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Evolution of increased complexity in a molecular machine


Many cellular processes are carried out by molecular ‘machines’—assemblies of multiple differentiated proteins that physically interact to execute biological functions1,2,3,4,5,6,7,8. Despite much speculation, strong evidence of the mechanisms by which these assemblies evolved is lacking. Here we use ancestral gene resurrection9,10,11 and manipulative genetic experiments to determine how the complexity of an essential molecular machine—the hexameric transmembrane ring of the eukaryotic V-ATPase proton pump—increased hundreds of millions of years ago. We show that the ring of Fungi, which is composed of three paralogous proteins, evolved from a more ancient two-paralogue complex because of a gene duplication that was followed by loss in each daughter copy of specific interfaces by which it interacts with other ring proteins. These losses were complementary, so both copies became obligate components with restricted spatial roles in the complex. Reintroducing a single historical mutation from each paralogue lineage into the resurrected ancestral proteins is sufficient to recapitulate their asymmetric degeneration and trigger the requirement for the more elaborate three-component ring. Our experiments show that increased complexity in an essential molecular machine evolved because of simple, high-probability evolutionary processes, without the apparent evolution of novel functions. They point to a plausible mechanism for the evolution of complexity in other multi-paralogue protein complexes.

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Figure 1: Structure and evolution of the V-ATPase complex.
Figure 2: Two reconstructed ancestral V 0 subunits functionally replace the three-paralogue ring in extant yeast.
Figure 3: Increasing complexity by complementary loss of interactions in the fungal V 0 ring.
Figure 4: Genetic basis for functional differentiation of Anc.3 and Anc.11.


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This study was supported by National Institutes of Health (NIH) grants R01-GM081592 (to J.W.T.) and R01-GM38006 (to T.H.S.), National Science Foundation (NSF) grants IOB-0546906 (to J.W.T.) and DEB-0516530 (to J.W.T.), NIH Genetics Training grant T32-GM007257 (to G.C.F.), NSF IGERT grant DGE-9972830 (to V.H.-S.) and the Howard Hughes Medical Institute (J.W.T.). We thank L. Graham, G. Butler and B. Houser for generating yeast strains and other assistance. We thank members of the Stevens and Thornton laboratories for helpful comments.

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V.H.-S. performed the phylogenetic analysis and statistical reconstructions. G.C.F. performed functional experiments. All authors conceived the experiments, interpreted the results and wrote the paper.

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Correspondence to Joseph W. Thornton.

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The authors declare no competing financial interests.

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Supplementary Information

This file contains the Protein Sequences and Yeast Strains used in this study, together with 7 Supplementary Figures with legends. (PDF 957 kb)

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Finnigan, G., Hanson-Smith, V., Stevens, T. et al. Evolution of increased complexity in a molecular machine. Nature 481, 360–364 (2012).

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