51
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Li D, Wang J. Ribosome heterogeneity in stem cells and development. J Cell Biol 2020; 219:e202001108. [PMID: 32330234 PMCID: PMC7265316 DOI: 10.1083/jcb.202001108] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Revised: 04/03/2020] [Accepted: 04/06/2020] [Indexed: 02/08/2023] Open
Abstract
Translation control is critical to regulate protein expression. By directly adjusting protein levels, cells can quickly respond to dynamic transitions during stem cell differentiation and embryonic development. Ribosomes are multisubunit cellular assemblies that mediate translation. Previously seen as invariant machines with the same composition of components in all conditions, recent studies indicate that ribosomes are heterogeneous and that different ribosome types can preferentially translate specific subsets of mRNAs. Such heterogeneity and specialized translation functions are very important in stem cells and development, as they allow cells to quickly respond to stimuli through direct changes of protein abundance. In this review, we discuss ribosome heterogeneity that arises from multiple features of rRNAs, including rRNA variants and rRNA modifications, and ribosomal proteins, including their stoichiometry, compositions, paralogues, and posttranslational modifications. We also discuss alterations of ribosome-associated proteins (RAPs), with a particular focus on their consequent specialized translational control in stem cells and development.
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Affiliation(s)
- Dan Li
- Department of Cell, Developmental and Regenerative Biology, The Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY
- The Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Jianlong Wang
- Department of Cell, Developmental and Regenerative Biology, The Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY
- The Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY
- Department of Medicine, Columbia Center for Human Development, Columbia University Irving Medical Center, New York, NY
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52
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Cialek CA, Koch AL, Galindo G, Stasevich TJ. Lighting up single-mRNA translation dynamics in living cells. Curr Opin Genet Dev 2020; 61:75-82. [PMID: 32408104 PMCID: PMC7508770 DOI: 10.1016/j.gde.2020.04.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Revised: 03/12/2020] [Accepted: 04/08/2020] [Indexed: 12/11/2022]
Abstract
Over the past five years, technological advances have made it possible to image the translation of single mRNA in the natural context of living cells. With these advances, researchers are beginning to shed light on when, where, and to what degree mRNA are translated with single-molecule precision. These works provide insight into the heterogeneity of translation amongst single transcripts, behavior that is averaged out in complementary bulk assays. In this review, we discuss the rapidly maturing field of live-cell, single-mRNA imaging of translation, beginning with a brief overview of recent technological advances. The remainder of the review focuses on the new biological insights gained from these technologies. We conclude with a discussion of the future of this technology.
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Affiliation(s)
- Charlotte A Cialek
- Department of Biochemistry & Molecular Biology, Colorado State University, Fort Collins, Colorado 80523, USA
| | - Amanda L Koch
- Department of Biochemistry & Molecular Biology, Colorado State University, Fort Collins, Colorado 80523, USA
| | - Gabriel Galindo
- Department of Biochemistry & Molecular Biology, Colorado State University, Fort Collins, Colorado 80523, USA
| | - Timothy J Stasevich
- Department of Biochemistry & Molecular Biology, Colorado State University, Fort Collins, Colorado 80523, USA; World Research Hub Initiative, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama 2268503, Japan.
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53
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Tao J, Hao Y, Li X, Yin H, Nie X, Zhang J, Xu B, Chen Q, Li B. Systematic Identification of Housekeeping Genes Possibly Used as References in Caenorhabditis elegans by Large-Scale Data Integration. Cells 2020; 9:E786. [PMID: 32213971 PMCID: PMC7140892 DOI: 10.3390/cells9030786] [Citation(s) in RCA: 13] [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: 01/24/2020] [Revised: 03/11/2020] [Accepted: 03/11/2020] [Indexed: 12/20/2022] Open
Abstract
For accurate gene expression quantification, normalization of gene expression data against reliable reference genes is required. It is known that the expression levels of commonly used reference genes vary considerably under different experimental conditions, and therefore, their use for data normalization is limited. In this study, an unbiased identification of reference genes in Caenorhabditis elegans was performed based on 145 microarray datasets (2296 gene array samples) covering different developmental stages, different tissues, drug treatments, lifestyle, and various stresses. As a result, thirteen housekeeping genes (rps-23, rps-26, rps-27, rps-16, rps-2, rps-4, rps-17, rpl-24.1, rpl-27, rpl-33, rpl-36, rpl-35, and rpl-15) with enhanced stability were comprehensively identified by using six popular normalization algorithms and RankAggreg method. Functional enrichment analysis revealed that these genes were significantly overrepresented in GO terms or KEGG pathways related to ribosomes. Validation analysis using recently published datasets revealed that the expressions of newly identified candidate reference genes were more stable than the commonly used reference genes. Based on the results, we recommended using rpl-33 and rps-26 as the optimal reference genes for microarray and rps-2 and rps-4 for RNA-sequencing data validation. More importantly, the most stable rps-23 should be a promising reference gene for both data types. This study, for the first time, successfully displays a large-scale microarray data driven genome-wide identification of stable reference genes for normalizing gene expression data and provides a potential guideline on the selection of universal internal reference genes in C. elegans, for quantitative gene expression analysis.
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Affiliation(s)
- Jingxin Tao
- College of Life Sciences, Chongqing Normal University, Chongqing 401331, China; (J.T.); (Y.H.); (X.L.); (H.Y.); (X.N.); (J.Z.); (B.X.)
| | - Youjin Hao
- College of Life Sciences, Chongqing Normal University, Chongqing 401331, China; (J.T.); (Y.H.); (X.L.); (H.Y.); (X.N.); (J.Z.); (B.X.)
| | - Xudong Li
- College of Life Sciences, Chongqing Normal University, Chongqing 401331, China; (J.T.); (Y.H.); (X.L.); (H.Y.); (X.N.); (J.Z.); (B.X.)
| | - Huachun Yin
- College of Life Sciences, Chongqing Normal University, Chongqing 401331, China; (J.T.); (Y.H.); (X.L.); (H.Y.); (X.N.); (J.Z.); (B.X.)
| | - Xiner Nie
- College of Life Sciences, Chongqing Normal University, Chongqing 401331, China; (J.T.); (Y.H.); (X.L.); (H.Y.); (X.N.); (J.Z.); (B.X.)
| | - Jie Zhang
- College of Life Sciences, Chongqing Normal University, Chongqing 401331, China; (J.T.); (Y.H.); (X.L.); (H.Y.); (X.N.); (J.Z.); (B.X.)
| | - Boying Xu
- College of Life Sciences, Chongqing Normal University, Chongqing 401331, China; (J.T.); (Y.H.); (X.L.); (H.Y.); (X.N.); (J.Z.); (B.X.)
| | - Qiao Chen
- Scientific Research Office, Chongqing Normal University, Chongqing 401331, China;
| | - Bo Li
- College of Life Sciences, Chongqing Normal University, Chongqing 401331, China; (J.T.); (Y.H.); (X.L.); (H.Y.); (X.N.); (J.Z.); (B.X.)
