3101
|
Pei XY, Dendooven T, Sonnleitner E, Chen S, Bläsi U, Luisi BF. Architectural principles for Hfq/Crc-mediated regulation of gene expression. eLife 2019; 8:e43158. [PMID: 30758287 PMCID: PMC6422490 DOI: 10.7554/elife.43158] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2018] [Accepted: 02/11/2019] [Indexed: 12/24/2022] Open
Abstract
In diverse bacterial species, the global regulator Hfq contributes to post-transcriptional networks that control expression of numerous genes. Hfq of the opportunistic pathogen Pseudomonas aeruginosa inhibits translation of target transcripts by forming a regulatory complex with the catabolite repression protein Crc. This repressive complex acts as part of an intricate mechanism of preferred nutrient utilisation. We describe high-resolution cryo-EM structures of the assembly of Hfq and Crc bound to the translation initiation site of a target mRNA. The core of the assembly is formed through interactions of two cognate RNAs, two Hfq hexamers and a Crc pair. Additional Crc protomers are recruited to the core to generate higher-order assemblies with demonstrated regulatory activity in vivo. This study reveals how Hfq cooperates with a partner protein to regulate translation, and provides a structural basis for an RNA code that guides global regulators to interact cooperatively and regulate different RNA targets.
Collapse
Affiliation(s)
- Xue Yuan Pei
- Department of BiochemistryUniversity of CambridgeCambridgeUnited Kingdom
| | - Tom Dendooven
- Department of BiochemistryUniversity of CambridgeCambridgeUnited Kingdom
| | - Elisabeth Sonnleitner
- Department of Microbiology, Immunobiology and Genetics, Max F Perutz Laboratories, Center of Molecular BiologyUniversity of Vienna, Vienna BiocenterViennaAustria
| | - Shaoxia Chen
- MRC Laboratory of Molecular BiologyCambridgeUnited Kingdom
| | - Udo Bläsi
- Department of Microbiology, Immunobiology and Genetics, Max F Perutz Laboratories, Center of Molecular BiologyUniversity of Vienna, Vienna BiocenterViennaAustria
| | - Ben F Luisi
- Department of BiochemistryUniversity of CambridgeCambridgeUnited Kingdom
| |
Collapse
|
3102
|
Structure of the complex I-like molecule NDH of oxygenic photosynthesis. Nature 2019; 566:411-414. [PMID: 30742075 DOI: 10.1038/s41586-019-0921-0] [Citation(s) in RCA: 89] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Accepted: 01/14/2019] [Indexed: 12/20/2022]
Abstract
Cyclic electron flow around photosystem I (PSI) is a mechanism by which photosynthetic organisms balance the levels of ATP and NADPH necessary for efficient photosynthesis1,2. NAD(P)H dehydrogenase-like complex (NDH) is a key component of this pathway in most oxygenic photosynthetic organisms3,4 and is the last large photosynthetic membrane-protein complex for which the structure remains unknown. Related to the respiratory NADH dehydrogenase complex (complex I), NDH transfers electrons originating from PSI to the plastoquinone pool while pumping protons across the thylakoid membrane, thereby increasing the amount of ATP produced per NADP+ molecule reduced4,5. NDH possesses 11 of the 14 core complex I subunits, as well as several oxygenic-photosynthesis-specific (OPS) subunits that are conserved from cyanobacteria to plants3,6. However, the three core complex I subunits that are involved in accepting electrons from NAD(P)H are notably absent in NDH3,5,6, and it is therefore not clear how NDH acquires and transfers electrons to plastoquinone. It is proposed that the OPS subunits-specifically NdhS-enable NDH to accept electrons from its electron donor, ferredoxin3-5,7. Here we report a 3.1 Å structure of the 0.42-MDa NDH complex from the thermophilic cyanobacterium Thermosynechococcus elongatus BP-1, obtained by single-particle cryo-electron microscopy. Our maps reveal the structure and arrangement of the principal OPS subunits in the NDH complex, as well as an unexpected cofactor close to the plastoquinone-binding site in the peripheral arm. The location of the OPS subunits supports a role in electron transfer and defines two potential ferredoxin-binding sites at the apex of the peripheral arm. These results suggest that NDH could possess several electron transfer routes, which would serve to maximize plastoquinone reduction and avoid deleterious off-target chemistry of the semi-plastoquinone radical.
