to characterize the structural requirements of the U3 snoRNA 3′-hinge interaction with region E1 of the external transcribed spacer (ETS) of pre-rRNA. This interaction is crucial for docking to initiate rRNA processing. 18S rRNA production was inhibited when fewer than 6 of the 8 bp of the U3 3′–hinge complex with the ETS could form; moreover, base pairing involving the right side of the 3′-hinge was more important than the left. Increasing the length of the U3 hinge–ETS interaction by 9 bp impaired rRNA processing. Formation of 18S rRNA was also inhibited by swapping the U3 5′- and 3′-hinge interactions with the ETS or by shifting the base pairing of the U3 3′-hinge to the sequence directly adjacent to ETS region E1. However, 18S rRNA production was partially restored by a compensatory shift that allowed the sequence adjacent to the U3 3′-hinge to pair with the eight bases directly adjacent to ETS region E1. The results suggest that the geometry of the U3 snoRNA interaction with the ETS is critical for rRNA processing.
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MESH Headings
- Animals
- Base Pairing
- Base Sequence
- Binding Sites
- Evolution, Molecular
- Molecular Sequence Data
- Mutation
- RNA Precursors/chemistry
- RNA Precursors/genetics
- RNA Precursors/metabolism
- RNA Processing, Post-Transcriptional
- RNA, Ribosomal, 18S/chemistry
- RNA, Ribosomal, 18S/genetics
- RNA, Ribosomal, 18S/metabolism
- RNA, Small Nucleolar/chemistry
- RNA, Small Nucleolar/genetics
- RNA, Small Nucleolar/metabolism
- Xenopus laevis
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Affiliation(s)
| | - Susan A. Gerbi
- To whom correspondence should be addressed. Tel: +1 401 863 2359; Fax: +1 401 863 1348;
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28
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Vos HR, Faber AW, de Gier MD, Vos JC, Raué HA. Deletion of the three distal S1 motifs of Saccharomyces cerevisiae Rrp5p abolishes pre-rRNA processing at site A(2) without reducing the production of functional 40S subunits. EUKARYOTIC CELL 2005; 3:1504-12. [PMID: 15590824 PMCID: PMC539016 DOI: 10.1128/ec.3.6.1504-1512.2004] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Yeast Rrp5p, one of the few trans-acting proteins required for the biogenesis of both ribosomal subunits, has a remarkable two-domain structure. Its C-terminal region consists of seven tetratricopeptide motifs, several of which are crucial for cleavages at sites A(0) to A(2) and thus for the formation of 18S rRNA. The N-terminal region, on the other hand, contains 12 S1 RNA-binding motifs, most of which are required for processing at site A(3) and thus for the production of the short form of 5.8S rRNA. Yeast cells expressing a mutant Rrp5p protein that lacks S1 motifs 10 to 12 (mutant rrp5Delta6) have a normal growth rate and wild-type steady-state levels of the mature rRNA species, suggesting that these motifs are irrelevant for ribosome biogenesis. Here we show that, nevertheless, in the rrp5Delta6 mutant, pre-rRNA processing follows an alternative pathway that does not include the cleavage of 32S pre-rRNA at site A(2). Instead, the 32S precursor is processed directly at site A(3), producing exclusively 21S rather than 20S pre-rRNA. This is the first evidence that the 21S precursor, which was observed previously only in cells showing a substantial growth defect or as a minor species in addition to the normal 20S precursor, is an efficient substrate for 18S rRNA synthesis. Maturation of the 21S precursor occurs via the same endonucleolytic cleavage at site D as that used for 20S pre-rRNA maturation. The resulting D-A(3) fragment, however, is degraded by both 5'-->3' and 3'-->5' exonuclease digestions, the latter involving the exosome, in contrast to the exclusively 5'-->3' exonucleolytic digestion of the D-A(2) fragment. We also show that rrp5Delta6 cells are hypersensitive to both hygromycin B and cycloheximide, suggesting that, despite their wild-type growth rate, their preribosomes or ribosomes may be structurally abnormal.
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Affiliation(s)
- Harmjan R Vos
- Section of Biochemistry and Molecular Biology, FEW, Vrije Universiteit, de Boelelaan 1083, 1081 HV Amsterdam, The Netherlands.
