Comparative evolutionary analysis of protein complexes in E. coli and yeast.

BMC Genomics
Adam J ReidChristine Orengo

Abstract

Proteins do not act in isolation; they frequently act together in protein complexes to carry out concerted cellular functions. The evolution of complexes is poorly understood, especially in organisms other than yeast, where little experimental data has been available. We generated accurate, high coverage datasets of protein complexes for E. coli and yeast in order to study differences in the evolution of complexes between these two species. We show that substantial differences exist in how complexes have evolved between these organisms. A previously proposed model of complex evolution identified complexes with cores of interacting homologues. We support findings of the relative importance of this mode of evolution in yeast, but find that it is much less common in E. coli. Additionally it is shown that those homologues which do cluster in complexes are involved in eukaryote-specific functions. Furthermore we identify correlated pairs of non-homologous domains which occur in multiple protein complexes. These were identified in both yeast and E. coli and we present evidence that these too may represent complex cores in yeast but not those of E. coli. Our results suggest that there are differences in the way protein complexes have ...Continue Reading

References

Aug 1, 1995·Current Biology : CB·D M Rubin, D Finley
Feb 1, 1997·Nature Structural Biology·X Yu, E H Egelman
Oct 27, 1998·Trends in Biochemical Sciences·K Henrick, J M Thornton
Apr 29, 1996·Physical Review Letters·M BlattE Domany
Oct 6, 2000·Annual Review of Microbiology·A Ishihama
Aug 24, 2001·Journal of Molecular Biology·S A TeichmannC Chothia
Mar 28, 2002·Nucleic Acids Research·A J EnrightC A Ouzounis
Jan 10, 2003·Nucleic Acids Research·Gary D BaderChristopher W V Hogue
Jun 14, 2003·Science·S L Baldauf
Dec 16, 2003·Proceedings of the National Academy of Sciences of the United States of America·Christian von MeringPeer Bork
Jan 6, 2004·Proteins·Jose B Pereira-LealChristos A Ouzounis
Mar 3, 2004·Genome Research·Berend Snel, Martijn A Huynen
Apr 21, 2004·Journal of Molecular Biology·Christine VogelSarah A Teichmann
Jun 8, 2004·Bioinformatics·A D KingI Jurisica
Jul 21, 2004·Bioinformatics·Doron BetelChristopher W V Hogue
Dec 21, 2004·Nucleic Acids Research·Paul KerseyRolf Apweiler
Feb 1, 2005·Trends in Genetics : TIG·Howard OchmanEmmanuelle Lerat
Feb 25, 2005·Nature·Roger Guimerà, Luís A Nunes Amaral
Apr 5, 2005·Genome Research·José B Pereira-Leal, Sarah A Teichmann
Apr 22, 2005·Journal of Molecular Biology·Toni GabaldónMartijn A Huynen
Jun 29, 2005·Nucleic Acids Research·Iaroslav IspolatovSergei Maslov
Oct 27, 2005·Heredity·J A G Ranea
Dec 31, 2005·Nucleic Acids Research·UNKNOWN Gene Ontology Consortium
Dec 31, 2005·Nucleic Acids Research·Chris StarkMike Tyers
Jan 24, 2006·Nature·Anne-Claude GavinGiulio Superti-Furga
Mar 24, 2006·Nature·Nevan J KroganJack F Greenblatt
Apr 12, 2006·Genome Research·Mohammad ArifuzzamanHirotada Mori
Jul 21, 2006·PLoS Computational Biology·Sven Mika, Burkhard Rost
Oct 6, 2006·Journal of Molecular Evolution·Juan A G RaneaChristine A Orengo
Nov 8, 2006·BMC Bioinformatics·Sylvain Brohée, Jacques van Helden
Nov 14, 2006·Nucleic Acids Research·Christian von MeringPeer Bork
Nov 23, 2006·PLoS Computational Biology·Emmanuel D LevySarah A Teichmann
Dec 1, 2006·Nucleic Acids Research·Andrew Chatr-aryamontriGianni Cesareni
Dec 6, 2006·Nucleic Acids Research·S KerrienH Hermjakob
Apr 7, 2007·Genome Biology·Jose B Pereira-LealSarah A Teichmann

❮ Previous
Next ❯

Citations

Nov 5, 2010·Proceedings of the National Academy of Sciences of the United States of America·Kosuke Hashimoto, Anna R Panchenko
Dec 7, 2011·Molecular Biology and Evolution·Michael Lynch
Jul 16, 2011·Annual Review of Genomics and Human Genetics·Michael LynchMina Rho
Mar 19, 2013·Biochimica Et Biophysica Acta·Benoit H DessaillyChristine A Orengo
Oct 10, 2015·Current Opinion in Genetics & Development·Sayoni DasChristine A Orengo
Jun 17, 2014·Progress in Biophysics and Molecular Biology·Alexander GoncearencoAnna R Panchenko
Dec 11, 2014·Annual Review of Biochemistry·Joseph A Marsh, Sarah A Teichmann
Jun 12, 2021·Frontiers in Molecular Biosciences·Jiří KoubekGünter Kramer

❮ Previous
Next ❯

Methods Mentioned

BETA
Tandem Affinity Purification
Two-Hybrid
Tandem
pull-down
co-immunoprecipitation
MDA
phylogenetic profiling

Software Mentioned

TAP
IntAct
MCL
MINT
Gene3D
MCODE
FunCat
BIND
GO

Related Concepts

Related Feeds

Archaeogenetics

Recent advances in genomic sequencing has led to the discovery of new strains of Archaea and shed light on their evolutionary history. Discover the latest research on Archaeogenetics here.

Alternative splicing

Alternative splicing a regulated gene expression process that allows a single genetic sequence to code for multiple proteins. Here is that latest research.