Collapse
|
3103
|
dal Maso E, Glukhova A, Zhu Y, Garcia-Nafria J, Tate CG, Atanasio S, Reynolds CA, Ramírez-Aportela E, Carazo JM, Hick CA, Furness SGB, Hay DL, Liang YL, Miller LJ, Christopoulos A, Wang MW, Wootten D, Sexton PM. The Molecular Control of Calcitonin Receptor Signaling. ACS Pharmacol Transl Sci 2019; 2:31-51. [PMID: 32219215 PMCID: PMC7088896 DOI: 10.1021/acsptsci.8b00056] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Indexed: 12/12/2022]
Abstract
The calcitonin receptor (CTR) is a class B G protein-coupled receptor (GPCR) that responds to the peptide hormone calcitonin (CT). CTs are clinically approved for the treatment of bone diseases. We previously reported a 4.1 Å structure of the activated CTR bound to salmon CT (sCT) and heterotrimeric Gs protein by cryo-electron microscopy (Liang, Y.-L., et al. Phase-plate cryo- EM structure of a class B GPCR-G protein complex. Nature 2017, 546, 118-123). In the current study, we have reprocessed the electron micrographs to yield a 3.3 Å map of the complex. This has allowed us to model extracellular loops (ECLs) 2 and 3, and the peptide N-terminus that previously could not be resolved. We have also performed alanine scanning mutagenesis of ECL1 and the upper segment of transmembrane helix 1 (TM1) and its extension into the receptor extracellular domain (TM1 stalk), with effects on peptide binding and function assessed by cAMP accumulation and ERK1/2 phosphorylation. These data were combined with previously published alanine scanning mutagenesis of ECL2 and ECL3 and the new structural information to provide a comprehensive 3D map of the molecular surface of the CTR that controls binding and signaling of distinct CT and related peptides. The work highlights distinctions in how different, related, class B receptors may be activated. The new mutational data on the TM1 stalk and ECL1 have also provided critical insights into the divergent control of cAMP versus pERK signaling and, collectively with previous mutagenesis data, offer evidence that the conformations linked to these different signaling pathways are, in many ways, mutually exclusive. This study furthers our understanding of the complex nature of signaling elicited by GPCRs and, in particular, that of the therapeutically important class B subfamily.
Collapse
Affiliation(s)
- Emma dal Maso
- Drug
Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville 3052, Victoria Australia
| | - Alisa Glukhova
- Drug
Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville 3052, Victoria Australia
| | - Yue Zhu
- The
National Center for Drug Screening and CAS Key Laboratory of Receptor
Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- University
of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China
| | - Javier Garcia-Nafria
- MRC
Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, U.K.
| | - Christopher G. Tate
- MRC
Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, U.K.
| | - Silvia Atanasio
- School
of Biological Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, U.K.
| | | | - Erney Ramírez-Aportela
- Biocomputing
Unit, National Center for Biotechnology
(CNB-CSIC), C/Darwin,
3, Campus Universidad Autónoma, 28049 Cantoblanco, Madrid Spain
| | - Jose-Maria Carazo
- Biocomputing
Unit, National Center for Biotechnology
(CNB-CSIC), C/Darwin,
3, Campus Universidad Autónoma, 28049 Cantoblanco, Madrid Spain
| | - Caroline A. Hick
- Drug
Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville 3052, Victoria Australia
| | - Sebastian G. B. Furness
- Drug
Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville 3052, Victoria Australia
| | - Debbie L. Hay
- The
University of Auckland, School of Biological
Sciences, 3 Symonds Street, Auckland 1142, New Zealand
| | - Yi-Lynn Liang
- Drug
Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville 3052, Victoria Australia
| | - Laurence J. Miller
- Department
of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Scottsdale, Arizona 85259, United States
| | - Arthur Christopoulos
- Drug
Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville 3052, Victoria Australia
| | - Ming-Wei Wang
- The
National Center for Drug Screening and CAS Key Laboratory of Receptor
Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- University
