General trends in the utilization of structural factors contributing to biological complexity

Molecular Biology and Evolution
Dong YangFuchu He

Abstract

During evolution, proteins containing newly emerged domains and the increasing proportion of multidomain proteins in the full genome-encoded proteome (GEP) have substantially contributed to increasing biological complexity. However, it is not known how these two potential structural factors are preferentially utilized at given physiological states. Here, we classified proteins according to domain number and domain age and explored the general trends across species for the utilization of proteins from GEP to various certain-state proteomes (CSPs, i.e., all the proteins expressed at certain physiological states). We found that multidomain proteins or only older domain-containing proteins are significantly overrepresented in CSPs compared with GEP, which is a trend that is stronger in multicellular organisms than in unicellular organisms. Interestingly, the strengths of overrepresentation decreased during evolution of multicellular eukaryotes. When comparing across CSPs, we found that multidomain proteins are more overrepresented in complex tissues than in simpler ones, whereas no difference among proteins with domains of different ages is evident between complex and simple tissues. Thus, biological complexity under certain condit...Continue Reading

References

Nov 21, 1997·Computer Applications in the Biosciences : CABIOS·Z Yang
Apr 14, 1999·Proceedings of the National Academy of Sciences of the United States of America·L Duret, D Mouchiroud
Apr 26, 2000·Proceedings of the National Academy of Sciences of the United States of America·C AdamiT C Collier
Aug 16, 2001·Molecular Biology and Evolution·S Wuchty
Jul 23, 2002·Nature Genetics·Cristian I Castillo-DavisFyodor A Kondrashov
Aug 15, 2002·Trends in Genetics : TIG·Laurence D Hurst
Nov 15, 2002·Nature·Eugene V KooninGeorgy P Karev
Dec 20, 2002·Bioinformatics·Earl HubbellRui Mei
Jun 14, 2003·Science·Cyrus ChothiaSarah A Teichmann
Jul 10, 2003·Trends in Genetics : TIG·Eli Eisenberg, Erez Y Levanon
Sep 17, 2003·Genome Research·Araxi O Urrutia, Laurence D Hurst
Nov 25, 2003·Science·Michael Lynch, John S Conery
Apr 13, 2004·Proceedings of the National Academy of Sciences of the United States of America·Andrew I SuJohn B Hogenesch
Apr 28, 2004·Trends in Genetics : TIG·Alexander E Vinogradov
May 7, 2004·Nature·Markus W CovertBernhard O Palsson
Aug 4, 2004·Genome Research·Jacob D JaffeGeorge M Church
Sep 15, 2004·Trends in Genetics : TIG·Ben Lehner, Andrew G Fraser
Jan 25, 2005·Journal of Molecular Biology·Christine VogelJose Pereira-Leal
Mar 11, 2005·Molecular Biology and Evolution·Andreas Wagner
Mar 31, 2005·Trends in Genetics : TIG·Inbar Cohen-GihonItai Yanai
Jul 7, 2005·Genome Research·C Victor JongeneelThomas J Vasicek
Dec 31, 2005·Nucleic Acids Research·Ivica LetunicPeer Bork
Dec 31, 2005·Nucleic Acids Research·Feng ChenDavid S Roos
May 31, 2006·PLoS Computational Biology·Christine Vogel, Cyrus Chothia
Dec 7, 2006·Nucleic Acids Research·Donna MaglottTatiana Tatusova
May 31, 2007·Nature Genetics·Venkateswara R ChintapalliJulian A T Dow
Sep 13, 2007·Genome Biology·Rebecca M FoxDavid M Miller
Nov 28, 2007·Nucleic Acids Research·Robert D FinnAlex Bateman
Jan 31, 2008·Genome Research·Malay Kumar BasuEugene V Koonin
May 20, 2008·Science·Christopher J CardinaleEvgeny Nudler
Oct 23, 2008·Nucleic Acids Research·Tanya BarrettRon Edgar
Nov 6, 2008·Nucleic Acids Research·Aron Marchler-BauerStephen H Bryant
Jan 21, 2009·Current Opinion in Genetics & Development·Todd H Oakley, Ajna S Rivera
Feb 14, 2009·Nucleic Acids Research·Eugene V Koonin
Apr 9, 2009·Proceedings of the National Academy of Sciences of the United States of America·Yuri I WolfDavid J Lipman
Jun 19, 2009·Nature·Amir MitchellYitzhak Pilpel

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