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Lei J, Ma-Lauer Y, Han Y, Thoms M, Buschauer R, Jores J, Thiel V, Beckmann R, Deng W, Leonhardt H, Hilgenfeld R, von Brunn A. The SARS-unique domain (SUD) of SARS-CoV and SARS-CoV-2 interacts with human Paip1 to enhance viral RNA translation. EMBO J 2021; 40:e102277. [PMID: 33876849 PMCID: PMC8167360 DOI: 10.15252/embj.2019102277] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Revised: 03/04/2021] [Accepted: 03/17/2021] [Indexed: 02/05/2023] Open
Abstract
The ongoing outbreak of severe acute respiratory syndrome (SARS) coronavirus 2 (SARS‐CoV‐2) demonstrates the continuous threat of emerging coronaviruses (CoVs) to public health. SARS‐CoV‐2 and SARS‐CoV share an otherwise non‐conserved part of non‐structural protein 3 (Nsp3), therefore named as “SARS‐unique domain” (SUD). We previously found a yeast‐2‐hybrid screen interaction of the SARS‐CoV SUD with human poly(A)‐binding protein (PABP)‐interacting protein 1 (Paip1), a stimulator of protein translation. Here, we validate SARS‐CoV SUD:Paip1 interaction by size‐exclusion chromatography, split‐yellow fluorescent protein, and co‐immunoprecipitation assays, and confirm such interaction also between the corresponding domain of SARS‐CoV‐2 and Paip1. The three‐dimensional structure of the N‐terminal domain of SARS‐CoV SUD (“macrodomain II”, Mac2) in complex with the middle domain of Paip1, determined by X‐ray crystallography and small‐angle X‐ray scattering, provides insights into the structural determinants of the complex formation. In cellulo, SUD enhances synthesis of viral but not host proteins via binding to Paip1 in pBAC‐SARS‐CoV replicon‐transfected cells. We propose a possible mechanism for stimulation of viral translation by the SUD of SARS‐CoV and SARS‐CoV‐2.
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Affiliation(s)
- Jian Lei
- Institute of Biochemistry, Center for Structural and Cell Biology in Medicine, University of Lübeck, Lübeck, Germany.,German Center for Infection Research (DZIF), Hamburg-Lübeck- Borstel-Riems Site, University of Lübeck, Lübeck, Germany.,State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, China
| | - Yue Ma-Lauer
- Max-von-Pettenkofer Institute, Ludwig-Maximilians-University Munich, Munich, Germany.,German Center for Infection Research (DZIF), Munich, Germany
| | - Yinze Han
- State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, China
| | - Matthias Thoms
- Gene Center Munich, Department of Biochemistry, Ludwig-Maximilians-University Munich, Munich, Germany
| | - Robert Buschauer
- Gene Center Munich, Department of Biochemistry, Ludwig-Maximilians-University Munich, Munich, Germany
| | - Joerg Jores
- Institute of Veterinary Bacteriology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Volker Thiel
- Institute of Virology and Immunology, University of Bern, Bern, Switzerland
| | - Roland Beckmann
- Gene Center Munich, Department of Biochemistry, Ludwig-Maximilians-University Munich, Munich, Germany
| | - Wen Deng
- Department of Biology and Center for Integrated Protein Science, Ludwig-Maximilians-University Munich, Planegg-Martinsried, Germany.,College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, China
| | - Heinrich Leonhardt
- Department of Biology and Center for Integrated Protein Science, Ludwig-Maximilians-University Munich, Planegg-Martinsried, Germany
| | - Rolf Hilgenfeld
- Institute of Biochemistry, Center for Structural and Cell Biology in Medicine, University of Lübeck, Lübeck, Germany.,German Center for Infection Research (DZIF), Hamburg-Lübeck- Borstel-Riems Site, University of Lübeck, Lübeck, Germany.,Institute of Molecular Medicine, University of Lübeck, Lübeck, Germany
