Literature DB >> 33060197

Comparative host-coronavirus protein interaction networks reveal pan-viral disease mechanisms.

David E Gordon1,2,3,4, Joseph Hiatt1,4,5,6,7, Mehdi Bouhaddou1,2,3,4, Veronica V Rezelj8, Svenja Ulferts9, Hannes Braberg1,2,3,4, Alexander S Jureka10, Kirsten Obernier1,2,3,4, Jeffrey Z Guo1,2,3,4, Jyoti Batra1,2,3,4, Robyn M Kaake1,2,3,4, Andrew R Weckstein11, Tristan W Owens12, Meghna Gupta12, Sergei Pourmal12, Erron W Titus12, Merve Cakir1,2,3,4, Margaret Soucheray1,2,3,4, Michael McGregor1,2,3,4, Zeynep Cakir1,2,3,4, Gwendolyn Jang1,2,3,4, Matthew J O'Meara13, Tia A Tummino1,2,14, Ziyang Zhang1,2,3,15, Helene Foussard1,2,3,4, Ajda Rojc1,2,3,4, Yuan Zhou1,2,3,4, Dmitry Kuchenov1,2,3,4, Ruth Hüttenhain1,2,3,4, Jiewei Xu1,2,3,4, Manon Eckhardt1,2,3,4, Danielle L Swaney1,2,3,4, Jacqueline M Fabius1,2, Manisha Ummadi1,2,3,4, Beril Tutuncuoglu1,2,3,4, Ujjwal Rathore1,2,3,4, Maya Modak1,2,3,4, Paige Haas1,2,3,4, Kelsey M Haas1,2,3,4, Zun Zar Chi Naing1,2,3,4, Ernst H Pulido1,2,3,4, Ying Shi1,2,3,15, Inigo Barrio-Hernandez16, Danish Memon16, Eirini Petsalaki16, Alistair Dunham16, Miguel Correa Marrero16, David Burke16, Cassandra Koh8, Thomas Vallet8, Jesus A Silvas10, Caleigh M Azumaya12, Christian Billesbølle12, Axel F Brilot12, Melody G Campbell12,17, Amy Diallo12, Miles Sasha Dickinson12, Devan Diwanji12, Nadia Herrera12, Nick Hoppe12, Huong T Kratochvil12, Yanxin Liu12, Gregory E Merz12, Michelle Moritz12, Henry C Nguyen12, Carlos Nowotny12, Cristina Puchades12, Alexandrea N Rizo12, Ursula Schulze-Gahmen12, Amber M Smith12, Ming Sun12,18, Iris D Young12, Jianhua Zhao12, Daniel Asarnow12, Justin Biel12, Alisa Bowen12, Julian R Braxton12, Jen Chen12, Cynthia M Chio12, Un Seng Chio12, Ishan Deshpande12, Loan Doan12, Bryan Faust12, Sebastian Flores12, Mingliang Jin12, Kate Kim12, Victor L Lam12, Fei Li12, Junrui Li12, Yen-Li Li12, Yang Li12, Xi Liu12, Megan Lo12, Kyle E Lopez12, Arthur A Melo12, Frank R Moss12, Phuong Nguyen12, Joana Paulino12, Komal Ishwar Pawar12, Jessica K Peters12, Thomas H Pospiech12, Maliheh Safari12, Smriti Sangwan12, Kaitlin Schaefer12, Paul V Thomas12, Aye C Thwin12, Raphael Trenker12, Eric Tse12, Tsz Kin Martin Tsui12, Feng Wang12, Natalie Whitis12, Zanlin Yu12, Kaihua Zhang12, Yang Zhang12, Fengbo Zhou12, Daniel Saltzberg1,2,19, Anthony J Hodder20, Amber S Shun-Shion20, Daniel M Williams20, Kris M White21,22, Romel Rosales21,22, Thomas Kehrer21,22, Lisa Miorin21,22, Elena Moreno21,22, Arvind H Patel23, Suzannah Rihn23, Mir M Khalid4, Albert Vallejo-Gracia4, Parinaz Fozouni4,5,7, Camille R Simoneau4,7, Theodore L Roth5,6,7, David Wu5,7, Mohd Anisul Karim24,25, Maya Ghoussaini24,25, Ian Dunham16,25, Francesco Berardi26, Sebastian Weigang27, Maxime Chazal28, Jisoo Park29, James Logue30, Marisa McGrath30, Stuart Weston30, Robert Haupt30, C James Hastie31, Matthew Elliott31, Fiona Brown31, Kerry A Burness31, Elaine Reid31, Mark Dorward31, Clare Johnson31, Stuart G Wilkinson31, Anna Geyer31, Daniel M Giesel31, Carla Baillie31, Samantha Raggett31, Hannah Leech31, Rachel Toth31, Nicola Goodman31, Kathleen C Keough4, Abigail L Lind4, Reyna J Klesh32, Kafi R Hemphill33, Jared Carlson-Stevermer34, Jennifer Oki34, Kevin Holden34, Travis Maures34, Katherine S Pollard4,35,36, Andrej Sali1,2,14,19, David A Agard1,2,12,37, Yifan Cheng1,2,12,15,37, James S Fraser1,2,12,19, Adam Frost1,2,12,37, Natalia Jura1,2,3,12,38, Tanja Kortemme1,2,12,19,39, Aashish Manglik1,2,12,14, Daniel R Southworth1,12,37, Robert M Stroud1,2,12,37, Dario R Alessi31, Paul Davies31, Matthew B Frieman30, Trey Ideker29,40, Carmen Abate26, Nolwenn Jouvenet27,28, Georg Kochs27, Brian Shoichet1,2,14, Melanie Ott4,41, Massimo Palmarini23, Kevan M Shokat1,2,3,15, Adolfo García-Sastre42,22,43,44, Jeremy A Rassen45, Robert Grosse46,47, Oren S Rosenberg48,2,12,36,37,41, Kliment A Verba48,2,12,14, Christopher F Basler49, Marco Vignuzzi50, Andrew A Peden51, Pedro Beltrao52, Nevan J Krogan48,2,3,4,21.   

