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Tingey M, Li Y, Yu W, Young A, Yang W. Spelling out the roles of individual nucleoporins in nuclear export of mRNA. Nucleus 2022; 13:170-193. [PMID: 35593254 PMCID: PMC9132428 DOI: 10.1080/19491034.2022.2076965] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 05/08/2022] [Accepted: 05/09/2022] [Indexed: 11/01/2022] Open
Abstract
The Nuclear Pore Complex (NPC) represents a critical passage through the nuclear envelope for nuclear import and export that impacts nearly every cellular process at some level. Recent technological advances in the form of Auxin Inducible Degron (AID) strategies and Single-Point Edge-Excitation sub-Diffraction (SPEED) microscopy have enabled us to provide new insight into the distinct functions and roles of nuclear basket nucleoporins (Nups) upon nuclear docking and export for mRNAs. In this paper, we provide a review of our recent findings as well as an assessment of new techniques, updated models, and future perspectives in the studies of mRNA's nuclear export.
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Affiliation(s)
- Mark Tingey
- Department of Biology, Temple University, Philadelphia, Pennsylvania, USA
| | - Yichen Li
- Department of Genetics, Yale School of Medicine, Yale University, New Haven, Connecticut, USA
| | - Wenlan Yu
- Department of Biology, Temple University, Philadelphia, Pennsylvania, USA
| | - Albert Young
- Department of Biology, Temple University, Philadelphia, Pennsylvania, USA
| | - Weidong Yang
- Department of Biology, Temple University, Philadelphia, Pennsylvania, USA
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2
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Klama S, Hirsch AG, Schneider UM, Zander G, Seel A, Krebber H. A guard protein mediated quality control mechanism monitors 5'-capping of pre-mRNAs. Nucleic Acids Res 2022; 50:11301-11314. [PMID: 36305816 PMCID: PMC9638935 DOI: 10.1093/nar/gkac952] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 09/30/2022] [Accepted: 10/12/2022] [Indexed: 07/26/2023] Open
Abstract
Efficient gene expression requires properly matured mRNAs for functional transcript translation. Several factors including the guard proteins monitor maturation and act as nuclear retention factors for unprocessed pre-mRNAs. Here we show that the guard protein Npl3 monitors 5'-capping. In its absence, uncapped transcripts resist degradation, because the Rat1-Rai1 5'-end degradation factors are not efficiently recruited to these faulty transcripts. Importantly, in npl3Δ, these improperly capped transcripts escape this quality control checkpoint and leak into the cytoplasm. Our data suggest a model in which Npl3 associates with the Rai1 bound pre-mRNAs. In case the transcript was properly capped and is thus CBC (cap binding complex) bound, Rai1 dissociates from Npl3 allowing the export factor Mex67 to interact with this guard protein and support nuclear export. In case Npl3 does not detect proper capping through CBC attachment, Rai1 binding persists and Rat1 can join this 5'-complex to degrade the faulty transcript.
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Affiliation(s)
| | | | - Ulla M Schneider
- Abteilung für Molekulare Genetik, Institut für Mikrobiologie und Genetik, Göttinger Zentrum für Molekulare Biowissenschaften (GZMB), Georg-August Universität Göttingen, Göttingen 37077, Germany
| | - Gesa Zander
- Abteilung für Molekulare Genetik, Institut für Mikrobiologie und Genetik, Göttinger Zentrum für Molekulare Biowissenschaften (GZMB), Georg-August Universität Göttingen, Göttingen 37077, Germany
| | - Anika Seel
- Abteilung für Molekulare Genetik, Institut für Mikrobiologie und Genetik, Göttinger Zentrum für Molekulare Biowissenschaften (GZMB), Georg-August Universität Göttingen, Göttingen 37077, Germany
| | - Heike Krebber
- To whom correspondence should be addressed. Tel: +49 551 39 33801; Fax: +49 551 39 33805;
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3
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Wang Y, Li X, Chen X, Siewers V. CRISPR/Cas9-mediated point mutations improve α-amylase secretion in Saccharomyces cerevisiae. FEMS Yeast Res 2022; 22:6626025. [PMID: 35776981 PMCID: PMC9290899 DOI: 10.1093/femsyr/foac033] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Accepted: 06/28/2022] [Indexed: 11/12/2022] Open
Abstract
The rapid expansion of the application of pharmaceutical proteins and industrial enzymes requires robust microbial workhorses for high protein production. The budding yeast Saccharomyces cerevisiae is an attractive cell factory due to its ability to perform eukaryotic post-translational modifications and to secrete proteins. Many strategies have been used to engineer yeast platform strains for higher protein secretion capacity. Herein, we investigated a line of strains that have previously been selected after UV random mutagenesis for improved α-amylase secretion. A total of 42 amino acid altering point mutations identified in this strain line were reintroduced into the parental strain AAC to study their individual effects on protein secretion. These point mutations included missense mutations (amino acid substitution), nonsense mutations (stop codon generation), and frameshift mutations. For comparison, single gene deletions for the corresponding target genes were also performed in this study. A total of 11 point mutations and seven gene deletions were found to effectively improve α-amylase secretion. These targets were involved in several bioprocesses, including cellular stresses, protein degradation, transportation, mRNA processing and export, DNA replication, and repair, which indicates that the improved protein secretion capacity in the evolved strains is the result of the interaction of multiple intracellular processes. Our findings will contribute to the construction of novel cell factories for recombinant protein secretion.
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Affiliation(s)
- Yanyan Wang
- Department of Biology and Biological Engineering, Chalmers University of Technology, Kemivägen 10, SE-41296 Gothenburg, Sweden
| | - Xiaowei Li
- Department of Biology and Biological Engineering, Chalmers University of Technology, Kemivägen 10, SE-41296 Gothenburg, Sweden
| | - Xin Chen
- Department of Biology and Biological Engineering, Chalmers University of Technology, Kemivägen 10, SE-41296 Gothenburg, Sweden
- Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, Kemivägen 10, SE-41296 Gothenburg, Sweden
| | - Verena Siewers
- Corresponding author. Department of Biology and Biological Engineering, Chalmers University of Technology, Kemivägen 10, SE-41296 Gothenburg, Sweden. Tel: +46 (0)317723853; E-mail:
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4
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Sáez Moreno D, Udi Q, Azeredo J, Domingues L. Towards T7 RNA polymerase (T7RNAP)-based expression system in yeast: challenges and opportunities. Bioengineered 2022; 13:14947-14959. [PMID: 37105766 DOI: 10.1080/21655979.2023.2180579] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/29/2023] Open
Abstract
During the last decades, we have witnessed unprecedented advances in biological engineering and synthetic biology. These disciplines aim to take advantage of gene pathway regulation and gene expression in different organisms, to enable cells to perform desired functions. Yeast has been widely utilized as a model for the study of eukaryotic protein expression while bacteriophage T7RNAP and its promoter constitute the preferred system for prokaryotic protein expression (such as pET-based expression systems). The ability to integrate a T7RNAP-based expression system in yeast could allow for a better understanding of gene regulation in eukaryotic cells, and potentially increase the efficiency and processivity of yeast as an expression system. However, the attempts for the creation of such a system have been unsuccessful to date. This review aims to: (i) summarize the efforts that, for many years, have been devoted to the creation of a T7RNAP-based yeast expression system and ii) provide an overview of the latest advances in knowledge of eukaryotic transcription and translation that could lead to the construction of a successful T7RNAP expression system in yeast. The completion of this new expression system would allow to further expand the toolkit of yeast in synthetic biology and ultimately contribute to boost yeast usage as a key cell factory in sustainable biorefinery and circular economy.
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Affiliation(s)
- David Sáez Moreno
- CEB-Centre of Biological Engineering, University of Minho, 4710-057, Braga, Portugal
- LABBELS-Associate Laboratory, 4835-198, Guimarães, Braga, Portugal
| | - Qimron Udi
- Department of Clinical Microbiology and Immunology, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Joana Azeredo
- CEB-Centre of Biological Engineering, University of Minho, 4710-057, Braga, Portugal
- LABBELS-Associate Laboratory, 4835-198, Guimarães, Braga, Portugal
| | - Lucília Domingues
- CEB-Centre of Biological Engineering, University of Minho, 4710-057, Braga, Portugal
- LABBELS-Associate Laboratory, 4835-198, Guimarães, Braga, Portugal
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5
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Nuclear mRNA Export and Aging. Int J Mol Sci 2022; 23:ijms23105451. [PMID: 35628261 PMCID: PMC9142925 DOI: 10.3390/ijms23105451] [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: 04/12/2022] [Revised: 05/10/2022] [Accepted: 05/12/2022] [Indexed: 02/04/2023] Open
Abstract
The relationship between transcription and aging is one that has been studied intensively and experimentally with diverse attempts. However, the impact of the nuclear mRNA export on the aging process following its transcription is still poorly understood, although the nuclear events after transcription are coupled closely with the transcription pathway because the essential factors required for mRNA transport, namely TREX, TREX-2, and nuclear pore complex (NPC), physically and functionally interact with various transcription factors, including the activator/repressor and pre-mRNA processing factors. Dysregulation of the mediating factors for mRNA export from the nucleus generally leads to the aberrant accumulation of nuclear mRNA and further impairment in the vegetative growth and normal lifespan and the pathogenesis of neurodegenerative diseases. The optimal stoichiometry and density of NPC are destroyed during the process of cellular aging, and their damage triggers a defect of function in the nuclear permeability barrier. This review describes recent findings regarding the role of the nuclear mRNA export in cellular aging and age-related neurodegenerative disorders.
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6
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De Magistris P. The Great Escape: mRNA Export through the Nuclear Pore Complex. Int J Mol Sci 2021; 22:ijms222111767. [PMID: 34769195 PMCID: PMC8583845 DOI: 10.3390/ijms222111767] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 10/18/2021] [Accepted: 10/21/2021] [Indexed: 12/30/2022] Open
Abstract
Nuclear export of messenger RNA (mRNA) through the nuclear pore complex (NPC) is an indispensable step to ensure protein translation in the cytoplasm of eukaryotic cells. mRNA is not translocated on its own, but it forms ribonuclear particles (mRNPs) in association with proteins that are crucial for its metabolism, some of which; like Mex67/MTR2-NXF1/NXT1; are key players for its translocation to the cytoplasm. In this review, I will summarize our current body of knowledge on the basic characteristics of mRNA export through the NPC. To be granted passage, the mRNP cargo needs to bind transport receptors, which facilitate the nuclear export. During NPC transport, mRNPs undergo compositional and conformational changes. The interactions between mRNP and the central channel of NPC are described; together with the multiple quality control steps that mRNPs undergo at the different rings of the NPC to ensure only proper export of mature transcripts to the cytoplasm. I conclude by mentioning new opportunities that arise from bottom up approaches for a mechanistic understanding of nuclear export.
