1
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Badonyi M, Marsh JA. Hallmarks and evolutionary drivers of cotranslational protein complex assembly. FEBS J 2024; 291:3557-3567. [PMID: 37202910 DOI: 10.1111/febs.16869] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Revised: 05/11/2023] [Accepted: 05/18/2023] [Indexed: 05/20/2023]
Abstract
Recent discoveries have highlighted the prevalence of cotranslational assembly in proteomes, revealing a range of mechanisms that enables the assembly of protein complex subunits on the ribosome. Structural analyses have uncovered emergent properties that may inherently control whether a subunit undergoes cotranslational assembly. However, the evolutionary paths that have yielded such complexes over an extended timescale remain largely unclear. In this review, we reflect on historical experiments that contributed to the field, including breakthroughs that have made possible the proteome-wide detection of cotranslational assembly, and the technical challenges yet to be overcome. We introduce a simple framework that encapsulates the hallmarks of cotranslational assembly and discuss how results from new experiments are shaping our view of the mechanistic, structural and evolutionary factors driving the phenomenon.
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Affiliation(s)
- Mihaly Badonyi
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, UK
| | - Joseph A Marsh
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, UK
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2
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Crawford RA, Eastham M, Pool MR, Ashe MP. Orchestrated centers for the production of proteins or "translation factories". WILEY INTERDISCIPLINARY REVIEWS. RNA 2024; 15:e1867. [PMID: 39048533 DOI: 10.1002/wrna.1867] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Revised: 05/20/2024] [Accepted: 06/07/2024] [Indexed: 07/27/2024]
Abstract
The mechanics of how proteins are generated from mRNA is increasingly well understood. However, much less is known about how protein production is coordinated and orchestrated within the crowded intracellular environment, especially in eukaryotic cells. Recent studies suggest that localized sites exist for the coordinated production of specific proteins. These sites have been termed "translation factories" and roles in protein complex formation, protein localization, inheritance, and translation regulation have been postulated. In this article, we review the evidence supporting the translation of mRNA at these sites, the details of their mechanism of formation, and their likely functional significance. Finally, we consider the key uncertainties regarding these elusive structures in cells. This article is categorized under: Translation Translation > Mechanisms RNA Export and Localization > RNA Localization Translation > Regulation.
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Affiliation(s)
- Robert A Crawford
- Division of Molecular and Cellular Function, Faculty of Biology Medicine and Health, Manchester Academic Health Science Centre, The University of Manchester, Manchester, UK
| | - Matthew Eastham
- Division of Molecular and Cellular Function, Faculty of Biology Medicine and Health, Manchester Academic Health Science Centre, The University of Manchester, Manchester, UK
| | - Martin R Pool
- Division of Molecular and Cellular Function, Faculty of Biology Medicine and Health, Manchester Academic Health Science Centre, The University of Manchester, Manchester, UK
| | - Mark P Ashe
- Division of Molecular and Cellular Function, Faculty of Biology Medicine and Health, Manchester Academic Health Science Centre, The University of Manchester, Manchester, UK
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3
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Venezian J, Bar-Yosef H, Ben-Arie Zilberman H, Cohen N, Kleifeld O, Fernandez-Recio J, Glaser F, Shiber A. Diverging co-translational protein complex assembly pathways are governed by interface energy distribution. Nat Commun 2024; 15:2638. [PMID: 38528060 DOI: 10.1038/s41467-024-46881-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Accepted: 03/12/2024] [Indexed: 03/27/2024] Open
Abstract
Protein-protein interactions are at the heart of all cellular processes, with the ribosome emerging as a platform, orchestrating the nascent-chain interplay dynamics. Here, to study the characteristics governing co-translational protein folding and complex assembly, we combine selective ribosome profiling, imaging, and N-terminomics with all-atoms molecular dynamics. Focusing on conserved N-terminal acetyltransferases (NATs), we uncover diverging co-translational assembly pathways, where highly homologous subunits serve opposite functions. We find that only a few residues serve as "hotspots," initiating co-translational assembly interactions upon exposure at the ribosome exit tunnel. These hotspots are characterized by high binding energy, anchoring the entire interface assembly. Alpha-helices harboring hotspots are highly thermolabile, folding and unfolding during simulations, depending on their partner subunit to avoid misfolding. In vivo hotspot mutations disrupted co-translational complexation, leading to aggregation. Accordingly, conservation analysis reveals that missense NATs variants, causing neurodevelopmental and neurodegenerative diseases, disrupt putative hotspot clusters. Expanding our study to include phosphofructokinase, anthranilate synthase, and nucleoporin subcomplex, we employ AlphaFold-Multimer to model the complexes' complete structures. Computing MD-derived interface energy profiles, we find similar trends. Here, we propose a model based on the distribution of interface energy as a strong predictor of co-translational assembly.
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Affiliation(s)
- Johannes Venezian
- Faculty of Biology, Technion Israel institute of Technology, Haifa, Israel
| | - Hagit Bar-Yosef
- Faculty of Biology, Technion Israel institute of Technology, Haifa, Israel
| | | | - Noam Cohen
- Faculty of Biology, Technion Israel institute of Technology, Haifa, Israel
| | - Oded Kleifeld
- Faculty of Biology, Technion Israel institute of Technology, Haifa, Israel
| | - Juan Fernandez-Recio
- Instituto de Ciencias de la Vid y del Vino (ICVV), CSIC-Universidad de La Rioja-Gobierno de La Rioja, Logroño, Spain
| | - Fabian Glaser
- Lorry I. Lokey Interdisciplinary Center for Life Sciences & Engineering, Haifa, Israel
| | - Ayala Shiber
- Faculty of Biology, Technion Israel institute of Technology, Haifa, Israel.
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4
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Bernardini A, Tora L. Co-translational Assembly Pathways of Nuclear Multiprotein Complexes Involved in the Regulation of Gene Transcription. J Mol Biol 2024; 436:168382. [PMID: 38061625 DOI: 10.1016/j.jmb.2023.168382] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 11/24/2023] [Accepted: 12/01/2023] [Indexed: 12/18/2023]
Abstract
Most factors that regulate gene transcription in eukaryotic cells are multimeric, often large, protein complexes. The understanding of the biogenesis pathways of such large and heterogeneous protein assemblies, as well as the dimerization partner choice among transcription factors, is crucial to interpret and control gene expression programs and consequent cell fate decisions. Co-translational assembly (Co-TA) is thought to play key roles in the biogenesis of protein complexes by directing complex formation during protein synthesis. In this review we discuss the principles of Co-TA with a special focus for the assembly of transcription regulatory complexes. We outline the expected molecular advantages of establishing co-translational interactions, pointing at the available, or missing, evidence for each of them. We hypothesize different molecular mechanisms based on Co-TA to explain the allocation "dilemma" of paralog proteins and subunits shared by different transcription complexes. By taking as a paradigm the different assembly pathways employed by three related transcription regulatory complexes (TFIID, SAGA and ATAC), we discuss alternative Co-TA strategies for nuclear multiprotein complexes and the widespread - yet specific - use of Co-TA for the formation of nuclear complexes involved in gene transcription. Ultimately, we outlined a series of open questions which demand well-defined lines of research to investigate the principles of gene regulation that rely on the coordinated assembly of protein complexes.
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Affiliation(s)
- Andrea Bernardini
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France; Centre National de la Recherche Scientifique, UMR7104, Illkirch, France; Institut National de la Santé et de la Recherche Médicale, U964 Illkirch, France; Université de Strasbourg, Illkirch, France.
| | - László Tora
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France; Centre National de la Recherche Scientifique, UMR7104, Illkirch, France; Institut National de la Santé et de la Recherche Médicale, U964 Illkirch, France; Université de Strasbourg, Illkirch, France.
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5
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Huber M, Vogel N, Borst A, Pfeiffer F, Karamycheva S, Wolf YI, Koonin EV, Soppa J. Unidirectional gene pairs in archaea and bacteria require overlaps or very short intergenic distances for translational coupling via termination-reinitiation and often encode subunits of heteromeric complexes. Front Microbiol 2023; 14:1291523. [PMID: 38029211 PMCID: PMC10666635 DOI: 10.3389/fmicb.2023.1291523] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2023] [Accepted: 10/25/2023] [Indexed: 12/01/2023] Open
Abstract
Genomes of bacteria and archaea contain a much larger fraction of unidirectional (serial) gene pairs than convergent or divergent gene pairs. Many of the unidirectional gene pairs have short overlaps of -4 nt and -1 nt. As shown previously, translation of the genes in overlapping unidirectional gene pairs is tightly coupled. Two alternative models for the fate of the post-termination ribosome predict either that overlaps or very short intergenic distances are essential for translational coupling or that the undissociated post-termination ribosome can scan through long intergenic regions, up to hundreds of nucleotides. We aimed to experimentally resolve the contradiction between the two models by analyzing three native gene pairs from the model archaeon Haloferax volcanii and three native pairs from Escherichia coli. A two reporter gene system was used to quantify the reinitiation frequency, and several stop codons in the upstream gene were introduced to increase the intergenic distances. For all six gene pairs from two species, an extremely strong dependence of the reinitiation efficiency on the intergenic distance was unequivocally demonstrated, such that even short intergenic distances of about 20 nt almost completely abolished translational coupling. Bioinformatic analysis of the intergenic distances in all unidirectional gene pairs in the genomes of H. volcanii and E. coli and in 1,695 prokaryotic species representative of 49 phyla showed that intergenic distances of -4 nt or -1 nt (= short gene overlaps of 4 nt or 1 nt) were by far most common in all these groups of archaea and bacteria. A small set of genes in E. coli, but not in H. volcanii, had intergenic distances of around +10 nt. Our experimental and bioinformatic analyses clearly show that translational coupling requires short gene overlaps, whereas scanning of intergenic regions by the post-termination ribosome occurs rarely, if at all. Short overlaps are enriched among genes that encode subunits of heteromeric complexes, and co-translational complex formation requiring precise subunit stoichiometry likely confers an evolutionary advantage that drove the formation and conservation of overlapping gene pairs during evolution.
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Affiliation(s)
- Madeleine Huber
- Institute for Molecular Biosciences, Biocentre, Goethe-University, Frankfurt, Germany
| | - Nico Vogel
- Institute for Molecular Biosciences, Biocentre, Goethe-University, Frankfurt, Germany
| | - Andreas Borst
- Institute for Molecular Biosciences, Biocentre, Goethe-University, Frankfurt, Germany
| | - Friedhelm Pfeiffer
- Computational Biology Group, Max-Planck-Institute of Biochemistry, Martinsried, Germany
| | - Svetlana Karamycheva
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, United States
| | - Yuri I. Wolf
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, United States
| | - Eugene V. Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, United States
| | - Jörg Soppa
- Institute for Molecular Biosciences, Biocentre, Goethe-University, Frankfurt, Germany
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6
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Penzo A, Palancade B. Puzzling out nuclear pore complex assembly. FEBS Lett 2023; 597:2705-2727. [PMID: 37548888 DOI: 10.1002/1873-3468.14713] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Revised: 07/12/2023] [Accepted: 07/17/2023] [Indexed: 08/08/2023]
Abstract
Nuclear pore complexes (NPCs) are sophisticated multiprotein assemblies embedded within the nuclear envelope and controlling the exchanges of molecules between the cytoplasm and the nucleus. In this review, we summarize the mechanisms by which these elaborate complexes are built from their subunits, the nucleoporins, based on our ever-growing knowledge of NPC structural organization and on the recent identification of additional features of this process. We present the constraints faced during the production of nucleoporins, their gathering into oligomeric complexes, and the formation of NPCs within nuclear envelopes, and review the cellular strategies at play, from co-translational assembly to the enrolment of a panel of cofactors. Remarkably, the study of NPCs can inform our perception of the biogenesis of multiprotein complexes in general - and vice versa.
