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      Evolution of increased complexity in a molecular machine.

      Nature
      Algorithms, Computational Biology, Evolution, Molecular, Extinction, Biological, Fungi, classification, enzymology, genetics, Gene Duplication, Models, Biological, Mutagenesis, Phylogeny, Protein Conformation, Saccharomyces cerevisiae, Vacuolar Proton-Translocating ATPases, chemistry, metabolism

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          Abstract

          Many cellular processes are carried out by molecular 'machines'-assemblies of multiple differentiated proteins that physically interact to execute biological functions. Despite much speculation, strong evidence of the mechanisms by which these assemblies evolved is lacking. Here we use ancestral gene resurrection 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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          Most cited references26

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          Using an appropriate model of amino acid replacement is very important for the study of protein evolution and phylogenetic inference. We have built a tool for the selection of the best-fit model of evolution, among a set of candidate models, for a given protein sequence alignment. ProtTest is available under the GNU license from http://darwin.uvigo.es
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              Three new dominant drug resistance cassettes for gene disruption in Saccharomyces cerevisiae.

              Disruption-deletion cassettes are powerful tools used to study gene function in many organisms, including Saccharomyces cerevisiae. Perhaps the most widely useful of these are the heterologous dominant drug resistance cassettes, which use antibiotic resistance genes from bacteria and fungi as selectable markers. We have created three new dominant drug resistance cassettes by replacing the kanamycin resistance (kan(r)) open reading frame from the kanMX3 and kanMX4 disruption-deletion cassettes (Wach et al., 1994) with open reading frames conferring resistance to the antibiotics hygromycin B (hph), nourseothricin (nat) and bialaphos (pat). The new cassettes, pAG25 (natMX4), pAG29 (patMX4), pAG31 (patMX3), pAG32 (hphMX4), pAG34 (hphMX3) and pAG35 (natMX3), are cloned into pFA6, and so are in all other respects identical to pFA6-kanMX3 and pFA6-kanMX4. Most tools and techniques used with the kanMX plasmids can also be used with the hph, nat and patMX containing plasmids. These new heterologous dominant drug resistance cassettes have unique antibiotic resistance phenotypes and do not affect growth when inserted into the ho locus. These attributes make the cassettes ideally suited for creating S. cerevisiae strains with multiple mutations within a single strain. Copyright 1999 John Wiley & Sons, Ltd.
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                Author and article information

                Comments

                added an editorial note to Evolutionary Cell Biology

                Multi-protein molecular machines are often surprisingly complex, and it is often assumed- and argued- that this complexity must be adaptive. Since complex interactions do not appear instantaneously this also raises a paradox because most mutations are either neutral or have deleterious effects on fitness. Alternatives to the adaptationist argument that can resolve this paradox, such as the theory of constructive neutral evolution (CNE), have existed for decades but are not widely discussed outside of the evolutionary biology community. The authors here use ancestral reconstruction and functional studies to provide actual experimental support for the CNE model. 

                They show that the ring of the fungal V-ATPase proton pump, a hexamer composed of three different paralogues, evolved from a simpler 2 paralogue version through a duplication followed by a series of high-likelihood mutations that degraded interactions with other ring proteins. These made the duplicated proteins dependent on each other, leading to an almost-irreversible increase in complexity (a "neutral evolutionary ratchet"). 

                See also Doolittle's news & views article on the paper. 

                More on CNE and neutral ratchets here: 
                How a neutral evolutionary ratchet can build evolutionary complexity 
                 

                 

                 

                 

                2016-04-20 14:56 UTC
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