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Hoogenboom BW, Hough LE, Lemke EA, Lim RYH, Onck PR, Zilman A. Physics of the Nuclear Pore Complex: Theory, Modeling and Experiment. PHYSICS REPORTS 2021; 921:1-53. [PMID: 35892075 PMCID: PMC9306291 DOI: 10.1016/j.physrep.2021.03.003] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
The hallmark of eukaryotic cells is the nucleus that contains the genome, enclosed by a physical barrier known as the nuclear envelope (NE). On the one hand, this compartmentalization endows the eukaryotic cells with high regulatory complexity and flexibility. On the other hand, it poses a tremendous logistic and energetic problem of transporting millions of molecules per second across the nuclear envelope, to facilitate their biological function in all compartments of the cell. Therefore, eukaryotes have evolved a molecular "nanomachine" known as the Nuclear Pore Complex (NPC). Embedded in the nuclear envelope, NPCs control and regulate all the bi-directional transport between the cell nucleus and the cytoplasm. NPCs combine high molecular specificity of transport with high throughput and speed, and are highly robust with respect to molecular noise and structural perturbations. Remarkably, the functional mechanisms of NPC transport are highly conserved among eukaryotes, from yeast to humans, despite significant differences in the molecular components among various species. The NPC is the largest macromolecular complex in the cell. Yet, despite its significant complexity, it has become clear that its principles of operation can be largely understood based on fundamental physical concepts, as have emerged from a combination of experimental methods of molecular cell biology, biophysics, nanoscience and theoretical and computational modeling. Indeed, many aspects of NPC function can be recapitulated in artificial mimics with a drastically reduced complexity compared to biological pores. We review the current physical understanding of the NPC architecture and function, with the focus on the critical analysis of experimental studies in cells and artificial NPC mimics through the lens of theoretical and computational models. We also discuss the connections between the emerging concepts of NPC operation and other areas of biophysics and bionanotechnology.
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Affiliation(s)
- Bart W. Hoogenboom
- London Centre for Nanotechnology and Department of Physics and Astronomy, University College London, London WC1E 6BT, United Kingdom
| | - Loren E. Hough
- Department of Physics and BioFrontiers Institute, University of Colorado, Boulder CO 80309, United States of America
| | - Edward A. Lemke
- Biocenter Mainz, Departments of Biology and Chemistry, Johannes Gutenberg University and Institute of Molecular Biology, 55128 Mainz, Germany
| | - Roderick Y. H. Lim
- Biozentrum and the Swiss Nanoscience Institute, University of Basel, 4056 Basel, Switzerland
| | - Patrick R. Onck
- Zernike Institute for Advanced Materials, University of Groningen, 9747 AG Groningen, The Netherlands
| | - Anton Zilman
- Department of Physics and Institute for Biomedical Engineering (IBME), University of Toronto, Toronto, ON M5S 1A7, Canada
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Eyboulet F, Jeronimo C, Côté J, Robert F. The deubiquitylase Ubp15 couples transcription to mRNA export. eLife 2020; 9:e61264. [PMID: 33226341 PMCID: PMC7682988 DOI: 10.7554/elife.61264] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Accepted: 11/04/2020] [Indexed: 12/16/2022] Open
Abstract
Nuclear export of messenger RNAs (mRNAs) is intimately coupled to their synthesis. pre-mRNAs assemble into dynamic ribonucleoparticles as they are being transcribed, processed, and exported. The role of ubiquitylation in this process is increasingly recognized but, while a few E3 ligases have been shown to regulate nuclear export, evidence for deubiquitylases is currently lacking. Here we identified deubiquitylase Ubp15 as a regulator of nuclear export in Saccharomyces cerevisiae. Ubp15 interacts with both RNA polymerase II and the nuclear pore complex, and its deletion reverts the nuclear export defect of E3 ligase Rsp5 mutants. The deletion of UBP15 leads to hyper-ubiquitylation of the main nuclear export receptor Mex67 and affects its association with THO, a complex coupling transcription to mRNA processing and involved in the recruitment of mRNA export factors to nascent transcripts. Collectively, our data support a role for Ubp15 in coupling transcription to mRNA export.
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Affiliation(s)
- Fanny Eyboulet
- Institut de recherches cliniques de MontréalMontréalCanada
- St-Patrick Research Group in Basic Oncology, Laval University Cancer Research Center, Axe Oncologie du Centre de Recherche du CHU de Québec-Université LavalQuébec CityCanada
| | - Célia Jeronimo
- Institut de recherches cliniques de MontréalMontréalCanada
| | - Jacques Côté
- St-Patrick Research Group in Basic Oncology, Laval University Cancer Research Center, Axe Oncologie du Centre de Recherche du CHU de Québec-Université LavalQuébec CityCanada
| | - François Robert
- Institut de recherches cliniques de MontréalMontréalCanada
- Département de Médecine, Faculté de Médecine, Université de MontréalMontréalCanada
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9
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Xie Y, Ren Y. Mechanisms of nuclear mRNA export: A structural perspective. Traffic 2019; 20:829-840. [PMID: 31513326 DOI: 10.1111/tra.12691] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Accepted: 08/26/2019] [Indexed: 12/28/2022]
Abstract
Export of mRNA from the nucleus to the cytoplasm is a critical process for all eukaryotic gene expression. As mRNA is synthesized, it is packaged with a myriad of RNA-binding proteins to form ribonucleoprotein particles (mRNPs). For each step in the processes of maturation and export, mRNPs must have the correct complement of proteins. Much of the mRNA export pathway revolves around the heterodimeric export receptor yeast Mex67•Mtr2/human NXF1•NXT1, which is recruited to signal the completion of nuclear mRNP assembly, mediates mRNP targeting/translocation through the nuclear pore complex (NPC), and is displaced at the cytoplasmic side of the NPC to release the mRNP into the cytoplasm. Directionality of the transport is governed by at least two DEAD-box ATPases, yeast Sub2/human UAP56 in the nucleus and yeast Dbp5/human DDX19 at the cytoplasmic side of the NPC, which respectively mediate the association and dissociation of Mex67•Mtr2/NXF1•NXT1 onto the mRNP. Here we review recent progress from structural studies of key constituents in different steps of nuclear mRNA export. These findings have laid the foundation for further studies to obtain a comprehensive mechanistic view of the mRNA export pathway.
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Affiliation(s)
- Yihu Xie
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - Yi Ren
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee
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10
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Abstract
In eukaryotes, the separation of translation from transcription by the nuclear envelope enables mRNA modifications such as capping, splicing, and polyadenylation. These modifications are mediated by a spectrum of ribonuclear proteins that associate with preRNA transcripts, coordinating the different steps and coupling them to nuclear export, ensuring that only mature transcripts reach the cytoplasmic translation machinery. Although the components of this machinery have been identified and considerable functional insight has been achieved, a number of questions remain outstanding about mRNA nuclear export and how it is integrated into the nuclear phase of the gene expression pathway. Nuclear export factors mediate mRNA transit through nuclear pores to the cytoplasm, after which these factors are removed from the mRNA, preventing transcripts from returning to the nucleus. However, as outlined in this review, several aspects of the mechanism by which transport factor binding and release are mediated remain unclear, as are the roles of accessory nuclear components in these processes. Moreover, the mechanisms by which completion of mRNA splicing and polyadenylation are recognized, together with how they are coordinated with nuclear export, also remain only partially characterized. One attractive hypothesis is that dissociating poly(A) polymerase from the cleavage and polyadenylation machinery could signal completion of mRNA maturation and thereby provide a mechanism for initiating nuclear export. The impressive array of genetic, molecular, cellular, and structural data that has been generated about these systems now provides many of the tools needed to define the precise mechanisms involved in these processes and how they are integrated.
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Affiliation(s)
- Murray Stewart
- From the MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, United Kingdom
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11
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Fasken MB, Corbett AH, Stewart M. Structure-function relationships in the Nab2 polyadenosine-RNA binding Zn finger protein family. Protein Sci 2019; 28:513-523. [PMID: 30578643 PMCID: PMC6371209 DOI: 10.1002/pro.3565] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Revised: 12/15/2018] [Accepted: 12/17/2018] [Indexed: 12/12/2022]
Abstract
The poly(A) RNA binding Zn finger ribonucleoprotein Nab2 functions to control the length of 3' poly(A) tails in Saccharomyces cerevisiae as well as contributing to the integration of the nuclear export of mature mRNA with preceding steps in the nuclear phase of the gene expression pathway. Nab2 is constructed from an N-terminal PWI-fold domain, followed by QQQP and RGG motifs and then seven CCCH Zn fingers. The nuclear pore-associated proteins Gfd1 and Mlp1 bind to opposite sides of the Nab2 N-terminal domain and function in the nuclear export of mRNA, whereas the Zn fingers, especially fingers 5-7, bind to A-rich regions of mature transcripts and function to regulate poly(A) tail length as well as mRNA compaction prior to nuclear export. Nab2 Zn fingers 5-7 have a defined spatial arrangement, with fingers 5 and 7 arranged on one side of the cluster and finger 6 on the other side. This spatial arrangement facilitates the dimerization of Nab2 when bound to adenine-rich RNAs and regulates both the termination of 3' polyadenylation and transcript compaction. Nab2 also functions to coordinate steps in the nuclear phase of the gene expression pathway, such as splicing and polyadenylation, with the generation of mature mRNA and its nuclear export. Nab2 orthologues in higher Eukaryotes have similar domain structures and play roles associated with the regulation of splicing and polyadenylation. Importantly, mutations in the gene encoding the human Nab2 orthologue ZC3H14 and cause intellectual disability.
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Affiliation(s)
- Milo B Fasken
- Department of Biology, Emory University, Atlanta, Georgia 30322
| | - Anita H Corbett
- Department of Biology, Emory University, Atlanta, Georgia 30322
| | - Murray Stewart
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge CB2 0QH, United Kingdom
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Mechanism and Regulation of Co-transcriptional mRNP Assembly and Nuclear mRNA Export. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1203:1-31. [DOI: 10.1007/978-3-030-31434-7_1] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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13
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Abstract
The Three prime repair exonuclease 2 (TREX-2) complex functions as a platform to which many of the components of the nuclear mRNA processing machinery bind, facilitating integration of this phase of the gene expression pathway, as well as mediating the re-positioning of highly regulated actively transcribing genes (such as GAL1) to nuclear pores (NPCs) to accelerate their activation. In Saccharomyces cerevisiae the TREX-2 complex is based on a Sac3 scaffold to which Thp1, Sem1, Cdc31 and two Sus1 chains are bound. A combination of X-ray crystallography and electron microscopy studies have established the structure of two major regions of this complex: the M-region that functions to bind nucleic acids and the CID region that functions to link the complex to nuclear pores. These structures have facilitated the engineering of mutants that have been used to define the contributions made by the TREX-2 complex to locating high-expressed genes to nuclear pores and the contributions made to mRNA nuclear export.