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Affiliation(s)
- Arianna Penzo
- Université Paris Cité, CNRS, Institut Jacques Monod, Paris, France
| | - Benoit Palancade
- Université Paris Cité, CNRS, Institut Jacques Monod, Paris, France
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7
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Jameson MB, Ríos-Pérez EB, Liu F, Eichel CA, Robertson GA. Pairwise biosynthesis of ion channels stabilizes excitability and mitigates arrhythmias. Proc Natl Acad Sci U S A 2023; 120:e2305295120. [PMID: 37816059 PMCID: PMC10589643 DOI: 10.1073/pnas.2305295120] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Accepted: 08/14/2023] [Indexed: 10/12/2023] Open
Abstract
Coordinated expression of ion channels is crucial for cardiac rhythms, neural signaling, and cell cycle progression. Perturbation of this balance results in many disorders including cardiac arrhythmias. Prior work revealed association of mRNAs encoding cardiac NaV1.5 (SCN5A) and hERG1 (KCNH2), but the functional significance of this association was not established. Here, we provide a more comprehensive picture of KCNH2, SCN5A, CACNA1C, and KCNQ1 transcripts collectively copurifying with nascent hERG1, NaV1.5, CaV1.2, or KCNQ1 channel proteins. Single-molecule fluorescence in situ hybridization (smFISH) combined with immunofluorescence reveals that the channel proteins are synthesized predominantly as heterotypic pairs from discrete molecules of mRNA, not as larger cotranslational complexes. Puromycin disrupted colocalization of mRNA with its encoded protein, as expected, but remarkably also pairwise mRNA association, suggesting that transcript association relies on intact translational machinery or the presence of the nascent protein. Targeted depletion of KCHN2 by specific shRNA resulted in concomitant reduction of all associated mRNAs, with a corresponding reduction in the encoded channel currents. This co-knockdown effect, originally described for KCNH2 and SCN5A, thus appears to be a general phenomenon among transcripts encoding functionally related proteins. In multielectrode array recordings, proarrhythmic behavior arose when IKr was reduced by the selective blocker dofetilide at IC50 concentrations, but not when equivalent reductions were mediated by shRNA, suggesting that co-knockdown mitigates proarrhythmic behavior expected from the selective reduction of a single channel species. We propose that coordinated, cotranslational association of functionally related ion channel mRNAs confers electrical stability by co-regulating complementary ion channels in macromolecular complexes.
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Affiliation(s)
- Margaret B. Jameson
- Department of Neuroscience, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI53705
| | - Erick B. Ríos-Pérez
- Department of Neuroscience, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI53705
| | - Fang Liu
- Department of Neuroscience, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI53705
| | - Catherine A. Eichel
- Department of Neuroscience, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI53705
| | - Gail A. Robertson
- Department of Neuroscience, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI53705
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8
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Yayli G, Bernardini A, Mendoza Sanchez PK, Scheer E, Damilot M, Essabri K, Morlet B, Negroni L, Vincent SD, Timmers HTM, Tora L. ATAC and SAGA co-activator complexes utilize co-translational assembly, but their cellular localization properties and functions are distinct. Cell Rep 2023; 42:113099. [PMID: 37682711 PMCID: PMC10591836 DOI: 10.1016/j.celrep.2023.113099] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Revised: 06/19/2023] [Accepted: 08/22/2023] [Indexed: 09/10/2023] Open
Abstract
To understand the function of multisubunit complexes, it is of key importance to uncover the precise mechanisms that guide their assembly. Nascent proteins can find and bind their interaction partners during their translation, leading to co-translational assembly. Here, we demonstrate that the core modules of ATAC (ADA-two-A-containing) and SAGA (Spt-Ada-Gcn5-acetyltransferase), two lysine acetyl transferase-containing transcription co-activator complexes, assemble co-translationally in the cytoplasm of mammalian cells. In addition, a SAGA complex containing all of its modules forms in the cytoplasm and acetylates non-histone proteins. In contrast, ATAC complex subunits cannot be detected in the cytoplasm of mammalian cells. However, an endogenous ATAC complex containing two functional modules forms and functions in the nucleus. Thus, the two related co-activators, ATAC and SAGA, assemble using co-translational pathways, but their subcellular localization, cytoplasmic abundance, and functions are distinct.
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Affiliation(s)
- Gizem Yayli
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France; Centre National de la Recherche Scientifique, UMR7104, Illkirch, France; Institut National de la Santé et de la Recherche Médicale, U1258, Illkirch, France; Université de Strasbourg, Illkirch, France
| | - Andrea Bernardini
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France; Centre National de la Recherche Scientifique, UMR7104, Illkirch, France; Institut National de la Santé et de la Recherche Médicale, U1258, Illkirch, France; Université de Strasbourg, Illkirch, France
| | - Paulina Karen Mendoza Sanchez
- German Cancer Consortium (DKTK) Partner Site Freiburg, German Cancer Research Center (DKFZ), Freiburg, Germany; Department of Urology, Medical Center-University of Freiburg, Freiburg, Germany
| | - Elisabeth Scheer
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France; Centre National de la Recherche Scientifique, UMR7104, Illkirch, France; Institut National de la Santé et de la Recherche Médicale, U1258, Illkirch, France; Université de Strasbourg, Illkirch, France
| | - Mylène Damilot
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France; Centre National de la Recherche Scientifique, UMR7104, Illkirch, France; Institut National de la Santé et de la Recherche Médicale, U1258, Illkirch, France; Université de Strasbourg, Illkirch, France
| | - Karim Essabri
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France; Centre National de la Recherche Scientifique, UMR7104, Illkirch, France; Institut National de la Santé et de la Recherche Médicale, U1258, Illkirch, France; Université de Strasbourg, Illkirch, France
| | - Bastien Morlet
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France; Centre National de la Recherche Scientifique, UMR7104, Illkirch, France; Institut National de la Santé et de la Recherche Médicale, U1258, Illkirch, France; Université de Strasbourg, Illkirch, France
| | - Luc Negroni
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France; Centre National de la Recherche Scientifique, UMR7104, Illkirch, France; Institut National de la Santé et de la Recherche Médicale, U1258, Illkirch, France; Université de Strasbourg, Illkirch, France
| | - Stéphane D Vincent
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France; Centre National de la Recherche Scientifique, UMR7104, Illkirch, France; Institut National de la Santé et de la Recherche Médicale, U1258, Illkirch, France; Université de Strasbourg, Illkirch, France
| | - H T Marc Timmers
- German Cancer Consortium (DKTK) Partner Site Freiburg, German Cancer Research Center (DKFZ), Freiburg, Germany; Department of Urology, Medical Center-University of Freiburg, Freiburg, Germany
| | - László Tora
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France; Centre National de la Recherche Scientifique, UMR7104, Illkirch, France; Institut National de la Santé et de la Recherche Médicale, U1258, Illkirch, France; Université de Strasbourg, Illkirch, France.
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9
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Höpfler M, Hegde RS. Control of mRNA fate by its encoded nascent polypeptide. Mol Cell 2023; 83:2840-2855. [PMID: 37595554 PMCID: PMC10501990 DOI: 10.1016/j.molcel.2023.07.014] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Revised: 07/03/2023] [Accepted: 07/11/2023] [Indexed: 08/20/2023]
Abstract
Cells tightly regulate mRNA processing, localization, and stability to ensure accurate gene expression in diverse cellular states and conditions. Most of these regulatory steps have traditionally been thought to occur before translation by the action of RNA-binding proteins. Several recent discoveries highlight multiple co-translational mechanisms that modulate mRNA translation, localization, processing, and stability. These mechanisms operate by recognition of the nascent protein, which is necessarily coupled to its encoding mRNA during translation. Hence, the distinctive sequence or structure of a particular nascent chain can recruit recognition factors with privileged access to the corresponding mRNA in an otherwise crowded cellular environment. Here, we draw on both well-established and recent examples to provide a conceptual framework for how cells exploit nascent protein recognition to direct mRNA fate. These mechanisms allow cells to dynamically and specifically regulate their transcriptomes in response to changes in cellular states to maintain protein homeostasis.
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10
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Yayli G, Bernardini A, Sanchez PKM, Scheer E, Damilot M, Essabri K, Morlet B, Negroni L, Vincent SD, Timmers HTM, Tora L. ATAC and SAGA coactivator complexes utilize co-translational assembly, but their cellular localization properties and functions are distinct. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.03.551787. [PMID: 37577620 PMCID: PMC10418265 DOI: 10.1101/2023.08.03.551787] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/15/2023]
Abstract
To understand the function of multisubunit complexes it is of key importance to uncover the precise mechanisms that guide their assembly. Nascent proteins can find and bind their interaction partners during their translation, leading to co-translational assembly. Here we demonstrate that the core modules of ATAC (ADA-Two-A-Containing) and SAGA (Spt-Ada-Gcn5-acetyltransferase), two lysine acetyl transferase-containing transcription coactivator complexes, assemble co-translationally in the cytoplasm of mammalian cells. In addition, SAGA complex containing all of its modules forms in the cytoplasm and acetylates non-histones proteins. In contrast, fully assembled ATAC complex cannot be detected in the cytoplasm of mammalian cells. However, endogenous ATAC complex containing two functional modules forms and functions in the nucleus. Thus, the two related coactivators, ATAC and SAGA, assemble by using co-translational pathways, but their subcellular localization, cytoplasmic abundance and functions are distinct.
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Affiliation(s)
- Gizem Yayli
- Institut de Génétique et de Biologie Moleculaire et Cellulaire, Illkirch, France
- Centre National de la Recherche Scientifique, UMR7104, Illkirch, France
- Institut National de la Santé et de la Recherche Medicale, U1258, Illkirch, France
- Universite de Strasbourg, Illkirch, France
| | - Andrea Bernardini
- Institut de Génétique et de Biologie Moleculaire et Cellulaire, Illkirch, France
- Centre National de la Recherche Scientifique, UMR7104, Illkirch, France
- Institut National de la Santé et de la Recherche Medicale, U1258, Illkirch, France
- Universite de Strasbourg, Illkirch, France
| | - Paulina Karen Mendoza Sanchez
- German Cancer Consortium (DKTK) partner site Freiburg, German Cancer Research, Center (DKFZ) and Department of Urology, Medical Center-University of Freiburg, Freiburg, Germany
| | - Elisabeth Scheer
- Institut de Génétique et de Biologie Moleculaire et Cellulaire, Illkirch, France
- Centre National de la Recherche Scientifique, UMR7104, Illkirch, France
- Institut National de la Santé et de la Recherche Medicale, U1258, Illkirch, France
- Universite de Strasbourg, Illkirch, France
| | - Mylène Damilot
- Institut de Génétique et de Biologie Moleculaire et Cellulaire, Illkirch, France
- Centre National de la Recherche Scientifique, UMR7104, Illkirch, France
- Institut National de la Santé et de la Recherche Medicale, U1258, Illkirch, France
- Universite de Strasbourg, Illkirch, France
| | - Karim Essabri
- Institut de Génétique et de Biologie Moleculaire et Cellulaire, Illkirch, France
- Centre National de la Recherche Scientifique, UMR7104, Illkirch, France
- Institut National de la Santé et de la Recherche Medicale, U1258, Illkirch, France
- Universite de Strasbourg, Illkirch, France
| | - Bastien Morlet
- Institut de Génétique et de Biologie Moleculaire et Cellulaire, Illkirch, France
- Centre National de la Recherche Scientifique, UMR7104, Illkirch, France
- Institut National de la Santé et de la Recherche Medicale, U1258, Illkirch, France
- Universite de Strasbourg, Illkirch, France
| | - Luc Negroni
- Institut de Génétique et de Biologie Moleculaire et Cellulaire, Illkirch, France
- Centre National de la Recherche Scientifique, UMR7104, Illkirch, France
- Institut National de la Santé et de la Recherche Medicale, U1258, Illkirch, France
- Universite de Strasbourg, Illkirch, France
| | - Stéphane D. Vincent
- Institut de Génétique et de Biologie Moleculaire et Cellulaire, Illkirch, France
- Centre National de la Recherche Scientifique, UMR7104, Illkirch, France
- Institut National de la Santé et de la Recherche Medicale, U1258, Illkirch, France
- Universite de Strasbourg, Illkirch, France
| | - HT Marc Timmers
- German Cancer Consortium (DKTK) partner site Freiburg, German Cancer Research, Center (DKFZ) and Department of Urology, Medical Center-University of Freiburg, Freiburg, Germany
| | - László Tora
- Institut de Génétique et de Biologie Moleculaire et Cellulaire, Illkirch, France
- Centre National de la Recherche Scientifique, UMR7104, Illkirch, France
- Institut National de la Santé et de la Recherche Medicale, U1258, Illkirch, France
- Universite de Strasbourg, Illkirch, France
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11
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Bernardini A, Mukherjee P, Scheer E, Kamenova I, Antonova S, Mendoza Sanchez PK, Yayli G, Morlet B, Timmers HTM, Tora L. Hierarchical TAF1-dependent co-translational assembly of the basal transcription factor TFIID. Nat Struct Mol Biol 2023; 30:1141-1152. [PMID: 37386215 PMCID: PMC10442232 DOI: 10.1038/s41594-023-01026-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Accepted: 05/31/2023] [Indexed: 07/01/2023]
Abstract
Large heteromeric multiprotein complexes play pivotal roles at every step of gene expression in eukaryotic cells. Among them, the 20-subunit basal transcription factor TFIID nucleates the RNA polymerase II preinitiation complex at gene promoters. Here, by combining systematic RNA-immunoprecipitation (RIP) experiments, single-molecule imaging, proteomics and structure-function analyses, we show that human TFIID biogenesis occurs co-translationally. We discovered that all protein heterodimerization steps happen during protein synthesis. We identify TAF1-the largest protein in the complex-as a critical factor for TFIID assembly. TAF1 acts as a flexible scaffold that drives the co-translational recruitment of TFIID submodules preassembled in the cytoplasm. Altogether, our data suggest a multistep hierarchical model for TFIID biogenesis that culminates with the co-translational assembly of the complex onto the nascent TAF1 polypeptide. We envision that this assembly strategy could be shared with other large heteromeric protein complexes.
