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Open Access Highly Accessed Research article

Complex fate of paralogs

Radek Szklarczyk1, Martijn A Huynen1 and Berend Snel23*

Author Affiliations

1 Centre for Molecular and Biomolecular Informatics, NCMLS, Radboud University Medical Centre, PO Box 9101, 6500 HB Nijmegen, the Netherlands

2 Bioinformatics, Department of Biology, Faculty of Science, Utrecht University, Padualaan 8, 3584 CH, the Netherlands

3 Academic Biomedical Centre, Utrecht University, Yalelaan 1, 3584 CL Utrecht, the Netherlands

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BMC Evolutionary Biology 2008, 8:337  doi:10.1186/1471-2148-8-337

Published: 18 December 2008



Thanks to recent high coverage mass-spectrometry studies and reconstructed protein complexes, we are now in an unprecedented position to study the evolution of biological systems. Gene duplications, known to be a major source of innovation in evolution, can now be readily examined in the context of protein complexes.


We observe that paralogs operating in the same complex fulfill different roles: mRNA dosage increase for more than a hundred cytosolic ribosomal proteins, mutually exclusive participation of at least 54 paralogs resulting in alternative forms of complexes, and 24 proteins contributing to bona fide structural growth. Inspection of paralogous proteins participating in two independent complexes shows that an ancient, pre-duplication protein functioned in both multi-protein assemblies and a gene duplication event allowed the respective copies to specialize and split their roles.


Variants with conditionally assembled, paralogous subunits likely have played a role in yeast's adaptation to anaerobic conditions. In a number of cases the gene duplication has given rise to one duplicate that is no longer part of a protein complex and shows an accelerated rate of evolution. Such genes could provide the raw material for the evolution of new functions.