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Affiliation(s)
- Murray Stewart
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge, CB2 0QH, UK.
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Lari A, Farzam F, Bensidoun P, Oeffinger M, Zenklusen D, Grunwald D, Montpetit B. Live-Cell Imaging of mRNP-NPC Interactions in Budding Yeast. Methods Mol Biol 2019; 2038:131-150. [PMID: 31407282 DOI: 10.1007/978-1-4939-9674-2_9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Single-molecule resolution imaging has become an important tool in the study of cell biology. Aptamer-based approaches (e.g., MS2 and PP7) allow for detection of single RNA molecules in living cells and have been used to study various aspects of mRNA metabolism, including mRNP nuclear export. Here we outline an imaging protocol for the study of interactions between mRNPs and nuclear pore complexes (NPCs) in the yeast S. cerevisiae, including mRNP export. We describe in detail the steps that allow for high-resolution live-cell mRNP imaging and measurement of mRNP interactions with NPCs using simultaneous two-color imaging. Our protocol discusses yeast strain construction, choice of marker proteins to label the nuclear pore complex, as well as imaging conditions that allow high signal-to-noise data acquisition. Moreover, we describe various aspects of postacquisition image analysis for single molecule tracking and image registration allowing for the characterization of mRNP-NPC interactions.
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Affiliation(s)
- Azra Lari
- Department of Cell Biology, University of Alberta, Edmonton, Canada
| | - Farzin Farzam
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA, USA
| | - Pierre Bensidoun
- Département de Biochimie et Médecine Moléculaire, Université de Montréal, Montréal, QC, Canada
- Institut de Recherches Cliniques de Montréal, Montréal, QC, Canada
| | - Marlene Oeffinger
- Département de Biochimie et Médecine Moléculaire, Université de Montréal, Montréal, QC, Canada
- Institut de Recherches Cliniques de Montréal, Montréal, QC, Canada
- Faculty of Medicine, Division of Experimental Medicine, McGill University, Montréal, QC, Canada
| | - Daniel Zenklusen
- Département de Biochimie et Médecine Moléculaire, Université de Montréal, Montréal, QC, Canada
| | - David Grunwald
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA, USA
| | - Ben Montpetit
- Department of Cell Biology, University of Alberta, Edmonton, Canada.
- Department of Viticulture and Enology, University of California, Davis, Davis, CA, USA.
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15
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Brambilla M, Martani F, Bertacchi S, Vitangeli I, Branduardi P. The Saccharomyces cerevisiae
poly (A) binding protein (Pab1): Master regulator of mRNA metabolism and cell physiology. Yeast 2018; 36:23-34. [DOI: 10.1002/yea.3347] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Revised: 06/26/2018] [Accepted: 07/06/2018] [Indexed: 12/15/2022] Open
Affiliation(s)
- Marco Brambilla
- Department of Biotechnology and Biosciences; University of Milano-Bicocca; Piazza della Scienza 2 20126 Milan Italy
| | - Francesca Martani
- Department of Biotechnology and Biosciences; University of Milano-Bicocca; Piazza della Scienza 2 20126 Milan Italy
| | - Stefano Bertacchi
- Department of Biotechnology and Biosciences; University of Milano-Bicocca; Piazza della Scienza 2 20126 Milan Italy
| | - Ilaria Vitangeli
- Department of Biotechnology and Biosciences; University of Milano-Bicocca; Piazza della Scienza 2 20126 Milan Italy
| | - Paola Branduardi
- Department of Biotechnology and Biosciences; University of Milano-Bicocca; Piazza della Scienza 2 20126 Milan Italy
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16
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Xiao C, Yu Q, Zhang B, Li J, Zhang D, Li M. The mRNA export factor Sac3 maintains nuclear homeostasis and regulates cytoskeleton organization in Candida albicans. Future Microbiol 2018; 13:283-296. [PMID: 29436239 DOI: 10.2217/fmb-2017-0191] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
AIM In eukaryotes, the nuclear export of mRNAs is essential for gene expression and regulations of numerous cellular processes. This study aimed to identify the mRNA export factor Sac3 in Candida albicans. MATERIALS & METHODS A sac3Δ/Δ mutant was obtained using PCR-mediated homologous recombination. RESULTS Disruption of SAC3 caused abnormal accumulation of mRNA in the nuclei. Further investigations revealed that sac3Δ/Δ mutant exhibited a severely growth defect, which was related to abnormal aggregation of microtubules. Moreover, loss of Sac3 caused a defect in hyphal polarized growth, which was associated with depolarization of actin cytoskeleton. In addition, the virulence of sac3Δ/Δ mutant was seriously attenuated. CONCLUSION Our findings provide new insights into the mRNA export factor Sac3 in C. albicans.
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Affiliation(s)
- Chenpeng Xiao
- Key Laboratory of Molecular Microbiology & Technology, Ministry of Education, Department of Microbiology, College of Life Sciences, Nankai University, Tianjin 300071, PR China
| | - Qilin Yu
- Key Laboratory of Molecular Microbiology & Technology, Ministry of Education, Department of Microbiology, College of Life Sciences, Nankai University, Tianjin 300071, PR China
| | - Bing Zhang
- Key Laboratory of Molecular Microbiology & Technology, Ministry of Education, Department of Microbiology, College of Life Sciences, Nankai University, Tianjin 300071, PR China
| | - Jianrong Li
- Key Laboratory of Molecular Microbiology & Technology, Ministry of Education, Department of Microbiology, College of Life Sciences, Nankai University, Tianjin 300071, PR China
| | - Dan Zhang
- Key Laboratory of Molecular Microbiology & Technology, Ministry of Education, Department of Microbiology, College of Life Sciences, Nankai University, Tianjin 300071, PR China
| | - Mingchun Li
- Key Laboratory of Molecular Microbiology & Technology, Ministry of Education, Department of Microbiology, College of Life Sciences, Nankai University, Tianjin 300071, PR China
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17
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Zander G, Krebber H. Quick or quality? How mRNA escapes nuclear quality control during stress. RNA Biol 2017; 14:1642-1648. [PMID: 28708448 PMCID: PMC5731798 DOI: 10.1080/15476286.2017.1345835] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Revised: 06/19/2017] [Accepted: 06/20/2017] [Indexed: 10/19/2022] Open
Abstract
Understanding the mechanisms for mRNA production under normal conditions and in response to cytotoxic stresses has been subject of numerous studies for several decades. The shutdown of canonical mRNA transcription, export and translation is required to have enough free resources for the immediate production of heat shock proteins that act as chaperones to sustain cellular processes. In recent work we uncovered a simple mechanism, in which the export block of regular mRNAs and a fast export of heat shock mRNAs is achieved by deactivation of the nuclear mRNA quality control mediated by the guard proteins. In this point of view we combine long known data with recently gathered information that support this novel model, in which cells omit quality control of stress responsive transcripts to ensure survival.
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Affiliation(s)
- Gesa Zander
- Abteilung für Molekulare Genetik, Institut für Mikrobiologie und Genetik, Göttinger Zentrum für Molekulare Biowissenschaften (GZMB), Georg-August Universität Göttingen, Göttingen, Germany
| | - Heike Krebber
- Abteilung für Molekulare Genetik, Institut für Mikrobiologie und Genetik, Göttinger Zentrum für Molekulare Biowissenschaften (GZMB), Georg-August Universität Göttingen, Göttingen, Germany
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18
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Aibara S, Gordon JMB, Riesterer AS, McLaughlin SH, Stewart M. Structural basis for the dimerization of Nab2 generated by RNA binding provides insight into its contribution to both poly(A) tail length determination and transcript compaction in Saccharomyces cerevisiae. Nucleic Acids Res 2017; 45:1529-1538. [PMID: 28180315 PMCID: PMC5388407 DOI: 10.1093/nar/gkw1224] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2016] [Revised: 11/08/2016] [Accepted: 11/23/2016] [Indexed: 12/26/2022] Open
Abstract
In Saccharomyces cerevisiae generation of export-competent mRNPs terminates the nuclear phase of the gene expression pathway and facilitates transport to the cytoplasm for translation. Nab2 functions in this process to control both mRNP compaction that facilitates movement through nuclear pore complexes and the length of transcript poly(A) tails. Nab2 has a modular structure that includes seven CCCH Zn fingers that bind to A-rich RNAs and fingers 5–7 are critical for these functions. Here, we demonstrate, using both biophysical and structural methods, that binding A11G RNA induces dimerization of Zn fingers 5–7 mediated by the novel spatial arrangement of the fingers promoting each RNA chain binding two protein chains. The dimerization of Nab2 induced by RNA binding provides a basis for understanding its function in both poly(A) tail length regulation and in the compaction of mature transcripts to facilitate nuclear export.
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Affiliation(s)
- Shintaro Aibara
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge, UK
| | - James M B Gordon
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge, UK
| | - Anja S Riesterer
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge, UK
| | - Stephen H McLaughlin
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge, UK
| | - Murray Stewart
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge, UK
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19
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Dargemont C, Babour A. Novel functions for chromatin dynamics in mRNA biogenesis beyond transcription. Nucleus 2017; 8:482-488. [PMID: 28816581 DOI: 10.1080/19491034.2017.1342916] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022] Open
Abstract
The first step of gene expression results in the production of mRNA ribonucleoparticles (mRNPs) that are exported to the cytoplasm via the NPC for translation into the cytoplasm. During this process, the mRNA molecule synthesized by RNA polymerase II (Pol II) undergoes extensive maturation, folding and packaging events that are intimately coupled to its synthesis. All these events take place in a chromatin context and it is therefore not surprising that a growing number of studies recently reported specific contributions of chromatin dynamics to various steps of mRNP biogenesis. In this extra view, we replace our recent findings highlighting the contribution of the yeast chromatin remodeling complex ISW1 to nuclear mRNA quality control in the context of the recent literature.