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Affiliation(s)
- Andrea Bernardini
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France
- Centre National de la Recherche Scientifique, Illkirch, France
- Institut National de la Santé et de la Recherche Médicale, Illkirch, France
- Université de Strasbourg, Illkirch, France
| | - Pooja Mukherjee
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France
- Centre National de la Recherche Scientifique, Illkirch, France
- Institut National de la Santé et de la Recherche Médicale, Illkirch, France
- Université de Strasbourg, Illkirch, France
- Innovative Genomics Institute, University of California, Berkeley, CA, USA
| | - Elisabeth Scheer
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France
- Centre National de la Recherche Scientifique, Illkirch, France
- Institut National de la Santé et de la Recherche Médicale, Illkirch, France
- Université de Strasbourg, Illkirch, France
| | - Ivanka Kamenova
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France
- Centre National de la Recherche Scientifique, Illkirch, France
- Institut National de la Santé et de la Recherche Médicale, Illkirch, France
- Université de Strasbourg, Illkirch, France
- Nature Protocols, London, UK
| | - Simona Antonova
- German Cancer Consortium (DKTK) partner site Freiburg, German Cancer Research Center (DKFZ) and Department of Urology, Medical Center-University of Freiburg, Freiburg, Germany
- The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Paulina Karen Mendoza Sanchez
- German Cancer Consortium (DKTK) partner site Freiburg, German Cancer Research Center (DKFZ) and Department of Urology, Medical Center-University of Freiburg, Freiburg, Germany
| | - Gizem Yayli
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France
- Centre National de la Recherche Scientifique, Illkirch, France
- Institut National de la Santé et de la Recherche Médicale, Illkirch, France
- Université de Strasbourg, Illkirch, France
| | - Bastien Morlet
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France
- Centre National de la Recherche Scientifique, Illkirch, France
- Institut National de la Santé et de la Recherche Médicale, Illkirch, France
- Université de Strasbourg, Illkirch, France
| | - H T Marc Timmers
- German Cancer Consortium (DKTK) partner site Freiburg, German Cancer Research Center (DKFZ) and Department of Urology, Medical Center-University of Freiburg, Freiburg, Germany
| | - László Tora
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France.
- Centre National de la Recherche Scientifique, Illkirch, France.
- Institut National de la Santé et de la Recherche Médicale, Illkirch, France.
- Université de Strasbourg, Illkirch, France.
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12
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Seidel M, Romanov N, Obarska-Kosinska A, Becker A, Trevisan Doimo de Azevedo N, Provaznik J, Nagaraja SR, Landry JJM, Benes V, Beck M. Co-translational binding of importins to nascent proteins. Nat Commun 2023; 14:3418. [PMID: 37296145 PMCID: PMC10256725 DOI: 10.1038/s41467-023-39150-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Accepted: 05/26/2023] [Indexed: 06/12/2023] Open
Abstract
Various cellular quality control mechanisms support proteostasis. While, ribosome-associated chaperones prevent the misfolding of nascent chains during translation, importins were shown to prevent the aggregation of specific cargoes in a post-translational mechanism prior the import into the nucleoplasm. Here, we hypothesize that importins may already bind ribosome-associated cargo in a co-translational manner. We systematically measure the nascent chain association of all importins in Saccharomyces cerevisiae by selective ribosome profiling. We identify a subset of importins that bind to a wide range of nascent, often uncharacterized cargoes. This includes ribosomal proteins, chromatin remodelers and RNA binding proteins that are aggregation prone in the cytosol. We show that importins act consecutively with other ribosome-associated chaperones. Thus, the nuclear import system is directly intertwined with nascent chain folding and chaperoning.
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Affiliation(s)
- Maximilian Seidel
- Department of Molecular Sociology, Max Planck Institute of Biophysics, Frankfurt, Germany
- Faculty of Bioscience, Heidelberg University, Heidelberg, Germany
| | - Natalie Romanov
- Department of Molecular Sociology, Max Planck Institute of Biophysics, Frankfurt, Germany
| | | | - Anja Becker
- Department of Molecular Sociology, Max Planck Institute of Biophysics, Frankfurt, Germany
| | | | - Jan Provaznik
- Genomics Core Facility, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Sankarshana R Nagaraja
- Department of Molecular Sociology, Max Planck Institute of Biophysics, Frankfurt, Germany
| | - Jonathan J M Landry
- Genomics Core Facility, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Vladimir Benes
- Genomics Core Facility, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Martin Beck
- Department of Molecular Sociology, Max Planck Institute of Biophysics, Frankfurt, Germany.
- Institute of Biochemistry, Goethe University Frankfurt, Frankfurt, Germany.
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13
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Khan K, Fox PL. Benefits of co-translational complex assembly for cellular fitness. Bioessays 2023; 45:e2300024. [PMID: 36916749 PMCID: PMC10121914 DOI: 10.1002/bies.202300024] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 02/27/2023] [Accepted: 03/01/2023] [Indexed: 03/16/2023]
Abstract
Complexes of two or more proteins form many, if not most, of the intracellular "machines" that execute physical and chemical work, and transmit information. Complexes can form from stochastic post-translational interactions of fully formed proteins, but recent attention has shifted to co-translational interactions in which the most common mechanism involves binding of a mature constituent to an incomplete polypeptide emerging from a translating ribosome. Studies in yeast have revealed co-translational interactions during formation of multiple major complexes, and together with recent mammalian cell studies, suggest widespread utilization of the mechanism. These translation-dependent interactions can involve a single or multiple mRNA templates, can be uni- or bi-directional, and can use multi-protein sub-complexes as a binding component. Here, we discuss benefits of co-translational complex assembly including accuracy and efficiency, overcoming hidden interfaces, localized and hierarchical assembly, and reduction of orphan protein degradation, toxicity, and dominant-negative pathogenesis, all serving to improve cell fitness.
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Affiliation(s)
- Krishnendu Khan
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, USA
| | - Paul L Fox
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, USA
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14
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Bernardini A, Mukherjee P, Scheer E, Kamenova I, Antonova S, Sanchez PKM, Yayli G, Morlet B, Timmers HM, Tora L. Hierarchical TAF1-dependent co-translational assembly of the basal transcription factor TFIID. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.05.535704. [PMID: 37066372 PMCID: PMC10104070 DOI: 10.1101/2023.04.05.535704] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 04/28/2023]
Abstract
Large heteromeric multiprotein complexes play pivotal roles at every step of gene expression in eukaryotic cells. Among them, the 20-subunit basal transcription factor TFIID nucleates RNA polymerase II preinitiation complex at gene promoters. Here, by combining systematic RNA-immunoprecipitation (RIP) experiments, single-molecule imaging, proteomics and structure-function analyses, we show that TFIID biogenesis occurs co-translationally. We discovered that all protein heterodimerization steps happen during protein synthesis. We identify TAF1 - the largest protein in the complex - as a critical factor for TFIID assembly. TAF1 acts as a flexible scaffold that drives the co-translational recruitment of TFIID submodules preassembled in the cytoplasm. Altogether, our data suggest a multistep hierarchical model for TFIID biogenesis that culminates with the co-translational assembly of the complex onto the nascent TAF1 polypeptide. We envision that this assembly strategy could be shared with other large heteromeric protein complexes.
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Affiliation(s)
- Andrea Bernardini
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France
- Centre National de la Recherche Scientifique, UMR7104, Illkirch, France
- Institut National de la Santé et de la Recherche Médicale, U964, Illkirch, France
- Université de Strasbourg, Illkirch, France
| | - Pooja Mukherjee
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France
- Centre National de la Recherche Scientifique, UMR7104, Illkirch, France
- Institut National de la Santé et de la Recherche Médicale, U964, Illkirch, France
- Université de Strasbourg, Illkirch, France
| | - Elisabeth Scheer
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France
- Centre National de la Recherche Scientifique, UMR7104, Illkirch, France
- Institut National de la Santé et de la Recherche Médicale, U964, Illkirch, France
- Université de Strasbourg, Illkirch, France
| | - Ivanka Kamenova
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France
- Centre National de la Recherche Scientifique, UMR7104, Illkirch, France
- Institut National de la Santé et de la Recherche Médicale, U964, Illkirch, France
- Université de Strasbourg, Illkirch, France
| | - Simona Antonova
- German Cancer Consortium (DKTK) partner site Freiburg, German Cancer Research Center (DKFZ) and Department of Urology, Medical Center-University of Freiburg, Germany
| | - Paulina Karen Mendoza Sanchez
- German Cancer Consortium (DKTK) partner site Freiburg, German Cancer Research Center (DKFZ) and Department of Urology, Medical Center-University of Freiburg, Germany
| | - Gizem Yayli
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France
- Centre National de la Recherche Scientifique, UMR7104, Illkirch, France
- Institut National de la Santé et de la Recherche Médicale, U964, Illkirch, France
- Université de Strasbourg, Illkirch, France
| | - Bastien Morlet
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France
- Centre National de la Recherche Scientifique, UMR7104, Illkirch, France
- Institut National de la Santé et de la Recherche Médicale, U964, Illkirch, France
- Université de Strasbourg, Illkirch, France
| | - H.T. Marc Timmers
- German Cancer Consortium (DKTK) partner site Freiburg, German Cancer Research Center (DKFZ) and Department of Urology, Medical Center-University of Freiburg, Germany
| | - László Tora
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France
- Centre National de la Recherche Scientifique, UMR7104, Illkirch, France
- Institut National de la Santé et de la Recherche Médicale, U964, Illkirch, France
- Université de Strasbourg, Illkirch, France
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15
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Rong Y, Jensen SI, Lindorff-Larsen K, Nielsen AT. Folding of heterologous proteins in bacterial cell factories: Cellular mechanisms and engineering strategies. Biotechnol Adv 2023; 63:108079. [PMID: 36528238 DOI: 10.1016/j.biotechadv.2022.108079] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2022] [Revised: 11/20/2022] [Accepted: 12/09/2022] [Indexed: 12/23/2022]
Abstract
The expression of correctly folded and functional heterologous proteins is important in many biotechnological production processes, whether it is enzymes, biopharmaceuticals or biosynthetic pathways for production of sustainable chemicals. For industrial applications, bacterial platform organisms, such as E. coli, are still broadly used due to the availability of tools and proven suitability at industrial scale. However, expression of heterologous proteins in these organisms can result in protein aggregation and low amounts of functional protein. This review provides an overview of the cellular mechanisms that can influence protein folding and expression, such as co-translational folding and assembly, chaperone binding, as well as protein quality control, across different model organisms. The knowledge of these mechanisms is then linked to different experimental methods that have been applied in order to improve functional heterologous protein folding, such as codon optimization, fusion tagging, chaperone co-production, as well as strain and protein engineering strategies.
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Affiliation(s)
- Yixin Rong
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, 2800 Kgs. Lyngby, Denmark
| | - Sheila Ingemann Jensen
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, 2800 Kgs. Lyngby, Denmark
| | - Kresten Lindorff-Larsen
- Structural Biology and NMR Laboratory, Department of Biology, University of Copenhagen, Ole Maaloes Vej 5, 2200 Copenhagen N, Denmark
| | - Alex Toftgaard Nielsen
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, 2800 Kgs. Lyngby, Denmark.
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16
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Lankeit J, Förste S, Rudorf S. Dominance analysis of competing protein assembly pathways. PLoS One 2023; 18:e0281964. [PMID: 36827413 PMCID: PMC9956869 DOI: 10.1371/journal.pone.0281964] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Accepted: 02/04/2023] [Indexed: 02/26/2023] Open
Abstract
Most proteins form complexes consisting of two or more subunits, where complex assembly can proceed via two competing pathways: co-translational assembly of a mature and a nascent subunit, and post-translational assembly by two mature protein subunits. Assembly pathway dominance, i.e., which of the two pathways is predominant under which conditions, is poorly understood. Here, we introduce a reaction-diffusion system that describes protein complex formation via post- and co-translational assembly and use it to analyze the dominance of both pathways. Special features of this new system are (i) spatially inhomogeneous sources of reacting species, (ii) a combination of diffusing and immobile species, and (iii) an asymmetric binding competition between the species. We study assembly pathway dominance for the spatially homogeneous system and find that the ratio of production rates of the two protein subunits determines the long-term pathway dominance. This result is independent of the binding rate constants for post- and co-translational assembly and implies that a system with an initial post-translational assembly dominance can eventually exhibit co-translational assembly dominance and vice versa. For exactly balanced production of both subunits, the assembly pathway dominance is determined by the steady state concentration of the subunit that can bind both nascent and mature partners. The introduced system of equations can be applied to describe general dynamics of assembly processes involving both diffusing and immobile components.