Abstract

The COVID-19 pandemic, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is a grave threat to public health and the global economy. SARS-CoV-2 is closely related to the more lethal but less transmissible coronaviruses SARS-CoV-1 and Middle East respiratory syndrome coronavirus (MERS-CoV). Here, we have carried out comparative viral-human protein-protein interaction and viral protein localization analyses for all three viruses. Subsequent functional genetic screening identified host factors that functionally impinge on coronavirus proliferation, including Tom70, a mitochondrial chaperone protein that interacts with both SARS-CoV-1 and SARS-CoV-2 ORF9b, an interaction we structurally characterized using cryo-electron microscopy. Combining genetically validated host factors with both COVID-19 patient genetic data and medical billing records identified molecular mechanisms and potential drug treatments that merit further molecular and clinical study.
Copyright © 2020 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works.

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Year:  2020        PMID: 33060197      PMCID: PMC7808408          DOI: 10.1126/science.abe9403

Source DB:  PubMed          Journal:  Science        ISSN: 0036-8075            Impact factor:   47.728


  92 in total

1.  Domain organization of the monomeric form of the Tom70 mitochondrial import receptor.

Authors:  Ryan D Mills; Jill Trewhella; Theresa Wenli Qiu; Thomas Welte; Timothy M Ryan; Tracey Hanley; Robert B Knott; Trevor Lithgow; Terrence D Mulhern
Journal:  J Mol Biol       Date:  2009-04-07       Impact factor: 5.469

2.  Optimized atomic statistical potentials: assessment of protein interfaces and loops.

Authors:  Guang Qiang Dong; Hao Fan; Dina Schneidman-Duhovny; Ben Webb; Andrej Sali
Journal:  Bioinformatics       Date:  2013-09-27       Impact factor: 6.937

3.  PhastWeb: a web interface for evolutionary conservation scoring of multiple sequence alignments using phastCons and phyloP.

Authors:  Ritika Ramani; Katie Krumholz; Yi-Fei Huang; Adam Siepel
Journal:  Bioinformatics       Date:  2019-07-01       Impact factor: 6.937

Review 4.  Biological functions and therapeutic opportunities of soluble cytokine receptors.

