Focus Issue on Metabolism: Metabolites, Metabolites Everywhere

Abstract

Metabolic studies have arguably been conducted since the 13th century with Ibn al-Nafis stating that “the body and its parts are in a continuous state of dissolution and nourishment, so they are inevitably undergoing permanent change” (Mahdi, 1974). However, it was studies in yeast in the last decades of the 19th century and the first decades of the 20th century (Kühne, 1877; Buchner, 1897; Sumner, 1926) that identified enzymes and thus mechanically defined metabolism. Many key findings that have provided the foundation of our current understanding of the biosynthesis and degradation of some of the hundreds of thousand metabolites of the plant kingdom have been published in the pages of Plant Physiology. This is particularly true regarding the core of chemical reactions, involving several thousands of reactions and metabolites, found with few exceptions in all free-living plants and therefore defined as primary metabolism. There have been so many such articles that highlighting only a handful is highly subjective. Nevertheless, important studies such as that characterizing the pathways of Glc oxidation in carrot (Daucus carota; Gibbs and Beevers, 1955) and those detailing the isolation and characterization of oxidative properties of plant mitochondria (Douce et al., 1977) and their interaction with photosynthesis (Hanning and Heldt, 1993) warrant special mention. Similarly, the pregenome use of mutants of Arabidopsis (Arabidopsis thaliana) to characterize photorespiration and lipid and starch biosynthesis (Somerville and Ogren, 1981; Caspar et al., 1985; Browse et al., 1986) represented considerable breakthroughs in our understanding of primary metabolism. Regarding what was once called, for complicated although ultimately incorrect reasoning, secondary metabolism (Fraenkel, 1959; Pichersky and Lewinsohn, 2011), defined in the past as the part of metabolism not present in nonplant organisms or variously as the part of plant metabolism not required for simple growth and development, Plant Physiology was actually a late comer. This was perhaps due to the erroneous belief on the part of self-respecting plant physiologists that such chemicals had no role in the life of the plant and were merely waste products and that any suggestions otherwise were teleological (Hartmann, 2008). Thus, the first mention of secondary metabolites in the pages of Plant Physiology was probably in 1982 (Hrazdina et al., 1982), at least two decades after extensive work on the metabolism of plant compounds such as lignin, flavonoids, alkaloids, and terpenes had begun to be published elsewhere. Nonetheless, with the advent of first molecular biology and then genomics, plant biologists have come to the realization that each plant species devotes a substantial portion of its genome to genes encoding enzymes involved in what is now defined as specialized metabolism (Pichersky and Lewinsohn, 2011), the portion of the metabolic network of each species that generates a lineage-specific set of metabolites with roles in various ecological interactions, most likely evolved as adaptations due to specific selection pressure. With this realization, specialized metabolism, which on aggregate encompasses many more genes and enzymes than those involved in primary metabolism, is regularly and extensively covered in Plant Physiology, as this Focus Issue will attest. Whereas the recent quantum leap in our ability to study plant metabolism began with the development of transcriptomics and genomic sequencing, proteomics and metabolomics followed swiftly thereafter, with early examples of the application of these approaches also being published in Plant Physiology (Girke et al., 2000; Zhu and Wang, 2000; Gallardo et al., 2001; Roessner et al., 2001). These developing technologies have both confirmed a number of long-held hypotheses and additionally provided novel insights into plant function. Moreover, the emergence of cost-efficient sequencing technologies has effectively removed previous barriers that prevented the adaptation of molecular approaches within certain species. As such, it seemed highly timely to develop a Focus Issue on the state of the art in plant metabolism focusing, but not exclusively so, on advances brought about by applications of these technologies and the data emanating from them. The Update by Weber (2015) provides a comprehensive review of RNA sequencing technologies and their advantages over micorarrays as well as bioinformatics approaches for transcriptome assembly. It additionally provides an important list of caveats of this approach before detailing how it has been used to refine our understanding of plant metabolism and discusses in detail one study, that of Ponnala et al. (2014), which indicates that RNA sequencing data can be used as a proxy for protein abundance. Recent advances in proteomic research have dramatically improved its capacity to identify proteins, although its detection level is still by no means as good as t