of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China
- School
of Pharmacy, Fudan University, Shanghai 201203, China
| | - Denise Wootten
- Drug
Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville 3052, Victoria Australia
- School
of Pharmacy, Fudan University, Shanghai 201203, China
| | - Patrick M. Sexton
- Drug
Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville 3052, Victoria Australia
- School
of Pharmacy, Fudan University, Shanghai 201203, China
| |
Collapse
|
3104
|
Zhang W, Falcon B, Murzin AG, Fan J, Crowther RA, Goedert M, Scheres SH. Heparin-induced tau filaments are polymorphic and differ from those in Alzheimer's and Pick's diseases. eLife 2019; 8:43584. [PMID: 30720432 PMCID: PMC6375701 DOI: 10.7554/elife.43584] [Citation(s) in RCA: 263] [Impact Index Per Article: 52.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Accepted: 01/31/2019] [Indexed: 12/17/2022] Open
Abstract
Assembly of microtubule-associated protein tau into filamentous inclusions underlies a range of neurodegenerative diseases. Tau filaments adopt different conformations in Alzheimer’s and Pick’s diseases. Here, we used cryo- and immuno- electron microscopy to characterise filaments that were assembled from recombinant full-length human tau with four (2N4R) or three (2N3R) microtubule-binding repeats in the presence of heparin. 2N4R tau assembles into multiple types of filaments, and the structures of three types reveal similar ‘kinked hairpin’ folds, in which the second and third repeats pack against each other. 2N3R tau filaments are structurally homogeneous, and adopt a dimeric core, where the third repeats of two tau molecules pack in a parallel manner. The heparin-induced tau filaments differ from those of Alzheimer’s or Pick’s disease, which have larger cores with different repeat compositions. Our results illustrate the structural versatility of amyloid filaments, and raise questions about the relevance of in vitro assembly.
Collapse
Affiliation(s)
- Wenjuan Zhang
- MRC Laboratory of Molecular Biology, Cambridge, United Kingdom
| | - Benjamin Falcon
- MRC Laboratory of Molecular Biology, Cambridge, United Kingdom
| | - Alexey G Murzin
- MRC Laboratory of Molecular Biology, Cambridge, United Kingdom
| | - Juan Fan
- MRC Laboratory of Molecular Biology, Cambridge, United Kingdom
| | | | - Michel Goedert
- MRC Laboratory of Molecular Biology, Cambridge, United Kingdom
| | | |
Collapse
|
3105
|
Fica SM, Oubridge C, Wilkinson ME, Newman AJ, Nagai K. A human postcatalytic spliceosome structure reveals essential roles of metazoan factors for exon ligation. Science 2019; 363:710-714. [PMID: 30705154 DOI: 10.1126/science.aaw5569] [Citation(s) in RCA: 66] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2019] [Accepted: 01/21/2019] [Indexed: 12/11/2022]
Abstract
During exon ligation, the Saccharomyces cerevisiae spliceosome recognizes the 3'-splice site (3'SS) of precursor messenger RNA (pre-mRNA) through non-Watson-Crick pairing with the 5'SS and the branch adenosine, in a conformation stabilized by Prp18 and Prp8. Here we present the 3.3-angstrom cryo-electron microscopy structure of a human postcatalytic spliceosome just after exon ligation. The 3'SS docks at the active site through conserved RNA interactions in the absence of Prp18. Unexpectedly, the metazoan-specific FAM32A directly bridges the 5'-exon and intron 3'SS of pre-mRNA and promotes exon ligation, as shown by functional assays. CACTIN, SDE2, and NKAP-factors implicated in alternative splicing-further stabilize the catalytic conformation of the spliceosome during exon ligation. Together these four proteins act as exon ligation factors. Our study reveals how the human spliceosome has co-opted additional proteins to modulate a conserved RNA-based mechanism for 3'SS selection and to potentially fine-tune alternative splicing at the exon ligation stage.
Collapse
Affiliation(s)
- Sebastian M Fica
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK.
| | - Chris Oubridge
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Max E Wilkinson
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Andrew J Newman
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Kiyoshi Nagai
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK.