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55
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Ford D. Ribosomal heterogeneity - A new inroad for pharmacological innovation. Biochem Pharmacol 2020; 175:113874. [PMID: 32105657 DOI: 10.1016/j.bcp.2020.113874] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2020] [Accepted: 02/20/2020] [Indexed: 12/13/2022]
Abstract
The paradigm of ribosome usage in protein translation has shifted from a stance proposed as scientists began to unpick the genetic code that each mRNA was partnered by its own, unique ribosome to a rapid reversal of this view that ribosomes are completely interchangeable and simply recruited to mRNAs from a completely homogenous cellular pool. Evidence that the ribosomal proteome, ribosomal gene transcriptome and ribosome protein and RNA modifications differ between cells and tissues points to the fact that ribosomes are heterogeneous in their composition and have a degree of specialisation in their function. It has also been posited that the tissue-specificity of ribosome diseases provides an indication of functional ribosome heterogeneity, but there are substantial caveats to this interpretation. Only now have proteomic technologies developed to a level enabling accurate stoichiometric comparison of the abundance of specific ribosomal proteins in actively translating ribosomes and to measure protein in non-denatured ribosomes. This poises the field for the provocation that ribosome heterogeneity offers a novel and powerful inroad for the pharmacological targeting of disease. Such ribosome-targeted treatments may extend beyond specific ribosomopathies through strategies such as targeting features of ribosomes that are unique to diseased cells, particularly cancer cells, or to activated immune cells, as well as augmenting the action of other drugs through weakening the production of new proteins in target tissues. We may also be able to harness the potential power in ribosome diversity and specialism to better tune synthetic biology for the production of pharmaceutical proteins.
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Affiliation(s)
- Dianne Ford
- Northumbria University, Northumberland Building, Northumberland Road, Newcastle upon Tyne, NE1 8ST, United Kingdom.
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56
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Dougherty SE, Maduka AO, Inada T, Silva GM. Expanding Role of Ubiquitin in Translational Control. Int J Mol Sci 2020; 21:E1151. [PMID: 32050486 PMCID: PMC7037965 DOI: 10.3390/ijms21031151] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2020] [Revised: 02/04/2020] [Accepted: 02/05/2020] [Indexed: 12/22/2022] Open
Abstract
The eukaryotic proteome has to be precisely regulated at multiple levels of gene expression, from transcription, translation, and degradation of RNA and protein to adjust to several cellular conditions. Particularly at the translational level, regulation is controlled by a variety of RNA binding proteins, translation and associated factors, numerous enzymes, and by post-translational modifications (PTM). Ubiquitination, a prominent PTM discovered as the signal for protein degradation, has newly emerged as a modulator of protein synthesis by controlling several processes in translation. Advances in proteomics and cryo-electron microscopy have identified ubiquitin modifications of several ribosomal proteins and provided numerous insights on how this modification affects ribosome structure and function. The variety of pathways and functions of translation controlled by ubiquitin are determined by the various enzymes involved in ubiquitin conjugation and removal, by the ubiquitin chain type used, by the target sites of ubiquitination, and by the physiologic signals triggering its accumulation. Current research is now elucidating multiple ubiquitin-mediated mechanisms of translational control, including ribosome biogenesis, ribosome degradation, ribosome-associated protein quality control (RQC), and redox control of translation by ubiquitin (RTU). This review discusses the central role of ubiquitin in modulating the dynamism of the cellular proteome and explores the molecular aspects responsible for the expanding puzzle of ubiquitin signals and functions in translation.
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Affiliation(s)
- Shannon E. Dougherty
- Department of Biology, Duke University, Durham, NC 27708-0338, USA; (S.E.D.); (A.O.M.)
| | - Austin O. Maduka
- Department of Biology, Duke University, Durham, NC 27708-0338, USA; (S.E.D.); (A.O.M.)
| | - Toshifumi Inada
- Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai 980-8578, Japan;
| | - Gustavo M. Silva
- Department of Biology, Duke University, Durham, NC 27708-0338, USA; (S.E.D.); (A.O.M.)
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57
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Beese CJ, Brynjólfsdóttir SH, Frankel LB. Selective Autophagy of the Protein Homeostasis Machinery: Ribophagy, Proteaphagy and ER-Phagy. Front Cell Dev Biol 2020; 7:373. [PMID: 32039200 PMCID: PMC6985035 DOI: 10.3389/fcell.2019.00373] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Accepted: 12/16/2019] [Indexed: 01/06/2023] Open
Abstract
The eukaryotic cell has developed intricate machineries that monitor and maintain proteome homeostasis in order to ensure cellular functionality. This involves the carefully coordinated balance between protein synthesis and degradation pathways, which are dynamically regulated in order to meet the constantly changing demands of the cell. Ribosomes, together with the endoplasmic reticulum (ER), are the key drivers of protein synthesis, folding, maturation and sorting, while the proteasome plays a pivotal role in terminating the existence of thousands of proteins that are misfolded, damaged or otherwise obsolete. The synthesis, structure and function of these dedicated machines has been studied for decades, however, much less is understood about the mechanisms that control and execute their own turnover. Autophagy, an evolutionarily conserved catabolic pathway, mediates degradation of a large variety of cytosolic substrates, ranging from single proteins to entire organelles or multi-subunit macromolecular complexes. In this review, we focus on selective autophagy of three key components of the protein homeostasis machinery: ribosomes, ER and proteasomes, through the selective autophagy pathways of ribophagy, ER-phagy, and proteaphagy. We discuss newly discovered mechanisms for the selective clearance of these substrates, which are often stress-dependent and involve specialized signals for cargo recognition by a growing number of receptors. We further discuss the interplay between these pathways and their biological impact on key aspects of proteome homeostasis and cellular function in health and disease.
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Affiliation(s)
- Carsten J Beese
- Biotech Research and Innovation Centre, University of Copenhagen, Copenhagen, Denmark.,Danish Cancer Society Research Center, Copenhagen, Denmark
| | | | - Lisa B Frankel
- Biotech Research and Innovation Centre, University of Copenhagen, Copenhagen, Denmark.,Danish Cancer Society Research Center, Copenhagen, Denmark
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58
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DiGiuseppe S, Rollins MG, Bartom ET, Walsh D. ZNF598 Plays Distinct Roles in Interferon-Stimulated Gene Expression and Poxvirus Protein Synthesis. Cell Rep 2019; 23:1249-1258. [PMID: 29719242 PMCID: PMC5951170 DOI: 10.1016/j.celrep.2018.03.132] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2017] [Revised: 02/20/2018] [Accepted: 03/29/2018] [Indexed: 10/25/2022] Open
Abstract
Post-translational modification of ribosomal subunit proteins (RPs) is emerging as an important means of regulating gene expression. Recently, regulatory ubiquitination of small RPs RPS10 and RPS20 by the ubiquitin ligase ZNF598 was found to function in ribosome sensing and stalling on internally polyadenylated mRNAs during ribosome quality control (RQC). Here, we reveal that ZNF598 and RPS10 negatively regulate interferon-stimulated gene (ISG) expression in primary cells, depletion of which induced ISG expression and a broad antiviral state. However, cell lines lacking interferon responses revealed that ZNF598 E3 ligase activity and ubiquitination of RPS20, but not RPS10, were specifically required for poxvirus replication and synthesis of poxvirus proteins whose encoding mRNAs contain unusual 5' poly(A) leaders. Our findings reveal distinct functions for ZNF598 and its downstream RPS targets, one that negatively regulates ISG expression and infection by a range of viruses while the other is positively exploited by poxviruses.
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Affiliation(s)
- Stephen DiGiuseppe
- Department of Microbiology-Immunology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Madeline G Rollins
- Department of Microbiology-Immunology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Elizabeth T Bartom
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Derek Walsh
- Department of Microbiology-Immunology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA.
