Evolutionary Diversification of Plant Shikimate Kinase Gene Duplicates

Abstract

Shikimate kinase (SK; EC 2.7.1.71) catalyzes the fifth reaction of the shikimate pathway, which directs carbon from the central metabolism pool to a broad range of secondary metabolites involved in plant development, growth, and stress responses. In this study, we demonstrate the role of plant SK gene duplicate evolution in the diversification of metabolic regulation and the acquisition of novel and physiologically essential function. Phylogenetic analysis of plant SK homologs resolves an orthologous cluster of plant SKs and two functionally distinct orthologous clusters. These previously undescribed genes, shikimate kinase-like 1 (SKL1) and -2 (SKL2), do not encode SK activity, are present in all major plant lineages, and apparently evolved under positive selection following SK gene duplication over 400 MYA. This is supported by functional assays using recombinant SK, SKL1, and SKL2 from Arabidopsis thaliana (At) and evolutionary analyses of the diversification of SK-catalytic and -substrate binding sites based on theoretical structure models. AtSKL1 mutants yield albino and novel variegated phenotypes, which indicate SKL1 is required for chloroplast biogenesis. Extant SKL2 sequences show a strong genetic signature of positive selection, which is enriched in a protein–protein interaction module not found in other SK homologs. We also report the first kinetic characterization of plant SKs and show that gene expression diversification among the AtSK inparalogs is correlated with developmental processes and stress responses. This study examines the functional diversification of ancient and recent plant SK gene duplicates and highlights the utility of SKs as scaffolds for functional innovation.

Current Approaches for Enhanced Expression of Secondary Metabolites as Bioactive Compounds in Plants for Agronomic and Human Health Purposes

“…The long days and cool night temperature in the northern latitudes appear, for example, to increase production of aromatic compounds compared with the same plant species in the south [Fucile et al, 2008].…”

“…The shikimate pathway acts at a critical point between primary and secondary metabolism by transporting carbon from glycolysis and the pentose phosphate pathway towards the synthesis of a broad range of physiologically important aromatic compounds [Fucile et al, 2008;Chen et al, 2009]. The shikimate pathway is defi ned by seven metabolic steps beginning with the condensation of phosphoenolpyruvate (PEP) and erythrose 4-phosphate (E4P) and ending with the synthesis of chorismate [Vogt, 2010].…”

“…The demand for natural products has increased in recent years because of limitations in the process of obtaining drugs based on chemical synthesis [Fucile et al, 2008;Vogt, 2010]. To this is added the chemical diversity of these compounds on synthetic and intense biological activity.…”

Arabidopsis Hexokinase-Like1 and Hexokinase1 Form a Critical Node in Mediating Plant Glucose and Ethylene Responses

“…Their presence as multiple distinct plant lineages implies that there is a selective advantage in maintaining their functions. These proteins might represent a more general paradigm that expressed noncatalytic enzyme homologs have regulatory functions (Fucile et al, 2008;Vandesteene et al, 2010).…”

Shikimate dehydrogenase (E.C. 1.1.1. 25 ShDH) alleles as potential markers for flowering phenology in Pinus sylvestris

“…The function of shikimate dehydrogenase in plant metabolism is related to aromatic amino acid biosynthesis. The ShDH gene activities have been noted during plant growth and development processes and have been correlated with plant responses to biotic stress (Hermann and Weaver 1999;Fucile et al 2008), thus it may play an important role in plant flowering phenology.…”