| |
Collapse
|
3106
|
Walls AC, Xiong X, Park YJ, Tortorici MA, Snijder J, Quispe J, Cameroni E, Gopal R, Dai M, Lanzavecchia A, Zambon M, Rey FA, Corti D, Veesler D. Unexpected Receptor Functional Mimicry Elucidates Activation of Coronavirus Fusion. Cell 2019; 176:1026-1039.e15. [PMID: 30712865 PMCID: PMC6751136 DOI: 10.1016/j.cell.2018.12.028] [Citation(s) in RCA: 454] [Impact Index Per Article: 90.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Revised: 10/29/2018] [Accepted: 12/17/2018] [Indexed: 12/27/2022]
Abstract
Recent outbreaks of severe acute respiratory syndrome and Middle East respiratory syndrome, along with the threat of a future coronavirus-mediated pandemic, underscore the importance of finding ways to combat these viruses. The trimeric spike transmembrane glycoprotein S mediates entry into host cells and is the major target of neutralizing antibodies. To understand the humoral immune response elicited upon natural infections with coronaviruses, we structurally characterized the SARS-CoV and MERS-CoV S glycoproteins in complex with neutralizing antibodies isolated from human survivors. Although the two antibodies studied blocked attachment to the host cell receptor, only the anti-SARS-CoV S antibody triggered fusogenic conformational changes via receptor functional mimicry. These results provide a structural framework for understanding coronavirus neutralization by human antibodies and shed light on activation of coronavirus membrane fusion, which takes place through a receptor-driven ratcheting mechanism.
Collapse
Affiliation(s)
- Alexandra C Walls
- Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA
| | - Xiaoli Xiong
- Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA
| | - Young-Jun Park
- Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA
| | - M Alejandra Tortorici
- Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA; Institute Pasteur & CNRS UMR 3569, Unité de Virologie Structurale, 75015, Paris, France
| | - Joost Snijder
- Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA
| | - Joel Quispe
- Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA
| | | | - Robin Gopal
- National Infection Service, Public Health England, London NW9 5HT, UK
| | - Mian Dai
- Crick Worldwide Influenza Centre, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Antonio Lanzavecchia
- Institute for Research in Biomedicine, Faculty of Biomedical Sciences, Università della Svizzera italiana, 6500 Bellinzona, Switzerland
| | - Maria Zambon
- National Infection Service, Public Health England, London NW9 5HT, UK
| | - Félix A Rey
- Institute Pasteur & CNRS UMR 3569, Unité de Virologie Structurale, 75015, Paris, France
| | - Davide Corti
- Humabs Biomed SA, Vir Biotechnology, 6500 Bellinzona, Switzerland
| | - David Veesler
- Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA.
| |
Collapse
|
3107
|
Arragain B, Reguera J, Desfosses A, Gutsche I, Schoehn G, Malet H. High resolution cryo-EM structure of the helical RNA-bound Hantaan virus nucleocapsid reveals its assembly mechanisms. eLife 2019; 8:43075. [PMID: 30638449 PMCID: PMC6365055 DOI: 10.7554/elife.43075] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Accepted: 01/10/2019] [Indexed: 12/21/2022] Open
Abstract
Negative-strand RNA viruses condense their genome into helical nucleocapsids that constitute essential templates for viral replication and transcription. The intrinsic flexibility of nucleocapsids usually prevents their full-length structural characterisation at high resolution. Here, we describe purification of full-length recombinant metastable helical nucleocapsid of Hantaan virus (Hantaviridae family, Bunyavirales order) and determine its structure at 3.3 Å resolution by cryo-electron microscopy. The structure reveals the mechanisms of helical multimerisation via sub-domain exchanges between protomers and highlights nucleotide positions in a continuous positively charged groove compatible with viral genome binding. It uncovers key sites for future structure-based design of antivirals that are currently lacking to counteract life-threatening hantavirus infections. The structure also suggests a model of nucleoprotein-polymerase interaction that would enable replication and transcription solely upon local disruption of the nucleocapsid.
Collapse
Affiliation(s)
- Benoît Arragain
- Electron Microscopy and Methods Group, Université Grenoble Alpes, CNRS, CEA, Institute for Structural Biology, Grenoble, France
| | - Juan Reguera
- Complexes Macromoléculaires Viraux, Aix-Marseille Université, CNRS, INSERM, AFMB UMR 7257, Marseille, France
| | - Ambroise Desfosses
- Electron Microscopy and Methods Group, Université Grenoble Alpes, CNRS, CEA, Institute for Structural Biology, Grenoble, France
| | - Irina Gutsche
- Electron Microscopy and Methods Group, Université Grenoble Alpes, CNRS, CEA, Institute for Structural Biology, Grenoble, France
| | - Guy Schoehn
- Electron Microscopy and Methods Group, Université Grenoble Alpes, CNRS, CEA, Institute for Structural Biology, Grenoble, France
| | - Hélène Malet
- Electron Microscopy and Methods Group, Université Grenoble Alpes, CNRS, CEA, Institute for Structural Biology, Grenoble, France
| |
Collapse
|
3108
|
Bárdy P, Hrebík D, Pantůček R, Plevka P. Future prospects of structural studies to advance our understanding of phage biology. MICROBIOLOGY AUSTRALIA 2019. [DOI: 10.1071/ma19009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Bacteriophages, being the most abundant biological entities on the Earth, play a major role in regulating populations of bacteria and thus influence the evolution and stability of ecosystems. Phage infections of pathogenic bacteria can both exacerbate and alleviate the severity of the disease. The structural characterisations of phage particles and individual proteins have enabled the understanding of many aspects of phage biology. Due to methodological limitations, most of the structures were determined from purified samples in vitro. However, studies performed outside the cellular context cannot capture the complex and dynamic interactions of the macromolecules that are required for their biological functions. Current developments in structural biology, in particular cryo-electron microscopy, allow in situ high-resolution studies of phage-infected cells. Here we discuss open questions in phage biology that could be addressed by structural biology techniques and their potential to enable the use of tailed phages in industrial applications and human therapy.
