The authors used a bottom‑up thermodynamic modelling framework to investigate how plants decode calcium signals, starting from Ca2+ binding to EF‑hand proteins and extending to higher‑order decoding modules. They identified six universal Ca2+-decoding modules that can explain variations in calcium sensitivity among kinases and provide a theoretical basis for interpreting calcium signal amplitude and frequency in plant cells.

The study examines how ectopic accumulation of methionine in Arabidopsis thaliana leaves, driven by a deregulated AtCGS transgene under a seed‑specific promoter, reshapes metabolism, gene expression, and DNA methylation. High‑methionine lines exhibit increased amino acids and sugars, activation of stress‑hormone pathways, and reduced expression of DNA methyltransferases, while low‑methionine lines show heightened non‑CG methylation without major transcriptional changes. Integrated transcriptomic and methylomic analyses reveal a feedback loop linking sulfur‑carbon metabolism, stress adaptation, and epigenetic regulation.

The study uncovers a hidden, evolutionarily conserved disorder-containing START (dSTART) domain within plant HD-ZIPIII and HD-ZIPIV transcription factors, demonstrating that dSTART is essential for proper subcellular localization, DNA-binding specificity, and developmental function. It also identifies phosphatidylglycerol and phosphatidic acid species as candidate ligands, linking lipid binding to transcription factor regulation.

The study identifies a novel C-terminal FR motif in Lotus japonicus NODULE INCEPTION (NIN) that expands DNA‑binding specificity by stabilizing the RWP‑RK dimer, and shows that loss of this motif impairs nodulation and nitrogen fixation. Comparative analysis reveals that Arabidopsis NLP2 also possesses a NIN‑type FR, and phylogenetic data suggest the motif originated in early gymnosperms, indicating it predates the evolution of root nodule symbiosis.

The study shows that the SnRK1 catalytic subunit KIN10 directs tissue-specific growth‑defense programs in Arabidopsis thaliana by reshaping transcriptomes. kin10 knockout mutants exhibit altered root transcription, reduced root growth, and weakened defense against Pseudomonas syringae, whereas KIN10 overexpression activates shoot defense pathways, increasing ROS and salicylic acid signaling at the cost of growth.