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Affiliation(s)
- Johannes Lankeit
- Institute of Applied Mathematics, Leibniz University Hannover, Hannover, Germany
| | - Stefanie Förste
- Theory and Bio-Systems, Max Planck Institute of Colloids and Interfaces, Potsdam, Germany
| | - Sophia Rudorf
- Institute of Cell Biology and Biophysics, Leibniz University Hannover, Hannover, Germany
- * E-mail:
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17
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Luo Y, Pratihar S, Horste EH, Mitschka S, Mey ASJS, Al-Hashimi HM, Mayr C. mRNA interactions with disordered regions control protein activity. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.18.529068. [PMID: 36824771 PMCID: PMC9949118 DOI: 10.1101/2023.02.18.529068] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/21/2023]
Abstract
The cytoplasm is compartmentalized into different translation environments. mRNAs use their 3'UTRs to localize to distinct cytoplasmic compartments, including TIS granules (TGs). Many transcription factors, including MYC, are translated in TGs. It was shown that translation of proteins in TGs enables the formation of protein complexes that cannot be established when these proteins are translated in the cytosol, but the mechanism is poorly understood. Here we show that MYC protein complexes that involve binding to the intrinsically disordered region (IDR) of MYC are only formed when MYC is translated in TGs. TG-dependent protein complexes require TG-enriched mRNAs for assembly. These mRNAs bind to a new and widespread RNA-binding domain in neutral or negatively charged IDRs in several transcription factors, including MYC. RNA-IDR interaction changes the conformational ensemble of the IDR, enabling the formation of MYC protein complexes that act in the nucleus and control functions that cannot be accomplished by cytosolically-translated MYC. We propose that certain mRNAs have IDR chaperone activity as they control IDR conformations. In addition to post-translational modifications, we found a novel mode of protein activity regulation. Since RNA-IDR interactions are prevalent, we suggest that mRNA-dependent control of protein functional states is widespread.
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Affiliation(s)
- Yang Luo
- Cancer Biology and Genetics Program, Sloan Kettering Institute, New York, NY 10065, USA
| | - Supriya Pratihar
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
| | - Ellen H. Horste
- Cancer Biology and Genetics Program, Sloan Kettering Institute, New York, NY 10065, USA
- Gerstner Sloan Kettering Graduate School of Biomedical Sciences, New York, NY 10065, USA
| | - Sibylle Mitschka
- Cancer Biology and Genetics Program, Sloan Kettering Institute, New York, NY 10065, USA
| | | | - Hashim M. Al-Hashimi
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
| | - Christine Mayr
- Cancer Biology and Genetics Program, Sloan Kettering Institute, New York, NY 10065, USA
- Gerstner Sloan Kettering Graduate School of Biomedical Sciences, New York, NY 10065, USA
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18
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Multimodal cotranslational interactions direct assembly of the human multi-tRNA synthetase complex. Proc Natl Acad Sci U S A 2022; 119:e2205669119. [PMID: 36037331 PMCID: PMC9457175 DOI: 10.1073/pnas.2205669119] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Amino acid ligation to cognate transfer RNAs (tRNAs) is catalyzed by aminoacyl-tRNA synthetases (aaRSs)-essential interpreters of the genetic code during translation. Mammalian cells harbor 20 cytoplasmic aaRSs, out of which 9 (in 8 proteins), with 3 non-aaRS proteins, AIMPs 1 to 3, form the ∼1.25-MDa multi-tRNA synthetase complex (MSC). The function of MSC remains uncertain, as does its mechanism of assembly. Constituents of multiprotein complexes encounter obstacles during assembly, including inappropriate interactions, topological constraints, premature degradation of unassembled subunits, and suboptimal stoichiometry. To facilitate orderly and efficient complex formation, some complexes are assembled cotranslationally by a mechanism in which a fully formed, mature protein binds a nascent partner as it emerges from the translating ribosome. Here, we show out of the 121 possible interaction events between the 11 MSC constituents, 15 are cotranslational. AIMPs are involved in the majority of these cotranslational interactions, suggesting they are not only critical for MSC structure but also for assembly. Unexpectedly, several cotranslational events involve more than the usual dyad of interacting proteins. We show two modes of cotranslational interaction, namely a "multisite" mechanism in which two or more mature proteins bind the same nascent peptide at distinct sites and a second "piggy-back" mechanism in which a mature protein carries a second fully formed protein and binds to a single site on an emerging peptide. Multimodal mechanisms of cotranslational interaction offer a diversity of pathways for ordered, piecewise assembly of small subcomplexes into larger heteromultimeric complexes such as the mammalian MSC.
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19
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Falk F, Melo Palhares R, Waithaka A, Clayton C. Roles and interactions of the specialized initiation factors EIF4E2, EIF4E5 and EIF4E6 in Trypanosoma brucei: EIF4E2 maintains the abundances of S-phase mRNAs. Mol Microbiol 2022; 118:457-476. [PMID: 36056730 DOI: 10.1111/mmi.14978] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Revised: 08/14/2022] [Accepted: 08/30/2022] [Indexed: 11/29/2022]
Abstract
Trypanosoma brucei has six versions of the cap-binding translation initiation factor EIF4E. We investigated the functions of EIF4E2, EIF4E3, EIF4E5 and EIF4E6 in bloodstream forms. We confirmed the protein associations previously found in procyclic forms, and detected specific co-purification of some RNA-binding proteins. Bloodstream forms lacking EIF4E5 grew normally and differentiated to replication-incompetent procyclic forms. Depletion of EIF4E6 inhibited bloodstream-form trypanosome growth and translation. EIF4E2 co-purified only the putative RNA binding protein SLBP2. Bloodstream forms lacking EIF4E2 multiplied slowly, had a low maximal cell density, and expressed the stumpy-form marker PAD1, but showed no evidence for enhanced stumpy-form signalling. EIF4E2 knock-out cells differentiated readily to replication-competent procyclic forms. EIF4E2 was strongly associated with a subset of mRNAs that are maximally abundant in S-phase, and these all had decreased abundances in EIF4E2 knock-out cells. Three EIF4E2 target mRNAs are also bound and stabilized by the Pumilio domain protein PUF9. Yeast 2-hybrid results suggested that PUF9 interacts directly with SLBP2, but PUF9 was not detected in EIF4E2 pull-downs. We speculate that the EIF4E2-SLBP2 complex might interact with its target mRNAs, perhaps via PUF9, only early during G1/S, stabilizing the mRNAs in preparation for translation later in S-phase or in early G2.
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Affiliation(s)
- Franziska Falk
- Heidelberg University Centre for Molecular Biology (ZMBH), Im Neuenheimer Feld, Heidelberg, Germany
| | - Rafael Melo Palhares
- Heidelberg University Centre for Molecular Biology (ZMBH), Im Neuenheimer Feld, Heidelberg, Germany.,Institut für Mikro- und Molekularbiologie, Justus-Liebig-Universität Giessen, IFZ, Heinrich-Buff-Ring 26-32, 35392 Giessen, Germany
| | - Albina Waithaka
- Heidelberg University Centre for Molecular Biology (ZMBH), Im Neuenheimer Feld, Heidelberg, Germany
| | - Christine Clayton
- Heidelberg University Centre for Molecular Biology (ZMBH), Im Neuenheimer Feld, Heidelberg, Germany
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20
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Hibbard JVK, Vázquez N, Wallingford JB. Cilia proteins getting to work - how do they commute from the cytoplasm to the base of cilia? J Cell Sci 2022; 135:jcs259444. [PMID: 36073764 PMCID: PMC9482345 DOI: 10.1242/jcs.259444] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Cilia are multifunctional organelles that originated with the last eukaryotic common ancestor and play central roles in the life cycles of diverse organisms. The motile flagella that move single cells like sperm or unicellular organisms, the motile cilia on animal multiciliated cells that generate fluid flow in organs, and the immotile primary cilia that decorate nearly all cells in animals share many protein components in common, yet each also requires specialized proteins to perform their specialized functions. Despite a now-advanced understanding of how such proteins are transported within cilia, we still know very little about how they are transported from their sites of synthesis through the cytoplasm to the ciliary base. Here, we review the literature concerning this underappreciated topic in ciliary cell biology. We discuss both general mechanisms, as well as specific examples of motor-driven active transport and passive transport via diffusion-and-capture. We then provide deeper discussion of specific, illustrative examples, such as the diverse array of protein subunits that together comprise the intraflagellar transport (IFT) system and the multi-protein axonemal dynein motors that drive beating of motile cilia. We hope this Review will spur further work, shedding light not only on ciliogenesis and ciliary signaling, but also on intracellular transport in general.
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Affiliation(s)
| | | | - John B. Wallingford
- Department of Molecular Biosciences, University of Texas, Austin, TX 78751, USA
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21
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Morales-Polanco F, Lee JH, Barbosa NM, Frydman J. Cotranslational Mechanisms of Protein Biogenesis and Complex Assembly in Eukaryotes. Annu Rev Biomed Data Sci 2022; 5:67-94. [PMID: 35472290 PMCID: PMC11040709 DOI: 10.1146/annurev-biodatasci-121721-095858] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The formation of protein complexes is crucial to most biological functions. The cellular mechanisms governing protein complex biogenesis are not yet well understood, but some principles of cotranslational and posttranslational assembly are beginning to emerge. In bacteria, this process is favored by operons encoding subunits of protein complexes. Eukaryotic cells do not have polycistronic mRNAs, raising the question of how they orchestrate the encounter of unassembled subunits. Here we review the constraints and mechanisms governing eukaryotic co- and posttranslational protein folding and assembly, including the influence of elongation rate on nascent chain targeting, folding, and chaperone interactions. Recent evidence shows that mRNAs encoding subunits of oligomeric assemblies can undergo localized translation and form cytoplasmic condensates that might facilitate the assembly of protein complexes. Understanding the interplay between localized mRNA translation and cotranslational proteostasis will be critical to defining protein complex assembly in vivo.
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Affiliation(s)
| | - Jae Ho Lee
- Department of Biology, Stanford University, Stanford, California, USA;
| | - Natália M Barbosa
- Department of Biology, Stanford University, Stanford, California, USA;
| | - Judith Frydman
- Department of Biology, Stanford University, Stanford, California, USA;
- Department of Genetics, Stanford University, Stanford, California, USA
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22
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Esposito E, Weidemann DE, Rogers JM, Morton CM, Baybay EK, Chen J, Hauf S. Mitotic checkpoint gene expression is tuned by codon usage bias. EMBO J 2022; 41:e107896. [PMID: 35811551 PMCID: PMC9340482 DOI: 10.15252/embj.2021107896] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Revised: 05/30/2022] [Accepted: 06/06/2022] [Indexed: 11/09/2022] Open
Abstract
The mitotic checkpoint (also called spindle assembly checkpoint, SAC) is a signaling pathway that safeguards proper chromosome segregation. Correct functioning of the SAC depends on adequate protein concentrations and appropriate stoichiometries between SAC proteins. Yet very little is known about the regulation of SAC gene expression. Here, we show in the fission yeast Schizosaccharomyces pombe that a combination of short mRNA half-lives and long protein half-lives supports stable SAC protein levels. For the SAC genes mad2+ and mad3+ , their short mRNA half-lives are caused, in part, by a high frequency of nonoptimal codons. In contrast, mad1+ mRNA has a short half-life despite a higher frequency of optimal codons, and despite the lack of known RNA-destabilizing motifs. Hence, different SAC genes employ different strategies of expression. We further show that Mad1 homodimers form co-translationally, which may necessitate a certain codon usage pattern. Taken together, we propose that the codon usage of SAC genes is fine-tuned to ensure proper SAC function. Our work shines light on gene expression features that promote spindle assembly checkpoint function and suggests that synonymous mutations may weaken the checkpoint.