Authors:  Juliane Lokau; Christoph Garbers
Journal:  Cytokine Growth Factor Rev       Date:  2020-04-18       Impact factor: 7.638

5.  Clinical and immunological features of severe and moderate coronavirus disease 2019.

Authors:  Guang Chen; Di Wu; Wei Guo; Yong Cao; Da Huang; Hongwu Wang; Tao Wang; Xiaoyun Zhang; Huilong Chen; Haijing Yu; Xiaoping Zhang; Minxia Zhang; Shiji Wu; Jianxin Song; Tao Chen; Meifang Han; Shusheng Li; Xiaoping Luo; Jianping Zhao; Qin Ning
Journal:  J Clin Invest       Date:  2020-05-01       Impact factor: 14.808

6.  GRAMM-X public web server for protein-protein docking.

Authors:  Andrey Tovchigrechko; Ilya A Vakser
Journal:  Nucleic Acids Res       Date:  2006-07-01       Impact factor: 16.971

7.  PatchDock and SymmDock: servers for rigid and symmetric docking.

Authors:  Dina Schneidman-Duhovny; Yuval Inbar; Ruth Nussinov; Haim J Wolfson
Journal:  Nucleic Acids Res       Date:  2005-07-01       Impact factor: 16.971

8.  MitoFates: improved prediction of mitochondrial targeting sequences and their cleavage sites.

Authors:  Yoshinori Fukasawa; Junko Tsuji; Szu-Chin Fu; Kentaro Tomii; Paul Horton; Kenichiro Imai
Journal:  Mol Cell Proteomics       Date:  2015-02-10       Impact factor: 5.911

9.  Insights into SARS-CoV transcription and replication from the structure of the nsp7-nsp8 hexadecamer.

Authors:  Yujia Zhai; Fei Sun; Xuemei Li; Hai Pang; Xiaoling Xu; Mark Bartlam; Zihe Rao
Journal:  Nat Struct Mol Biol       Date:  2005-11       Impact factor: 15.369

10.  Automated structure refinement of macromolecular assemblies from cryo-EM maps using Rosetta.

Authors:  Ray Yu-Ruei Wang; Yifan Song; Benjamin A Barad; Yifan Cheng; James S Fraser; Frank DiMaio
Journal:  Elife       Date:  2016-09-26       Impact factor: 8.140

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  198 in total

1.  CryoEM and AI reveal a structure of SARS-CoV-2 Nsp2, a multifunctional protein involved in key host processes.

Authors:  Meghna Gupta; Caleigh M Azumaya; Michelle Moritz; Sergei Pourmal; Amy Diallo; Gregory E Merz; Gwendolyn Jang; Mehdi Bouhaddou; Andrea Fossati; Axel F Brilot; Devan Diwanji; Evelyn Hernandez; Nadia Herrera; Huong T Kratochvil; Victor L Lam; Fei Li; Yang Li; Henry C Nguyen; Carlos Nowotny; Tristan W Owens; Jessica K Peters; Alexandrea N Rizo; Ursula Schulze-Gahmen; Amber M Smith; Iris D Young; Zanlin Yu; Daniel Asarnow; Christian Billesbølle; Melody G Campbell; Jen Chen; Kuei-Ho Chen; Un Seng Chio; Miles Sasha Dickinson; Loan Doan; Mingliang Jin; Kate Kim; Junrui Li; Yen-Li Li; Edmond Linossi; Yanxin Liu; Megan Lo; Jocelyne Lopez; Kyle E Lopez; Adamo Mancino; Frank R Moss; Michael D Paul; Komal Ishwar Pawar; Adrian Pelin; Thomas H Pospiech; Cristina Puchades; Soumya Govinda Remesh; Maliheh Safari; Kaitlin Schaefer; Ming Sun; Mariano C Tabios; Aye C Thwin; Erron W Titus; Raphael Trenker; Eric Tse; Tsz Kin Martin Tsui; Feng Wang; Kaihua Zhang; Yang Zhang; Jianhua Zhao; Fengbo Zhou; Yuan Zhou; Lorena Zuliani-Alvarez; David A Agard; Yifan Cheng; James S Fraser; Natalia Jura; Tanja Kortemme; Aashish Manglik; Daniel R Southworth; Robert M Stroud; Danielle L Swaney; Nevan J Krogan; Adam Frost; Oren S Rosenberg; Kliment A Verba
Journal:  bioRxiv       Date:  2021-05-11

