Complex evolutionary footprints revealed in an analysis of reused protein segments of diverse lengths

Proceedings of the National Academy of Sciences of the United States of America
Sergey NepomnyachiyRachel Kolodny

Abstract

Proteins share similar segments with one another. Such "reused parts"-which have been successfully incorporated into other proteins-are likely to offer an evolutionary advantage over de novo evolved segments, as most of the latter will not even have the capacity to fold. To systematically explore the evolutionary traces of segment "reuse" across proteins, we developed an automated methodology that identifies reused segments from protein alignments. We search for "themes"-segments of at least 35 residues of similar sequence and structure-reused within representative sets of 15,016 domains [Evolutionary Classification of Protein Domains (ECOD) database] or 20,398 chains [Protein Data Bank (PDB)]. We observe that theme reuse is highly prevalent and that reuse is more extensive when the length threshold for identifying a theme is lower. Structural domains, the best characterized form of reuse in proteins, are just one of many complex and intertwined evolutionary traces. Others include long themes shared among a few proteins, which encompass and overlap with shorter themes that recur in numerous proteins. The observed complexity is consistent with evolution by duplication and divergence, and some of the themes might include descenda...Continue Reading

References

Jan 1, 1997·Nucleic Acids Research·T J HubbardC Chothia
Aug 15, 1997·Structure·C A OrengoJ M Thornton
Jan 1, 1999·BioEssays : News and Reviews in Molecular, Cellular and Developmental Biology·M B SwindellsJ M Thornton
Jun 14, 2000·Journal of Molecular Biology·Y I WolfE V Koonin
Oct 20, 2000·Bioinformatics·S J WheelanS H Bryant
Jun 19, 2001·Current Opinion in Structural Biology·P Koehl
Aug 16, 2001·Molecular Biology and Evolution·S Wuchty
Dec 18, 2001·Proteins·Andrew F W Coulson, John Moult
Oct 17, 2002·Journal of Molecular Biology·Rachel KolodnyMichael Levitt
Oct 18, 2002·Proceedings of the National Academy of Sciences of the United States of America·Nikolay V DokholyanEugene I Shakhnovich
Nov 6, 2002·Journal of Molecular Biology·Andrew HarrisonChristine Orengo
Jun 14, 2003·Science·Cyrus ChothiaSarah A Teichmann
Aug 26, 2003·BioEssays : News and Reviews in Molecular, Cellular and Developmental Biology·Johannes Söding, Andrei N Lupas
Sep 23, 2003·Protein Science : a Publication of the Protein Society·Ryan DayValerie Daggett
Apr 20, 2004·Current Opinion in Structural Biology·Christine VogelSarah A Teichmann
Apr 21, 2004·Journal of Molecular Biology·Christine VogelSarah A Teichmann
Nov 9, 2004·Bioinformatics·Johannes Söding
Dec 18, 2004·Bioinformatics·S Sri Krishna, Nick V Grishin
Feb 11, 2005·Journal of Molecular Biology·Rachel KolodnyMichael Levitt
Jun 16, 2005·Annual Review of Biochemistry·Christine A Orengo, Janet M Thornton
Oct 6, 2005·Bioinformatics·Joseph D SzustakowskiZhiping Weng
Feb 16, 2006·Proceedings of the National Academy of Sciences of the United States of America·Yang ZhangJeffrey Skolnick
May 9, 2006·Current Opinion in Structural Biology·Rachel KolodnyBarry Honig
May 30, 2006·Biophysical Journal·Yoshito Sawada, Shinya Honda
Oct 17, 2007·Annual Review of Physical Chemistry·Konstantin B Zeldovich, Eugene I Shakhnovich
Nov 6, 2007·Proteins·Indronil ChaudhuriAndrei N Lupas
Nov 15, 2007·Nucleic Acids Research·Antonina AndreevaAlexey G Murzin
Nov 21, 2007·Gene·Zakharia M Frenkel, Edward N Trifonov
Apr 21, 2009·BMC Structural Biology·Gergely CsabaRalf Zimmer
Apr 24, 2009·Current Opinion in Structural Biology·Edward N Trifonov, Zakharia M Frenkel
May 22, 2009·Nucleic Acids Research·Timothy L BaileyWilliam S Noble
Jun 23, 2009·Proceedings of the National Academy of Sciences of the United States of America·Michael Levitt
Oct 7, 2009·Proceedings of the National Academy of Sciences of the United States of America·Donald PetreyBarry Honig
Apr 28, 2010·PLoS Computational Biology·Narcis Fernandez-FuentesAndras Fiser
Sep 9, 2010·Bioinformatics·Alexander Goncearenco, Igor N Berezovsky
Oct 26, 2010·Nucleic Acids Research·Peter VanheeJoost Schymkowitz
Jul 5, 2011·Bioinformatics·Alexander Goncearenco, Igor N Berezovsky
Jan 29, 2013·Nature Methods·Predrag RadivojacIddo Friedberg
Mar 27, 2013·Annual Review of Biophysics·Rachel KolodnyMichael Levitt

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Citations

Dec 27, 2018·Journal of Biomolecular Structure & Dynamics·Dirk StratmannJacques Chomilier
Oct 11, 2019·Protein Science : a Publication of the Protein Society·Cameron MuraPhilip E Bourne
Apr 4, 2019·Bioinformatics·Mathilde Carpentier, Jacques Chomilier
Feb 23, 2020·Proceedings of the National Academy of Sciences of the United States of America·Aya NarunskyNir Ben-Tal
Oct 12, 2020·Protein Science : a Publication of the Protein Society·Rosalie Lipsh-SokolikSarel J Fleishman
Dec 19, 2020·Computational and Structural Biotechnology Journal·Jeroen P M VranckenArnout R D Voet
Jan 17, 2021·Current Opinion in Structural Biology·Sergio Romero-RomeroBirte Höcker
Jan 22, 2021·Current Opinion in Structural Biology·Rachel Kolodny
Apr 25, 2020·Journal of Molecular Biology·Noelia FerruzBirte Höcker
Mar 1, 2021·Algorithms for Molecular Biology : AMB·Peter Røgen
Jul 31, 2018·Structure·Meghan Whitney FranklinJoanna S G Slusky
May 18, 2021·Frontiers in Molecular Biosciences·Arun S KonagurthuArthur M Lesk
Jun 12, 2021·Frontiers in Molecular Biosciences·Jiří KoubekGünter Kramer
Dec 30, 2020·Current Opinion in Structural Biology·Bram MylemansJeremy Rh Tame
Nov 1, 2020·Current Opinion in Structural Biology·Jeffrey Skolnick, Mu Gao
Aug 13, 2021·Molecular Biology and Evolution·Claudia Alvarez-CarreñoLoren Dean Williams
Sep 7, 2021·Frontiers in Molecular Biosciences·Noelia FerruzBirte Höcker
Sep 28, 2021·Biophysical Journal·Victor Y ZhaoEugene I Shakhnovich
Oct 12, 2021·Expert Review of Proteomics·Gustavo Caetano-AnollésDerek Caetano-Anollés
Oct 30, 2021·PLoS Computational Biology·Petar I PenevLoren Dean Williams

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Software Mentioned

HMMER
ECOD
HHSearch

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