Quantifying the mechanisms of domain gain in animal proteins.

Genome Biology
Marija BuljanAlex Bateman

Abstract

Protein domains are protein regions that are shared among different proteins and are frequently functionally and structurally independent from the rest of the protein. Novel domain combinations have a major role in evolutionary innovation. However, the relative contributions of the different molecular mechanisms that underlie domain gains in animals are still unknown. By using animal gene phylogenies we were able to identify a set of high confidence domain gain events and by looking at their coding DNA investigate the causative mechanisms. Here we show that the major mechanism for gains of new domains in metazoan proteins is likely to be gene fusion through joining of exons from adjacent genes, possibly mediated by non-allelic homologous recombination. Retroposition and insertion of exons into ancestral introns through intronic recombination are, in contrast to previous expectations, only minor contributors to domain gains and have accounted for less than 1% and 10% of high confidence domain gain events, respectively. Additionally, exonization of previously non-coding regions appears to be an important mechanism for addition of disordered segments to proteins. We observe that gene duplication has preceded domain gain in at leas...Continue Reading

References

Oct 5, 1990·Journal of Molecular Biology·S F AltschulD J Lipman
Jan 11, 1982·Nucleic Acids Research·D SankoffW McKay
Dec 19, 1995·Proceedings of the National Academy of Sciences of the United States of America·M LongW Gilbert
Nov 1, 1996·Matrix Biology : Journal of the International Society for Matrix Biology·L Patthy
Nov 5, 1999·Journal of Molecular Biology·P E Wright, H J Dyson
Mar 24, 2000·Science·G M RubinS Lewis
Sep 5, 2001·Nature Biotechnology·A K Dunker, Z Obradovic
Dec 26, 2001·Nucleic Acids Research·Alex BatemanErik L L Sonnhammer
Jan 31, 2002·Trends in Genetics : TIG·Paweł Stankiewicz, James R Lupski
Feb 6, 2002·Current Opinion in Chemical Biology·Richard R CopleyPeer Bork
May 2, 2002·Proceedings of the National Academy of Sciences of the United States of America·Michael Lynch
Jun 5, 2002·Genome Research·W James KentDavid Haussler
Aug 10, 2002·Science·Jeffrey A BaileyEvan E Eichler
Nov 8, 2002·Genome Research·Henrik KaessmannWen-Hsiung Li
Nov 21, 2002·Protein Science : a Publication of the Protein Society·Russell L MarsdenDavid T Jones
Jun 14, 2003·Science·Cyrus ChothiaSarah A Teichmann
Nov 25, 2003·Nature Reviews. Genetics·Manyuan LongWen Wang
Jan 11, 2005·Nucleic Acids Research·Mingyi LiuAndrei Grigoriev
Feb 1, 2005·Trends in Genetics : TIG·Sarah K Kummerfeld, Sarah A Teichmann
Jul 15, 2005·BioEssays : News and Reviews in Molecular, Cellular and Developmental Biology·Jeffrey S Han, Jef D Boeke
Sep 1, 2005·PLoS Biology·Paramvir Dehal, Jeffrey L Boore
Oct 4, 2005·Journal of Molecular Biology·Asa K BjörklundArne Elofsson
Dec 14, 2005·Genome Research·Pinchas AkivaRotem Sorek
Dec 14, 2005·Genome Research·Genís ParraRoderic Guigó
Apr 7, 2006·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Teresa PrzytyckaDannie Durand
Apr 28, 2006·The FEBS Journal·January WeinerErich Bornberg-Bauer
May 5, 2006·Proceedings of the National Academy of Sciences of the United States of America·Richard CordauxCédric Feschotte
May 26, 2006·Genome Biology·Tine BlommeYves Van de Peer
May 31, 2006·PLoS Computational Biology·Christine Vogel, Cyrus Chothia
Jun 14, 2006·Nature Reviews. Genetics·Jeffrey A Bailey, Evan E Eichler
Jul 1, 2006·Genome Research·Jennifer L FreemanCharles Lee
Aug 30, 2006·Proceedings of the National Academy of Sciences of the United States of America·Xiang H-F Zhang, Lawrence A Chasin
Nov 4, 2006·Journal of Proteome Research·Zsuzsanna DosztányiPeter Tompa
Dec 15, 2006·Journal of Molecular Biology·Jessica H FongStephen H Bryant
Dec 29, 2006·Cellular and Molecular Life Sciences : CMLS·D V BabushokH H Kazazian
Sep 5, 2007·Nature Genetics·Donald F Conrad, Matthew E Hurles
Jul 12, 2007·Genome Research·Daria V BabushokHaig H Kazazian
Aug 11, 2007·Journal of Molecular Biology·Diana EkmanArne Elofsson
Oct 20, 2007·Genetics·Matthew W HahnSang-Gook Han
Nov 16, 2007·Nucleic Acids Research·L G WilmingJ L Harrow