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Affiliation(s)
- Catherine Dargemont
- a Université Paris Diderot, Sorbonne Paris Cité, INSERM UMR944, CNRS UMR7212 , Hôpital St. Louis 1, Paris , France
| | - Anna Babour
- a Université Paris Diderot, Sorbonne Paris Cité, INSERM UMR944, CNRS UMR7212 , Hôpital St. Louis 1, Paris , France
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20
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Krogh N, Pietschmann M, Schmid M, Jensen TH, Nielsen H. Lariat capping as a tool to manipulate the 5' end of individual yeast mRNA species in vivo. RNA (NEW YORK, N.Y.) 2017; 23:683-695. [PMID: 28159804 PMCID: PMC5393178 DOI: 10.1261/rna.059337.116] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/25/2016] [Accepted: 01/31/2017] [Indexed: 06/06/2023]
Abstract
The 5' cap structure of eukaryotic mRNA is critical for its processing, transport, translation, and stability. The many functions of the cap and the fact that most, if not all, mRNA carries the same type of cap makes it difficult to analyze cap function in vivo at individual steps of gene expression. We have used the lariat capping ribozyme (LCrz) from the myxomycete Didymium to replace the mRNA m7G cap of a single reporter mRNA species with a tiny lariat in which the first and the third nucleotide are joined by a 2', 5' phosphodiester bond. We show that the ribozyme functions in vivo in the budding yeast Saccharomyces cerevisiae presumably without cofactors and that lariat capping occurs cotranscriptionally. The lariat-capped reporter mRNA is efficiently exported to the cytoplasm where it is found to be oligoadenylated and evenly distributed. Both the oligoadenylated form and a lariat-capped mRNA with a templated poly(A) tail translates poorly, underlining the critical importance of the m7G cap in translation. Finally, the lariat-capped RNA exhibits a threefold longer half-life compared to its m7G-capped counterpart, consistent with a key role for the m7G cap in mRNA turnover. Our study emphasizes important activities of the m7G cap and suggests new utilities of lariat capping as a molecular tool in vivo.
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Affiliation(s)
- Nicolai Krogh
- Department of Cellular and Molecular Medicine, University of Copenhagen, DK-2200 Copenhagen N, Denmark
| | - Max Pietschmann
- Department of Cellular and Molecular Medicine, University of Copenhagen, DK-2200 Copenhagen N, Denmark
| | - Manfred Schmid
- Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus C, Denmark
| | - Torben Heick Jensen
- Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus C, Denmark
| | - Henrik Nielsen
- Department of Cellular and Molecular Medicine, University of Copenhagen, DK-2200 Copenhagen N, Denmark
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21
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The Chromatin Remodeler ISW1 Is a Quality Control Factor that Surveys Nuclear mRNP Biogenesis. Cell 2017; 167:1201-1214.e15. [PMID: 27863241 DOI: 10.1016/j.cell.2016.10.048] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2016] [Revised: 09/12/2016] [Accepted: 10/27/2016] [Indexed: 02/07/2023]
Abstract
Chromatin dynamics play an essential role in regulating DNA transaction processes, but it is unclear whether transcription-associated chromatin modifications control the mRNA ribonucleoparticles (mRNPs) pipeline from synthesis to nuclear exit. Here, we identify the yeast ISW1 chromatin remodeling complex as an unanticipated mRNP nuclear export surveillance factor that retains export-incompetent transcripts near their transcription site. This tethering activity of ISW1 requires chromatin binding and is independent of nucleosome sliding activity or changes in RNA polymerase II processivity. Combination of in vivo UV-crosslinking and genome-wide RNA immunoprecipitation assays show that Isw1 and its cofactors interact directly with premature mRNPs. Our results highlight that the concerted action of Isw1 and the nuclear exosome ensures accurate surveillance mechanism that proofreads the efficiency of mRNA biogenesis.
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22
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Bittencourt IDA, Serpeloni M, Hiraiwa PM, de Arruda Campos Brasil de Souza T, Ávila AR. Dissecting biochemical peculiarities of the ATPase activity of TcSub2, a component of the mRNA export pathway in Trypanosoma cruzi. Int J Biol Macromol 2017; 98:793-801. [PMID: 28212935 DOI: 10.1016/j.ijbiomac.2017.02.050] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2016] [Revised: 02/10/2017] [Accepted: 02/11/2017] [Indexed: 11/16/2022]
Abstract
The RNA helicase DEAD-box protein Sub2 (yeast)/UAP56 (mammals) is conserved across eukaryotes and is essential for mRNA export in trypanosomes. Despite the high conservation of Sub2 in lower eukaryotes such as Trypanosoma cruzi, the low conservation of other mRNA export factors raises questions regarding whether the mode of action of TcSub2 is similar to that of orthologs from other eukaryotes. Mutation of the conserved K87 residue of TcSub2 abolishes ATPase activity, showing that its ATPase domain is functional. However, the Vmax of TcSub2 was much higher than the Vmax described for the human protein UAP56, which suggests that the TcSub2 enzyme hydrolyzes ATP faster than its human homolog. Furthermore, we demonstrate that RNA association is less important to the activity of TcSub2 compared to UAP56. Our results show differences in activity of this protein, even though the structure of TcSub2 is very similar to UAP56. Functional complementation assays indicate that these differences may be common to other trypanosomatids. Distinct features of RNA influence and ATPase efficiency between UAP56 and TcSub2 may reflect distinct structures for functional sites of TcSub2. For this reason, ligand-based or structure-based methodologies can be applied to investigate the potential of TcSub2 as a target for new drugs.
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23
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Yang F, Hsu P, Lee SD, Yang W, Hoskinson D, Xu W, Moore C, Varani G. The C terminus of Pcf11 forms a novel zinc-finger structure that plays an essential role in mRNA 3'-end processing. RNA (NEW YORK, N.Y.) 2017; 23:98-107. [PMID: 27780845 PMCID: PMC5159653 DOI: 10.1261/rna.058354.116] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2016] [Accepted: 10/16/2016] [Indexed: 05/22/2023]
Abstract
3'-End processing of pre-mRNAs prior to packaging and export to the cytoplasm of the mature transcript is a highly regulated process executed by several tens of protein factors that recognize poorly conserved RNA signals. Among them is Pcf11, a highly conserved, multidomain protein that links transcriptional elongation, 3'-end processing, and transcription termination. Here we report the structure and biochemical function of Pcf11's C-terminal domain, which is conserved from yeast to humans. We identify a novel zinc-finger fold, resembling a trillium flower. Structural, biochemical, and genetic analyses reveal a highly conserved surface that plays a critical role in both cleavage and polyadenylation. These findings provide further insight into this important protein and its multiple functional roles during cotranscriptional RNA processing.
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Affiliation(s)
- Fan Yang
- Department of Chemistry, University of Washington, Seattle, Washington 98195, USA
| | - Peter Hsu
- Department of Chemistry, University of Washington, Seattle, Washington 98195, USA
| | - Susan D Lee
- Department of Developmental, Molecular, and Chemical Biology, Tufts University School of Medicine, Boston, Massachusetts 02111, USA
| | - Wen Yang
- Department of Chemistry, University of Washington, Seattle, Washington 98195, USA
| | - Derick Hoskinson
- Department of Developmental, Molecular, and Chemical Biology, Tufts University School of Medicine, Boston, Massachusetts 02111, USA
| | - Weihao Xu
- Department of Chemistry, University of Washington, Seattle, Washington 98195, USA
| | - Claire Moore
- Department of Developmental, Molecular, and Chemical Biology, Tufts University School of Medicine, Boston, Massachusetts 02111, USA
| | - Gabriele Varani
- Department of Chemistry, University of Washington, Seattle, Washington 98195, USA
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24
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Serpeloni M, Jiménez-Ruiz E, Vidal NM, Kroeber C, Andenmatten N, Lemgruber L, Mörking P, Pall GS, Meissner M, Ávila AR. UAP56 is a conserved crucial component of a divergent mRNA export pathway in Toxoplasma gondii. Mol Microbiol 2016; 102:672-689. [PMID: 27542978 PMCID: PMC5118106 DOI: 10.1111/mmi.13485] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/18/2016] [Indexed: 01/28/2023]
Abstract
Nucleo‐cytoplasmic RNA export is an essential post‐transcriptional step to control gene expression in eukaryotic cells and is poorly understood in apicomplexan parasites. With the exception of UAP56, a component of TREX (Transcription Export) complex, other components of mRNA export machinery are not well conserved in divergent supergroups. Here, we use Toxoplasma gondii as a model system to functionally characterize TgUAP56 and its potential interaction factors. We demonstrate that TgUAP56 is crucial for mRNA export and that functional interference leads to significant accumulation of mRNA in the nucleus. It was necessary to employ bioinformatics and phylogenetic analysis to identify orthologs related to mRNA export, which show a remarkable low level of conservation in T. gondii. We adapted a conditional Cas9/CRISPR system to carry out a genetic screen to verify if these factors were involved in mRNA export in T. gondii. Only the disruption of TgRRM_1330 caused accumulation of mRNA in the nucleus as found with TgUAP56. This protein is potentially a divergent partner of TgUAP56, and provides insight into a divergent mRNA export pathway in apicomplexans.
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Affiliation(s)
- Mariana Serpeloni
- Instituto Carlos Chagas, FIOCRUZ, Curitiba, Brazil.,Departamento de Biologia Celular e Molecular, Universidade Federal do Paraná, Curitiba, Brazil.,College of Medical, Veterinary and Life Sciences, Institute of Infection, Immunity & Inflammation, Wellcome Trust Centre for Molecular Parasitology, University of Glasgow, UK
| | - Elena Jiménez-Ruiz
- College of Medical, Veterinary and Life Sciences, Institute of Infection, Immunity & Inflammation, Wellcome Trust Centre for Molecular Parasitology, University of Glasgow, UK
| | - Newton Medeiros Vidal
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Constanze Kroeber
- College of Medical, Veterinary and Life Sciences, Institute of Infection, Immunity & Inflammation, Wellcome Trust Centre for Molecular Parasitology, University of Glasgow, UK
| | - Nicole Andenmatten
- College of Medical, Veterinary and Life Sciences, Institute of Infection, Immunity & Inflammation, Wellcome Trust Centre for Molecular Parasitology, University of Glasgow, UK
| | - Leandro Lemgruber
- College of Medical, Veterinary and Life Sciences, Institute of Infection, Immunity & Inflammation, Wellcome Trust Centre for Molecular Parasitology, University of Glasgow, UK
| | | | - Gurman S Pall
- College of Medical, Veterinary and Life Sciences, Institute of Infection, Immunity & Inflammation, Wellcome Trust Centre for Molecular Parasitology, University of Glasgow, UK
| | - Markus Meissner
- College of Medical, Veterinary and Life Sciences, Institute of Infection, Immunity & Inflammation, Wellcome Trust Centre for Molecular Parasitology, University of Glasgow, UK
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25
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Paul B, Montpetit B. Altered RNA processing and export lead to retention of mRNAs near transcription sites and nuclear pore complexes or within the nucleolus. Mol Biol Cell 2016; 27:2742-56. [PMID: 27385342 PMCID: PMC5007094 DOI: 10.1091/mbc.e16-04-0244] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2016] [Accepted: 06/29/2016] [Indexed: 01/17/2023] Open
Abstract
In a screen of >1000 essential gene mutants in Saccharomyces cerevisiae, 26 mutants are found that directly or indirectly affect mRNA processing and/or mRNA export. Single-molecule FISH data show that the majority of these mutants retain mRNAs at discrete locations within the nucleus, which include the nucleolus. Many protein factors are required for mRNA biogenesis and nuclear export, which are central to the eukaryotic gene expression program. It is unclear, however, whether all factors have been identified. Here we report on a screen of >1000 essential gene mutants in Saccharomyces cerevisiae for defects in mRNA processing and export, identifying 26 mutants with defects in this process. Single-molecule FISH data showed that the majority of these mutants accumulated mRNA within specific regions of the nucleus, which included 1) mRNAs within the nucleolus when nucleocytoplasmic transport, rRNA biogenesis, or RNA processing and surveillance was disrupted, 2) the buildup of mRNAs near transcription sites in 3′-end processing and chromosome segregation mutants, and 3) transcripts being enriched near nuclear pore complexes when components of the mRNA export machinery were mutated. These data show that alterations to various nuclear processes lead to the retention of mRNAs at discrete locations within the nucleus.