| | - Albrecht von Brunn
- Max-von-Pettenkofer Institute, Ludwig-Maximilians-University Munich, Munich, Germany.,German Center for Infection Research (DZIF), Munich, Germany
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Camillo dos Santos LP, de Matos BM, de Maman Ribeiro BC, Zanchin NIT, Guimarães BG. Crystal structure of the MIF4G domain of the Trypanosoma cruzi translation initiation factor EIF4G5. Acta Crystallogr F Struct Biol Commun 2019; 75:738-743. [PMID: 31797815 PMCID: PMC6891579 DOI: 10.1107/s2053230x19015061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Accepted: 11/07/2019] [Indexed: 11/10/2022] Open
Abstract
Kinetoplastida, a class of early-diverging eukaryotes that includes pathogenic Trypanosoma and Leishmania species, display key differences in their translation machinery compared with multicellular eukaryotes. One of these differences involves a larger number of genes encoding eIF4E and eIF4G homologs and the interaction pattern between the translation initiation factors. eIF4G is a scaffold protein which interacts with the mRNA cap-binding factor eIF4E, the poly(A)-binding protein, the RNA helicase eIF4A and the eIF3 complex. It contains the so-called middle domain of eIF4G (MIF4G), a multipurpose adaptor involved in different protein-protein and protein-RNA complexes. Here, the crystal structure of the MIF4G domain of T. cruzi EIF4G5 is described at 2.4 Å resolution, which is the first three-dimensional structure of a trypanosomatid MIF4G domain to be reported. Structural comparison with IF4G homologs from other eukaryotes and other MIF4G-containing proteins reveals differences that may account for the specific interaction mechanisms of MIF4G despite its highly conserved overall fold.
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Affiliation(s)
- Lucca Pietro Camillo dos Santos
- Carlos Chagas Institute, Oswaldo Cruz Foundation, Curitiba, Paraná, Brazil
- Biosciences and Biotechnology Postgraduate Program, Carlos Chagas Institute, Curitiba, Paraná, Brazil
| | - Bruno Moisés de Matos
- Carlos Chagas Institute, Oswaldo Cruz Foundation, Curitiba, Paraná, Brazil
- Biochemistry Postgraduate Program, Federal University of Paraná, Curitiba, Paraná, Brazil
| | | | | | - Beatriz Gomes Guimarães
- Carlos Chagas Institute, Oswaldo Cruz Foundation, Curitiba, Paraná, Brazil
- Biosciences and Biotechnology Postgraduate Program, Carlos Chagas Institute, Curitiba, Paraná, Brazil
- Biochemistry Postgraduate Program, Federal University of Paraná, Curitiba, Paraná, Brazil
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Chapat C, Corbo L. Novel roles of the CCR4-NOT complex. WILEY INTERDISCIPLINARY REVIEWS-RNA 2014; 5:883-901. [PMID: 25044499 DOI: 10.1002/wrna.1254] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2013] [Revised: 06/02/2014] [Accepted: 06/04/2014] [Indexed: 12/21/2022]
Abstract
The CCR4-NOT complex is a multi-subunit protein complex evolutionarily conserved across eukaryotes which regulates several aspects of gene expression. A fascinating model is emerging in which this complex acts as a regulation platform, controlling gene products 'from birth to death' through the coordination of different cellular machineries involved in diverse cellular functions. Recently the CCR4-NOT functions have been extended to the control of the innate immune response through the regulation of interferon signaling. Thus, a more comprehensive picture of how CCR4-NOT allows the rapid adaptation of cells to external stress, from transcription to mRNA and protein decay, is presented and discussed here. Overall, CCR4-NOT permits the efficient and rapid adaptation of cellular gene expression in response to changes in environmental conditions and stimuli.