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59
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Gao Y, Lee H, Kwon OK, Tan M, Kim KT, Lee S. Global Proteomic Analysis of Lysine Succinylation in Zebrafish (Danio rerio). J Proteome Res 2019; 18:3762-3769. [DOI: 10.1021/acs.jproteome.9b00462] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Yan Gao
- BK21 Plus KNU Multi-Omics Based Creative Drug Research Team, College of Pharmacy and Research Institute of Pharmaceutical Sciences, Kyungpook National University, Daegu 41566, Republic of Korea
| | | | - Oh Kwang Kwon
- BK21 Plus KNU Multi-Omics Based Creative Drug Research Team, College of Pharmacy and Research Institute of Pharmaceutical Sciences, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Minjia Tan
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | | | - Sangkyu Lee
- BK21 Plus KNU Multi-Omics Based Creative Drug Research Team, College of Pharmacy and Research Institute of Pharmaceutical Sciences, Kyungpook National University, Daegu 41566, Republic of Korea
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60
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Sirri V, Grob A, Berthelet J, Jourdan N, Roussel P. Sirtuin 7 promotes 45S pre-rRNA cleavage at site 2 and determines the processing pathway. J Cell Sci 2019; 132:jcs228601. [PMID: 31331964 PMCID: PMC6771141 DOI: 10.1242/jcs.228601] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Accepted: 07/10/2019] [Indexed: 01/06/2023] Open
Abstract
In humans, ribosome biogenesis mainly occurs in nucleoli following two alternative pre-rRNA processing pathways differing in the order in which cleavages take place but not by the sites of cleavage. To uncover the role of the nucleolar NAD+-dependent deacetylase sirtuin 7 in the synthesis of ribosomal subunits, pre-rRNA processing was analyzed after sirtinol-mediated inhibition of sirtuin 7 activity or depletion of sirtuin 7 protein. We thus reveal that sirtuin 7 activity is a critical regulator of processing of 45S, 32S and 30S pre-rRNAs. Sirtuin 7 protein is primarily essential to 45S pre-rRNA cleavage at site 2, which is the first step of processing pathway 2. Furthermore, we demonstrate that sirtuin 7 physically interacts with Nop56 and the GAR domain of fibrillarin, and propose that this could interfere with fibrillarin-dependent cleavage. Sirtuin 7 depletion results in the accumulation of 5' extended forms of 32S pre-rRNA, and also influences the localization of fibrillarin. Thus, we establish a close relationship between sirtuin 7 and fibrillarin, which might determine the processing pathway used for ribosome biogenesis.
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Affiliation(s)
- Valentina Sirri
- Université de Paris, Unité de Biologie Fonctionnelle et Adaptative (BFA), UMR 8251, CNRS, 4 rue Marie-Andrée Lagroua Weill-Hallé, F-75013 Paris, France
| | - Alice Grob
- Department of Life Sciences, Imperial College London, London SW7 2AZ, England, UK
| | - Jérémy Berthelet
- Université de Paris, Unité de Biologie Fonctionnelle et Adaptative (BFA), UMR 8251, CNRS, 4 rue Marie-Andrée Lagroua Weill-Hallé, F-75013 Paris, France
| | - Nathalie Jourdan
- Sorbonne Université, Institut de Biologie Paris-Seine (IBPS), UMR 8256, CNRS, 9 quai St Bernard, F-75005 Paris, France
| | - Pascal Roussel
- Université de Paris, Unité de Biologie Fonctionnelle et Adaptative (BFA), UMR 8251, CNRS, 4 rue Marie-Andrée Lagroua Weill-Hallé, F-75013 Paris, France
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61
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Genuth NR, Barna M. Heterogeneity and specialized functions of translation machinery: from genes to organisms. Nat Rev Genet 2019; 19:431-452. [PMID: 29725087 DOI: 10.1038/s41576-018-0008-z] [Citation(s) in RCA: 141] [Impact Index Per Article: 28.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Regulation of mRNA translation offers the opportunity to diversify the expression and abundance of proteins made from individual gene products in cells, tissues and organisms. Emerging evidence has highlighted variation in the composition and activity of several large, highly conserved translation complexes as a means to differentially control gene expression. Heterogeneity and specialized functions of individual components of the ribosome and of the translation initiation factor complexes eIF3 and eIF4F, which are required for recruitment of the ribosome to the mRNA 5' untranslated region, have been identified. In this Review, we summarize the evidence for selective mRNA translation by components of these macromolecular complexes as a means to dynamically control the translation of the proteome in time and space. We further discuss the implications of this form of gene expression regulation for a growing number of human genetic disorders associated with mutations in the translation machinery.
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Affiliation(s)
- Naomi R Genuth
- Departments of Genetics and Developmental Biology, Stanford University, Stanford, CA, USA.,Department of Biology, Stanford University, Stanford, CA, USA
| | - Maria Barna
- Departments of Genetics and Developmental Biology, Stanford University, Stanford, CA, USA.
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62
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Bohnsack KE, Bohnsack MT. Uncovering the assembly pathway of human ribosomes and its emerging links to disease. EMBO J 2019; 38:e100278. [PMID: 31268599 PMCID: PMC6600647 DOI: 10.15252/embj.2018100278] [Citation(s) in RCA: 133] [Impact Index Per Article: 26.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Revised: 02/18/2019] [Accepted: 04/26/2019] [Indexed: 12/12/2022] Open
Abstract
The essential cellular process of ribosome biogenesis is at the nexus of various signalling pathways that coordinate protein synthesis with cellular growth and proliferation. The fact that numerous diseases are caused by defects in ribosome assembly underscores the importance of obtaining a detailed understanding of this pathway. Studies in yeast have provided a wealth of information about the fundamental principles of ribosome assembly, and although many features are conserved throughout eukaryotes, the larger size of human (pre-)ribosomes, as well as the evolution of additional regulatory networks that can modulate ribosome assembly and function, have resulted in a more complex assembly pathway in humans. Notably, many ribosome biogenesis factors conserved from yeast appear to have subtly different or additional functions in humans. In addition, recent genome-wide, RNAi-based screens have identified a plethora of novel factors required for human ribosome biogenesis. In this review, we discuss key aspects of human ribosome production, highlighting differences to yeast, links to disease, as well as emerging concepts such as extra-ribosomal functions of ribosomal proteins and ribosome heterogeneity.
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Affiliation(s)
- Katherine E Bohnsack
- Department of Molecular BiologyUniversity Medical Center GöttingenGöttingenGermany
| | - Markus T Bohnsack
- Department of Molecular BiologyUniversity Medical Center GöttingenGöttingenGermany
- Göttingen Center for Molecular BiosciencesGeorg‐August UniversityGöttingenGermany
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63
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Teixeira FK, Lehmann R. Translational Control during Developmental Transitions. Cold Spring Harb Perspect Biol 2019; 11:cshperspect.a032987. [PMID: 30082467 DOI: 10.1101/cshperspect.a032987] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The many steps of gene expression, from the transcription of a gene to the production of its protein product, are well understood. Yet, transcriptional regulation has been the focal point for the study of gene expression during development. However, quantitative studies reveal that messenger RNA (mRNA) levels are not necessarily good predictors of the respective proteins' levels in a cell. This discrepancy is, at least in part, the result of developmentally regulated, translational mechanisms that control the spatiotemporal regulation of gene expression. In this review, we focus on translational regulatory mechanisms mediating global transitions in gene expression: the shift from the maternal to the embryonic developmental program in the early embryo and the switch from the self-renewal of stem cells to differentiation in the adult.
