Genetius

The study investigates autophagy’s protective role against cadmium stress in Arabidopsis thaliana by comparing wild-type, atg5 and atg7 autophagy-deficient mutants, and ATG5/ATG7 overexpression lines. Cadmium exposure triggered autophagy, shown by ATG8a-PE accumulation, GFP-ATG8a fluorescence and ATG gene up-regulation, with atg5 mutants displaying heightened Cd sensitivity and disrupted metal ion homeostasis, whereas overexpression had limited impact. Genotype-specific differences between Col-0 and Ws backgrounds were also observed.

The study introduces a native‑condition method combining cell fractionation and immuno‑isolation to purify autophagic compartments from Arabidopsis, followed by proteomic and lipidomic characterisation of the isolated phagophore membranes. Proteomic profiling identified candidate proteins linked to autophagy, membrane remodeling, vesicular trafficking and lipid metabolism, while lipidomics revealed a predominance of glycerophospholipids, especially phosphatidylcholine and phosphatidylglycerol, defining the unique composition of plant phagophores.

The study demonstrates that the chromatin remodeler DDM1 is essential for biomass heterosis in Arabidopsis thaliana hybrids, as loss of DDM1 function leads to reduced rosette growth and extensive genotype‑specific transcriptomic and DNA methylation changes. Whole‑genome bisulfite sequencing revealed widespread hypomethylation in ddm1 mutants, while salicylic acid levels were found unrelated to heterosis, indicating that epigenetic divergence, rather than SA signaling, underpins hybrid vigor.

A genome-wide association study of 166 Iberian Arabidopsis accessions identified loci, including ABA3 and GA2ox2, that modulate the inhibitory effect of the auxin precursor indole-3-acetamide (IAM) on primary root elongation. Integrating sequence analysis, transcriptomics, 3D protein modeling, and mutant physiology revealed that IAM promotes ABA biosynthesis and signaling, uncovering a novel node of hormone crosstalk.

The study identifies GyrB3 as a novel nuclear factor that interacts with histone deacetylases to regulate transposable element silencing in plants, acting as a suppressor of IBM1 deficiency–induced epigenetic defects. Loss of GyrB3 reduces DNA methylation and increases H3 acetylation at TEs, demonstrating the importance of histone deacetylation for genome stability.

The study identifies the Arabidopsis phospholipases LCAT3 and LCAT4 as essential components that hydrolyze membranes of autophagic bodies within the vacuole, a critical step for autophagy completion. Double mutants lacking both enzymes accumulate autophagic bodies and display diminished autophagic activity, while in vivo reconstitution shows LCAT3 initiates membrane hydrolysis, facilitating LCAT4’s function.

The study introduces a CRISPR/Cas9‑based restoration system (CiRBS) that reactivates a disabled luciferase reporter (LUC40Ins26bp) in transgenic Arabidopsis, enabling long‑term single‑cell bioluminescence monitoring. Restoration occurs within 24 h after particle‑bombardment‑mediated CRISPR delivery, with ~7 % of cells regaining luminescence and most restored cells carrying a single correctly edited chromosome, facilitating reliable analysis of cellular gene‑expression heterogeneity.

The study examines how autophagy-related genes AtATG5 and AtATG7 influence Arabidopsis seed germination and ABA responses, revealing that atg5 and atg7 mutants germinate more slowly and display altered lipid droplet and protein storage vacuole organization. Transcriptomic and immunolocalization analyses show delayed ABI5 decay and a direct interaction between ATG8 and the autophagy machinery, implicating autophagy in seed reserve mobilization via transcription factor turnover.

The study combined long‑read whole‑genome assembly, multi‑omics profiling (DNA methylation, mRNA, ribosome‑associated transcripts, tRNA abundance, and protein levels) in two Arabidopsis thaliana accessions to evaluate how genomic information propagates through the Central Dogma. Codon usage in gene sequences emerged as the strongest predictor of both mRNA and protein abundance, while methylation, tRNA levels, and ribosome‑associated transcripts contributed little additional information under stable conditions.

The study reveals that root hair cells rely on elevated autophagy to extend their lifespan, and that loss-of-function mutations in autophagy genes ATG2, ATG5, or ATG7 trigger premature, cell-autonomous death mediated by NAC transcription factors ANAC046 and ANAC087. This uncovers an antagonistic interaction between autophagy and a developmentally programmed cell death pathway that controls root hair longevity, highlighting a potential target for improving nutrient and water uptake in crops.