title: Evolution of a Catalytic Mechanism.
abstract: The means by which superfamilies of specialized enzymes arise by gene duplication and functional divergence are poorly understood. The escape from adaptive conflict hypothesis, which posits multiple copies of a gene encoding a primitive inefficient and highly promiscuous generalist ancestor, receives support from experiments showing that resurrected ancestral enzymes are indeed more substrate-promiscuous than their modern descendants. Here, we provide evidence in support of an alternative model, the innovation-amplification-divergence hypothesis, which posits a single-copied ancestor as efficient and specific as any modern enzyme. We argue that the catalytic mechanisms of plant esterases and descendent acetone cyanohydrin lyases are incompatible with each other (e.g., the reactive substrate carbonyl must bind in opposite orientations in the active site). We then show that resurrected ancestral plant esterases are as catalytically specific as modern esterases, that the ancestor of modern acetone cyanohydrin lyases was itself only very weakly promiscuous, and that improvements in lyase activity came at the expense of esterase activity. These observations support the innovation-amplification-divergence hypothesis, in which an ancestor gains a weak promiscuous activity that is improved by selection at the expense of the ancestral activity, and not the escape from adaptive conflict in which an inefficient generalist ancestral enzyme steadily loses promiscuity throughout the transition to a highly active specialized modern enzyme.
authors.affiliation: Department of Biochemistry, Molecular Biology & Biophysics and the Biotechnology Institute, University of Minnesota.
authors.forename: Alissa
authors.initials: A
authors.lastname: Rauwerdink
authors.affiliation: Department of Biochemistry, Molecular Biology & Biophysics and the Biotechnology Institute, University of Minnesota.
authors.forename: Mark
authors.initials: M
authors.lastname: Lunzer
authors.affiliation: Department of Biochemistry, Molecular Biology & Biophysics and the Biotechnology Institute, University of Minnesota.
authors.forename: Titu
authors.initials: T
authors.lastname: Devamani
authors.affiliation: Department of Biochemistry, Molecular Biology & Biophysics and the Biotechnology Institute, University of Minnesota.
authors.forename: Bryan
authors.initials: B
authors.lastname: Jones
authors.affiliation: Department of Biochemistry, Molecular Biology & Biophysics and the Biotechnology Institute, University of Minnesota.
authors.forename: Joanna
authors.initials: J
authors.lastname: Mooney
authors.affiliation: Department of Biochemistry, Molecular Biology & Biophysics and the Biotechnology Institute, University of Minnesota Department of Biotechnology, East China University of Science and Technology, Shanghai, PR China.
authors.forename: Zhi-Jun
authors.initials: ZJ
authors.lastname: Zhang
authors.affiliation: Department of Biochemistry, Molecular Biology & Biophysics and the Biotechnology Institute, University of Minnesota Department of Biotechnology, East China University of Science and Technology, Shanghai, PR China.
authors.forename: Jian-He
authors.initials: JH
authors.lastname: Xu
authors.affiliation: Department of Biochemistry, Molecular Biology & Biophysics and the Biotechnology Institute, University of Minnesota.
authors.forename: Romas J
authors.initials: RJ
authors.lastname: Kazlauskas
authors.affiliation: Department of Biochemistry, Molecular Biology & Biophysics and the Biotechnology Institute, University of Minnesota Department of Ecology, Evolution and Behavior, University of Minnesota College of Ecology and Evolution, Sun Yat-Sen University, Guangzhou, PR China dean@mail.sysu.edu.cn.
authors.forename: Antony M
authors.initials: AM
authors.lastname: Dean
mesh_terms: D000446:Aldehyde-Lyases / Q000235:genetics; D002384:Catalysis; D020134:Catalytic Domain; D019143:Evolution, Molecular; D020440:Gene Duplication; D014644:Genetic Variation; D006867:Hydrolases / Q000235:genetics*; D010802:Phylogeny
chemical_list: D006867:Hydrolases; D000446:Aldehyde-Lyases; C087495:acetone-cyanohydrin lyase
keywords: amplification; catalysis; divergence.; escape from adaptive conflict; gene duplication and divergence; innovation; transition state stabilization