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Affiliation(s)
| | - Ruth Lehmann
- Howard Hughes Medical Institute (HHMI) and Kimmel Center for Biology and Medicine of the Skirball Institute, Department of Cell Biology, New York University School of Medicine, New York, New York 10016
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64
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Prakash V, Carson BB, Feenstra JM, Dass RA, Sekyrova P, Hoshino A, Petersen J, Guo Y, Parks MM, Kurylo CM, Batchelder JE, Haller K, Hashimoto A, Rundqivst H, Condeelis JS, Allis CD, Drygin D, Nieto MA, Andäng M, Percipalle P, Bergh J, Adameyko I, Farrants AKÖ, Hartman J, Lyden D, Pietras K, Blanchard SC, Vincent CT. Ribosome biogenesis during cell cycle arrest fuels EMT in development and disease. Nat Commun 2019; 10:2110. [PMID: 31068593 PMCID: PMC6506521 DOI: 10.1038/s41467-019-10100-8] [Citation(s) in RCA: 129] [Impact Index Per Article: 25.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Accepted: 04/16/2019] [Indexed: 12/15/2022] Open
Abstract
Ribosome biogenesis is a canonical hallmark of cell growth and proliferation. Here we show that execution of Epithelial-to-Mesenchymal Transition (EMT), a migratory cellular program associated with development and tumor metastasis, is fueled by upregulation of ribosome biogenesis during G1/S arrest. This unexpected EMT feature is independent of species and initiating signal, and is accompanied by release of the repressive nucleolar chromatin remodeling complex (NoRC) from rDNA, together with recruitment of the EMT-driving transcription factor Snai1 (Snail1), RNA Polymerase I (Pol I) and the Upstream Binding Factor (UBF). EMT-associated ribosome biogenesis is also coincident with increased nucleolar recruitment of Rictor, an essential component of the EMT-promoting mammalian target of rapamycin complex 2 (mTORC2). Inhibition of rRNA synthesis in vivo differentiates primary tumors to a benign, Estrogen Receptor-alpha (ERα) positive, Rictor-negative phenotype and reduces metastasis. These findings implicate the EMT-associated ribosome biogenesis program with cellular plasticity, de-differentiation, cancer progression and metastatic disease.
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Affiliation(s)
- Varsha Prakash
- Department of Physiology and Pharmacology, Karolinska Institutet, 171 77, Stockholm, Sweden.,Department of Immunology, Genetics and Pathology, Uppsala University, 751 85, Uppsala, Sweden
| | - Brittany B Carson
- Department of Physiology and Pharmacology, Karolinska Institutet, 171 77, Stockholm, Sweden
| | - Jennifer M Feenstra
- Department of Physiology and Pharmacology, Karolinska Institutet, 171 77, Stockholm, Sweden.,Department of Immunology, Genetics and Pathology, Uppsala University, 751 85, Uppsala, Sweden
| | - Randall A Dass
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, 10065, USA
| | - Petra Sekyrova
- Department of Immunology, Genetics and Pathology, Uppsala University, 751 85, Uppsala, Sweden
| | - Ayuko Hoshino
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY, 10065, USA.,Department of Pediatrics and Cell and Developmental Biology, Weill Cornell Medicine College, New York, NY, 10065, USA
| | - Julian Petersen
- Department of Physiology and Pharmacology, Karolinska Institutet, 171 77, Stockholm, Sweden.,Department for Brain Research, Medical University of Vienna, 1090, Vienna, Austria
| | - Yuan Guo
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, S-10691, Stockholm, Sweden
| | - Matthew M Parks
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, 10065, USA.,Meyer Cancer Center, Weill Cornell Medicine, New York, NY, 10065, USA
| | - Chad M Kurylo
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, 10065, USA.,Meyer Cancer Center, Weill Cornell Medicine, New York, NY, 10065, USA
| | - Jake E Batchelder
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, 10065, USA.,Meyer Cancer Center, Weill Cornell Medicine, New York, NY, 10065, USA
| | - Kristian Haller
- Department of Laboratory Medicine, Center for Molecular Pathology, Lund University, Lund, SE-223 81, Sweden
| | - Ayako Hashimoto
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY, 10065, USA.,Department of Pediatrics and Cell and Developmental Biology, Weill Cornell Medicine College, New York, NY, 10065, USA
| | - Helene Rundqivst
- Department of Cell and Molecular Biology, Karolinska Institute, Stockholm, SE-171 77, Sweden
| | - John S Condeelis
- Gruss Lipper Biophotonics Center, Albert Einstein College of Medicine, Bronx, 10461, NY, USA.,Department of Pathology, Montefiore Medical Center, Bronx, 10461, NY, USA
| | - C David Allis
- Laboratory of Chromatin Biology and Epigenetics, The Rockefeller University, New York, NY, 10065, USA
| | - Denis Drygin
- Pimera, Inc, 3210 Merryfield Row, San Diego, CA, 92121, USA
| | - M Angela Nieto
- Instituto de Neurociencias, CSIC-UMH, Alicante, 03550, Spain
| | - Michael Andäng
- Department of Immunology, Genetics and Pathology, Uppsala University, 751 85, Uppsala, Sweden
| | - Piergiorgio Percipalle
- Science Division, Biology Program, New York University Abu Dhabi, Abu Dhabi, 129188, UAE
| | - Jonas Bergh
- Department of Oncology and Pathology, Karolinska Institutet and University Hospital, S-171 76, Solna, Sweden
| | - Igor Adameyko
- Department of Physiology and Pharmacology, Karolinska Institutet, 171 77, Stockholm, Sweden.,Department for Brain Research, Medical University of Vienna, 1090, Vienna, Austria
| | - Ann-Kristin Östlund Farrants
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, S-10691, Stockholm, Sweden
| | - Johan Hartman
- Department of Oncology and Pathology, Karolinska Institutet and University Hospital, S-171 76, Solna, Sweden
| | - David Lyden
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY, 10065, USA.,Department of Pediatrics and Cell and Developmental Biology, Weill Cornell Medicine College, New York, NY, 10065, USA
| | - Kristian Pietras
- Department of Laboratory Medicine, Center for Molecular Pathology, Lund University, Lund, SE-223 81, Sweden
| | - Scott C Blanchard
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, 10065, USA. .,Meyer Cancer Center, Weill Cornell Medicine, New York, NY, 10065, USA. .,Tri-Institutional Training Program in Chemical Biology, Weill Cornell Medicine, New York, NY, 10065, USA.
| | - C Theresa Vincent
- Department of Physiology and Pharmacology, Karolinska Institutet, 171 77, Stockholm, Sweden. .,Department of Immunology, Genetics and Pathology, Uppsala University, 751 85, Uppsala, Sweden. .,Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, 10065, USA. .,Meyer Cancer Center, Weill Cornell Medicine, New York, NY, 10065, USA.
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65
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Ferretti MB, Karbstein K. Does functional specialization of ribosomes really exist? RNA (NEW YORK, N.Y.) 2019; 25:521-538. [PMID: 30733326 PMCID: PMC6467006 DOI: 10.1261/rna.069823.118] [Citation(s) in RCA: 74] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
It has recently become clear that ribosomes are much more heterogeneous than previously thought, with diversity arising from rRNA sequence and modifications, ribosomal protein (RP) content and posttranslational modifications (PTMs), as well as bound nonribosomal proteins. In some cases, the existence of these diverse ribosome populations has been verified by biochemical or structural methods. Furthermore, knockout or knockdown of RPs can diversify ribosome populations, while also affecting the translation of some mRNAs (but not others) with biological consequences. However, the effects on translation arising from depletion of diverse proteins can be highly similar, suggesting that there may be a more general defect in ribosome function or stability, perhaps arising from reduced ribosome numbers. Consistently, overall reduced ribosome numbers can differentially affect subclasses of mRNAs, necessitating controls for specificity. Moreover, in order to study the functional consequences of ribosome diversity, perturbations including affinity tags and knockouts are introduced, which can also affect the outcome of the experiment. Here we review the available literature to carefully evaluate whether the published data support functional diversification, defined as diverse ribosome populations differentially affecting translation of distinct mRNA (classes). Based on these observations and the commonly observed cellular responses to perturbations in the system, we suggest a set of important controls to validate functional diversity, which should include gain-of-function assays and the demonstration of inducibility under physiological conditions.