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29
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Loar JW, Seiser RM, Sundberg AE, Sagerson HJ, Ilias N, Zobel-Thropp P, Craig EA, Lycan DE. Genetic and biochemical interactions among Yar1, Ltv1 and Rps3 define novel links between environmental stress and ribosome biogenesis in Saccharomyces cerevisiae. Genetics 2005; 168:1877-89. [PMID: 15611164 PMCID: PMC1448719 DOI: 10.1534/genetics.104.032656] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
In the yeast S. cerevisiae, ribosome assembly is linked to environmental conditions by the coordinate transcriptional regulation of genes required for ribosome biogenesis. In this study we show that two nonessential stress-responsive genes, YAR1 and LTV1, function in 40S subunit production. We provide genetic and biochemical evidence that Yar1, a small ankyrin-repeat protein, physically interacts with RpS3, a component of the 40S subunit, and with Ltv1, a protein recently identified as a substoichiometric component of a 43S preribosomal particle. We demonstrate that cells lacking YAR1 or LTV1 are hypersensitive to particular protein synthesis inhibitors and exhibit aberrant polysome profiles, with a reduced absolute number of 40S subunits and an excess of free 60S subunits. Surprisingly, both mutants are also hypersensitive to a variety of environmental stress conditions. Overexpression of RPS3 suppresses both the stress sensitivity and the ribosome biogenesis defect of Deltayar1 mutants, but does not suppress either defect in Deltaltv1 mutants. We propose that YAR1 and LTV1 play distinct, nonessential roles in 40S subunit production. The stress-sensitive phenotypes of strains lacking these genes reveal a hitherto unknown link between ribosome biogenesis factors and environmental stress sensitivity.
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Affiliation(s)
- Jesse W Loar
- Department of Biology, Lewis and Clark College, Portland, Oregon 97219, USA
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30
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Léger-Silvestre I, Milkereit P, Ferreira-Cerca S, Saveanu C, Rousselle JC, Choesmel V, Guinefoleau C, Gas N, Gleizes PE. The ribosomal protein Rps15p is required for nuclear exit of the 40S subunit precursors in yeast. EMBO J 2004; 23:2336-47. [PMID: 15167894 PMCID: PMC423291 DOI: 10.1038/sj.emboj.7600252] [Citation(s) in RCA: 90] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2004] [Accepted: 05/04/2004] [Indexed: 11/09/2022] Open
Abstract
We have conducted a genetic screen in order to identify ribosomal proteins of Saccharomyces cerevisiae involved in nuclear export of the small subunit precursors. This has led us to distinguish Rps15p as a protein dispensable for maturation of the pre-40S particles, but whose assembly into the pre-ribosomes is a prerequisite to their nuclear exit. Upon depletion of Rps15p, 20S pre-rRNA is released from the nucleolus and retained in the nucleus, without alteration of the pre-rRNA early cleavages. In contrast, Rps18p, which contacts Rps15p in the small subunit, is required upstream for pre-rRNA processing at site A2. Most pre-40S specific factors are correctly associated with the intermediate particles accumulating in the nucleus upon Rps15p depletion, except the late-binding proteins Tsr1p and Rio2p. Here we show that these two proteins are dispensable for nuclear exit; instead, they participate in 20S pre-rRNA processing in the cytoplasm. We conclude that, during the final maturation steps in the nucleus, incorporation of the ribosomal protein Rps15p is specifically required to render the pre-40S particles competent for translocation to the cytoplasm.
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Affiliation(s)
- Isabelle Léger-Silvestre
- Laboratoire de Biologie Moléculaire Eucaryote, CNRS and Université Paul Sabatier, Toulouse, France
| | - Philipp Milkereit
- Laboratoire de Biologie Moléculaire Eucaryote, CNRS and Université Paul Sabatier, Toulouse, France
| | - Sébastien Ferreira-Cerca
- Laboratoire de Biologie Moléculaire Eucaryote, CNRS and Université Paul Sabatier, Toulouse, France
| | - Cosmin Saveanu
- Génétique des Interactions Macromoléculaires, Institut Pasteur, Paris, France
| | | | - Valérie Choesmel
- Laboratoire de Biologie Moléculaire Eucaryote, CNRS and Université Paul Sabatier, Toulouse, France
| | - Cécile Guinefoleau
- Laboratoire de Biologie Moléculaire Eucaryote, CNRS and Université Paul Sabatier, Toulouse, France
| | - Nicole Gas
- Laboratoire de Biologie Moléculaire Eucaryote, CNRS and Université Paul Sabatier, Toulouse, France
| | - Pierre-Emmanuel Gleizes
- Laboratoire de Biologie Moléculaire Eucaryote, CNRS and Université Paul Sabatier, Toulouse, France
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