Collapse
|
3109
|
Masiulis S, Desai R, Uchański T, Serna Martin I, Laverty D, Karia D, Malinauskas T, Zivanov J, Pardon E, Kotecha A, Steyaert J, Miller KW, Aricescu AR. GABA A receptor signalling mechanisms revealed by structural pharmacology. Nature 2019; 565:454-459. [PMID: 30602790 PMCID: PMC6370056 DOI: 10.1038/s41586-018-0832-5] [Citation(s) in RCA: 333] [Impact Index Per Article: 66.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Accepted: 11/23/2018] [Indexed: 01/02/2023]
Abstract
Type-A γ-aminobutyric (GABAA) receptors are ligand-gated chloride channels with a very rich pharmacology. Some of their modulators, including benzodiazepines and general anaesthetics, are among the most successful drugs in clinical use and are common substances of abuse. Without reliable structural data, the mechanistic basis for the pharmacological modulation of GABAA receptors remains largely unknown. Here we report several high-resolution cryo-electron microscopy structures in which the full-length human α1β3γ2L GABAA receptor in lipid nanodiscs is bound to the channel-blocker picrotoxin, the competitive antagonist bicuculline, the agonist GABA (γ-aminobutyric acid), and the classical benzodiazepines alprazolam and diazepam. We describe the binding modes and mechanistic effects of these ligands, the closed and desensitized states of the GABAA receptor gating cycle, and the basis for allosteric coupling between the extracellular, agonist-binding region and the transmembrane, pore-forming region. This work provides a structural framework in which to integrate previous physiology and pharmacology research and a rational basis for the development of GABAA receptor modulators.
Collapse
Affiliation(s)
- Simonas Masiulis
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, UK.
| | - Rooma Desai
- Department of Anesthesia, Critical Care and Pain Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Tomasz Uchański
- Structural Biology Brussels, Vrije Universiteit Brussel (VUB), Brussels, Belgium
- VIB-VUB Center for Structural Biology, VIB, Brussels, Belgium
| | - Itziar Serna Martin
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Duncan Laverty
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, UK
| | - Dimple Karia
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Tomas Malinauskas
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Jasenko Zivanov
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, UK
| | - Els Pardon
- Structural Biology Brussels, Vrije Universiteit Brussel (VUB), Brussels, Belgium
- VIB-VUB Center for Structural Biology, VIB, Brussels, Belgium
| | - Abhay Kotecha
- Materials and Structural Analysis, Thermo Fisher Scientific, Eindhoven, The Netherlands
| | - Jan Steyaert
- Structural Biology Brussels, Vrije Universiteit Brussel (VUB), Brussels, Belgium
- VIB-VUB Center for Structural Biology, VIB, Brussels, Belgium
| | - Keith W Miller
- Department of Anesthesia, Critical Care and Pain Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA.
| | - A Radu Aricescu
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, UK.