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Affiliation(s)
- Max B Ferretti
- Department of Integrative Structural and Molecular Biology, The Scripps Research Institute, Jupiter, Florida 33458, USA
- The Skaggs Graduate School of Chemical and Biological Sciences, The Scripps Research Institute, Jupiter, Florida 33458, USA
| | - Katrin Karbstein
- Department of Integrative Structural and Molecular Biology, The Scripps Research Institute, Jupiter, Florida 33458, USA
- The Skaggs Graduate School of Chemical and Biological Sciences, The Scripps Research Institute, Jupiter, Florida 33458, USA
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66
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Koren SA, Hamm MJ, Meier SE, Weiss BE, Nation GK, Chishti EA, Arango JP, Chen J, Zhu H, Blalock EM, Abisambra JF. Tau drives translational selectivity by interacting with ribosomal proteins. Acta Neuropathol 2019; 137:571-583. [PMID: 30759285 PMCID: PMC6426815 DOI: 10.1007/s00401-019-01970-9] [Citation(s) in RCA: 67] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Revised: 01/31/2019] [Accepted: 02/01/2019] [Indexed: 12/23/2022]
Abstract
There is a fundamental gap in understanding the consequences of tau-ribosome interactions. Tau oligomers and filaments hinder protein synthesis in vitro, and they associate strongly with ribosomes in vivo. Here, we investigated the consequences of tau interactions with ribosomes in transgenic mice, in cells, and in human brain tissues to identify tau as a direct modulator of ribosomal selectivity. First, we performed microarrays and nascent proteomics to measure changes in protein synthesis. Using regulatable rTg4510 tau transgenic mice, we determined that tau expression differentially shifts both the transcriptome and the nascent proteome, and that the synthesis of ribosomal proteins is reversibly dependent on tau levels. We further extended these results to human brains and found that tau pathologically interacts with ribosomal protein S6 (rpS6 or S6), a crucial regulator of translation. Consequently, protein synthesis under translational control of rpS6 was reduced under tauopathic conditions in Alzheimer's disease brains. Our data establish tau as a driver of RNA translation selectivity. Moreover, since regulation of protein synthesis is critical for learning and memory, aberrant tau-ribosome interactions in disease could explain the linkage between tauopathies and cognitive impairment.
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Affiliation(s)
- Shon A Koren
- Department of Neuroscience and Center for Translational Research in Neurodegenerative Disease, University of Florida, 1275 Center Drive, BOX 100159, Gainesville, FL, 32610, USA
| | - Matthew J Hamm
- Department of Neuroscience and Center for Translational Research in Neurodegenerative Disease, University of Florida, 1275 Center Drive, BOX 100159, Gainesville, FL, 32610, USA
| | - Shelby E Meier
- Sanders Brown Center on Aging, Department of Physiology, Spinal Cord and Brain Injury Research Center, and Epilepsy Center, University of Kentucky, Lexington, KY, 40513, USA
| | - Blaine E Weiss
- Sanders Brown Center on Aging, Department of Physiology, Spinal Cord and Brain Injury Research Center, and Epilepsy Center, University of Kentucky, Lexington, KY, 40513, USA
| | - Grant K Nation
- Sanders Brown Center on Aging, Department of Physiology, Spinal Cord and Brain Injury Research Center, and Epilepsy Center, University of Kentucky, Lexington, KY, 40513, USA
| | - Emad A Chishti
- Sanders Brown Center on Aging, Department of Physiology, Spinal Cord and Brain Injury Research Center, and Epilepsy Center, University of Kentucky, Lexington, KY, 40513, USA
| | - Juan Pablo Arango
- Sanders Brown Center on Aging, Department of Physiology, Spinal Cord and Brain Injury Research Center, and Epilepsy Center, University of Kentucky, Lexington, KY, 40513, USA
| | - Jing Chen
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, KY, 40513, USA
| | - Haining Zhu
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, KY, 40513, USA
| | - Eric M Blalock
- Department of Pharmacology and Nutritional Sciences, University of Kentucky, Lexington, KY, 40513, USA
| | - Jose F Abisambra
- Department of Neuroscience and Center for Translational Research in Neurodegenerative Disease, University of Florida, 1275 Center Drive, BOX 100159, Gainesville, FL, 32610, USA.
- Sanders Brown Center on Aging, Department of Physiology, Spinal Cord and Brain Injury Research Center, and Epilepsy Center, University of Kentucky, Lexington, KY, 40513, USA.
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67
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Emerging Role of Eukaryote Ribosomes in Translational Control. Int J Mol Sci 2019; 20:ijms20051226. [PMID: 30862090 PMCID: PMC6429320 DOI: 10.3390/ijms20051226] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Revised: 03/06/2019] [Accepted: 03/08/2019] [Indexed: 12/15/2022] Open
Abstract
Translation is one of the final steps that regulate gene expression. The ribosome is the effector of translation through to its role in mRNA decoding and protein synthesis. Many mechanisms have been extensively described accounting for translational regulation. However it emerged only recently that ribosomes themselves could contribute to this regulation. Indeed, though it is well-known that the translational efficiency of the cell is linked to ribosome abundance, studies recently demonstrated that the composition of the ribosome could alter translation of specific mRNAs. Evidences suggest that according to the status, environment, development, or pathological conditions, cells produce different populations of ribosomes which differ in their ribosomal protein and/or RNA composition. Those observations gave rise to the concept of "specialized ribosomes", which proposes that a unique ribosome composition determines the translational activity of this ribosome. The current review will present how technological advances have participated in the emergence of this concept, and to which extent the literature sustains this concept today.
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68
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Song W, Joo M, Yeom JH, Shin E, Lee M, Choi HK, Hwang J, Kim YI, Seo R, Lee JE, Moore CJ, Kim YH, Eyun SI, Hahn Y, Bae J, Lee K. Divergent rRNAs as regulators of gene expression at the ribosome level. Nat Microbiol 2019; 4:515-526. [DOI: 10.1038/s41564-018-0341-1] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Accepted: 12/05/2018] [Indexed: 01/21/2023]
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69
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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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70
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High-Resolution Ribosome Profiling Defines Discrete Ribosome Elongation States and Translational Regulation during Cellular Stress. Mol Cell 2019; 73:959-970.e5. [PMID: 30686592 DOI: 10.1016/j.molcel.2018.12.009] [Citation(s) in RCA: 153] [Impact Index Per Article: 30.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Revised: 10/25/2018] [Accepted: 12/12/2018] [Indexed: 12/19/2022]
Abstract
Ribosomes undergo substantial conformational changes during translation elongation to accommodate incoming aminoacyl-tRNAs and translocate along the mRNA template. We used multiple elongation inhibitors and chemical probing to define ribosome conformational states corresponding to differently sized ribosome-protected mRNA fragments (RPFs) generated by ribosome profiling. We show, using various genetic and environmental perturbations, that short 20-22 or classical 27-29 nucleotide RPFs correspond to ribosomes with open or occupied ribosomal A sites, respectively. These distinct states of translation elongation are readily discerned by ribosome profiling in all eukaryotes we tested, including fungi, worms, and mammals. This high-resolution ribosome profiling approach reveals mechanisms of translation-elongation arrest during distinct stress conditions. Hyperosmotic stress inhibits translocation through Rck2-dependent eEF2 phosphorylation, whereas oxidative stress traps ribosomes in a pre-translocation state, independent of Rck2-driven eEF2 phosphorylation. These results provide insights and approaches for defining the molecular events that impact translation elongation throughout biology.
