Temporal dynamics of gene expression underpin responses to internal and environmental stimuli. In eukaryotes, regulation of gene induction includes changing chromatin states at target genes and recruiting the transcriptional machinery that includes transcription factors. As one of the most potent defense compounds in Arabidopsis thaliana, camalexin can be rapidly induced by bacterial and fungal infections. Though several transcription factors controlling camalexin biosynthesis genes have been characterized, how the rapid activation of genes in this pathway upon a pathogen signal is enabled remains unknown. By combining publicly available epigenomic data with in vivo chromatin modification mapping, we found that camalexin biosynthesis genes are marked with two epigenetic modifications with opposite effects on gene expression, trimethylation of lysine 27 of histone 3 (H3K27me3) (repression) and acetylation of lysine 18 of histone 3 (H3K18ac) (activation), to form a previously uncharacterized type of bivalent chromatin. Mutants with reduced H3K27me3 or H3K18ac suggested that both modifications were required to determine the timing of gene expression and metabolite accumulation at an early stage of the stress response. Our study indicates that the H3K27me3-H3K18ac bivalent chromatin, which we name as kairostat, plays an important role in controlling the timely induction of gene expression upon stress stimuli in plants.

Despite the ecological and agronomical importance of seed germination, how seeds integrate environmental signals to trigger germination remains enigmatic. Recently we reported that a protein called FLOE1 is involved in sensing and responding to water availability during germination. Here, we present a live-imaging protocol to assess the subcellular localization of a protein of interest during imbibition of desiccated Arabidopsis thaliana seeds with the goal of understanding protein dynamics during the early stages of water uptake. For complete details on the use and execution of this profile, please refer to Dorone etal. (2021).

Iron deficiency hampers photosynthesis and is associated with chlorosis. We recently showed that iron deficiency-induced chlorosis depends on phosphorus availability. How plants integrate these cues to control chlorophyll accumulation is unknown. Here, we show that iron limitation downregulates photosynthesis genes in a phosphorus-dependent manner. Using transcriptomics and genome-wide association analysis, we identify two genes, PHT4;4 encoding a chloroplastic ascorbate transporter and bZIP58, encoding a nuclear transcription factor, which prevent the downregulation of photosynthesis genes leading to the stay-green phenotype under iron-phosphorus deficiency. Joint limitation of these nutrients induces ascorbate accumulation by activating expression of an ascorbate biosynthesis gene, VTC4, which requires bZIP58. Furthermore, we demonstrate that chloroplastic ascorbate transport prevents the downregulation of photosynthesis genes under iron-phosphorus combined deficiency through modulation of ROS homeostasis. Our study uncovers a ROS-mediated chloroplastic retrograde signaling pathway to adapt photosynthesis to nutrient availability.

Sorghum [Sorghum bicolor (L.) Moench] is the fifth most important cereal crop globally by harvested area and production. Its drought and heat tolerance allow high yields with minimal input. It is a promising biomass crop for the production of biofuels and bioproducts. In addition, as an annual diploid with a relatively small genome compared with other C-4 grasses, and excellent germplasm diversity, sorghum is an excellent research species for other C-4 crops such as maize. As a result, an increasing number of researchers are looking to test the transferability of findings from other organisms such as Arabidopsis thaliana and Brachypodium distachyon to sorghum, as well as to engineer new biomass sorghum varieties. Here, we provide an overview of sorghum as a multipurpose feedstock crop which can support the growing bioeconomy, and as a monocot research model system. We review what makes sorghum such a successful crop and identify some key traits for future improvement. We assess recent progress in sorghum transformation and highlight how transformation limitations still restrict its widespread adoption. Finally, we summarize available sorghum genetic, genomic, and bioinformatics resources. This review is intended for researchers new to sorghum research, as well as those wishing to include non-food and forage applications in their research.

Photosynthetic organisms convert light energy into chemical energy stored in carbohydrates. To perform this process, an adequate supply of essential mineral elements, such as iron, is required in the chloroplast. Because iron plays a crucial role during electron transport and chlorophyll formation, iron deficiency alters photosynthesis and promotes chlorosis, or the yellowing of leaves. Intriguingly, iron deficiency-induced chlorosis can be reverted by the depletion of other micronutrients [i.e., manganese (Mn)] or macronutrients [i.e., sulfur (S) or phosphorus (P)], raising the question of how plants integrate nutrient status to control photosynthesis. Here, we review how improving our understanding of the complex relationship between nutrient homeostasis and photosynthesis has great potential for crop improvement.

Body size varies widely among species, populations and individuals, depending on the environment. Transitioning between proliferation and differentiation is a crucial determinant of final organ size, but how the timing of this transition is established and maintained remains unknown. Using cell proliferation markers and genetic analysis, we show that CHIQUITA1 (CHIQ1) is required to maintain the timing of the transition from proliferation to differentiation in Arabidopsis thaliana. Combining kinematic and cell lineage-tracking studies, we found that the number of actively dividing cells in chiquita1-1 plants decreases prematurely compared with wild-type plants, suggesting CHIQ1 maintains the proliferative capacity in dividing cells and ensures that cells divide a specific number of times. CHIQ1 belongs to a plant-specific gene family of unknown molecular function and genetically interacts with three close members of its family to control the timing of proliferation exit. Our work reveals the interdependency between cellular and organ-level processes underlying final organ size determination.

Plants produce a vast array of metabolites, the biosynthetic routes of which remain largely undetermined. Genome-scale enzyme and pathway annotations and omics technologies have revolutionized research to decrypt plant metabolism and produced a growing list of functionally characterized metabolic genes and pathways. However, what is known is still a tiny fraction of the metabolic capacity harbored by plants. Here, we review plant enzyme and pathway annotation resources and cutting-edge omics approaches to guide discovery and characterization of plant metabolic pathways. We also discuss strategies for improving enzyme function prediction by integrating protein 3D structure information and single cell omics. This review aims to serve as a primer for plant biologists to leverage omics datasets to facilitate understanding and engineering plant metabolism.

Understanding the molecular and physiological mechanisms of how plants respond to drought is paramount to breeding more drought resistant crops. Certain mutations or allelic variations result in plants with altered water-use requirements. To correctly identify genetic differences which confer a drought phenotype, plants with different genotypes must be subjected to equal levels of drought stress. Many reports of advantageous mutations conferring drought resistance do not control for soil water content variations across genotypes and may therefore need to be re-examined. Here, we reassessed the drought phenotype of the Arabidopsis (Arabidopsis thaliana) dwarf mutant, chiquita1-1 (chiq1-1, also called constitutively stressed 1 (cost1)), by growing mutant seedlings together with the wild type to ensure uniform soil water availability across genotypes. Our results demonstrate that the dwarf phenotype conferred by loss of CHIQ1 function results in constitutively lower water usage per plant, but not increased drought resistance. Our study provides an easily reproducible, low-cost method to measure and control for soil water content and to compare drought resistant genotypes more accurately.

The densities of RNA-seq reads (in reads per kilo-bases per million reads, RPKM) were normalized to the library size and the number of sites in 20bp sliding windows along the genome.