Gene duplication and functional diversification is a central driving force in the evolution of plant biochemical diversity. However, the latter process is not well understood. Here the diversification of the plant shikimate/quinate dehydrogenase (S/QDH) gene family was investigated in order to shed light on how duplicate genes functionally diversify. The shikimate pathway is the major biosynthetic route towards the aromatic amino acids, linking vital protein biosynthesis with the production of aromatic secondary metabolites. Dehydroquinate dehydratase/shikimate dehydrogenase (SDH) encodes the central enzyme of this pathway, catalyzing the production of shikimate. Quinate is a secondary metabolite synthesized using the same precursors as shikimate by quinate dehydrogenase (QDH). Gene duplication prior to the gymnosperm / angiosperm split generated two distinct clades in seed plants separating SDH and QDH functions whereas non-seed plants have a single copy SDH. In vitro biochemical characterization of a reconstructed ancestral enzyme was performed alongside extant members separated prior to duplication (from a lycopod, a bryophyte, and a chlorophyte) and afterwards (from a gymnosperm and an angiosperm). This revealed that novel quinate biosynthetic activity was gained in seed plants, providing evidence for the diversification of gene function via neofunctionalization. However, the ability to use both NAD(H) and NADP(H) seems to have developed in both SDH and QDH clade members of angiosperms. Finally, a method is described for analysing quinate and its derivative, chlorogenic acid in transgenic Arabidopsis. / Graduate / 2021-05-11

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The shikimate pathway connects primary metabolism with the biosynthesis of the three aromatic amino acids (phenylalanine, tyrosine and tryptophan), which are essential protein building blocks. This pathway also provides precursors for a wide array of plant secondary metabolites with adaptive functions in plant adaptation and defense. The third and fourth steps of the shikimate pathway (the conversion of shikimate from 3-dehydroquinate via 3-dehydroshikimate) are catalyzed by a bi-functional enzyme called 3-dehydroquinate dehydratase/shikimate dehydrogenase (DQD/SDH). DQD/SDHs have been biochemically characterized in a few plant species including Arabidopsis thaliana, Solanum lycopersicum and Nicotiana tabacum. The embryo-lethal phenotype of Arabidopsis null mutants lacking DQD/SDH highlights a critical role of shikimate in primary metabolism. Quinate shares high structural similarity with shikimate and is an important secondary metabolite present in many plant species. Quinate and its derivatives (e.g. chlorogenic acid) serve important functions in plant defense due to their astringent (i.e. bitterness) and antimicrobial properties. Quinate can be derived from 3-dehydroquinate, and this reaction is catalyzed by quinate dehydrogense (QDH), the reaction mechanism of which resembles that of SDH. With a functional genomics approach, I demonstrated that two of the five poplar putative DQD/SDHs (Poptr1 and Poptr5, poplar DQD/SDH1 and 2) have exclusive specificity for shikimate, while the other three (Poptr2 to Poptr4, poplar QDH1 to 3) are involved in quinate biosynthesis. Phylogenetic reconstruction of the DQD/SDH/QDH superfamily has identified two distinct clades in seed plants that may act preferentially on either shikimate or quinate, whereas lineages that have diverged prior to the angiosperm/gymnosperm split, only have a single copy DQD/SDH. An evolutionary analysis was carried out, and the sequence of the immediate pre-duplication ancestral DQD/SDH (>300MYA) was estimated and reconstructed. Protein structure modelling and in vitro biochemical characterization of the ancestral recombinant protein was performed along with some extant members of this family (pre-duplication representatives: Rhodopirellula baltica (Rhoba), Chlamydomonas reinhardtii (Chlre), Physcomitrella patens (Phypa) and Selaginella moellendorffii (Selmo); post-duplication species: Pinus taeda (Pinta1 & Pinta2) and Populus trichocarpa (Poptr1 & Poptr3). Together, the results indicate that quinate biosynthetic activity was gained prior to duplication and remained low until it became beneficial and favored by selection. The optimization of quinate biosynthetic activity was at the expense of losing some primary shikimate biosynthetic function creating a pleiotropic conflict. This was then resolved by gene duplication and further specialization leading to genes encoding specialized enzymes (either SDH or QDH). Diversification of the DQD/SDH/QDH superfamily likely occurred through sub-functionalization via a mechanism described as “Escape from Adaptive Conflict.” / Graduate / 0307 / guojia@uvic.ca