2.  Genetic interaction mapping informs integrative structure determination of protein complexes.

Authors:  Hannes Braberg; Ignacia Echeverria; Stefan Bohn; Peter Cimermancic; Anthony Shiver; Richard Alexander; Jiewei Xu; Michael Shales; Raghuvar Dronamraju; Shuangying Jiang; Gajendradhar Dwivedi; Derek Bogdanoff; Kaitlin K Chaung; Ruth Hüttenhain; Shuyi Wang; David Mavor; Riccardo Pellarin; Dina Schneidman; Joel S Bader; James S Fraser; John Morris; James E Haber; Brian D Strahl; Carol A Gross; Junbiao Dai; Jef D Boeke; Andrej Sali; Nevan J Krogan
Journal:  Science       Date:  2020-12-11       Impact factor: 47.728

Review 3.  Mechanisms of mitochondrial respiratory adaptation.

Authors:  Christopher F Bennett; Pedro Latorre-Muro; Pere Puigserver
Journal:  Nat Rev Mol Cell Biol       Date:  2022-07-08       Impact factor: 94.444

4.  Homozygosity for rs17775810 Minor Allele Associated With Reduced Mortality of COVID-19 in the UK Biobank Cohort.

Authors:  Steven Lehrer; Peter H Rheinstein
Journal:  In Vivo       Date:  2021 Mar-Apr       Impact factor: 2.155

5.  Chimeric spike mRNA vaccines protect against Sarbecovirus challenge in mice.

Authors:  David R Martinez; Alexandra Schäfer; Sarah R Leist; Gabriela De la Cruz; Ande West; Elena N Atochina-Vasserman; Lisa C Lindesmith; Norbert Pardi; Robert Parks; Maggie Barr; Dapeng Li; Boyd Yount; Kevin O Saunders; Drew Weissman; Barton F Haynes; Stephanie A Montgomery; Ralph S Baric
Journal:  Science       Date:  2021-06-22       Impact factor: 47.728

6.  Multilevel proteomics reveals host perturbations by SARS-CoV-2 and SARS-CoV.

Authors:  Alexey Stukalov; Virginie Girault; Vincent Grass; Ozge Karayel; Valter Bergant; Christian Urban; Darya A Haas; Yiqi Huang; Lila Oubraham; Anqi Wang; M Sabri Hamad; Antonio Piras; Fynn M Hansen; Maria C Tanzer; Igor Paron; Luca Zinzula; Thomas Engleitner; Maria Reinecke; Teresa M Lavacca; Rosina Ehmann; Roman Wölfel; Jörg Jores; Bernhard Kuster; Ulrike Protzer; Roland Rad; John Ziebuhr; Volker Thiel; Pietro Scaturro; Matthias Mann; Andreas Pichlmair
Journal:  Nature       Date:  2021-04-12       Impact factor: 49.962

7.  Comprehensive interactome analysis of the spike protein of swine acute diarrhea syndrome coronavirus.

Authors:  Qingxing Wang; Yun Luo; Weijuan Shang; Zhengli Shi; Gengfu Xiao; Leike Zhang
Journal:  Biosaf Health       Date:  2021-05-17

8.  Crystal structure of SARS-CoV-2 Orf9b in complex with human TOM70 suggests unusual virus-host interactions.

Authors:  Xiaopan Gao; Kaixiang Zhu; Bo Qin; Vincent Olieric; Meitian Wang; Sheng Cui
Journal:  Nat Commun       Date:  2021-05-14       Impact factor: 14.919

Review 9.  Recent advances in drug repurposing using machine learning.

Authors:  Fabio Urbina; Ana C Puhl; Sean Ekins
Journal:  Curr Opin Chem Biol       Date:  2021-07-16       Impact factor: 8.822

10.  TMEM41B is a host factor required for the replication of diverse coronaviruses including SARS-CoV-2.

Authors:  Joseph D Trimarco; Brook E Heaton; Ryan R Chaparian; Kaitlyn N Burke; Raquel A Binder; Gregory C Gray; Clare M Smith; Vineet D Menachery; Nicholas S Heaton
Journal:  PLoS Pathog       Date:  2021-05-27       Impact factor: 6.823

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