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Affiliation(s)
- Eric Esposito
- Department of Biological SciencesVirginia TechBlacksburgVAUSA
- Fralin Life Sciences InstituteVirginia TechBlacksburgVAUSA
| | - Douglas E Weidemann
- Department of Biological SciencesVirginia TechBlacksburgVAUSA
- Fralin Life Sciences InstituteVirginia TechBlacksburgVAUSA
| | - Jessie M Rogers
- Department of Biological SciencesVirginia TechBlacksburgVAUSA
- Fralin Life Sciences InstituteVirginia TechBlacksburgVAUSA
| | - Claire M Morton
- Department of Biological SciencesVirginia TechBlacksburgVAUSA
- Fralin Life Sciences InstituteVirginia TechBlacksburgVAUSA
| | - Erod Keaton Baybay
- Department of Biological SciencesVirginia TechBlacksburgVAUSA
- Fralin Life Sciences InstituteVirginia TechBlacksburgVAUSA
| | - Jing Chen
- Department of Biological SciencesVirginia TechBlacksburgVAUSA
- Fralin Life Sciences InstituteVirginia TechBlacksburgVAUSA
| | - Silke Hauf
- Department of Biological SciencesVirginia TechBlacksburgVAUSA
- Fralin Life Sciences InstituteVirginia TechBlacksburgVAUSA
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23
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Badonyi M, Marsh JA. Large protein complex interfaces have evolved to promote cotranslational assembly. eLife 2022; 11:79602. [PMID: 35899946 PMCID: PMC9365393 DOI: 10.7554/elife.79602] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Accepted: 07/27/2022] [Indexed: 11/13/2022] Open
Abstract
Assembly pathways of protein complexes should be precise and efficient to minimise misfolding and unwanted interactions with other proteins in the cell. One way to achieve this efficiency is by seeding assembly pathways during translation via the cotranslational assembly of subunits. While recent evidence suggests that such cotranslational assembly is widespread, little is known about the properties of protein complexes associated with the phenomenon. Here, using a combination of proteome-specific protein complex structures and publicly available ribosome profiling data, we show that cotranslational assembly is particularly common between subunits that form large intermolecular interfaces. To test whether large interfaces have evolved to promote cotranslational assembly, as opposed to cotranslational assembly being a non-adaptive consequence of large interfaces, we compared the sizes of first and last translated interfaces of heteromeric subunits in bacterial, yeast, and human complexes. When considering all together, we observe the N-terminal interface to be larger than the C-terminal interface 54% of the time, increasing to 64% when we exclude subunits with only small interfaces, which are unlikely to cotranslationally assemble. This strongly suggests that large interfaces have evolved as a means to maximise the chance of successful cotranslational subunit binding.
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Affiliation(s)
- Mihaly Badonyi
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, United Kingdom
| | - Joseph A Marsh
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, United Kingdom
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24
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Elías-Villalobos A, Duncan C, Mata J, Helmlinger D. Quantitative analysis of protein-RNA interactions in fission yeast. STAR Protoc 2022; 3:101373. [PMID: 35586315 PMCID: PMC9108979 DOI: 10.1016/j.xpro.2022.101373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Characterizing the interactions between RNAs and proteins in vivo is key to better understand how organisms regulate gene expression. Here, we describe a robust and quantitative protocol to measure specific RNA-protein interactions in a native context using RNA immunoprecipitation (RIP). We provide a comprehensive experimental framework to detect cotranslational interactions and detail the quantitative analysis of purified RNAs by PCR and high-throughput sequencing. Although we developed the protocol in fission yeast, it can be readily implemented in other yeast species. For complete details on the use and execution of this protocol, please refer to Toullec et al. (2021). Simple and robust detection of RNA-protein interactions in a native context Ribonucleoprotein complex isolated by immunoprecipitation Quantitative analysis of purified RNA by PCR or high-throughput sequencing Detailed experimental pipeline to demonstrate cotranslational interactions
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Affiliation(s)
- Alberto Elías-Villalobos
- CRBM, University of Montpellier, CNRS, Montpellier, France.,Instituto de Biomedicina de Sevilla (IBiS), Universidad de Sevilla-Hospital Universitario Virgen del Rocío-CSIC, Seville, Spain.,Departamento de Genética, Universidad de Sevilla, Seville, Spain
| | - Caia Duncan
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW, UK
| | - Juan Mata
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW, UK
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25
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Padovani C, Jevtić P, Rapé M. Quality control of protein complex composition. Mol Cell 2022; 82:1439-1450. [PMID: 35316660 DOI: 10.1016/j.molcel.2022.02.029] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 01/26/2022] [Accepted: 02/21/2022] [Indexed: 12/13/2022]
Abstract
Eukaryotic cells possess hundreds of protein complexes that contain multiple subunits and must be formed at the correct time and place during development. Despite specific assembly pathways, cells frequently encounter complexes with missing or aberrant subunits that can disrupt important signaling events. Cells, therefore, employ several ubiquitin-dependent quality control pathways that can prevent, correct, or degrade flawed complexes. In this review, we will discuss our emerging understanding of such quality control of protein complex composition.
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Affiliation(s)
- Chris Padovani
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, CA 94720, USA
| | - Predrag Jevtić
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, CA 94720, USA; Howard Hughes Medical Institute, University of California at Berkeley, Berkeley, CA 94720, USA
| | - Michael Rapé
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, CA 94720, USA; Howard Hughes Medical Institute, University of California at Berkeley, Berkeley, CA 94720, USA; California Institute for Quantitative Biosciences (QB3), University of California at Berkeley, Berkeley, CA 94720, USA.
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26
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Seidel M, Becker A, Pereira F, Landry JJM, de Azevedo NTD, Fusco CM, Kaindl E, Romanov N, Baumbach J, Langer JD, Schuman EM, Patil KR, Hummer G, Benes V, Beck M. Co-translational assembly orchestrates competing biogenesis pathways. Nat Commun 2022; 13:1224. [PMID: 35264577 PMCID: PMC8907234 DOI: 10.1038/s41467-022-28878-5] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Accepted: 02/11/2022] [Indexed: 12/27/2022] Open
Abstract
During the co-translational assembly of protein complexes, a fully synthesized subunit engages with the nascent chain of a newly synthesized interaction partner. Such events are thought to contribute to productive assembly, but their exact physiological relevance remains underexplored. Here, we examine structural motifs contained in nucleoporins for their potential to facilitate co-translational assembly. We experimentally test candidate structural motifs and identify several previously unknown co-translational interactions. We demonstrate by selective ribosome profiling that domain invasion motifs of beta-propellers, coiled-coils, and short linear motifs may act as co-translational assembly domains. Such motifs are often contained in proteins that are members of multiple complexes (moonlighters) and engage with closely related paralogs. Surprisingly, moonlighters and paralogs assemble co-translationally in only some but not all of the relevant biogenesis pathways. Our results highlight the regulatory complexity of assembly pathways.
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Affiliation(s)
- Maximilian Seidel
- Department of Molecular Sociology, Max Planck Institute of Biophysics, Frankfurt, Germany
- Faculty of Bioscience, Heidelberg University, Heidelberg, Germany
| | - Anja Becker
- Department of Molecular Sociology, Max Planck Institute of Biophysics, Frankfurt, Germany
| | - Filipa Pereira
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, USA
| | - Jonathan J M Landry
- Genomics Core Facility, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | | | - Claudia M Fusco
- Department of Synaptic Plasticity, Max Planck Institute for Brain Research, Frankfurt, Germany
| | - Eva Kaindl
- Department of Molecular Sociology, Max Planck Institute of Biophysics, Frankfurt, Germany
| | - Natalie Romanov
- Department of Molecular Sociology, Max Planck Institute of Biophysics, Frankfurt, Germany
| | - Janina Baumbach
- Department of Molecular Sociology, Max Planck Institute of Biophysics, Frankfurt, Germany
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Julian D Langer
- Department of Synaptic Plasticity, Max Planck Institute for Brain Research, Frankfurt, Germany
- Membrane Proteomics and Mass Spectrometry, Max Planck Institute of Biophysics, Frankfurt, Germany
- Mass Spectrometry, Max Planck Institute for Brain Research, Frankfurt, Germany
| | - Erin M Schuman
- Department of Synaptic Plasticity, Max Planck Institute for Brain Research, Frankfurt, Germany
| | - Kiran Raosaheb Patil
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
- Medical Research Council Toxicology Unit, University of Cambridge, Cambridge, United Kingdom
| | - Gerhard Hummer
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Frankfurt, Germany
- Institute of Biophysics, Goethe University Frankfurt, Frankfurt, Germany
| | - Vladimir Benes
- Genomics Core Facility, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Martin Beck
- Department of Molecular Sociology, Max Planck Institute of Biophysics, Frankfurt, Germany.
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany.
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27
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Cotranslational interaction of human EBP50 and ezrin overcomes masked binding site during complex assembly. Proc Natl Acad Sci U S A 2022; 119:2115799119. [PMID: 35140182 PMCID: PMC8851480 DOI: 10.1073/pnas.2115799119] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/23/2021] [Indexed: 12/13/2022] Open
Abstract
Multiprotein assemblages are the intracellular workhorses of many physiological processes. Assembly of constituents into complexes can be driven by stochastic, domain-dependent, posttranslational events in which mature, folded proteins specifically interact. However, inaccessibility of interacting surfaces in mature proteins (e.g., due to "buried" domains) can obstruct complex formation. Mechanisms by which multiprotein complex constituents overcome topological impediments remain enigmatic. For example, the heterodimeric complex formed by EBP50 and ezrin must address this issue as the EBP50-interacting domain in ezrin is obstructed by a self-interaction that occupies the EBP50 binding site. Here, we show that the EBP50-ezrin complex is formed by a cotranslational mechanism in which the C terminus of mature, fully formed EBP50 binds the emerging, ribosome-bound N-terminal FERM domain of ezrin during EZR mRNA translation. Consistent with this observation, a C-terminal EBP50 peptide mimetic reduces the cotranslational interaction and abrogates EBP50-ezrin complex formation. Phosphorylation of EBP50 at Ser339 and Ser340 abrogates the cotranslational interaction and inhibits complex formation. In summary, we show that the function of eukaryotic mRNA translation extends beyond "simple" generation of a linear peptide chain that folds into a tertiary structure, potentially for subsequent complex assembly; importantly, translation can facilitate interactions with sterically inaccessible domains to form functional multiprotein complexes.
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28
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Younus I, Kochkina S, Choi CC, Sun W, Ford RC. ATP-Binding Cassette Transporters: Snap-on Complexes? Subcell Biochem 2022; 99:35-82. [PMID: 36151373 DOI: 10.1007/978-3-031-00793-4_2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
ATP-binding cassette (ABC) transporters are one of the largest families of membrane proteins in prokaryotic organisms. Much is now understood about the structure of these transporters and many reviews have been written on that subject. In contrast, less has been written on the assembly of ABC transporter complexes and this will be a major focus of this book chapter. The complexes are formed from two cytoplasmic subunits that are highly conserved (in terms of their primary and three-dimensional structures) across the whole family. These ATP-binding subunits give rise to the name of the family. They must assemble with two transmembrane subunits that will typically form the permease component of the transporter. The transmembrane subunits have been found to be surprisingly diverse in structure when the whole family is examined, with seven distinct folds identified so far. Hence nucleotide-binding subunits appear to have been bolted on to a variety of transmembrane platforms during evolution, leading to a greater variety in function. Furthermore, many importers within the family utilise a further external substrate-binding component to trap scarce substrates and deliver them to the correct permease components. In this chapter, we will discuss whether assembly of the various ABC transporter subunits occurs with high fidelity within the crowded cellular environment and whether promiscuity in assembly of transmembrane and cytoplasmic components can occur. We also discuss the new AlphaFold protein structure prediction tool which predicts a new type of transmembrane domain fold within the ABC transporters that is associated with cation exporters of bacteria and plants.
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Affiliation(s)
- Iqra Younus
- Faculty of Biology, Medicine and Health, School of Biological Sciences, The University of Manchester, Manchester, UK
| | - Sofia Kochkina
- Faculty of Biology, Medicine and Health, School of Biological Sciences, The University of Manchester, Manchester, UK
| | - Cheri C Choi
- Faculty of Biology, Medicine and Health, School of Biological Sciences, The University of Manchester, Manchester, UK
| | - Wenjuan Sun
- Faculty of Biology, Medicine and Health, School of Biological Sciences, The University of Manchester, Manchester, UK
| | - Robert C Ford
- Faculty of Biology, Medicine and Health, School of Biological Sciences, The University of Manchester, Manchester, UK.
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29
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Toullec D, Elías-Villalobos A, Faux C, Noly A, Lledo G, Séveno M, Helmlinger D. The Hsp90 cochaperone TTT promotes cotranslational maturation of PIKKs prior to complex assembly. Cell Rep 2021; 37:109867. [PMID: 34686329 DOI: 10.1016/j.celrep.2021.109867] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Revised: 07/30/2021] [Accepted: 09/30/2021] [Indexed: 01/28/2023] Open
Abstract
Phosphatidylinositol 3-kinase-related kinases (PIKKs) are a family of kinases that control fundamental processes, including cell growth, DNA damage repair, and gene expression. Although their regulation and activities are well characterized, little is known about how PIKKs fold and assemble into active complexes. Previous work has identified a heat shock protein 90 (Hsp90) cochaperone, the TTT complex, that specifically stabilizes PIKKs. Here, we describe a mechanism by which TTT promotes their de novo maturation in fission yeast. We show that TTT recognizes newly synthesized PIKKs during translation. Although PIKKs form multimeric complexes, we find that they do not engage in cotranslational assembly with their partners. Rather, our findings suggest a model by which TTT protects nascent PIKK polypeptides from misfolding and degradation because PIKKs acquire their native state after translation is terminated. Thus, PIKK maturation and assembly are temporally segregated, suggesting that the biogenesis of large complexes requires both dedicated chaperones and cotranslational interactions between subunits.