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71
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Morisaki T, Stasevich TJ. Quantifying Single mRNA Translation Kinetics in Living Cells. Cold Spring Harb Perspect Biol 2018; 10:a032078. [PMID: 30385605 PMCID: PMC6211384 DOI: 10.1101/cshperspect.a032078] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
One of the last hurdles to quantifying the full central dogma of molecular biology in living cells with single-molecule resolution has been the imaging of single messenger RNA (mRNA) translation. Here we describe how recent advances in protein tagging and imaging technologies are being used to precisely visualize and quantify the synthesis of nascent polypeptide chains from single mRNA in living cells. We focus on recent applications of repeat-epitope tags and describe how they enable quantification of single mRNA ribosomal densities, translation initiation and elongation rates, and translation site mobility and higher-order structure. Together with complementary live-cell assays to monitor translation using fast-maturing fluorophores and mRNA-binding protein knockoff, single-molecule studies are beginning to uncover striking and unexpected heterogeneity in gene expression at the level of translation.
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Affiliation(s)
- Tatsuya Morisaki
- Institute of Genome Architecture and Function and Department of Biochemistry & Molecular Biology, Colorado State University, Fort Collins, Colorado 80523
| | - Timothy J Stasevich
- Institute of Genome Architecture and Function and Department of Biochemistry & Molecular Biology, Colorado State University, Fort Collins, Colorado 80523
- Cell Biology Unit, Institute of Innovative Research, Tokyo Institute of Technology, Midori-ku, Yokohama, Kanagawa, 226-8503, Japan
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72
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Imami K, Milek M, Bogdanow B, Yasuda T, Kastelic N, Zauber H, Ishihama Y, Landthaler M, Selbach M. Phosphorylation of the Ribosomal Protein RPL12/uL11 Affects Translation during Mitosis. Mol Cell 2018; 72:84-98.e9. [PMID: 30220558 DOI: 10.1016/j.molcel.2018.08.019] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2017] [Revised: 06/09/2018] [Accepted: 08/10/2018] [Indexed: 12/22/2022]
Abstract
Emerging evidence indicates that heterogeneity in ribosome composition can give rise to specialized functions. Until now, research mainly focused on differences in core ribosomal proteins and associated factors. The effect of posttranslational modifications has not been studied systematically. Analyzing ribosome heterogeneity is challenging because individual proteins can be part of different subcomplexes (40S, 60S, 80S, and polysomes). Here we develop polysome proteome profiling to obtain unbiased proteomic maps across ribosomal subcomplexes. Our method combines extensive fractionation by sucrose gradient centrifugation with quantitative mass spectrometry. The high resolution of the profiles allows us to assign proteins to specific subcomplexes. Phosphoproteomics on the fractions reveals that phosphorylation of serine 38 in RPL12/uL11, a known mitotic CDK1 substrate, is strongly depleted in polysomes. Follow-up experiments confirm that RPL12/uL11 phosphorylation regulates the translation of specific subsets of mRNAs during mitosis. Together, our results show that posttranslational modification of ribosomal proteins can regulate translation.
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Affiliation(s)
- Koshi Imami
- Max Delbrück Center for Molecular Medicine, Robert-Rössle-Str. 10, 13092 Berlin, Germany; Department of Molecular and Cellular BioAnalysis, Kyoto University, 606-8501 Kyoto, Japan.
| | - Miha Milek
- Max Delbrück Center for Molecular Medicine, Robert-Rössle-Str. 10, 13092 Berlin, Germany
| | - Boris Bogdanow
- Max Delbrück Center for Molecular Medicine, Robert-Rössle-Str. 10, 13092 Berlin, Germany
| | - Tomoharu Yasuda
- Max Delbrück Center for Molecular Medicine, Robert-Rössle-Str. 10, 13092 Berlin, Germany
| | - Nicolai Kastelic
- Max Delbrück Center for Molecular Medicine, Robert-Rössle-Str. 10, 13092 Berlin, Germany
| | - Henrik Zauber
- Max Delbrück Center for Molecular Medicine, Robert-Rössle-Str. 10, 13092 Berlin, Germany
| | - Yasushi Ishihama
- Department of Molecular and Cellular BioAnalysis, Kyoto University, 606-8501 Kyoto, Japan
| | - Markus Landthaler
- Max Delbrück Center for Molecular Medicine, Robert-Rössle-Str. 10, 13092 Berlin, Germany; IRI Life Sciences, Institute für Biologie, Humboldt Universität zu Berlin, Philippstraße 13, 10115 Berlin, Germany
| | - Matthias Selbach
- Max Delbrück Center for Molecular Medicine, Robert-Rössle-Str. 10, 13092 Berlin, Germany; Charité-Universitätsmedizin Berlin, 10117 Berlin, Germany.
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73
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Gerst JE. Pimp My Ribosome: Ribosomal Protein Paralogs Specify Translational Control. Trends Genet 2018; 34:832-845. [PMID: 30195580 DOI: 10.1016/j.tig.2018.08.004] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Revised: 08/06/2018] [Accepted: 08/10/2018] [Indexed: 12/12/2022]
Abstract
The ability of cells to grow and divide, differentiate and function, and even senesce is dependent on the fine-tuning of both gene and protein expression. Protein concentration in the cell is regulated not only at the transcriptional and post-translational levels, but also at the level of translation. Ribosomes, the molecular machines behind translation, were once considered to be an invariant driving force behind protein expression. However, studies over the past decade paint a rather different picture; namely, that ribosomes constitute an additional layer of regulatory control that might define which subsets of mRNAs are translated, to what extent, and to what purpose. Recent works summarized herein directly implicate ribosome heterogeneity and, in particular, ribosomal protein (RP) paralog specificity in regulating mRNA translation and control of the cellular translatome.
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Affiliation(s)
- Jeffrey E Gerst
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel.
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74
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A single N 1-methyladenosine on the large ribosomal subunit rRNA impacts locally its structure and the translation of key metabolic enzymes. Sci Rep 2018; 8:11904. [PMID: 30093689 PMCID: PMC6085284 DOI: 10.1038/s41598-018-30383-z] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Accepted: 06/29/2018] [Indexed: 12/18/2022] Open
Abstract
The entire chemical modification repertoire of yeast ribosomal RNAs and the enzymes responsible for it have recently been identified. Nonetheless, in most cases the precise roles played by these chemical modifications in ribosome structure, function and regulation remain totally unclear. Previously, we demonstrated that yeast Rrp8 methylates m1A645 of 25S rRNA in yeast. Here, using mung bean nuclease protection assays in combination with quantitative RP-HPLC and primer extension, we report that 25S/28S rRNA of S. pombe, C. albicans and humans also contain a single m1A methylation in the helix 25.1. We characterized nucleomethylin (NML) as a human homolog of yeast Rrp8 and demonstrate that NML catalyzes the m1A1322 methylation of 28S rRNA in humans. Our in vivo structural probing of 25S rRNA, using both DMS and SHAPE, revealed that the loss of the Rrp8-catalyzed m1A modification alters the conformation of domain I of yeast 25S rRNA causing translation initiation defects detectable as halfmers formation, likely because of incompetent loading of 60S on the 43S-preinitiation complex. Quantitative proteomic analysis of the yeast Δrrp8 mutant strain using 2D-DIGE, revealed that loss of m1A645 impacts production of specific set of proteins involved in carbohydrate metabolism, translation and ribosome synthesis. In mouse, NML has been characterized as a metabolic disease-associated gene linked to obesity. Our findings in yeast also point to a role of Rrp8 in primary metabolism. In conclusion, the m1A modification is crucial for maintaining an optimal 60S conformation, which in turn is important for regulating the production of key metabolic enzymes.