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Affiliation(s)
- Biplab Paul
- Department of Cell Biology, University of Alberta, Edmonton, AB T6G 2H7, Canada
| | - Ben Montpetit
- Department of Cell Biology, University of Alberta, Edmonton, AB T6G 2H7, Canada
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26
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Smith C, Lari A, Derrer CP, Ouwehand A, Rossouw A, Huisman M, Dange T, Hopman M, Joseph A, Zenklusen D, Weis K, Grunwald D, Montpetit B. In vivo single-particle imaging of nuclear mRNA export in budding yeast demonstrates an essential role for Mex67p. J Cell Biol 2016; 211:1121-30. [PMID: 26694837 PMCID: PMC4687877 DOI: 10.1083/jcb.201503135] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Single-particle imaging in budding yeast demonstrates that mRNP export is fast (∼200 ms) and that mRNPs are retained at NPCs and undergo retrograde transport in a mex67-5 mutant, proving an essential role for Mex67p in directional mRNP transport. Many messenger RNA export proteins have been identified; yet the spatial and temporal activities of these proteins and how they determine directionality of messenger ribonucleoprotein (mRNP) complex export from the nucleus remain largely undefined. Here, the bacteriophage PP7 RNA-labeling system was used in Saccharomyces cerevisiae to follow single-particle mRNP export events with high spatial precision and temporal resolution. These data reveal that mRNP export, consisting of nuclear docking, transport, and cytoplasmic release from a nuclear pore complex (NPC), is fast (∼200 ms) and that upon arrival in the cytoplasm, mRNPs are frequently confined near the nuclear envelope. Mex67p functions as the principal mRNP export receptor in budding yeast. In a mex67-5 mutant, delayed cytoplasmic release from NPCs and retrograde transport of mRNPs was observed. This proves an essential role for Mex67p in cytoplasmic mRNP release and directionality of transport.
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Affiliation(s)
- Carlas Smith
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA 01605 Department Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605
| | - Azra Lari
- Department of Cell Biology, University of Alberta, T6G 2H7 Edmonton, Alberta, Canada
| | | | - Anette Ouwehand
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA 01605 Department Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605 Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, 2628 CJ Delft, Netherlands
| | - Ammeret Rossouw
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA 01605 Department Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605 Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, 2628 CJ Delft, Netherlands
| | - Maximiliaan Huisman
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA 01605 Department Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605 Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, 2628 CJ Delft, Netherlands
| | - Thomas Dange
- Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, 2628 CJ Delft, Netherlands
| | - Mark Hopman
- Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, 2628 CJ Delft, Netherlands
| | - Aviva Joseph
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA 01605 Department Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605
| | - Daniel Zenklusen
- Departement de Biochimie et Medecine Moleculaire, Universite de Montreal, H3T 1J4 Montreal, Quebec, Canada
| | - Karsten Weis
- Department of Biology, Institute of Biochemistry, ETH Zurich, 8093 Zurich, Switzerland Department of Cell and Developmental Biology, University of California, Berkeley, Berkeley, CA 94720
| | - David Grunwald
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA 01605 Department Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605 Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, 2628 CJ Delft, Netherlands
| | - Ben Montpetit
- Department of Cell Biology, University of Alberta, T6G 2H7 Edmonton, Alberta, Canada
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27
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Wu J, Bao A, Chatterjee K, Wan Y, Hopper AK. Genome-wide screen uncovers novel pathways for tRNA processing and nuclear-cytoplasmic dynamics. Genes Dev 2016; 29:2633-44. [PMID: 26680305 PMCID: PMC4699390 DOI: 10.1101/gad.269803.115] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
In this resource, Wu et al. present the first comprehensive unbiased analysis of the role of nearly an entire proteome in tRNA biology and describe 162 novel and 12 previously known Saccharomyces cerevisiae gene products that function in tRNA processing, turnover, and subcellular movement. The findings from this genome-wide screen describe putative novel pathways for tRNA nuclear export and extensive links between tRNA biology and other aspects of cell physiology. Transfer ribonucleic acids (tRNAs) are essential for protein synthesis. However, key gene products involved in tRNA biogenesis and subcellular movement remain to be discovered. We conducted the first comprehensive unbiased analysis of the role of nearly an entire proteome in tRNA biology and describe 162 novel and 12 previously known Saccharomyces cerevisiae gene products that function in tRNA processing, turnover, and subcellular movement. tRNA nuclear export is of particular interest because it is essential, but the known tRNA exporters (Los1 [exportin-t] and Msn5 [exportin-5]) are unessential. We report that mutations of CRM1 (Exportin-1), MEX67/MTR2 (TAP/p15), and five nucleoporins cause accumulation of unspliced tRNA, a hallmark of defective tRNA nuclear export. CRM1 mutation genetically interacts with los1Δ and causes altered tRNA nuclear–cytoplasmic distribution. The data implicate roles for the protein and mRNA nuclear export machineries in tRNA nuclear export. Mutations of genes encoding actin cytoskeleton components and mitochondrial outer membrane proteins also cause accumulation of unspliced tRNA, likely due to defective splicing on mitochondria. Additional gene products, such as chromatin modification enzymes, have unanticipated effects on pre-tRNA end processing. Thus, this genome-wide screen uncovered putative novel pathways for tRNA nuclear export and extensive links between tRNA biology and other aspects of cell physiology.
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Affiliation(s)
- Jingyan Wu
- Department of Molecular Genetics, Center for RNA biology, The Ohio State University, Columbus, Ohio 43210, USA
| | | | - Kunal Chatterjee
- Department of Molecular Genetics, Center for RNA biology, The Ohio State University, Columbus, Ohio 43210, USA
| | - Yao Wan
- Department of Molecular Genetics, Center for RNA biology, The Ohio State University, Columbus, Ohio 43210, USA
| | - Anita K Hopper
- Department of Molecular Genetics, Center for RNA biology, The Ohio State University, Columbus, Ohio 43210, USA
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28
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Abstract
Nuclear pore proteins interact dynamically with chromatin to regulate gene activities. A key question is how nucleoporin interactions mechanistically alter a gene's intranuclear position and transcriptional output. We reported recently on a direct interaction between the nuclear pore-associated TREX-2 complex and promoter-bound Mediator. This highlights how nuclear-pore associated adaptors gain regulatory access to the core transcription machinery. In this Extra View, we discuss an additional implication that arises from our work and the recent literature: how promoter elements may regulate mRNA metabolism beyond transcription initiation.
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Affiliation(s)
- Tobias Schubert
- a Max F. Perutz Laboratories , Medical University of Vienna , Vienna Biocenter Campus (VBC) , Vienna, Austria
| | - Alwin Köhler
- a Max F. Perutz Laboratories , Medical University of Vienna , Vienna Biocenter Campus (VBC) , Vienna, Austria
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29
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Vogt C, Bohne J. The KSHV RNA regulator ORF57: target specificity and its role in the viral life cycle. WILEY INTERDISCIPLINARY REVIEWS-RNA 2016; 7:173-85. [PMID: 26769399 DOI: 10.1002/wrna.1323] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2015] [Revised: 11/12/2015] [Accepted: 11/13/2015] [Indexed: 12/14/2022]
Abstract
Kaposi's sarcoma-associated herpesvirus (KSHV) encodes ORF57, which enhances the expression of intron-less KSHV genes on multiple post-transcriptional levels mainly affecting RNA stability and export to the cytoplasm. Yet, it remains elusive how ORF57 recognizes viral RNAs and discriminates them from cellular messenger RNAs (mRNAs). Although one common binding motif on three separate KSHV RNAs has been described, most other lytic genes lack this sequence element. In this article we will review the sequence requirements for ORF57 to enhance RNA expression and discuss a model how ORF57 achieves specificity for viral RNAs. Finally, the role of ORF57 is integrated into the viral life cycle as a complex interplay with other viral and host factors and with implications for cellular gene expression.
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Affiliation(s)
- Carolin Vogt
- Institute for Virology, Hannover Medical School, Hannover, Germany
| | - Jens Bohne
- Institute for Virology, Hannover Medical School, Hannover, Germany
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30
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Trahan C, Oeffinger M. Targeted cross-linking-mass spectrometry determines vicinal interactomes within heterogeneous RNP complexes. Nucleic Acids Res 2015; 44:1354-69. [PMID: 26657640 PMCID: PMC4756821 DOI: 10.1093/nar/gkv1366] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2015] [Accepted: 11/24/2015] [Indexed: 02/06/2023] Open
Abstract
Proteomic and RNomic approaches have identified many components of different ribonucleoprotein particles (RNPs), yet still little is known about the organization and protein proximities within these heterogeneous and highly dynamic complexes. Here we describe a targeted cross-linking approach, which combines cross-linking from a known anchor site with affinity purification and mass spectrometry (MS) to identify the changing vicinity interactomes along RNP maturation pathways. Our method confines the reaction radius of a heterobifunctional cross-linker to a specific interaction surface, increasing the probability to capture low abundance conformations and transient vicinal interactors too infrequent for identification by traditional cross-linking-MS approaches, and determine protein proximities within RNPs. Applying the method to two conserved RNA-associated complexes in Saccharomyces cerevisae, the mRNA export receptor Mex67:Mtr2 and the pre-ribosomal Nop7 subcomplex, we identified dynamic vicinal interactomes within those complexes and along their changing pathway milieu. Our results therefore show that this method provides a new tool to study the changing spatial organization of heterogeneous dynamic RNP complexes.