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Affiliation(s)
- Damien Toullec
- CRBM, University of Montpellier, CNRS, Montpellier, France
| | | | - Céline Faux
- CRBM, University of Montpellier, CNRS, Montpellier, France
| | - Ambre Noly
- CRBM, University of Montpellier, CNRS, Montpellier, France
| | | | - Martial Séveno
- BioCampus Montpellier, University of Montpellier, CNRS, INSERM, Montpellier, France
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30
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Lashkevich KA, Dmitriev SE. mRNA Targeting, Transport and Local Translation in Eukaryotic Cells: From the Classical View to a Diversity of New Concepts. Mol Biol 2021; 55:507-537. [PMID: 34092811 PMCID: PMC8164833 DOI: 10.1134/s0026893321030080] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 02/26/2021] [Accepted: 03/12/2021] [Indexed: 12/28/2022]
Abstract
Spatial organization of protein biosynthesis in the eukaryotic cell has been studied for more than fifty years, thus many facts have already been included in textbooks. According to the classical view, mRNA transcripts encoding secreted and transmembrane proteins are translated by ribosomes associated with endoplasmic reticulum membranes, while soluble cytoplasmic proteins are synthesized on free polysomes. However, in the last few years, new data has emerged, revealing selective translation of mRNA on mitochondria and plastids, in proximity to peroxisomes and endosomes, in various granules and at the cytoskeleton (actin network, vimentin intermediate filaments, microtubules and centrosomes). There are also long-standing debates about the possibility of protein synthesis in the nucleus. Localized translation can be determined by targeting signals in the synthesized protein, nucleotide sequences in the mRNA itself, or both. With RNA-binding proteins, many transcripts can be assembled into specific RNA condensates and form RNP particles, which may be transported by molecular motors to the sites of active translation, form granules and provoke liquid-liquid phase separation in the cytoplasm, both under normal conditions and during cell stress. The translation of some mRNAs occurs in specialized "translation factories," assemblysomes, transperons and other structures necessary for the correct folding of proteins, interaction with functional partners and formation of oligomeric complexes. Intracellular localization of mRNA has a significant impact on the efficiency of its translation and presumably determines its response to cellular stress. Compartmentalization of mRNAs and the translation machinery also plays an important role in viral infections. Many viruses provoke the formation of specific intracellular structures, virus factories, for the production of their proteins. Here we review the current concepts of the molecular mechanisms of transport, selective localization and local translation of cellular and viral mRNAs, their effects on protein targeting and topogenesis, and on the regulation of protein biosynthesis in different compartments of the eukaryotic cell. Special attention is paid to new systems biology approaches, providing new cues to the study of localized translation.
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Affiliation(s)
- Kseniya A Lashkevich
- Belozersky Institute of Physico-Chemical Biology, Moscow State University, 119234 Moscow, Russia.,Faculty of Bioengineering and Bioinformatics, Moscow State University, 119234 Moscow, Russia
| | - Sergey E Dmitriev
- Belozersky Institute of Physico-Chemical Biology, Moscow State University, 119234 Moscow, Russia.,Faculty of Bioengineering and Bioinformatics, Moscow State University, 119234 Moscow, Russia.,Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
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31
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Koubek J, Schmitt J, Galmozzi CV, Kramer G. Mechanisms of Cotranslational Protein Maturation in Bacteria. Front Mol Biosci 2021; 8:689755. [PMID: 34113653 PMCID: PMC8185961 DOI: 10.3389/fmolb.2021.689755] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Accepted: 05/10/2021] [Indexed: 01/05/2023] Open
Abstract
Growing cells invest a significant part of their biosynthetic capacity into the production of proteins. To become functional, newly-synthesized proteins must be N-terminally processed, folded and often translocated to other cellular compartments. A general strategy is to integrate these protein maturation processes with translation, by cotranslationally engaging processing enzymes, chaperones and targeting factors with the nascent polypeptide. Precise coordination of all factors involved is critical for the efficiency and accuracy of protein synthesis and cellular homeostasis. This review provides an overview of the current knowledge on cotranslational protein maturation, with a focus on the production of cytosolic proteins in bacteria. We describe the role of the ribosome and the chaperone network in protein folding and how the dynamic interplay of all cotranslationally acting factors guides the sequence of cotranslational events. Finally, we discuss recent data demonstrating the coupling of protein synthesis with the assembly of protein complexes and end with a brief discussion of outstanding questions and emerging concepts in the field of cotranslational protein maturation.
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Affiliation(s)
- Jiří Koubek
- Center for Molecular Biology of Heidelberg University (ZMBH) and German Cancer Research Center (DKFZ), DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Jaro Schmitt
- Center for Molecular Biology of Heidelberg University (ZMBH) and German Cancer Research Center (DKFZ), DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Carla Veronica Galmozzi
- Center for Molecular Biology of Heidelberg University (ZMBH) and German Cancer Research Center (DKFZ), DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Günter Kramer
- Center for Molecular Biology of Heidelberg University (ZMBH) and German Cancer Research Center (DKFZ), DKFZ-ZMBH Alliance, Heidelberg, Germany
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32
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Pleiner T, Hazu M, Tomaleri GP, Januszyk K, Oania RS, Sweredoski MJ, Moradian A, Guna A, Voorhees RM. WNK1 is an assembly factor for the human ER membrane protein complex. Mol Cell 2021; 81:2693-2704.e12. [PMID: 33964204 DOI: 10.1016/j.molcel.2021.04.013] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 03/02/2021] [Accepted: 04/14/2021] [Indexed: 12/13/2022]
Abstract
The assembly of nascent proteins into multi-subunit complexes is a tightly regulated process that must occur at high fidelity to maintain cellular homeostasis. The ER membrane protein complex (EMC) is an essential insertase that requires seven membrane-spanning and two soluble cytosolic subunits to function. Here, we show that the kinase with no lysine 1 (WNK1), known for its role in hypertension and neuropathy, functions as an assembly factor for the human EMC. WNK1 uses a conserved amphipathic helix to stabilize the soluble subunit, EMC2, by binding to the EMC2-8 interface. Shielding this hydrophobic surface prevents promiscuous interactions of unassembled EMC2 and directly competes for binding of E3 ubiquitin ligases, permitting assembly. Depletion of WNK1 thus destabilizes both the EMC and its membrane protein clients. This work describes an unexpected role for WNK1 in protein biogenesis and defines the general requirements of an assembly factor that will apply across the proteome.
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Affiliation(s)
- Tino Pleiner
- Division of Biology and Biological Engineering, California Institute of Technology, 1200 E. California Blvd., Pasadena, CA 91125, USA
| | - Masami Hazu
- Division of Biology and Biological Engineering, California Institute of Technology, 1200 E. California Blvd., Pasadena, CA 91125, USA
| | - Giovani Pinton Tomaleri
- Division of Biology and Biological Engineering, California Institute of Technology, 1200 E. California Blvd., Pasadena, CA 91125, USA
| | - Kurt Januszyk
- Division of Biology and Biological Engineering, California Institute of Technology, 1200 E. California Blvd., Pasadena, CA 91125, USA
| | - Robert S Oania
- Division of Biology and Biological Engineering, California Institute of Technology, 1200 E. California Blvd., Pasadena, CA 91125, USA
| | - Michael J Sweredoski
- Division of Biology and Biological Engineering, California Institute of Technology, 1200 E. California Blvd., Pasadena, CA 91125, USA
| | - Annie Moradian
- Division of Biology and Biological Engineering, California Institute of Technology, 1200 E. California Blvd., Pasadena, CA 91125, USA
| | - Alina Guna
- Division of Biology and Biological Engineering, California Institute of Technology, 1200 E. California Blvd., Pasadena, CA 91125, USA
| | - Rebecca M Voorhees
- Division of Biology and Biological Engineering, California Institute of Technology, 1200 E. California Blvd., Pasadena, CA 91125, USA.
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33
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Lautier O, Penzo A, Rouvière JO, Chevreux G, Collet L, Loïodice I, Taddei A, Devaux F, Collart MA, Palancade B. Co-translational assembly and localized translation of nucleoporins in nuclear pore complex biogenesis. Mol Cell 2021; 81:2417-2427.e5. [PMID: 33838103 DOI: 10.1016/j.molcel.2021.03.030] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Revised: 02/24/2021] [Accepted: 03/18/2021] [Indexed: 01/03/2023]
Abstract
mRNA translation is coupled to multiprotein complex assembly in the cytoplasm or to protein delivery into intracellular compartments. Here, by combining systematic RNA immunoprecipitation and single-molecule RNA imaging in yeast, we have provided a complete depiction of the co-translational events involved in the biogenesis of a large multiprotein assembly, the nuclear pore complex (NPC). We report that binary interactions between NPC subunits can be established during translation, in the cytoplasm. Strikingly, the nucleoporins Nup1/Nup2, together with a number of nuclear proteins, are instead translated at nuclear pores, through a mechanism involving interactions between their nascent N-termini and nuclear transport receptors. Uncoupling this co-translational recruitment further triggers the formation of cytoplasmic foci of unassembled polypeptides. Altogether, our data reveal that distinct, spatially segregated modes of co-translational interactions foster the ordered assembly of NPC subunits and that localized translation can ensure the proper delivery of proteins to the pore and the nucleus.
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Affiliation(s)
- Ophélie Lautier
- Université de Paris, CNRS, Institut Jacques Monod, 75006 Paris, France
| | - Arianna Penzo
- Université de Paris, CNRS, Institut Jacques Monod, 75006 Paris, France
| | - Jérôme O Rouvière
- Université de Paris, CNRS, Institut Jacques Monod, 75006 Paris, France
| | - Guillaume Chevreux
- ProteoSeine@IJM, Université de Paris, CNRS, Institut Jacques Monod, 75006 Paris, France
| | - Louis Collet
- Université de Paris, CNRS, Institut Jacques Monod, 75006 Paris, France
| | - Isabelle Loïodice
- Institut Curie, PSL Research University, CNRS, Sorbonne Université, UMR3664 Nuclear Dynamics, Paris, France
| | - Angela Taddei
- Institut Curie, PSL Research University, CNRS, Sorbonne Université, UMR3664 Nuclear Dynamics, Paris, France
| | - Frédéric Devaux
- Sorbonne Université, CNRS, Institut de biologie Paris-Seine (IBPS), UMR 7238, Laboratoire de biologie computationnelle et quantitative, LCQB, 4 place Jussieu, 75005 Paris, France
| | - Martine A Collart
- Department of Microbiology and Molecular Medicine, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Benoit Palancade
- Université de Paris, CNRS, Institut Jacques Monod, 75006 Paris, France.
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34
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Morales-Polanco F, Bates C, Lui J, Casson J, Solari CA, Pizzinga M, Forte G, Griffin C, Garner KEL, Burt HE, Dixon HL, Hubbard S, Portela P, Ashe MP. Core Fermentation (CoFe) granules focus coordinated glycolytic mRNA localization and translation to fuel glucose fermentation. iScience 2021; 24:102069. [PMID: 33554071 PMCID: PMC7859310 DOI: 10.1016/j.isci.2021.102069] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Revised: 12/16/2020] [Accepted: 01/12/2021] [Indexed: 12/24/2022] Open
Abstract
Glycolysis is a fundamental metabolic pathway for glucose catabolism across biology, and glycolytic enzymes are among the most abundant proteins in cells. Their expression at such levels provides a particular challenge. Here we demonstrate that the glycolytic mRNAs are localized to granules in yeast and human cells. Detailed live cell and smFISH studies in yeast show that the mRNAs are actively translated in granules, and this translation appears critical for the localization. Furthermore, this arrangement is likely to facilitate the higher level organization and control of the glycolytic pathway. Indeed, the degree of fermentation required by cells is intrinsically connected to the extent of mRNA localization to granules. On this basis, we term these granules, core fermentation (CoFe) granules; they appear to represent translation factories, allowing high-level coordinated enzyme synthesis for a critical metabolic pathway.
