Structural analysis of SARS-CoV-2 genome and predictions of the human interactome

Nucleic Acids Research
A. VandelliGian Gaetano Tartaglia

Abstract

Specific elements of viral genomes regulate interactions within host cells. Here, we calculated the secondary structure content of >2000 coronaviruses and computed >100 000 human protein interactions with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The genomic regions display different degrees of conservation. SARS-CoV-2 domain encompassing nucleotides 22 500-23 000 is conserved both at the sequence and structural level. The regions upstream and downstream, however, vary significantly. This part of the viral sequence codes for the Spike S protein that interacts with the human receptor angiotensin-converting enzyme 2 (ACE2). Thus, variability of Spike S is connected to different levels of viral entry in human cells within the population. Our predictions indicate that the 5' end of SARS-CoV-2 is highly structured and interacts with several human proteins. The binding proteins are involved in viral RNA processing, include double-stranded RNA specific editases and ATP-dependent RNA-helicases and have strong propensity to form stress granules and phase-separated assemblies. We propose that these proteins, also implicated in viral infections such as HIV, are selectively recruited by SARS-CoV-2 genome to alter transc...Continue Reading

References

Jan 9, 1999·The Journal of Biological Chemistry·S N SarkarG C Sen
May 18, 1999·Journal of Molecular Biology·Y T KwakR B Gaynor
Aug 28, 1999·The Journal of Biological Chemistry·S N SarkarG C Sen
Sep 23, 2003·BMC Microbiology·Yossef Kliger, Erez Y Levanon
Aug 4, 2004·Seminars in Cancer Biology·S Diane Hayward
Nov 30, 2004·Virology·Jianhua FangRoger J Pomerantz
Feb 15, 2008·Journal of Virology·José L MorenoIsabel Sola
Apr 27, 2010·Journal of Molecular Biology·Gian Gaetano TartagliaMichele Vendruscolo
Jun 25, 2010·RNA·Katrin SchäfflerUtz Fischer
Dec 31, 2010·Nature Reviews. Genetics·Fatih Ozsolak, Patrice M Milos
May 31, 2011·Nature Methods·Matteo BellucciGian Gaetano Tartaglia
Jul 19, 2011·Journal of Molecular Biology·Kun LuMichael F Summers
Dec 1, 2009·Viruses·Kunj B Pathak, Peter D Nagy
Nov 5, 2011·Journal of Molecular Biology·Stephen P EdgcombJames R Williamson
Nov 26, 2011·Algorithms for Molecular Biology : AMB·Ronny LorenzIvo L Hofacker
Mar 13, 2012·Trends in Microbiology·James P White, Richard E Lloyd
Jun 5, 2012·Cell·Alfredo CastelloMatthias W Hentze
Oct 25, 2012·Nucleic Acids Research·Federico AgostiniGian Gaetano Tartaglia
Dec 26, 2012·Trends in Microbiology·Neil M Bell, Andrew M L Lever
Aug 27, 2013·Bioinformatics·Federico AgostiniGian Gaetano Tartaglia
Sep 7, 2013·Bioinformatics·Eric P Nawrocki, Sean R Eddy
Feb 28, 2015·Methods in Molecular Biology·Anthony R Fehr, Stanley Perlman
Mar 5, 2015·Virus Research·Dong Yang, Julian L Leibowitz
May 21, 2016·Wiley Interdisciplinary Reviews. RNA·Radmila HrdlickovaBin Tian

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Citations

Dec 8, 2020·BioEssays : News and Reviews in Molecular, Cellular and Developmental Biology·Alexandros ArmaosGian Gaetano Tartaglia
Jan 19, 2021·Journal of Basic Microbiology·Swapnil B KadamVitthal T Barvkar
Dec 29, 2020·Biochemical Society Transactions·Ilaria Manfredonia, Danny Incarnato
Feb 4, 2021·Molecules : a Journal of Synthetic Chemistry and Natural Product Chemistry·Isabella RomeoStefano Alcaro
Mar 5, 2021·Frontiers in Molecular Biosciences·Mattia MiottoEdoardo Milanetti
May 11, 2021·Journal of Cellular and Molecular Medicine·Maryam Moazzam-JaziMaryam S Daneshpour
May 18, 2021·Frontiers in Immunology·Yuqing LiWeijie Dong
Jun 19, 2021·Briefings in Bioinformatics·Sagnik SenUjjwal Maulik
Jun 15, 2021·Frontiers in Cardiovascular Medicine·Randa M Breikaa, Brenda Lilly

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Methods Mentioned

BETA
bronchoalveolar lavage
X-ray
affinity purification
deamination

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