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK.
| |
Collapse
|
3110
|
Structure of the post-translational protein translocation machinery of the ER membrane. Nature 2018; 566:136-139. [PMID: 30644436 PMCID: PMC6367035 DOI: 10.1038/s41586-018-0856-x] [Citation(s) in RCA: 81] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2018] [Accepted: 12/18/2018] [Indexed: 11/09/2022]
Abstract
Many proteins must translocate through the protein-conducting Sec61 channel in the eukaryotic endoplasmic reticulum membrane or the SecY channel in the prokaryotic plasma membrane1,2. Proteins with highly hydrophobic signal sequences are first recognized by the signal recognition particle (SRP)3,4 and then moved co-translationally through the Sec61 or SecY channel by the associated translating ribosome. Substrates with less hydrophobic signal sequences bypass the SRP and are moved through the channel post-translationally5,6. In eukaryotic cells, post-translational translocation is mediated by the association of the Sec61 channel with another membrane protein complex, the Sec62-Sec63 complex7-9, and substrates are moved through the channel by the luminal BiP ATPase9. How the Sec62-Sec63 complex activates the Sec61 channel for post-translational translocation is not known. Here we report the electron cryo-microscopy structure of the Sec complex from Saccharomyces cerevisiae, consisting of the Sec61 channel and the Sec62, Sec63, Sec71 and Sec72 proteins. Sec63 causes wide opening of the lateral gate of the Sec61 channel, priming it for the passage of low-hydrophobicity signal sequences into the lipid phase, without displacing the channel's plug domain. Lateral channel opening is triggered by Sec63 interacting both with cytosolic loops in the C-terminal half of Sec61 and transmembrane segments in the N-terminal half of the Sec61 channel. The cytosolic Brl domain of Sec63 blocks ribosome binding to the channel and recruits Sec71 and Sec72, positioning them for the capture of polypeptides associated with cytosolic Hsp7010. Our structure shows how the Sec61 channel is activated for post-translational protein translocation.
Collapse
|
3111
|
Farnung L, Vos SM, Cramer P. Structure of transcribing RNA polymerase II-nucleosome complex. Nat Commun 2018; 9:5432. [PMID: 30575770 PMCID: PMC6303367 DOI: 10.1038/s41467-018-07870-y] [Citation(s) in RCA: 66] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Accepted: 12/05/2018] [Indexed: 01/08/2023] Open
Abstract
Transcription of eukaryotic protein-coding genes requires passage of RNA polymerase II (Pol II) through nucleosomes, but it is unclear how this is achieved. Here we report the cryo-EM structure of transcribing Saccharomyces cerevisiae Pol II engaged with a downstream nucleosome core particle at an overall resolution of 4.4 Å. Pol II and the nucleosome are observed in a defined relative orientation that is not predicted. Pol II contacts both sides of the nucleosome dyad using its clamp head and lobe domains. Structural comparisons reveal that the elongation factors TFIIS, DSIF, NELF, SPT6, and PAF1 complex can be accommodated on the Pol II surface in the presence of the oriented nucleosome. Our results provide a starting point for analysing the mechanisms of chromatin transcription. Eukaryotic transcription requires passage of RNA polymerase II (Pol II) through chromatin, which is impaired by nucleosomes. Here the authors report the cryo-EM structure of transcribing Pol II engaged with a downstream nucleosome core particle at an overall resolution of 4.4 Å, providing insights into the mechanism of chromatin transcription.
Collapse
Affiliation(s)
- Lucas Farnung
- Max Planck Institute for Biophysical Chemistry, Department of Molecular Biology, Am Fassberg 11, 37077, Göttingen, Germany
| | - Seychelle M Vos
- Max Planck Institute for Biophysical Chemistry, Department of Molecular Biology, Am Fassberg 11, 37077, Göttingen, Germany
| | - Patrick Cramer
- Max Planck Institute for Biophysical Chemistry, Department of Molecular Biology, Am Fassberg 11, 37077, Göttingen, Germany.
| |
Collapse
|
3112
|
Schuller JM, Birrell JA, Tanaka H, Konuma T, Wulfhorst H, Cox N, Schuller SK, Thiemann J, Lubitz W, Sétif P, Ikegami T, Engel BD, Kurisu G, Nowaczyk MM. Structural adaptations of photosynthetic complex I enable ferredoxin-dependent electron transfer. Science 2018; 363:257-260. [PMID: 30573545 DOI: 10.1126/science.aau3613] [Citation(s) in RCA: 127] [Impact Index Per Article: 21.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Accepted: 12/06/2018] [Indexed: 12/22/2022]
Abstract
Photosynthetic complex I enables cyclic electron flow around photosystem I, a regulatory mechanism for photosynthetic energy conversion. We report a 3.3-angstrom-resolution cryo-electron microscopy structure of photosynthetic complex I from the cyanobacterium Thermosynechococcus elongatus. The model reveals structural adaptations that facilitate binding and electron transfer from the photosynthetic electron carrier ferredoxin. By mimicking cyclic electron flow with isolated components in vitro, we demonstrate that ferredoxin directly mediates electron transfer between photosystem I and complex I, instead of using intermediates such as NADPH (the reduced form of nicotinamide adenine dinucleotide phosphate). A large rate constant for association of ferredoxin to complex I indicates efficient recognition, with the protein subunit NdhS being the key component in this process.
