A transposon-derived transcription factor senses ionic stress through phase separation to govern plant autophagy.

Abstract

Salt stress severely impairs plant growth through two distinct cellular insults: osmotic stress caused by water limitation and ionic toxicity resulting from excessive Na+ accumulation. Although plant osmosensors have been identified, the mechanisms underlying ionic stress perception remain elusive. Salt stress also activates autophagy, a conserved degradation pathway that removes damaged organelles and protein aggregates to promote stress tolerance. In animals, master regulators such as transcription factor EB (TFEB) coordinate this response by activating autophagy genes across the pathway, but no analogous regulator has been identified in plants. Here, we show that MUSTANG4 (MUG4), a transcription factor derived from Mutator-like element (MULE) transposons, functions as an ionic stress sensor and the primary transcriptional driver of salt-induced autophagy in Arabidopsis. MUG4 responds to elevated monovalent cation concentrations, but not chloride anions or osmotic stress, thereby distinguishing ionic from osmotic stress. Ionic stress compacts the intrinsically disordered region (IDR) of MUG4 and drives liquid-liquid phase separation of the full-length protein, as demonstrated by Förster resonance energy transfer-fluorescence lifetime imaging, in vitro assays, and coarse-grained molecular dynamics simulations. Genome-wide in vivo CUT&Tag sequencing and RNA sequencing reveal that MUG4 directly and coordinately activates autophagy genes spanning multiple functional stages of the pathway. IDR deletion abolishes phase separation, reduces autophagy gene activation and autophagic flux, and prevents the truncated protein from rescuing the salt-sensitive phenotype of mug4 mutants. These findings identify a dedicated plant ionic stress sensor and establish a mechanistic link between exapted transposable elements, phase separation, and transcriptional stress responses, thereby integrating ionic stress perception with autophagy activation.