Small molecules: from structural diversity to signalling and regulatory roles

Abstract

For many years, the role of low molecular weight chemicals in plant signaling and regulation was restricted to a small set of molecules, largely those considered phytohormones including auxins, cytokinines, abscisates, gibberellins, and more. Yet, small molecules belonging to diverse chemical classes that are not defined as hormones have been demonstrated to act as mediators of signaling and regulatory cascades. While it is currently difficult to estimate how many such molecules function in plants, it might be that those identified to date are only a small portion of the ones functioning in a single plant. Small molecules could be acting not only at the level of proteins and membranes, but could also mediate mechanisms associated with DNA, mRNA, and small and long non-coding RNAs. Identifying such molecules is a difficult task partially due to the limited availability of methodologies to conduct large-scale in vivo detection of direct interactions with small molecules as well as the classically acknowledged low abundance of these molecules. At the same time, in contrast to what is generally recognized, a certain portion of signaling and regulatory small molecules accumulate to significant levels rather than at low levels, particularly lipid and carbohydrates derivatives. Even in cases when a certain molecule is associated with a particular process, the in vivo activity and role of its derivatives, conjugates and catabolites typically remain unresolved. Adding to the complexity of the role of small molecules in signaling and regulation is their intra-organismal transport that can take place in the same cell, between connected cells, in between nearby unconnected cells and distant cells. It may also be extraorganismal as in the case of volatiles and secreted chemicals.Despite the many challenges in detecting and functionally characterizing small molecules, genomics advances paired with increasingly sophisticated metabolomics approaches have led to a steady increase in the discovery of metabolites of diverse structure and roles in signaling and regulatory processes. This special issue will highlight recent advances and discoveries in the field of small molecule research ranging from signaling metabolites in primary metabolism to molecules with roles in inter-or intra-specific interactions in plants and algae. The reader will find traditional functional classifications of small molecules to become increasingly blurred since many chemicals act as exogenous signals and simultaneously serve important endogenous functions in plant physiology and development.In the first paper of this special issue, Lunn et al. (2014) describe particular sugars, namely trehalose and its phosphorylated intermediate trehalose 6-phosphate (Tre6P), as potential signaling metabolites. The non-reducing disaccharide trehalose is renown in many organisms as an osmoprotectant while in plants it is currently implicated in signaling associated with abiotic stress response as well as below and above ground interactions. Reports on a tight correlatio...

Allantoin, a stress-related purine metabolite, can activate jasmonate signaling in a MYC2-regulated and abscisic acid-dependent manner

“…The importance of various effects on plant development and physiology has been documented for certain molecular species of sugars, amino acids, polyamines, and other kinds of small compounds that are not considered to be phytohormones (see the Introduction). Currently, the number of such small metabolites is limited, but is estimated to be much higher than that reported in the literature ( Tholl and Aharoni, 2014 ). Thus, it seems possible that allantoin could serve in either nitrogen metabolism or stress protection, depending on the circumstances where plants live.…”

PROMIS, global analysis of PROtein–metabolite interactions using size separation in Arabidopsis thaliana

“…In fact, one way to see the cell is as “an entity in which proteins are embedded in a sea of metabolites” ( 1 ). In line with this, it has been speculated that many more small molecules than known today interact, and by doing so they modulate the function of their protein partners ( 2 , 3 ).…”

Recent advances in bio‐chemical, molecular and physiological aspects of membrane lipid derivatives in plant pathology

“…The regulatory lipids are a class of lipids which have been actively demonstrated as mediators of signalling and regulatory cascades and are capable of functioning effectively at low concentrations (Tholl & Aharoni, 2014). Examples of these classes of bioactive lipids include polyunsaturated fatty acid derivatives such as oxylipins, eicosanoids, as well as jasmonic acid.…”

“…For example, lipids may differ in fatty acid chain length and the level of unsaturation. Various lipids may help to either eliminate disease-causing organisms or curb their spread in the plant(Wältermann & Steinbüchel, 2005).Other signalling molecules are phytohormones like salicylic acid and ethylene, which are capable of defending plants against herbivores and necrotrophic pathogens(Tholl & Aharoni, 2014;Yang, Dong, & Hammock, 2011). As essential components of unicellular and multicellular membranes, lipids serve as structural components of plasma membranes.…”