❮ Previous
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Citations

Feb 1, 2013·Bioinformatics·Pierre-Alain JachietEric Bapteste
Mar 19, 2013·Bioinformatics·Chia-Chin WuAleksandar Milosavljevic
Jul 21, 2012·Genome Biology and Evolution·Lucas Leclère, Fabian Rentzsch
Oct 22, 2011·Molecular Biology and Evolution·Andrew D Moore, Erich Bornberg-Bauer
Nov 30, 2010·BMC Evolutionary Biology·Andreas Leidenroth, Jane E Hewitt
Feb 22, 2013·BMC Evolutionary Biology·Macarena Toll-Riera, M Mar Albà
Jul 16, 2010·Genome Biology·Joseph A Marsh, Sarah A Teichmann
May 19, 2011·PLoS Computational Biology·Dan Siegal-GaskinsErich Grotewold
Jul 6, 2013·Bioinformatics·Nicolas TerraponErich Bornberg-Bauer
Apr 3, 2014·Molecular Biology and Evolution·Adam J SardarOwen J L Rackham
Feb 5, 2013·Biochimica Et Biophysica Acta·Andrew D MooreErich Bornberg-Bauer
Jun 19, 2014·Human Molecular Genetics·Iakes EzkurdiaMichael L Tress
Sep 1, 2011·Nature Reviews. Genetics·Diethard Tautz, Tomislav Domazet-Lošo
Jun 12, 2014·Nature·Alexander A MyburgJeremy Schmutz
Apr 9, 2013·Current Opinion in Structural Biology·Erich Bornberg-Bauer, M Mar Albà
Apr 30, 2014·Chemical Reviews·Robin van der LeeM Madan Babu
Oct 10, 2015·Current Opinion in Genetics & Development·Andrea Scaiewicz, Michael Levitt
Aug 11, 2015·Scientific Reports·Zhen-Na ZhangCheng-Gang Zou
Feb 2, 2011·IEEE/ACM Transactions on Computational Biology and Bioinformatics·John WiedenhoeftOliver Eulenstein
May 28, 2015·Cellular and Molecular Life Sciences : CMLS·Saligram Prabhakar BhargavInari Kursula
Nov 22, 2015·Nucleic Acids Research·Malini NagulapalliJitendra K Thakur
Jun 5, 2015·Frontiers in Molecular Biosciences·Gabriel Thieulin-PardoBrigitte Gontero
Dec 11, 2014·Annual Review of Biochemistry·Joseph A Marsh, Sarah A Teichmann
May 1, 2015·Genome Biology·Ananth Prakash, Alex Bateman
Jun 17, 2016·Current Opinion in Structural Biology·Jonathan G LeesChristine A Orengo
Oct 30, 2016·Trends in Biochemical Sciences·Rita Pancsa, Peter Tompa
Feb 6, 2017·ELife·Thomas BadetSylvain Raffaele
Aug 6, 2016·Bioinformatics and Biology Insights·Steffen KlasbergLudovic Mallet
May 29, 2018·The FEBS Journal·Steffen KlasbergErich Bornberg-Bauer
Oct 11, 2017·Journal of Molecular Cell Biology·Maximilian J GerhardtSarah Melissa P Jacobo
Jun 10, 2017·Cellular and Molecular Life Sciences : CMLS·Joseph B AhrensJessica Siltberg-Liberles
Jan 9, 2019·Frontiers in Immunology·Paloma Gómez-FernándezKoen Vandenbroeck
Jun 24, 2017·Nature Ecology & Evolution·Benjamin A WilsonJoanna Masel
Jun 26, 2020·Frontiers in Genetics·Xuan XiaoWang-Ren Qiu

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Datasets Mentioned

BETA
AP000365.1

Methods Mentioned

BETA
nucleotide exchange

Software Mentioned

Wu
TreeFam
Ensembl
IUPred
Belvu viewer
Pfam
DAVID
TreeFam API
blastp
profile comparer

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