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Affiliation(s)
- Christian Trahan
- Department for Systems Biology, Institut de recherches cliniques de Montréal, Montréal, Québec H2W 1R7, Canada Département de biochimie, Faculté de médecine, Université de Montréal, Montréal, Québec H3T 1J4, Canada
| | - Marlene Oeffinger
- Department for Systems Biology, Institut de recherches cliniques de Montréal, Montréal, Québec H2W 1R7, Canada Département de biochimie, Faculté de médecine, Université de Montréal, Montréal, Québec H3T 1J4, Canada Division of Experimental Medicine, Faculty of Medicine, McGill University, Montréal, Québec H3A 1A3, Canada
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Guet D, Burns LT, Maji S, Boulanger J, Hersen P, Wente SR, Salamero J, Dargemont C. Combining Spinach-tagged RNA and gene localization to image gene expression in live yeast. Nat Commun 2015; 6:8882. [PMID: 26582123 PMCID: PMC4673486 DOI: 10.1038/ncomms9882] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2015] [Accepted: 10/13/2015] [Indexed: 11/14/2022] Open
Abstract
Although many factors required for the formation of export-competent mRNPs have been described, an integrative view of the spatiotemporal coordinated cascade leading mRNPs from their site of transcription to their site of nuclear exit, at a single cell level, is still partially missing due to technological limitations. Here we report that the RNA Spinach aptamer is a powerful tool for mRNA imaging in live S. cerevisiae with high spatial-temporal resolution and no perturbation of the mRNA biogenesis properties. Dedicated image processing workflows are developed to allow detection of very low abundance of transcripts, accurate quantitative dynamic studies, as well as to provide a localization precision close to 100 nm at consistent time scales. Combining these approaches has provided a state-of-the-art analysis of the osmotic shock response in live yeast by localizing induced transcription factors, target gene loci and corresponding transcripts. Measuring single-cell mRNA dynamics is critical to understand gene expression. Here, using RNA Spinach technique to detect very low abundant mRNAs, Guet et al. report an analysis of the osmotic shock response in live yeast by localizing induced transcription factors, target gene loci and corresponding transcripts.
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Affiliation(s)
- David Guet
- Univ Paris Diderot, Sorbonne Paris Cité, INSERM UMR944, CNRS UMR7212, Equipe labellisée Ligue contre le cancer, Hôpital St Louis, 1 Avenue Claude Vellefaux, 75475 Paris Cedex 10, 75475, France
| | - Laura T Burns
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, 205 Kirkland Hall, Nashville, Tennessee 37232-8240, USA
| | - Suman Maji
- Univ Paris Diderot, Sorbonne Paris Cité, INSERM UMR944, CNRS UMR7212, Equipe labellisée Ligue contre le cancer, Hôpital St Louis, 1 Avenue Claude Vellefaux, 75475 Paris Cedex 10, 75475, France
| | - Jérôme Boulanger
- Team-Space Time Imaging of Endomembranes and Organelles Dynamics, UMR144 CNRS, Univ Pierre et Marie Curie, Institut Curie, 12 rue Lhomond, Paris 75005, France
| | - Pascal Hersen
- Univ Paris Diderot, Sorbonne Paris Cité, CNRS UMR7057, Laboratoire Matière et Systèmes Complexes, 10 rue Alice Domon et Léonie Duquet, Paris 75013, France
| | - Susan R Wente
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, 205 Kirkland Hall, Nashville, Tennessee 37232-8240, USA
| | - Jean Salamero
- Team-Space Time Imaging of Endomembranes and Organelles Dynamics, UMR144 CNRS, Univ Pierre et Marie Curie, Institut Curie, 12 rue Lhomond, Paris 75005, France.,PICT-IBiSA Imaging Core Facility, Institut Curie, 12 rue Lhomond, Paris 75005, France
| | - Catherine Dargemont
- Univ Paris Diderot, Sorbonne Paris Cité, INSERM UMR944, CNRS UMR7212, Equipe labellisée Ligue contre le cancer, Hôpital St Louis, 1 Avenue Claude Vellefaux, 75475 Paris Cedex 10, 75475, France
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Burton ZF. The Old and New Testaments of gene regulation. Evolution of multi-subunit RNA polymerases and co-evolution of eukaryote complexity with the RNAP II CTD. Transcription 2015; 5:e28674. [PMID: 25764332 PMCID: PMC4215175 DOI: 10.4161/trns.28674] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
I relate a story of genesis told from the point of view of multi-subunit RNA polymerases (RNAPs) including an Old Testament (core RNAP motifs in all cellular life) and a New Testament (the RNAP II heptad repeat carboxy terminal domain (CTD) and CTD interactome in eukarya). The Old Testament: at their active site, one class of eukaryotic interfering RNAP and ubiquitous multi-subunit RNAPs each have two-double psi β barrel (DPBB) motifs (a distinct pattern for compact 6-β sheet barrels). Between β sheets 2 and 3 of the β subunit type DPBB of all multi-subunit RNAPs is a sandwich barrel hybrid motif (SBHM) that interacts with conserved initiation and elongation factors required to utilize a DNA template. Analysis of RNAP core protein motifs, therefore, indicates that RNAP evolution can be traced from the RNA-protein world to LUCA (the last universal common ancestor) branching to LECA (the last eukaryotic common ancestor) and to the present day, spanning about 4 billion years. The New Testament: in the eukaryotic lineage, I posit that splitting RNAP functions into RNAPs I, II and III and innovations developed around the CTD heptad repeat of RNAP II and the extensive CTD interactome helps to describe how greater structural, cell cycle, epigenetic and signaling complexity co-evolved in eukaryotes relative to eubacteria and archaea.
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Affiliation(s)
- Zachary F Burton
- a Department of Biochemistry and Molecular Biology; Michigan State University; East Lansing, MI USA
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Sloan KE, Gleizes PE, Bohnsack MT. Nucleocytoplasmic Transport of RNAs and RNA-Protein Complexes. J Mol Biol 2015; 428:2040-59. [PMID: 26434509 DOI: 10.1016/j.jmb.2015.09.023] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2015] [Revised: 09/26/2015] [Accepted: 09/28/2015] [Indexed: 12/15/2022]
Abstract
RNAs and ribonucleoprotein complexes (RNPs) play key roles in mediating and regulating gene expression. In eukaryotes, most RNAs are transcribed, processed and assembled with proteins in the nucleus and then either function in the cytoplasm or also undergo a cytoplasmic phase in their biogenesis. This compartmentalization ensures that sequential steps in gene expression and RNP production are performed in the correct order and it allows important quality control mechanisms that prevent the involvement of aberrant RNAs/RNPs in these cellular pathways. The selective exchange of RNAs/RNPs between the nucleus and cytoplasm is enabled by nuclear pore complexes, which function as gateways between these compartments. RNA/RNP transport is facilitated by a range of nuclear transport receptors and adaptors, which are specifically recruited to their cargos and mediate interactions with nucleoporins to allow directional translocation through nuclear pore complexes. While some transport factors are only responsible for the export/import of a certain class of RNA/RNP, others are multifunctional and, in the case of large RNPs, several export factors appear to work together to bring about export. Recent structural studies have revealed aspects of the mechanisms employed by transport receptors to enable specific cargo recognition, and genome-wide approaches have provided the first insights into the diverse composition of pre-mRNPs during export. Furthermore, the regulation of RNA/RNP export is emerging as an important means to modulate gene expression under stress conditions and in disease.
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Affiliation(s)
- Katherine E Sloan
- Institute for Molecular Biology, Goettingen University Medical Department, 37073 Goettingen, Germany
| | - Pierre-Emmanuel Gleizes
- Laboratoire de Biologie Moléculaire Eucaryote, UMR 5099, Université de Toulouse-Paul Sabatier, CNRS, Toulouse, France
| | - Markus T Bohnsack
- Institute for Molecular Biology, Goettingen University Medical Department, 37073 Goettingen, Germany; Goettingen Centre for Molecular Biosciences, Georg-August-University, 37075 Goettingen, Germany.
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Wickramasinghe VO, Laskey RA. Control of mammalian gene expression by selective mRNA export. Nat Rev Mol Cell Biol 2015; 16:431-42. [PMID: 26081607 DOI: 10.1038/nrm4010] [Citation(s) in RCA: 147] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Nuclear export of mRNAs is a crucial step in the regulation of gene expression, linking transcription in the nucleus to translation in the cytoplasm. Although important components of the mRNA export machinery are well characterized, such as transcription-export complexes TREX and TREX-2, recent work has shown that, in some instances, mammalian mRNA export can be selective and can regulate crucial biological processes such as DNA repair, gene expression, maintenance of pluripotency, haematopoiesis, proliferation and cell survival. Such findings show that mRNA export is an unexpected, yet potentially important, mechanism for the control of gene expression and of the mammalian transcriptome.
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Affiliation(s)
- Vihandha O Wickramasinghe
- Medical Research Centre (MRC) Cancer Unit, Hutchison/MRC Research Centre, Box 197, Biomedical Campus, Cambridge CB2 0XZ, UK
| | - Ronald A Laskey
- Department of Zoology, University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK
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Oeffinger M, Montpetit B. Emerging properties of nuclear RNP biogenesis and export. Curr Opin Cell Biol 2015; 34:46-53. [PMID: 25938908 DOI: 10.1016/j.ceb.2015.04.007] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2014] [Revised: 03/23/2015] [Accepted: 04/14/2015] [Indexed: 01/02/2023]
Abstract
RNA biology has recently seen an explosion of data due to advances in RNA sequencing, proteomic, and RNA imaging technologies. In this review, we highlight progress that has been made using these approaches in the area of nuclear RNP biogenesis and export. Excitingly, the ability to collect quantitative data at the 'omics' scale combined with measurements of transcription, decay, and transport kinetics is providing the information needed to address RNP biogenesis at a systems level. We believe this to be a necessary and critical next step that will lead to a better understanding of how RNP quality, diversity, and fate emerge from a defined set of nuclear RNP assembly and maturation steps.
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Affiliation(s)
- Marlene Oeffinger
- Institut de recherches cliniques de Montréal, 110 Avenue des Pins Ouest, Montréal, Québec, Canada H2W 1R7; Département de biochimie et médicine moléculaire, Université de Montréal, Montréal, Québec, Canada H3T 1J4; Faculty of Medicine, Division of Experimental Medicine, McGill University, Montréal, Québec, Canada H3A 1A3.
| | - Ben Montpetit
- Department of Cell Biology, University of Alberta, 5-14 Medical Sciences Building, Edmonton, Alberta, Canada T6G 2H7.
