A recent origin of Orf3a from M protein across the coronavirus lineage arising by sharp divergence.

Computational and Structural Biotechnology Journal
Christos A Ouzounis


The genome of SARS-CoV-2, the coronavirus responsible for the Covid-19 pandemic, encodes a number of accessory genes. The longest accessory gene, Orf3a, plays important roles in the virus lifecycle indicated by experimental findings, known polymorphisms, its evolutionary trajectory and a distinct three-dimensional fold. Here we show that supervised, sensitive database searches with Orf3a detect weak, yet significant and highly specific similarities to the M proteins of coronaviruses. The similarity profiles can be used to derive low-resolution three-dimensional models for M proteins based on Orf3a as a structural template. The models also explain the emergence of Orf3a from M proteins and suggest a recent origin across the coronavirus lineage, enunciated by its restricted phylogenetic distribution. This study provides evidence for the common origin of M and Orf3a families and proposes for the first time a working model for the structure of the universally distributed M proteins in coronaviruses, consistent with the properties of both protein families.


Sep 1, 1997·Nucleic Acids Research·S F AltschulD J Lipman
Jun 20, 1998·Bioinformatics·N P BrownC Sander
Jul 21, 2004·Journal of Computational Chemistry·Eric F PettersenThomas E Ferrin
Feb 8, 2005·Proceedings of the National Academy of Sciences of the United States of America·Huai-Dong SongGuo-Ping Zhao
Mar 15, 2005·Virus Research·Xiaoling YuanYuwen Cong
Aug 9, 2006·Proceedings of the National Academy of Sciences of the United States of America·Wei LuBing Sun
Jan 20, 2009·Bioinformatics·Andrew M WaterhouseGeoffrey J Barton
Mar 13, 2010·PloS One·Morgan N PriceAdam P Arkin
Aug 20, 2010·Journal of Virology·Ariel L ArndtBrenda G Hogue
Dec 8, 2010·Bioinformatics·Pascal BenkertTorsten Schwede
Jul 8, 2011·Nucleic Acids Research·Lukasz JaroszewskiAdam Godzik
Oct 14, 2011·Bioinformatics·Alex StivalaPeter J Stuckey
Jul 4, 2012·Nature Reviews. Microbiology·José Luis NievaLuis Carrasco
Mar 5, 2016·Scientific Reports·Vasilis J PromponasChristos A Ouzounis
Oct 3, 2017·Briefings in Bioinformatics·Kazutaka KatohKazunori D Yamada
May 23, 2018·Nucleic Acids Research·Andrew WaterhouseTorsten Schwede
Oct 26, 2018·Nucleic Acids Research·Sara El-GebaliRobert D Finn
Dec 12, 2018·Nature Biotechnology·Etienne BechtEvan W Newell
Dec 12, 2018·Nature Reviews. Microbiology·Jie CuiZheng-Li Shi
Feb 23, 2019·Viruses·Antonio C P WongPatrick C Y Woo
Apr 2, 2019·Nucleic Acids Research·Ivica Letunic, Peer Bork
Apr 28, 2019·Nucleic Acids Research·Frédéric LemoineOlivier Gascuel
Oct 12, 2019·Nucleic Acids Research·Eric W SayersJames Ostell
Oct 14, 2019·Protein Science : a Publication of the Protein Society·Liisa Holm
Jan 25, 2020·The New England Journal of Medicine·Na ZhuUNKNOWN China Novel Coronavirus Investigating and Research Team
Mar 4, 2020·Nature Microbiology·UNKNOWN Coronaviridae Study Group of the International Committee on Taxonomy of Viruses
Mar 24, 2020·Future Virology·Entedar A J Alsaadi, Ian M Jones
Jun 13, 2020·Nature Reviews. Microbiology·Michael LetkoVincent J Munster
Jul 16, 2020·Nature Communications·Sepideh SadeghJan Baumbach

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