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Affiliation(s)
- Fabian Morales-Polanco
- School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester Academic Health Science Centre, Michael Smith Building, Oxford Road, Manchester M13 9PT, UK
| | - Christian Bates
- School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester Academic Health Science Centre, Michael Smith Building, Oxford Road, Manchester M13 9PT, UK
| | - Jennifer Lui
- School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester Academic Health Science Centre, Michael Smith Building, Oxford Road, Manchester M13 9PT, UK
| | - Joseph Casson
- School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester Academic Health Science Centre, Michael Smith Building, Oxford Road, Manchester M13 9PT, UK
| | - Clara A Solari
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, IQUIBICEN-CONICET, Buenos Aires, Argentina
| | - Mariavittoria Pizzinga
- School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester Academic Health Science Centre, Michael Smith Building, Oxford Road, Manchester M13 9PT, UK
| | - Gabriela Forte
- School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester Academic Health Science Centre, Michael Smith Building, Oxford Road, Manchester M13 9PT, UK
| | - Claire Griffin
- School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester Academic Health Science Centre, Michael Smith Building, Oxford Road, Manchester M13 9PT, UK
| | - Kirsten E L Garner
- School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester Academic Health Science Centre, Michael Smith Building, Oxford Road, Manchester M13 9PT, UK
| | - Harriet E Burt
- School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester Academic Health Science Centre, Michael Smith Building, Oxford Road, Manchester M13 9PT, UK
| | - Hannah L Dixon
- School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester Academic Health Science Centre, Michael Smith Building, Oxford Road, Manchester M13 9PT, UK
| | - Simon Hubbard
- School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester Academic Health Science Centre, Michael Smith Building, Oxford Road, Manchester M13 9PT, UK
| | - Paula Portela
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, IQUIBICEN-CONICET, Buenos Aires, Argentina
| | - Mark P Ashe
- School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester Academic Health Science Centre, Michael Smith Building, Oxford Road, Manchester M13 9PT, UK
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Heidenreich M, Georgeson JM, Locatelli E, Rovigatti L, Nandi SK, Steinberg A, Nadav Y, Shimoni E, Safran SA, Doye JPK, Levy ED. Designer protein assemblies with tunable phase diagrams in living cells. Nat Chem Biol 2020; 16:939-945. [PMID: 32661377 DOI: 10.1038/s41589-020-0576-z] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Accepted: 05/22/2020] [Indexed: 12/14/2022]
Abstract
Protein self-organization is a hallmark of biological systems. Although the physicochemical principles governing protein-protein interactions have long been known, the principles by which such nanoscale interactions generate diverse phenotypes of mesoscale assemblies, including phase-separated compartments, remain challenging to characterize. To illuminate such principles, we create a system of two proteins designed to interact and form mesh-like assemblies. We devise a new strategy to map high-resolution phase diagrams in living cells, which provide self-assembly signatures of this system. The structural modularity of the two protein components allows straightforward modification of their molecular properties, enabling us to characterize how interaction affinity impacts the phase diagram and material state of the assemblies in vivo. The phase diagrams and their dependence on interaction affinity were captured by theory and simulations, including out-of-equilibrium effects seen in growing cells. Finally, we find that cotranslational protein binding suffices to recruit a messenger RNA to the designed micron-scale structures.
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Affiliation(s)
- Meta Heidenreich
- Department of Structural Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Joseph M Georgeson
- Department of Structural Biology, Weizmann Institute of Science, Rehovot, Israel
| | | | - Lorenzo Rovigatti
- Physical & Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, Oxford, UK.
- Department of Physics, Sapienza Università di Roma, Rome, Italy.
| | - Saroj Kumar Nandi
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot, Israel
- TIFR Centre for Interdisciplinary Sciences, Tata Institute of Fundamental Research, Hyderabad, India
| | - Avital Steinberg
- Department of Structural Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Yotam Nadav
- Department of Structural Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Eyal Shimoni
- Department of Chemical Research Support, Weizmann Institute of Science, Rehovot, Israel
| | - Samuel A Safran
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot, Israel.
| | - Jonathan P K Doye
- Physical & Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, Oxford, UK.
| | - Emmanuel D Levy
- Department of Structural Biology, Weizmann Institute of Science, Rehovot, Israel.
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Ren C, Deng K, Wang Z, Deng M, Fan Y, Zhang Y, Ma J, Wang S, Liu Z, Wang F. Reinterpreting sheep muscle strand-specific RNA sequencing data showing extensive 3'UTR extensions. Anim Genet 2020; 51:788-798. [PMID: 32696483 DOI: 10.1111/age.12987] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Revised: 05/16/2020] [Accepted: 06/23/2020] [Indexed: 12/01/2022]
Abstract
The more complex 3' UTR in higher organisms may have the function of increasing post-transcriptional gene regulation. Recent RNA sequencing technologies have provided us with the possibility to capture the complete 3' UTR landscape of different species and cells. However, no systematic analysis of sheep-related 3' UTR has been performed. Here, we conducted a detailed analysis of the 3' UTR with the primary goal of identifying intact 3' UTR landscapes in the sheep muscles of the three developmental stages. Based on strand-specific RNA sequencing (ssRNA-seq) data, we found that thousands of genes in sheep muscle are continuously transcribed after the UTR of the reference genome (Oar_v4.0). More than 66% of the 3' UTR extensions exhibit similar expression trends to their upstream gene exons. These 3' UTR extensions strongly enrich thousands of conserved microRNA binding sites. The 3' UTR extension-associated RNA of PFKM (PuaRNA) was predicted to be derived from the 3' UTR of PFKM. In sheep myocytes, myotubes and various tissues, the expression pattern of PuaRNA is positively correlated with that of PFKM. Taken together, these new 3' UTR annotations greatly extend the range of mammalian post-transcriptional regulatory networks, which have a particular impact on the regulation of sheep muscle development.
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Affiliation(s)
- Caifang Ren
- Institute of Sheep and Goat Science, Nanjing Agricultural University, Weigang Street, Xuanwu District, Nanjing, Jiangsu, 210095, China.,School of Medicine, Jiangsu University, Zhengjiang, Jiangsu, 212013, China
| | - Kaiping Deng
- Institute of Sheep and Goat Science, Nanjing Agricultural University, Weigang Street, Xuanwu District, Nanjing, Jiangsu, 210095, China
| | - Zhibo Wang
- Institute of Sheep and Goat Science, Nanjing Agricultural University, Weigang Street, Xuanwu District, Nanjing, Jiangsu, 210095, China
| | - Mingtian Deng
- Institute of Sheep and Goat Science, Nanjing Agricultural University, Weigang Street, Xuanwu District, Nanjing, Jiangsu, 210095, China
| | - Yixuan Fan
- Institute of Sheep and Goat Science, Nanjing Agricultural University, Weigang Street, Xuanwu District, Nanjing, Jiangsu, 210095, China
| | - Yanli Zhang
- Institute of Sheep and Goat Science, Nanjing Agricultural University, Weigang Street, Xuanwu District, Nanjing, Jiangsu, 210095, China
| | - Jianyu Ma
- Institute of Sheep and Goat Science, Nanjing Agricultural University, Weigang Street, Xuanwu District, Nanjing, Jiangsu, 210095, China
| | - Shuting Wang
- Institute of Sheep and Goat Science, Nanjing Agricultural University, Weigang Street, Xuanwu District, Nanjing, Jiangsu, 210095, China
| | - Zifei Liu
- Institute of Sheep and Goat Science, Nanjing Agricultural University, Weigang Street, Xuanwu District, Nanjing, Jiangsu, 210095, China
| | - Feng Wang
- Institute of Sheep and Goat Science, Nanjing Agricultural University, Weigang Street, Xuanwu District, Nanjing, Jiangsu, 210095, China
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eIF3 Associates with 80S Ribosomes to Promote Translation Elongation, Mitochondrial Homeostasis, and Muscle Health. Mol Cell 2020; 79:575-587.e7. [PMID: 32589965 DOI: 10.1016/j.molcel.2020.06.003] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2019] [Revised: 12/06/2019] [Accepted: 06/01/2020] [Indexed: 12/28/2022]
Abstract
eIF3, a multi-subunit complex with numerous functions in canonical translation initiation, is known to interact with 40S and 60S ribosomal proteins and translation elongation factors, but a direct involvement in translation elongation has never been demonstrated. We found that eIF3 deficiency reduced early ribosomal elongation speed between codons 25 and 75 on a set of ∼2,700 mRNAs encoding proteins associated with mitochondrial and membrane functions, resulting in defective synthesis of their encoded proteins. To promote elongation, eIF3 interacts with 80S ribosomes translating the first ∼60 codons and serves to recruit protein quality-control factors, functions required for normal mitochondrial physiology. Accordingly, eIF3e+/- mice accumulate defective mitochondria in skeletal muscle and show a progressive decline in muscle strength. Hence, eIF3 interacts with 80S ribosomes to enhance, at the level of early elongation, the synthesis of proteins with membrane-associated functions, an activity that is critical for mitochondrial physiology and muscle health.
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38
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Collart MA, Weiss B. Ribosome pausing, a dangerous necessity for co-translational events. Nucleic Acids Res 2020; 48:1043-1055. [PMID: 31598688 PMCID: PMC7026645 DOI: 10.1093/nar/gkz763] [Citation(s) in RCA: 87] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Revised: 08/13/2019] [Accepted: 08/21/2019] [Indexed: 12/31/2022] Open
Abstract
In recent years translation elongation has emerged as an important contributor to the regulation of gene expression. There are multiple quality control checkpoints along the way of producing mature proteins and targeting them to the right cellular compartment, or associating them correctly with their partners. Ribosomes pause to allow co-translational protein folding, protein targeting or protein interactions, and the pausing is dictated by a combination of the mRNA sequence and structure, the tRNA availability and the nascent peptide. However, ribosome pausing can also lead to ribosome collisions and co-translational degradation of both mRNA and nascent chain. Understanding how the translating ribosome tunes the different maturation steps that nascent proteins must undergo, what the timing of these maturation events is, and how degradation can be avoided when pausing is needed, is now possible by the emergence of methods to follow ribosome dynamics in vivo. This review summarizes some of the recent studies that have advanced our knowledge about co-translational events using the power of ribosome profiling, and some of the questions that have emerged from these studies.
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Affiliation(s)
- Martine A Collart
- Department of Microbiology and Molecular Medicine, Faculty of Medicine, University of Geneva, Institute of Genetics and Genomics, Geneva, 1 rue Michel Servet, 1211 Genève 4, Switzerland
| | - Benjamin Weiss
- Department of Microbiology and Molecular Medicine, Faculty of Medicine, University of Geneva, Institute of Genetics and Genomics, Geneva, 1 rue Michel Servet, 1211 Genève 4, Switzerland
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Cotranslational Folding of Proteins on the Ribosome. Biomolecules 2020; 10:biom10010097. [PMID: 31936054 PMCID: PMC7023365 DOI: 10.3390/biom10010097] [Citation(s) in RCA: 61] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Revised: 12/20/2019] [Accepted: 12/25/2019] [Indexed: 02/04/2023] Open
Abstract
Many proteins in the cell fold cotranslationally within the restricted space of the polypeptide exit tunnel or at the surface of the ribosome. A growing body of evidence suggests that the ribosome can alter the folding trajectory in many different ways. In this review, we summarize the recent examples of how translation affects folding of single-domain, multiple-domain and oligomeric proteins. The vectorial nature of translation, the spatial constraints of the exit tunnel, and the electrostatic properties of the ribosome-nascent peptide complex define the onset of early folding events. The ribosome can facilitate protein compaction, induce the formation of intermediates that are not observed in solution, or delay the onset of folding. Examples of single-domain proteins suggest that early compaction events can define the folding pathway for some types of domain structures. Folding of multi-domain proteins proceeds in a domain-wise fashion, with each domain having its role in stabilizing or destabilizing neighboring domains. Finally, the assembly of protein complexes can also begin cotranslationally. In all these cases, the ribosome helps the nascent protein to attain a native fold and avoid the kinetic traps of misfolding.
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40
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Eichel CA, Ríos-Pérez EB, Liu F, Jameson MB, Jones DK, Knickelbine JJ, Robertson GA. A microtranslatome coordinately regulates sodium and potassium currents in the human heart. eLife 2019; 8:52654. [PMID: 31670657 PMCID: PMC6867827 DOI: 10.7554/elife.52654] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Accepted: 10/23/2019] [Indexed: 12/16/2022] Open
Abstract
Catastrophic arrhythmias and sudden cardiac death can occur with even a small imbalance between inward sodium currents and outward potassium currents, but mechanisms establishing this critical balance are not understood. Here, we show that mRNA transcripts encoding INa and IKr channels (SCN5A and hERG, respectively) are associated in defined complexes during protein translation. Using biochemical, electrophysiological and single-molecule fluorescence localization approaches, we find that roughly half the hERG translational complexes contain SCN5A transcripts. Moreover, the transcripts are regulated in a way that alters functional expression of both channels at the membrane. Association and coordinate regulation of transcripts in discrete ‘microtranslatomes’ represents a new paradigm controlling electrical activity in heart and other excitable tissues.