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Bonnet A, Bretes H, Palancade B. Nuclear pore components affect distinct stages of intron-containing gene expression. Nucleic Acids Res 2015; 43:4249-61. [PMID: 25845599 PMCID: PMC4417180 DOI: 10.1093/nar/gkv280] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2015] [Accepted: 03/20/2015] [Indexed: 12/20/2022] Open
Abstract
Several nuclear pore-associated factors, including the SUMO-protease Ulp1, have been proposed to prevent the export of intron-containing messenger ribonucleoparticles (mRNPs) in yeast. However, the molecular mechanisms of this nuclear pore-dependent mRNA quality control, including the sumoylated targets of Ulp1, have remained unidentified. Here, we demonstrate that the apparent 'pre-mRNA leakage' phenotype arising upon ULP1 inactivation is shared by sumoylation mutants of the THO complex, an early mRNP biogenesis factor. Importantly, we establish that alteration of THO complex activity differentially impairs the expression of intronless and intron-containing reporter genes, rather than triggering bona fide 'pre-mRNA leakage'. Indeed, we show that the presence of introns within THO target genes attenuates the effect of THO inactivation on their transcription. Epistasis analyses further clarify that different nuclear pore components influence intron-containing gene expression at distinct stages. Ulp1, whose maintenance at nuclear pores depends on the Nup84 complex, impacts on THO-dependent gene expression, whereas the nuclear basket-associated Mlp1/Pml39 proteins prevent pre-mRNA export at a later stage, contributing to mRNA quality control. Our study thus highlights the multiplicity of mechanisms by which nuclear pores contribute to gene expression, and further provides the first evidence that intronic sequences can alleviate early mRNP biogenesis defects.
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Affiliation(s)
- Amandine Bonnet
- Institut Jacques Monod, CNRS, UMR 7592, Univ Paris Diderot, Sorbonne Paris Cité, F-75205 Paris, France
| | - Hugo Bretes
- Institut Jacques Monod, CNRS, UMR 7592, Univ Paris Diderot, Sorbonne Paris Cité, F-75205 Paris, France Ecole Doctorale Gènes Génomes Cellules, Université Paris Sud-11, 91400 Orsay, France
| | - Benoit Palancade
- Institut Jacques Monod, CNRS, UMR 7592, Univ Paris Diderot, Sorbonne Paris Cité, F-75205 Paris, France
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37
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ORF57 overcomes the detrimental sequence bias of Kaposi's sarcoma-associated herpesvirus lytic genes. J Virol 2015; 89:5097-109. [PMID: 25694606 DOI: 10.1128/jvi.03264-14] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2014] [Accepted: 02/17/2015] [Indexed: 12/24/2022] Open
Abstract
UNLABELLED Kaposi's sarcoma-associated herpesvirus (KSHV) encodes ORF57, which enhances the expression of intronless KSHV genes on multiple posttranscriptional levels. However, it remains elusive how ORF57 recognizes viral RNAs. Here, we demonstrate that ORF57 also increases the expression of the multiple intron-containing K15 gene. The nucleotide bias of the K15 cDNA revealed an unusual high AT content. Thus, we optimized the K15 cDNA by raising the frequency of GC nucleotides, yielding an ORF57-independent version. To further prove the importance of the sequence bias of ORF57-dependent RNAs, we grouped KSHV mRNAs according to their AT content and found a correlation between AT-richness and ORF57 dependency. More importantly, latent genes, which have to be expressed in the absence of ORF57, have a low AT content and are indeed ORF57 independent. The nucleotide composition of K15 resembles that of HIV gag, which cannot be expressed unless RNA export is facilitated by the HIV Rev protein. Interestingly, ORF57 can partially rescue HIV Gag expression. Thus, the KSHV target RNAs of ORF57 and HIV gag RNA may share certain motifs based on the nucleotide bias. A bioinformatic comparison between wild-type and sequence-optimized K15 revealed a higher density for hnRNP-binding motifs in the former. We speculate that binding of particular hnRNPs to KSHV lytic transcripts is the prerequisite for ORF57 to enhance their expression. IMPORTANCE The mostly intronless genes of KSHV are only expressed in the presence of the viral regulator protein ORF57, but how ORF57 recognizes viral RNAs remains elusive. We focused on the multiple intron-containing KSHV gene K15 and revealed that its expression is also increased by ORF57. Moreover, sequences in the K15 cDNA mediate this enhancement. The quest for a target sequence or a response element for ORF57 in the lytic genes was not successful. Instead, we found the nucleotide bias to be the critical determinant of ORF57 dependency. Based on the fact that ORF57 has only a weak affinity for nucleic acids, we speculate that a cellular RNA-binding protein provides the sequence preference for ORF57. This study provides evidence that herpesviral RNA regulator proteins use the sequence bias of lytic genes and the resulting composition of the viral mRNP to distinguish between viral and cellular mRNAs.
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Aibara S, Katahira J, Valkov E, Stewart M. The principal mRNA nuclear export factor NXF1:NXT1 forms a symmetric binding platform that facilitates export of retroviral CTE-RNA. Nucleic Acids Res 2015; 43:1883-93. [PMID: 25628361 PMCID: PMC4330390 DOI: 10.1093/nar/gkv032] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
The NXF1:NXT1 complex (also known as TAP:p15) is a general mRNA nuclear export factor that is conserved from yeast to humans. NXF1 is a modular protein constructed from four domains (RRM, LRR, NTF2-like and UBA domains). It is currently unclear how NXF1:NXT1 binds transcripts and whether there is higher organization of the NXF1 domains. We report here the 3.4 Å resolution crystal structure of the first three domains of human NXF1 together with NXT1 that has two copies of the complex in the asymmetric unit arranged to form an intimate domain-swapped dimer. In this dimer, the linkers between the NXF1 LRR and NTF2-like domains interact with NXT1, generating a 2-fold symmetric platform in which the RNA-binding RRM, LRR and NTF2-like domains are arranged on one face. In addition to bulk transcripts, NXF1:NXT1 also facilitates the export of unspliced retroviral genomic RNA from simple type-D retroviruses such as SRV-1 that contain a constitutive transport element (CTE), a cis-acting 2-fold symmetric RNA stem–loop motif. Complementary structural, biochemical and cellular techniques indicated that the formation of a symmetric RNA binding platform generated by dimerization of NXF1:NXT1 facilitates the recognition of CTE-RNA and promotes its nuclear export.
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Affiliation(s)
- Shintaro Aibara
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK
| | - Jun Katahira
- Biomolecular Networks Laboratories, Graduate School of Frontier Biosciences, Osaka University, 1-3 Yamadoka, Suita, Osaka 565-0871, Japan Department of Biochemistry, Graduate School of Medicine, Osaka University, 2-2 Yamadaoka Suita, Osaka 565-0871, Japan
| | - Eugene Valkov
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK
| | - Murray Stewart
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK
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Tran EJ, King MC, Corbett AH. Macromolecular transport between the nucleus and the cytoplasm: Advances in mechanism and emerging links to disease. BIOCHIMICA ET BIOPHYSICA ACTA 2014; 1843:2784-2795. [PMID: 25116306 PMCID: PMC4161953 DOI: 10.1016/j.bbamcr.2014.08.003] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2014] [Revised: 08/01/2014] [Accepted: 08/02/2014] [Indexed: 01/08/2023]
Abstract
Transport of macromolecules between the cytoplasm and the nucleus is critical for the function of all eukaryotic cells. Large macromolecular channels termed nuclear pore complexes that span the nuclear envelope mediate the bidirectional transport of cargoes between the nucleus and cytoplasm. However, the influence of macromolecular trafficking extends past the nuclear pore complex to transcription and RNA processing within the nucleus and signaling pathways that reach into the cytoplasm and beyond. At the Mechanisms of Nuclear Transport biennial meeting held from October 18 to 23, 2013 in Woods Hole, MA, researchers in the field met to report on their recent findings. The work presented highlighted significant advances in understanding nucleocytoplasmic trafficking including how transport receptors and cargoes pass through the nuclear pore complex, the many signaling pathways that impinge on transport pathways, interplay between the nuclear envelope, nuclear pore complexes, and transport pathways, and numerous links between transport pathways and human disease. The goal of this review is to highlight newly emerging themes in nuclear transport and underscore the major questions that are likely to be the focus of future research in the field.
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Affiliation(s)
- Elizabeth J Tran
- Department of Biochemistry, Purdue University, 175 S. University Street, West Lafayette, IN 47907, USA; Purdue University Center for Cancer Research, Purdue University, Hansen Life Sciences Research Building, Room 141, 201 S. University Street, West Lafayette, IN 47907, USA.
| | - Megan C King
- Department of Cell Biology, Yale School of Medicine, 333 Cedar Street, New Haven, CT 06520, USA
| | - Anita H Corbett
- Department of Biochemistry, Emory University School of Medicine, 4117 Rollins Research Center, 1510 Clifton Road, NE, Atlanta, GA 30322, USA.
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40
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Wu H, Becker D, Krebber H. Telomerase RNA TLC1 shuttling to the cytoplasm requires mRNA export factors and is important for telomere maintenance. Cell Rep 2014; 8:1630-1638. [PMID: 25220466 DOI: 10.1016/j.celrep.2014.08.021] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2014] [Revised: 07/09/2014] [Accepted: 08/08/2014] [Indexed: 12/23/2022] Open
Abstract
Telomerases protect the ends of linear chromosomes from shortening. They are composed of an RNA (TLC1 in S. cerevisiae) and several proteins. TLC1 undergoes several maturation steps before it is exported into the cytoplasm to recruit the Est proteins for complete assembly. The mature telomerase is subsequently reimported into the nucleus, where it fulfills its function on telomeres. Here, we show that TLC1 export into the cytoplasm requires not only the Ran GTPase-dependent karyopherin Crm1/Xpo1 but also the mRNA export machinery. mRNA export factor mutants accumulate mature and export-competent TLC1 RNAs in their nuclei. Moreover, TLC1 physically interacts with the mRNA transport factors Mex67 and Dbp5/Rat8. Most importantly, we show that the nuclear export of TLC1 is an essential step for the formation of the functional RNA containing enzyme, because blocking TLC1 export in the mex67-5 xpo1-1 double mutant prevents its cytoplasmic maturation and leads to telomere shortening.
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Affiliation(s)
- Haijia Wu
- Abteilung für Molekulare Genetik, Institut für Mikrobiologie und Genetik, Göttinger Zentrum für Molekulare Biowissenschaften (GZMB), Georg-August Universität Göttingen, 37077 Göttingen, Germany
| | - Daniel Becker
- Abteilung für Molekulare Genetik, Institut für Mikrobiologie und Genetik, Göttinger Zentrum für Molekulare Biowissenschaften (GZMB), Georg-August Universität Göttingen, 37077 Göttingen, Germany
| | - Heike Krebber
- Abteilung für Molekulare Genetik, Institut für Mikrobiologie und Genetik, Göttinger Zentrum für Molekulare Biowissenschaften (GZMB), Georg-August Universität Göttingen, 37077 Göttingen, Germany.
