The shikimate pathway provides carbon skeletons for the aromatic amino acids L-tryptophan, L-phenylalanine, and L-tyrosine. It is a high flux bearing pathway and it has been estimated that greater than 30% of all fixed carbon is directed through this pathway. These combined pathways have been subjected to considerable research attention due to the fact that mammals are unable to synthesize these amino acids and the fact that one of the enzymes of the shikimate pathway is a very effective herbicide target. However, in addition to these characteristics these pathways additionally provide important precursors for a wide range of important secondary metabolites including chlorogenic acid, alkaloids, glucosinolates, auxin, tannins, suberin, lignin and lignan, tocopherols, and betalains. Here we review the shikimate pathway of the green lineage and compare and contrast its evolution and ubiquity with that of the more specialized phenylpropanoid metabolism which this essential pathway fuels.

In Arabidopsis (Arabidopsis thaliana), TREHALOSE-6-PHOSPHATE SYNTHASE1 (TPS1) catalyzes the synthesis of the sucrose-signaling metabolite trehalose 6-phosphate (Tre6P) and is essential for embryogenesis and normal postembryonic growth and development. To understand its molecular functions, we transformed the embryo-lethal tps1-1 null mutant with various forms of TPS1 and with a heterologous TPS (OtsA) from Escherichia coli, under the control of the TPS1 promoter, and tested for complementation. TPS1 protein localized predominantly in the phloem-loading zone and guard cells in leaves, root vasculature, and shoot apical meristem, implicating it in both local and systemic signaling of Suc status. The protein is targeted mainly to the nucleus. Restoring Tre6P synthesis was both necessary and sufficient to rescue the tps1-1 mutant through embryogenesis. However, postembryonic growth and the sucrose-Tre6P relationship were disrupted in some complementation lines. A point mutation (A119W) in the catalytic domain or truncating the C-terminal domain of TPS1 severely compromised growth. Despite having high Tre6P levels, these plants never flowered, possibly because Tre6P signaling was disrupted by two unidentified disaccharide-monophosphates that appeared in these plants. The noncatalytic domains of TPS1 ensure its targeting to the correct subcellular compartment and its catalytic fidelity and are required for appropriate signaling of Suc status by Tre6P.

A genomics analysis on sulphur metabolism has been conducted at the level of transcriptomics and metabolomics. The analysis of these data after applying bioinformatic tools is to reveal novel findings. The findings are discussed and the knowledge obtained from comparable analyses on sulphur metabolism and other plant nutrient genomic studies is reviewed. The analysis of the response of the transcriptome and metabolome to sulphur deprivation in the growth medium provides a tool set for the analysis of comparable genomics studies of other nutrients. The goal of this ‘sulphobolomics’ (i.e. sulphur genomics and metabolome analysis) approach, and of other investigations, is to describe in a holistic way the biochemical, molecular, and physiological response of a plant to nutrient starvation, here sulphate, or, more generally, to alterations and imbalances in nutrient availability. Eventually, this analysis will provide a case study for a systems biology approach.

Plants display manifold metabolic changes on sulfate deficiency (S deficiency) with all sulfur-containing pools of primary and secondary metabolism affected. O-Acetylserine (OAS), whose levels are rapidly altered on S deficiency, is correlated tightly with novel regulators of plant sulfur metabolism that have key roles in balancing plant sulfur pools, including the Sulfur Deficiency Induced genes (SDI1 and SDI2), More Sulfur Accumulation1 (MSA1), and GGCT2;1. Despite the importance of OAS in the coordination of S pools under stress, mechanisms of OAS perception and signaling have remained elusive. Here, we put particular focus on the general OAS-responsive genes but also elaborate on the specific roles of SDI1 and SDI2 genes, which downregulate the glucosinolate (GSL) pool size. We also highlight the key open questions in sulfur partitioning.

Sulphur is an essential macronutrient for plant growth and development. Reaching a thorough understanding of the molecular basis for changes in plant metabolism depending on the sulphur-nutritional status at the systems level will advance our basic knowledge and help target future crop improvement. Although the transcriptional responses induced by sulphate starvation have been studied in the past, knowledge of the regulation of sulphur metabolism is still fragmentary. This work focuses on the discovery of candidates for regulatory genes such as transcription factors (TFs) using ‘omics technologies. For this purpose a short term sulphate-starvation / re-supply approach was used. ATH1 microarray studies and metabolite determinations yielded 21 TFs which responded more than 2-fold at the transcriptional level to sulphate starvation. Categorization by response behaviors under sulphate-starvation / re-supply and other nutrient starvations such as nitrate and phosphate allowed determination of whether the TF genes are specific for or common between distinct mineral nutrient depletions. Extending this co-behavior analysis to the whole transcriptome data set enabled prediction of putative downstream genes. Additionally, combinations of transcriptome and metabolome data allowed identification of relationships between TFs and downstream responses, namely, expression changes in biosynthetic genes and subsequent metabolic responses. Effect chains on glucosinolate and polyamine biosynthesis are discussed in detail. The knowledge gained from this study provides a blueprint for an integrated analysis of transcriptomics and metabolomics and application for the identification of uncharacterized genes.

Nutrients are critical for plants to grow and develop, and nutrient depletion severely affects crop yield. In order to optimize nutrient acquisition, plants adapt their growth and root architecture. Changes in growth are determined by modifications in the cell walls surrounding every plant cell. The plant cell wall, which is largely composed of complex polysaccharides, is essential for plants to attain their shape and to protect cells against the environment. Within the cell wall, cellulose strands form microfibrils that act as a framework for other wall components, including hemicelluloses, pectins, proteins, and, in some cases, callose, lignin, and suberin. Cell wall composition varies, depending on cell and tissue type. It is governed by synthesis, deposition and remodeling of wall components, and determines the physical and structural properties of the cell wall. How nutrient status affects cell wall synthesis and organization, and thus plant growth and morphology, remains poorly understood. In this review, we aim to summarize and synthesize research on the adaptation of root cell walls in response to nutrient availability and the potential role of cell walls in nutrient sensing.