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75
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Genuth NR, Barna M. The Discovery of Ribosome Heterogeneity and Its Implications for Gene Regulation and Organismal Life. Mol Cell 2018; 71:364-374. [PMID: 30075139 DOI: 10.1016/j.molcel.2018.07.018get] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Revised: 07/08/2018] [Accepted: 07/16/2018] [Indexed: 05/27/2023]
Abstract
The ribosome has recently transitioned from being viewed as a passive, indiscriminate machine to a more dynamic macromolecular complex with specialized roles in the cell. Here, we discuss the historical milestones from the discovery of the ribosome itself to how this ancient machinery has gained newfound appreciation as a more regulatory participant in the central dogma of gene expression. The first emerging examples of direct changes in ribosome composition at the RNA and protein level, coupled with an increased awareness of the role individual ribosomal components play in the translation of specific mRNAs, is opening a new field of study centered on ribosome-mediated control of gene regulation. In this Perspective, we discuss our current understanding of the known functions for ribosome heterogeneity, including specialized translation of individual transcripts, and its implications for the regulation and expression of key gene regulatory networks. In addition, we suggest what the crucial next steps are to ascertain the extent of ribosome heterogeneity and specialization and its importance for regulation of the proteome within subcellular space, across different cell types, and during multi-cellular organismal development.
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Affiliation(s)
- Naomi R Genuth
- Department of Developmental Biology, Stanford University, Stanford, CA, 94305, USA; Department of Genetics, Stanford University, Stanford, CA, 94305, USA; Department of Biology, Stanford University, Stanford, CA, 94305, USA
| | - Maria Barna
- Department of Developmental Biology, Stanford University, Stanford, CA, 94305, USA; Department of Genetics, Stanford University, Stanford, CA, 94305, USA.
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76
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Genuth NR, Barna M. The Discovery of Ribosome Heterogeneity and Its Implications for Gene Regulation and Organismal Life. Mol Cell 2018; 71:364-374. [PMID: 30075139 PMCID: PMC6092941 DOI: 10.1016/j.molcel.2018.07.018] [Citation(s) in RCA: 259] [Impact Index Per Article: 43.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Revised: 07/08/2018] [Accepted: 07/16/2018] [Indexed: 12/24/2022]
Abstract
The ribosome has recently transitioned from being viewed as a passive, indiscriminate machine to a more dynamic macromolecular complex with specialized roles in the cell. Here, we discuss the historical milestones from the discovery of the ribosome itself to how this ancient machinery has gained newfound appreciation as a more regulatory participant in the central dogma of gene expression. The first emerging examples of direct changes in ribosome composition at the RNA and protein level, coupled with an increased awareness of the role individual ribosomal components play in the translation of specific mRNAs, is opening a new field of study centered on ribosome-mediated control of gene regulation. In this Perspective, we discuss our current understanding of the known functions for ribosome heterogeneity, including specialized translation of individual transcripts, and its implications for the regulation and expression of key gene regulatory networks. In addition, we suggest what the crucial next steps are to ascertain the extent of ribosome heterogeneity and specialization and its importance for regulation of the proteome within subcellular space, across different cell types, and during multi-cellular organismal development.
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Affiliation(s)
- Naomi R Genuth
- Department of Developmental Biology, Stanford University, Stanford, CA, 94305, USA; Department of Genetics, Stanford University, Stanford, CA, 94305, USA; Department of Biology, Stanford University, Stanford, CA, 94305, USA
| | - Maria Barna
- Department of Developmental Biology, Stanford University, Stanford, CA, 94305, USA; Department of Genetics, Stanford University, Stanford, CA, 94305, USA.
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77
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Identification and manipulation of a novel locus to improve cell tolerance to short-chain alcohols in Escherichia coli. ACTA ACUST UNITED AC 2018; 45:589-598. [DOI: 10.1007/s10295-017-1996-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Accepted: 12/09/2017] [Indexed: 12/30/2022]
Abstract
Abstract
Escherichia coli KO11 is a popular ethanologenic strain, but is more sensitive to ethanol than other producers. Here, an ethanol-tolerant mutant EM was isolated from ultraviolet mutagenesis library of KO11. Comparative genomic analysis added by piecewise knockout strategy and complementation assay revealed EKO11_3023 (espA) within the 36.6-kb deletion from KO11 was the only locus responsible for ethanol sensitivity. Interestingly, when espA was deleted in strain W (the parent strain of KO11), ethanol tolerance was dramatically elevated to the level of espA-free hosts [e.g., MG1655 and BL21(DE3)]. And overexpression of espA in strains MG1655 and BL21(DE3) led to significantly enhanced ethanol sensitivity. In addition to ethanol, deletion of espA also improved cell tolerance to other short-chain (C2–C4) alcohols, including methanol, isopropanol, n-butanol, isobutanol and 2-butanol. Therefore, espA was responsible for short-chain alcohol sensitivity of W-strains compared to other cells, which provides a potential engineering target for alcohols production.
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78
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Digital Gene Expression Profiling Analysis of Aged Mice under Moxibustion Treatment. EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE 2018; 2018:4767328. [PMID: 29853953 PMCID: PMC5954890 DOI: 10.1155/2018/4767328] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Accepted: 04/10/2018] [Indexed: 11/17/2022]
Abstract
Aging is closely connected with death, progressive physiological decline, and increased risk of diseases, such as cancer, arteriosclerosis, heart disease, hypertension, and neurodegenerative diseases. It is reported that moxibustion can treat more than 300 kinds of diseases including aging related problems and can improve immune function and physiological functions. The digital gene expression profiling of aged mice with or without moxibustion treatment was investigated and the mechanisms of moxibustion in aged mice were speculated by gene ontology and pathway analysis in the study. Almost 145 million raw reads were obtained by digital gene expression analysis and about 140 million (96.55%) were clean reads. Five differentially expressed genes with an adjusted P value < 0.05 and |log2(fold change)| > 1 were identified between the control and moxibustion groups. They were Gm6563, Gm8116, Rps26-ps1, Nat8f4, and Igkv3-12. Gene ontology analysis was carried out by the GOseq R package and functional annotations of the differentially expressed genes related to translation, mRNA export from nucleus, mRNA transport, nuclear body, acetyltransferase activity, and so on. Kyoto Encyclopedia of Genes and Genomes database was used for pathway analysis and ribosome was the most significantly enriched pathway term.