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Affiliation(s)
- Clément Chapat
- Université Lyon 1, Lyon, France; CNRS UMR 5286, Lyon, France; Inserm U1052, Lyon, France; Cancer Research Center of Lyon, Centre Léon Bérard, Lyon, France
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Ren W, Chen H, Sun Q, Tang X, Lim SC, Huang J, Song H. Structural basis of SOSS1 complex assembly and recognition of ssDNA. Cell Rep 2014; 6:982-991. [PMID: 24630995 DOI: 10.1016/j.celrep.2014.02.020] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2014] [Revised: 02/06/2014] [Accepted: 02/14/2014] [Indexed: 01/03/2023] Open
Abstract
The SOSS1 complex comprising SOSSA, SOSSB1, and SOSSC senses single-stranded DNA (ssDNA) and promotes repair of DNA double-strand breaks (DSBs). But how SOSS1 is assembled and recognizes ssDNA remains elusive. The crystal structure of the N-terminal half of SOSSA (SOSSAN) in complex with SOSSB1 and SOSSC showed that SOSSAN serves as a scaffold to bind both SOSSB1 and SOSSC for assembly of the SOSS1 complex. The structures of SOSSAN/B1 in complex with a 12 nt ssDNA and SOSSAN/B1/C in complex with a 35 nt ssDNA showed that SOSSB1 interacts with both SOSSAN and ssDNA via two distinct surfaces. Recognition of ssDNA with a length of up to nine nucleotides is mediated solely by SOSSB1, whereas neither SOSSC nor SOSSAN are critical for ssDNA binding. These results reveal the structural basis of SOSS1 assembly and provide a framework for further study of the mechanism governing longer ssDNA recognition by the SOSS1 complex during DSB repair.
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Affiliation(s)
- Wendan Ren
- Life Sciences Institute, Zhejiang University, 388 Yuhangtang Road, Hangzhou 310058, China; Institute of Molecular and Cell Biology, 61 Biopolis Drive, Singapore 138673, Singapore
| | - Hongxia Chen
- Life Sciences Institute, Zhejiang University, 388 Yuhangtang Road, Hangzhou 310058, China
| | - Qiangzu Sun
- Life Sciences Institute, Zhejiang University, 388 Yuhangtang Road, Hangzhou 310058, China
| | - Xuhua Tang
- Institute of Molecular and Cell Biology, 61 Biopolis Drive, Singapore 138673, Singapore
| | - Siew Choo Lim
- Institute of Molecular and Cell Biology, 61 Biopolis Drive, Singapore 138673, Singapore
| | - Jun Huang
- Life Sciences Institute, Zhejiang University, 388 Yuhangtang Road, Hangzhou 310058, China.
| | - Haiwei Song
- Life Sciences Institute, Zhejiang University, 388 Yuhangtang Road, Hangzhou 310058, China; Institute of Molecular and Cell Biology, 61 Biopolis Drive, Singapore 138673, Singapore; Department of Biochemistry, National University of Singapore, 14 Science Drive, Singapore 117543, Singapore.
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Petit AP, Wohlbold L, Bawankar P, Huntzinger E, Schmidt S, Izaurralde E, Weichenrieder O. The structural basis for the interaction between the CAF1 nuclease and the NOT1 scaffold of the human CCR4-NOT deadenylase complex. Nucleic Acids Res 2012; 40:11058-72. [PMID: 22977175 PMCID: PMC3510486 DOI: 10.1093/nar/gks883] [Citation(s) in RCA: 100] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The CCR4–NOT complex plays a crucial role in post-transcriptional mRNA regulation in eukaryotic cells. It catalyzes the removal of mRNA poly(A) tails, thereby repressing translation and committing mRNAs to decay. The conserved core of the complex consists of a catalytic module comprising two deadenylases (CAF1/POP2 and CCR4a/b) and the NOT module, which contains at least NOT1, NOT2 and NOT3. NOT1 bridges the interaction between the two modules and therefore, acts as a scaffold protein for the assembly of the complex. Here, we present the crystal structures of the CAF1-binding domain of human NOT1 alone and in complex with CAF1. The NOT1 domain comprises five helical hairpins that adopt an MIF4G (middle portion of eIF4G) fold. This NOT1 MIF4G domain binds CAF1 through a pre-formed interface and leaves the CAF1 catalytic site fully accessible to RNA substrates. The conservation of critical structural and interface residues suggests that the NOT1 MIF4G domain adopts a similar fold and interacts with CAF1 in a similar manner in all eukaryotes. Our findings shed light on the assembly of the CCR4–NOT complex and provide the basis for dissecting the role of the NOT module in mRNA deadenylation.
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Affiliation(s)
- Alain-Pierre Petit
- Department of Biochemistry, Max Planck Institute for Developmental Biology, Spemannstrasse 35, 72076 Tübingen, Germany
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