The authors created a high‑throughput yeast two‑hybrid platform using Arabidopsis F‑box and U‑box E3 decoys to map E3‑substrate interactions, screening 283 E3 variants against 21 core circadian clock regulators and identifying 77 candidate pairs. They validated that PUB18 interacts with LHY and JMJD5, promotes their ubiquitination in planta, and that PUB18 and its homolog PUB19 redundantly regulate the circadian clock, demonstrating the utility of the decoy system for dissecting ubiquitination networks.

The study shows that the membrane lipids PI4P, PI(4,5)P2, and phosphatidylserine have distinct spatial and temporal dynamics during lateral root primordium formation in Arabidopsis thaliana, with PI4P acting as a stable basal lipid, PI(4,5)P2 serving as a negative regulator of initiation, and phosphatidylserine increasing after founder cell activation. Using live-cell biosensors, genetic mutants, and an inducible PI(4,5)P2 depletion system, the authors demonstrate that reducing PI(4,5)P2 enhances lateral root initiation and development.

The study reveals that early PAMP-triggered immune responses, such as flg22‑induced FRK1 transcription and ROS production, are heightened at subjective dusk compared to dawn in Arabidopsis. Overexpression of the clock gene TOC1 dampens these defenses and increases susceptibility to Pseudomonas syringae, while flg22 and elf18 treatments reset the rhythmic expression of core clock genes CCA1 and TOC1.

The study engineers Type‑B response regulators to alter their transcriptional activity and cytokinin sensitivity, enabling precise modulation of cytokinin‑dependent traits. Using tissue‑specific promoters, the synthetic transcription factors were deployed in Arabidopsis thaliana to reliably increase or decrease lateral root numbers, demonstrating a modular platform for controlling developmental phenotypes.

The study presents the first single‑nucleus transcriptome atlas for the CAM plant Mesembryanthemum crystallinum, revealing cell‑type specific transcriptional changes during the C3‑to‑CAM transition. Integrating snRNA‑seq with a 24‑hour bulk RNA‑seq time course identified PPCK1 within a circadian‑enriched co‑expression network, and functional assays showed that the ice‑plant HY5 directly activates PPCK1, a regulatory relationship absent in Arabidopsis thaliana. These findings highlight a rewiring of transcriptional regulation underlying CAM evolution and provide a target for engineering drought‑resilient crops.

The study characterizes the tomato class B heat shock factor SlHSFB3a, revealing its age‑dependent expression in roots and its role in enhancing lateral root density by modulating auxin homeostasis. Overexpression of SlHSFB3a increases lateral root emergence, while CRISPR‑mediated knockouts produce the opposite phenotype, indicating that SlHSFB3a regulates auxin signaling through repression of auxin repressors and activation of the ARF7/LOB20 pathway.

The study demonstrates that phosphorylation of the core circadian repressor TOC1, especially at serine 175, is essential for its interaction with FHY3 and PIF5 at the CCA1 promoter, thereby modulating CCA1 repression. While TOC1 phosphorylation is required for CCA1 regulation, LHY expression depends on TOC1 but not on its phosphostate, indicating distinct repression mechanisms. Genome-wide analyses reveal that TOC1’s phosphostate enhances chromatin association and robust rhythmic transcription.

The study demonstrates that dihydroxy B‑ring flavonoids modulate the amplitude of the core circadian clock gene reporter TOC1:LUC in Arabidopsis by affecting cellular H2O2 levels, rather than auxin transport. Reducing reactive oxygen species restored normal TOC1:LUC amplitude in flavonoid‑deficient seedlings, and altered chloroplast Ca2+ levels suggest a retrograde signaling component.