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79
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Harvey RF, Smith TS, Mulroney T, Queiroz RML, Pizzinga M, Dezi V, Villenueva E, Ramakrishna M, Lilley KS, Willis AE. Trans-acting translational regulatory RNA binding proteins. WILEY INTERDISCIPLINARY REVIEWS. RNA 2018; 9:e1465. [PMID: 29341429 PMCID: PMC5947564 DOI: 10.1002/wrna.1465] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Revised: 10/31/2017] [Accepted: 12/04/2017] [Indexed: 12/13/2022]
Abstract
The canonical molecular machinery required for global mRNA translation and its control has been well defined, with distinct sets of proteins involved in the processes of translation initiation, elongation and termination. Additionally, noncanonical, trans-acting regulatory RNA-binding proteins (RBPs) are necessary to provide mRNA-specific translation, and these interact with 5' and 3' untranslated regions and coding regions of mRNA to regulate ribosome recruitment and transit. Recently it has also been demonstrated that trans-acting ribosomal proteins direct the translation of specific mRNAs. Importantly, it has been shown that subsets of RBPs often work in concert, forming distinct regulatory complexes upon different cellular perturbation, creating an RBP combinatorial code, which through the translation of specific subsets of mRNAs, dictate cell fate. With the development of new methodologies, a plethora of novel RNA binding proteins have recently been identified, although the function of many of these proteins within mRNA translation is unknown. In this review we will discuss these methodologies and their shortcomings when applied to the study of translation, which need to be addressed to enable a better understanding of trans-acting translational regulatory proteins. Moreover, we discuss the protein domains that are responsible for RNA binding as well as the RNA motifs to which they bind, and the role of trans-acting ribosomal proteins in directing the translation of specific mRNAs. This article is categorized under: RNA Interactions with Proteins and Other Molecules > RNA-Protein Complexes Translation > Translation Regulation Translation > Translation Mechanisms.
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Affiliation(s)
| | - Tom S. Smith
- Cambridge Centre for Proteomics, Department of BiochemistryUniversity of CambridgeCambridgeUK
| | | | - Rayner M. L. Queiroz
- Cambridge Centre for Proteomics, Department of BiochemistryUniversity of CambridgeCambridgeUK
| | | | | | - Eneko Villenueva
- Cambridge Centre for Proteomics, Department of BiochemistryUniversity of CambridgeCambridgeUK
| | | | - Kathryn S. Lilley
- Cambridge Centre for Proteomics, Department of BiochemistryUniversity of CambridgeCambridgeUK
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80
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Dolezal JM, Dash AP, Prochownik EV. Diagnostic and prognostic implications of ribosomal protein transcript expression patterns in human cancers. BMC Cancer 2018. [PMID: 29530001 PMCID: PMC5848553 DOI: 10.1186/s12885-018-4178-z] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Background Ribosomes, the organelles responsible for the translation of mRNA, are comprised of four rRNAs and ~ 80 ribosomal proteins (RPs). Although canonically assumed to be maintained in equivalent proportions, some RPs have been shown to possess differential expression across tissue types. Dysregulation of RP expression occurs in a variety of human diseases, notably in many cancers, and altered expression of some RPs correlates with different tumor phenotypes and patient survival. Little work has been done, however, to characterize overall patterns of RP transcript (RPT) expression in human cancers. Methods To investigate the impact of global RPT expression patterns on tumor phenotypes, we analyzed RPT expression of ~ 10,000 human tumors and over 700 normal tissues from The Cancer Genome Atlas (TCGA) using t-distributed stochastic neighbor embedding (t-SNE). Clusters of tumors identified by t-SNE were then analyzed with chi-squared and t-tests to compare phenotypic data, ANOVA to compare individual RPT expression, and Kaplan-Meier curves to assess survival differences. Results Normal tissues and cancers possess distinct and readily discernible RPT expression patterns that are independent of their absolute levels of expression. In tumors, RPT patterning is distinct from that of normal tissues, identifies heretofore unrecognized tumor subtypes, and in many cases correlates with molecular, pathological, and clinical features, including survival. Conclusions RPT expression patterns are both tissue-specific and tumor-specific. These could be used as a powerful and novel method of tumor classification, offering a potential clinical tool for prognosis and therapeutic stratification. Electronic supplementary material The online version of this article (10.1186/s12885-018-4178-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- James M Dolezal
- Division of Hematology/Oncology, Children's Hospital of Pittsburgh of UPMC, Pittsburgh, PA, USA.
| | - Arie P Dash
- Division of Hematology/Oncology, Children's Hospital of Pittsburgh of UPMC, Pittsburgh, PA, USA
| | - Edward V Prochownik
- Division of Hematology/Oncology, Children's Hospital of Pittsburgh of UPMC, Pittsburgh, PA, USA.,Department of Microbiology and Molecular Genetics, The University of Pittsburgh Medical Center; The University of Pittsburgh Hillman Cancer Center, Pittsburgh, PA, USA
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81
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Immunoribosomes: Where's there's fire, there's fire. Mol Immunol 2018; 113:38-42. [PMID: 29361306 DOI: 10.1016/j.molimm.2017.12.026] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2017] [Accepted: 12/31/2017] [Indexed: 01/13/2023]
Abstract
The MHC class I antigen presentation pathway enables T cell immunosurveillance of cancer cells, viruses and other intracellular pathogens. Rapidly degraded newly synthesized proteins (DRiPs) are a major source of self-, and particularly, viral antigenic peptides. A number of findings support the idea that a substantial fraction of antigenic peptides are synthesized by "immunoribosomes", a subset of translating ribosomes that generate class I peptides with enhanced efficiency. Here, we review the evidence for the immunoribosome hypothesis.
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82
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Simsek D, Tiu GC, Flynn RA, Byeon GW, Leppek K, Xu AF, Chang HY, Barna M. The Mammalian Ribo-interactome Reveals Ribosome Functional Diversity and Heterogeneity. Cell 2017; 169:1051-1065.e18. [PMID: 28575669 PMCID: PMC5548193 DOI: 10.1016/j.cell.2017.05.022] [Citation(s) in RCA: 252] [Impact Index Per Article: 36.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2016] [Revised: 03/13/2017] [Accepted: 05/14/2017] [Indexed: 11/19/2022]
Abstract
During eukaryotic evolution, ribosomes have considerably increased in size, forming a surface-exposed ribosomal RNA (rRNA) shell of unknown function, which may create an interface for yet uncharacterized interacting proteins. To investigate such protein interactions, we establish a ribosome affinity purification method that unexpectedly identifies hundreds of ribosome-associated proteins (RAPs) from categories including metabolism and cell cycle, as well as RNA- and protein-modifying enzymes that functionally diversify mammalian ribosomes. By further characterizing RAPs, we discover the presence of ufmylation, a metazoan-specific post-translational modification (PTM), on ribosomes and define its direct substrates. Moreover, we show that the metabolic enzyme, pyruvate kinase muscle (PKM), interacts with sub-pools of endoplasmic reticulum (ER)-associated ribosomes, exerting a non-canonical function as an RNA-binding protein in the translation of ER-destined mRNAs. Therefore, RAPs interconnect one of life's most ancient molecular machines with diverse cellular processes, providing an additional layer of regulatory potential to protein expression.
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Affiliation(s)
- Deniz Simsek
- Department of Developmental Biology, Stanford University, Stanford, CA 94305, USA; Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Gerald C Tiu
- Department of Developmental Biology, Stanford University, Stanford, CA 94305, USA; Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Ryan A Flynn
- Center for Personal Dynamic Regulomes and Program in Epithelial Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Gun W Byeon
- Department of Developmental Biology, Stanford University, Stanford, CA 94305, USA; Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Kathrin Leppek
- Department of Developmental Biology, Stanford University, Stanford, CA 94305, USA; Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Adele F Xu
- Department of Developmental Biology, Stanford University, Stanford, CA 94305, USA; Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Howard Y Chang
- Center for Personal Dynamic Regulomes and Program in Epithelial Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Maria Barna
- Department of Developmental Biology, Stanford University, Stanford, CA 94305, USA; Department of Genetics, Stanford University, Stanford, CA 94305, USA.
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