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Affiliation(s)
- Catherine A Eichel
- Department of Neuroscience and Cardiovascular Research Center, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, United States
| | - Erick B Ríos-Pérez
- Department of Neuroscience and Cardiovascular Research Center, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, United States
| | - Fang Liu
- Department of Neuroscience and Cardiovascular Research Center, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, United States
| | - Margaret B Jameson
- Department of Neuroscience and Cardiovascular Research Center, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, United States
| | - David K Jones
- Department of Neuroscience and Cardiovascular Research Center, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, United States
| | - Jennifer J Knickelbine
- Department of Neuroscience and Cardiovascular Research Center, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, United States
| | - Gail A Robertson
- Department of Neuroscience and Cardiovascular Research Center, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, United States
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41
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Omomyc Reveals New Mechanisms To Inhibit the MYC Oncogene. Mol Cell Biol 2019; 39:MCB.00248-19. [PMID: 31501275 PMCID: PMC6817756 DOI: 10.1128/mcb.00248-19] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Accepted: 08/07/2019] [Indexed: 11/21/2022] Open
Abstract
The MYC oncogene is upregulated in human cancers by translocation, amplification, and mutation of cellular pathways that regulate Myc. Myc/Max heterodimers bind to E box sequences in the promoter regions of genes and activate transcription. The MYC oncogene is upregulated in human cancers by translocation, amplification, and mutation of cellular pathways that regulate Myc. Myc/Max heterodimers bind to E box sequences in the promoter regions of genes and activate transcription. The MYC inhibitor Omomyc can reduce the ability of MYC to bind specific box sequences in promoters of MYC target genes by binding directly to E box sequences as demonstrated by chromatin immunoprecipitation (CHIP). Here, we demonstrate by both a proximity ligation assay (PLA) and double chromatin immunoprecipitation (ReCHIP) that Omomyc preferentially binds to Max, not Myc, to mediate inhibition of MYC-mediated transcription by replacing MYC/MAX heterodimers with Omomyc/MAX heterodimers. The formation of Myc/Max and Omomyc/Max heterodimers occurs cotranslationally; Myc, Max, and Omomyc can interact with ribosomes and Max RNA under conditions in which ribosomes are intact. Taken together, our data suggest that the mechanism of action of Omomyc is to bind DNA as either a homodimer or a heterodimer with Max that is formed cotranslationally, revealing a novel mechanism to inhibit the MYC oncogene. We find that in vivo, Omomyc distributes quickly to kidneys and liver and has a short effective half-life in plasma, which could limit its use in vivo.
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42
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The Benefits of Cotranslational Assembly: A Structural Perspective. Trends Cell Biol 2019; 29:791-803. [DOI: 10.1016/j.tcb.2019.07.006] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2019] [Revised: 07/13/2019] [Accepted: 07/15/2019] [Indexed: 12/20/2022]
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Abstract
3' untranslated regions (3' UTRs) of messenger RNAs (mRNAs) are best known to regulate mRNA-based processes, such as mRNA localization, mRNA stability, and translation. In addition, 3' UTRs can establish 3' UTR-mediated protein-protein interactions (PPIs), and thus can transmit genetic information encoded in 3' UTRs to proteins. This function has been shown to regulate diverse protein features, including protein complex formation or posttranslational modifications, but is also expected to alter protein conformations. Therefore, 3' UTR-mediated information transfer can regulate protein features that are not encoded in the amino acid sequence. This review summarizes both 3' UTR functions-the regulation of mRNA and protein-based processes-and highlights how each 3' UTR function was discovered with a focus on experimental approaches used and the concepts that were learned. This review also discusses novel approaches to study 3' UTR functions in the future by taking advantage of recent advances in technology.
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Affiliation(s)
- Christine Mayr
- Department of Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, New York 10065
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44
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Bera M, Kalyana Sundaram RV. Chromosome Territorial Organization Drives Efficient Protein Complex Formation: A Hypothesis. THE YALE JOURNAL OF BIOLOGY AND MEDICINE 2019; 92:541-548. [PMID: 31543715 PMCID: PMC6747946] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
In eukaryotes, chromosomes often form a transcriptional kissing loop during interphase. We propose that these kissing loops facilitate the formation of protein complexes. mRNA transcripts from these loops could cluster together into phase-separated nuclear granules. Their export into the ER could be ensured by guided diffusion through the inter-chromatin space followed by association with nuclear baskets and export factors. Inside the ER, these mRNAs would form a translation hub. Juxtaposed translation of these mRNAs would increase the cis/trans protein complex assembly among the nascent protein chains. Eukaryotes might employ this pathway to increase complex formation efficiency.
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Affiliation(s)
- Manindra Bera
- To whom all correspondence should be addressed: Manindra Bera, Department of Cell Biology, Yale University School of Medicine, 333 Cedar Street, New Haven, CT USA, 06520; Tel: 203-737-3269,
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45
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Abrusán G, Marsh JA. Ligand Binding Site Structure Shapes Folding, Assembly and Degradation of Homomeric Protein Complexes. J Mol Biol 2019; 431:3871-3888. [PMID: 31306664 PMCID: PMC6739599 DOI: 10.1016/j.jmb.2019.07.014] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Revised: 07/04/2019] [Accepted: 07/08/2019] [Indexed: 12/20/2022]
Abstract
Ligand binding site structure has profound consequences for the evolution of function of protein complexes, particularly in homomers—complexes comprising multiple copies of the same protein. Previously, we have shown that homomers with multichain binding sites (MBSs) are characterized by more conserved binding sites and quaternary structure, and qualitatively different allosteric pathways than homomers with single-chain binding sites (SBSs) or monomers. Here, using computational methods, we show that the folds of single-domain MBS and SBS homomers are different, and SBS homomers are likely to be folded cotranslationally, while MBS homomers are more likely to form post-translationally and rely on more advanced folding-assistance and quality control mechanisms, which include chaperonins. In addition, our findings demonstrate that MBS homomers are qualitatively different from monomers, while SBS homomers are much less distinct, supporting the hypothesis that the evolution of quaternary structure in SBS homomers is significantly influenced by stochastic processes.
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Affiliation(s)
- György Abrusán
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Crewe Road, Edinburgh, EH4 2XU, UK.
| | - Joseph A Marsh
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Crewe Road, Edinburgh, EH4 2XU, UK
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46
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Stein KC, Kriel A, Frydman J. Nascent Polypeptide Domain Topology and Elongation Rate Direct the Cotranslational Hierarchy of Hsp70 and TRiC/CCT. Mol Cell 2019; 75:1117-1130.e5. [PMID: 31400849 DOI: 10.1016/j.molcel.2019.06.036] [Citation(s) in RCA: 67] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Revised: 05/24/2019] [Accepted: 06/25/2019] [Indexed: 02/03/2023]
Abstract
Cotranslational protein folding requires assistance from elaborate ribosome-associated chaperone networks. It remains unclear how the changing information in a growing nascent polypeptide dictates the recruitment of functionally distinct chaperones. Here, we used ribosome profiling to define the principles governing the cotranslational action of the chaperones TRiC/CCT and Hsp70/Ssb. We show that these chaperones are sequentially recruited to specific sites within domain-encoding regions of select nascent polypeptides. Hsp70 associates first, binding select sites throughout domains, whereas TRiC associates later, upon the emergence of nearly complete domains that expose an unprotected hydrophobic surface. This suggests that transient topological properties of nascent folding intermediates drive sequential chaperone association. Moreover, cotranslational recruitment of both TRiC and Hsp70 correlated with translation elongation slowdowns. We propose that the temporal modulation of the nascent chain structural landscape is coordinated with local elongation rates to regulate the hierarchical action of Hsp70 and TRiC for cotranslational folding.
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Affiliation(s)
- Kevin C Stein
- Department of Biology, Stanford University, Stanford, CA 94305, USA
| | - Allison Kriel
- Department of Biology, Stanford University, Stanford, CA 94305, USA
| | - Judith Frydman
- Department of Biology, Stanford University, Stanford, CA 94305, USA; Department of Genetics, Stanford University, Stanford, CA 94305, USA.
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47
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Kramer G, Shiber A, Bukau B. Mechanisms of Cotranslational Maturation of Newly Synthesized Proteins. Annu Rev Biochem 2019; 88:337-364. [DOI: 10.1146/annurev-biochem-013118-111717] [Citation(s) in RCA: 98] [Impact Index Per Article: 19.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The timely production of functional proteins is of critical importance for the biological activity of cells. To reach the functional state, newly synthesized polypeptides have to become enzymatically processed, folded, and assembled into oligomeric complexes and, for noncytosolic proteins, translocated across membranes. Key activities of these processes occur cotranslationally, assisted by a network of machineries that transiently engage nascent polypeptides at distinct phases of translation. The sequence of events is tuned by intrinsic features of the nascent polypeptides and timely association of factors with the translating ribosome. Considering the dynamics of translation, the heterogeneity of cellular proteins, and the diversity of interaction partners, it is a major cellular achievement that these processes are temporally and spatially so precisely coordinated, minimizing the generation of damaged proteins. This review summarizes the current progress we have made toward a comprehensive understanding of the cotranslational interactions of nascent chains, which pave the way to their functional state.
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Affiliation(s)
- Günter Kramer
- Center for Molecular Biology of Heidelberg University (ZMBH) and German Cancer Research Center (DKFZ), DKFZ-ZMBH Alliance, D-69120 Heidelberg, Germany;,
| | - Ayala Shiber
- Center for Molecular Biology of Heidelberg University (ZMBH) and German Cancer Research Center (DKFZ), DKFZ-ZMBH Alliance, D-69120 Heidelberg, Germany;,
| | - Bernd Bukau
- Center for Molecular Biology of Heidelberg University (ZMBH) and German Cancer Research Center (DKFZ), DKFZ-ZMBH Alliance, D-69120 Heidelberg, Germany;,
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48
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Co-translational assembly of mammalian nuclear multisubunit complexes. Nat Commun 2019; 10:1740. [PMID: 30988355 PMCID: PMC6465333 DOI: 10.1038/s41467-019-09749-y] [Citation(s) in RCA: 68] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Accepted: 03/29/2019] [Indexed: 01/07/2023] Open
Abstract
Cells dedicate significant energy to build proteins often organized in multiprotein assemblies with tightly regulated stoichiometries. As genes encoding subunits assembling in a multisubunit complex are dispersed in the genome of eukaryotes, it is unclear how these protein complexes assemble. Here, we show that mammalian nuclear transcription complexes (TFIID, TREX-2 and SAGA) composed of a large number of subunits, but lacking precise architectural details are built co-translationally. We demonstrate that dimerization domains and their positions in the interacting subunits determine the co-translational assembly pathway (simultaneous or sequential). The lack of co-translational interaction can lead to degradation of the partner protein. Thus, protein synthesis and complex assembly are linked in building mammalian multisubunit complexes, suggesting that co-translational assembly is a general principle in mammalian cells to avoid non-specific interactions and protein aggregation. These findings will also advance structural biology by defining endogenous co-translational building blocks in the architecture of multisubunit complexes. Genes encoding protein complex subunits are often dispersed in the genome of eukaryotes, raising the question how these protein complexes assemble. Here, the authors provide evidence that mammalian nuclear transcription complexes are formed co-translationally to ensure specific and functional interactions.
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Co-translational assembly of proteasome subunits in NOT1-containing assemblysomes. Nat Struct Mol Biol 2019; 26:110-120. [PMID: 30692646 DOI: 10.1038/s41594-018-0179-5] [Citation(s) in RCA: 74] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Accepted: 12/06/2018] [Indexed: 01/31/2023]
Abstract
The assembly of large multimeric complexes in the crowded cytoplasm is challenging. Here we reveal a mechanism that ensures accurate production of the yeast proteasome, involving ribosome pausing and co-translational assembly of Rpt1 and Rpt2. Interaction of nascent Rpt1 and Rpt2 then lifts ribosome pausing. We show that the N-terminal disordered domain of Rpt1 is required to ensure efficient ribosome pausing and association of nascent Rpt1 protein complexes into heavy particles, wherein the nascent protein complexes escape ribosome quality control. Immunofluorescence and in situ hybridization studies indicate that Rpt1- and Rpt2-encoding messenger RNAs co-localize in these particles that contain, and are dependent on, Not1, the scaffold of the Ccr4-Not complex. We refer to these particles as Not1-containing assemblysomes, as they are smaller than and distinct from other RNA granules such as stress granules and GW- or P-bodies. Synthesis of Rpt1 with ribosome pausing and Not1-containing assemblysome induction is conserved from yeast to human cells.
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Diepold A. Assembly and Post-assembly Turnover and Dynamics in the Type III Secretion System. Curr Top Microbiol Immunol 2019; 427:35-66. [PMID: 31218503 DOI: 10.1007/82_2019_164] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The type III secretion system (T3SS) is one of the largest transmembrane complexes in bacteria, comprising several intricately linked and embedded substructures. The assembly of this nanomachine is a hierarchical process which is regulated and controlled by internal and external cues at several critical points. Recently, it has become obvious that the assembly of the T3SS is not a unidirectional and deterministic process, but that parts of the T3SS constantly exchange or rearrange. This article aims to give an overview on the assembly and post-assembly dynamics of the T3SS, with a focus on emerging general concepts and adaptations of the general assembly pathway.
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Affiliation(s)
- Andreas Diepold
- Department of Ecophysiology, Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Straße 10, 35043, Marburg, Germany.
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