Collapse
Affiliation(s)
- Jan M Schuller
- Department of Structural Cell Biology, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany.
| | - James A Birrell
- Max Planck Institute for Chemical Energy Conversion, 45470 Mülheim an der Ruhr, Germany
| | - Hideaki Tanaka
- Institute for Protein Research, Osaka University, Suita, Osaka 565-0871, Japan.,Department of Macromolecular Science, Graduate School of Science, Osaka University, Toyonaka 560-0043, Japan
| | - Tsuyoshi Konuma
- Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Hannes Wulfhorst
- Plant Biochemistry, Faculty of Biology and Biotechnology, Ruhr University Bochum, 44780 Bochum, Germany.,Daiichi Sankyo Deutschland GmbH, Zielstattstr. 48, 81379 München, Germany
| | - Nicholas Cox
- Max Planck Institute for Chemical Energy Conversion, 45470 Mülheim an der Ruhr, Germany.,Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
| | - Sandra K Schuller
- Gene Center and Department of Biochemistry, Ludwig-Maximilians-Universität München, Feodor-Lynen-Str. 25, 81377 Munich, Germany
| | - Jacqueline Thiemann
- Plant Biochemistry, Faculty of Biology and Biotechnology, Ruhr University Bochum, 44780 Bochum, Germany
| | - Wolfgang Lubitz
- Max Planck Institute for Chemical Energy Conversion, 45470 Mülheim an der Ruhr, Germany
| | - Pierre Sétif
- Institut de Biologie Intégrative de la Cellule (I2BC), IBITECS, CEA, CNRS, Université Paris-Saclay, F-91198 Gif-sur-Yvette, France
| | - Takahisa Ikegami
- Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Benjamin D Engel
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Genji Kurisu
- Institute for Protein Research, Osaka University, Suita, Osaka 565-0871, Japan. .,Department of Macromolecular Science, Graduate School of Science, Osaka University, Toyonaka 560-0043, Japan
| | - Marc M Nowaczyk
- Plant Biochemistry, Faculty of Biology and Biotechnology, Ruhr University Bochum, 44780 Bochum, Germany.
| |
Collapse
|
3113
|
Soczek KM, Grant T, Rosenthal PB, Mondragón A. CryoEM structures of open dimers of gyrase A in complex with DNA illuminate mechanism of strand passage. eLife 2018; 7:41215. [PMID: 30457554 PMCID: PMC6286129 DOI: 10.7554/elife.41215] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Accepted: 11/09/2018] [Indexed: 11/13/2022] Open
Abstract
Gyrase is a unique type IIA topoisomerase that uses ATP hydrolysis to maintain the negatively supercoiled state of bacterial DNA. In order to perform its function, gyrase undergoes a sequence of conformational changes that consist of concerted gate openings, DNA cleavage, and DNA strand passage events. Structures where the transported DNA molecule (T-segment) is trapped by the A subunit have not been observed. Here we present the cryoEM structures of two oligomeric complexes of open gyrase A dimers and DNA. The protein subunits in these complexes were solved to 4 Å and 5.2 Å resolution. One of the complexes traps a linear DNA molecule, a putative T-segment, which interacts with the open gyrase A dimers in two states, representing steps either prior to or after passage through the DNA-gate. The structures locate the T-segment in important intermediate conformations of the catalytic cycle and provide insights into gyrase-DNA interactions and mechanism.
Collapse
Affiliation(s)
- Katarzyna M Soczek
- Department of Molecular Biosciences, Northwestern University, Evanston, United States
| | - Tim Grant
- Division of Physical Biochemistry, MRC National Institute for Medical Research, London, United Kingdom
| | - Peter B Rosenthal
- Division of Physical Biochemistry, MRC National Institute for Medical Research, London, United Kingdom.,Structural Biology of Cells and Viruses Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Alfonso Mondragón
- Department of Molecular Biosciences, Northwestern University, Evanston, United States
| |
Collapse
|