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41
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Bonnet A, Palancade B. Regulation of mRNA trafficking by nuclear pore complexes. Genes (Basel) 2014; 5:767-91. [PMID: 25184662 PMCID: PMC4198930 DOI: 10.3390/genes5030767] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2014] [Revised: 08/25/2014] [Accepted: 08/26/2014] [Indexed: 11/17/2022] Open
Abstract
Over the last two decades, multiple studies have explored the mechanisms governing mRNA export out of the nucleus, a crucial step in eukaryotic gene expression. During transcription and processing, mRNAs are assembled into messenger ribonucleoparticles (mRNPs). mRNPs are then exported through nuclear pore complexes (NPCs), which are large multiprotein assemblies made of several copies of a limited number of nucleoporins. A considerable effort has been put into the dissection of mRNA export through NPCs at both cellular and molecular levels, revealing the conserved contributions of a subset of nucleoporins in this process, from yeast to vertebrates. Several reports have also demonstrated the ability of NPCs to sort out properly-processed mRNPs for entry into the nuclear export pathway. Importantly, changes in mRNA export have been associated with post-translational modifications of nucleoporins or changes in NPC composition, depending on cell cycle progression, development or exposure to stress. How NPC modifications also impact on cellular mRNA export in disease situations, notably upon viral infection, is discussed.
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Affiliation(s)
- Amandine Bonnet
- Institut Jacques Monod, CNRS, UMR 7592, University Paris Diderot, Sorbonne Paris Cité, Paris F-75205, France.
| | - Benoit Palancade
- Institut Jacques Monod, CNRS, UMR 7592, University Paris Diderot, Sorbonne Paris Cité, Paris F-75205, France.
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42
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Björk P, Wieslander L. Mechanisms of mRNA export. Semin Cell Dev Biol 2014; 32:47-54. [PMID: 24813364 DOI: 10.1016/j.semcdb.2014.04.027] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2014] [Accepted: 04/17/2014] [Indexed: 02/02/2023]
Abstract
Release of properly processed and assembled mRNPs from the actively transcribing genes, movement of the mRNPs through the interchromatin and interaction with the Nuclear Pore Complexes, leading to cytoplasmic export, are essential steps of eukaryotic gene expression. Here, we review these intranuclear gene expression steps.
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Affiliation(s)
- Petra Björk
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, SE-106 91 Stockholm, Sweden.
| | - Lars Wieslander
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, SE-106 91 Stockholm, Sweden.
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43
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From hypothesis to mechanism: uncovering nuclear pore complex links to gene expression. Mol Cell Biol 2014; 34:2114-20. [PMID: 24615017 DOI: 10.1128/mcb.01730-13] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
The gene gating hypothesis put forth by Blobel in 1985 was an alluring proposal outlining functions for the nuclear pore complex (NPC) in transcription and nuclear architecture. Over the past several decades, collective studies have unveiled a full catalog of nucleoporins (Nups) that comprise the NPC, structural arrangements of Nups in the nuclear pore, and mechanisms of nucleocytoplasmic transport. With this foundation, investigations of the gene gating hypothesis have now become possible. Studies of several model organisms provide credence for Nup functions in transcription, mRNA export, and genome organization. Surprisingly, Nups are not only involved in transcriptional events that occur at the nuclear periphery, but there are also novel roles for dynamic Nups within the nucleoplasmic compartment. Several tenants of the original gene gating hypothesis have yet to be addressed. Knowledge of whether the NPC impacts the organization of the genome to control subsets of genes is limited, and the cooperating molecular machinery or specific genomic anchoring sequences are not fully resolved. This minireview summarizes the current evidence for gene gating in Saccharomyces cerevisiae, Caenorhabditis elegans, Drosophila melanogaster, and mammalian model systems. These examples highlight new and unpredicted mechanisms for Nup impacts on transcription and questions that are left to be explored.
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44
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Hérissant L, Moehle EA, Bertaccini D, Van Dorsselaer A, Schaeffer-Reiss C, Guthrie C, Dargemont C. H2B ubiquitylation modulates spliceosome assembly and function in budding yeast. Biol Cell 2014; 106:126-38. [PMID: 24476359 DOI: 10.1111/boc.201400003] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2014] [Accepted: 01/24/2014] [Indexed: 11/30/2022]
Abstract
BACKGROUND INFORMATION Commitment to splicing occurs co-transcriptionally, but a major unanswered question is the extent to which various modifications of chromatin, the template for transcription in vivo, contribute to the regulation of splicing. RESULTS Here, we perform genome-wide analyses showing that inhibition of specific marks - H2B ubiquitylation, H3K4 methylation and H3K36 methylation - perturbs splicing in budding yeast, with each modification exerting gene-specific effects. Furthermore, semi-quantitative mass spectrometry on purified nuclear mRNPs and chromatin immunoprecipitation analysis on intron-containing genes indicated that H2B ubiquitylation, but not Set1-, Set2- or Dot1-dependent H3 methylation, stimulates recruitment of the early splicing factors, namely U1 and U2 snRNPs, onto nascent RNAs. CONCLUSIONS These results suggest that histone modifications impact splicing of distinct subsets of genes using distinct pathways.
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Affiliation(s)
- Lucas Hérissant
- Pathologie Cellulaire, University Paris Diderot, Sorbonne Paris Cité, INSERM U944, CNRS UMR7212, Equipe labellisée Ligue contre le cancer, Hôpital Saint Louis, Paris, Cedex 10, France
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Schreieck A, Easter AD, Etzold S, Wiederhold K, Lidschreiber M, Cramer P, Passmore LA. RNA polymerase II termination involves C-terminal-domain tyrosine dephosphorylation by CPF subunit Glc7. Nat Struct Mol Biol 2014; 21:175-179. [PMID: 24413056 PMCID: PMC3917824 DOI: 10.1038/nsmb.2753] [Citation(s) in RCA: 63] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2013] [Accepted: 12/04/2013] [Indexed: 02/07/2023]
Abstract
At the 3′ end of protein-coding genes, RNA polymerase (Pol) II is dephosphorylated at tyrosine (Tyr1) residues of its C-terminal domain (CTD). In addition, the associated cleavage and polyadenylation (pA) factor (CPF) cleaves the transcript and adds a polyA tail. Whether these events are coordinated and how they lead to transcription termination remains poorly understood. Here we show that CPF from Saccharomyces cerevisiae is a Pol II CTD phosphatase and that the CPF subunit Glc7 dephosphorylates Tyr1 in vitro. In vivo, the activity of Glc7 is required for normal Tyr1 dephosphorylation at the pA site, for recruitment of termination factors Pcf11 and Rtt103, and for normal Pol II termination. These results show that transcription termination involves Tyr1 dephosphorylation of the CTD and indicate that pre-mRNA processing by CPF and transcription termination are coupled via Glc7-dependent Pol II Tyr1 dephosphorylation.
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Affiliation(s)
- Amelie Schreieck
- Gene Center Munich and Department of Biochemistry, Center for Integrated Protein Science Munich (CIPSM), Ludwig-Maximilians-Universität München, Munich, Germany
| | - Ashley D Easter
- Medical Research Council (MRC) Laboratory of Molecular Biology, Cambridge, United Kingdom
| | - Stefanie Etzold
- Gene Center Munich and Department of Biochemistry, Center for Integrated Protein Science Munich (CIPSM), Ludwig-Maximilians-Universität München, Munich, Germany
| | - Katrin Wiederhold
- Medical Research Council (MRC) Laboratory of Molecular Biology, Cambridge, United Kingdom
| | - Michael Lidschreiber
- Gene Center Munich and Department of Biochemistry, Center for Integrated Protein Science Munich (CIPSM), Ludwig-Maximilians-Universität München, Munich, Germany
| | - Patrick Cramer
- Gene Center Munich and Department of Biochemistry, Center for Integrated Protein Science Munich (CIPSM), Ludwig-Maximilians-Universität München, Munich, Germany
| | - Lori A Passmore
- Medical Research Council (MRC) Laboratory of Molecular Biology, Cambridge, United Kingdom
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Floch AG, Palancade B, Doye V. Fifty years of nuclear pores and nucleocytoplasmic transport studies: multiple tools revealing complex rules. Methods Cell Biol 2014; 122:1-40. [PMID: 24857723 DOI: 10.1016/b978-0-12-417160-2.00001-1] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Nuclear pore complexes (NPCs) are multiprotein assemblies embedded within the nuclear envelope and involved in the control of the bidirectional transport of proteins and ribonucleoparticles between the nucleus and the cytoplasm. Since their discovery more than 50 years ago, NPCs and nucleocytoplasmic transport have been the focus of intense research. Here, we review how the use of a multiplicity of structural, biochemical, genetic, and cell biology approaches have permitted the deciphering of the main features of this macromolecular complex, its mode of assembly as well as the rules governing nucleocytoplasmic exchanges. We first present the current knowledge of the ultrastructure of NPCs, which reveals that they are modular and repetitive assemblies of subunits referred to as nucleoporins, associated into stable subcomplexes and composed of a limited set of protein domains, including phenylalanine-glycine (FG) repeats and membrane-interacting domains. The outcome of investigations on nucleocytoplasmic trafficking will then be detailed, showing how it involves a limited number of molecular factors and common mechanisms, namely (i) indirect association of cargos with nuclear pores through receptors in the donor compartment, (ii) progression within the channel through dynamic hydrophobic interactions with FG-Nups, and (iii) NTPase-driven remodeling of transport complexes in the target compartment. Finally, we also discuss the outcome of more recent studies, which indicate that NPCs and the transport machinery are dynamic and versatile devices, whose biogenesis is tightly coordinated with the cell cycle, and which carry nonconventional duties, in particular, in mitosis, gene expression, and genetic stability.
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Affiliation(s)
- Aurélie G Floch
- Institut Jacques Monod, CNRS, UMR 7592, Univ. Paris Diderot, Sorbonne Paris Cité, F-75205 Paris, France; Ecole Doctorale Gènes Génomes Cellules, Université Paris Sud-11, Orsay, France
| | - Benoit Palancade
- Institut Jacques Monod, CNRS, UMR 7592, Univ. Paris Diderot, Sorbonne Paris Cité, F-75205 Paris, France
| | - Valérie Doye
- Institut Jacques Monod, CNRS, UMR 7592, Univ. Paris Diderot, Sorbonne Paris Cité, F-75205 Paris, France
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