CALMODULIN LIKE 38 is required for autophagy of hypoxia-induced cytoplasmic RNA granules in Arabidopsis thaliana

In response to the energy crisis resulting from submergence stress and hypoxia, the model plant Arabidopsis thaliana limits non-essential mRNA translation, and accumulates cytosolic stress granules. Stress granules are phase-separated mRNA-protein particles that partition transcripts for various fates: storage, degradation, or return to translation after stress alleviation. Another response by the plant cell to low oxygen stress is the induction of the turnover pathway autophagy. Stress granule regulation by autophagy occurs by a ‘granulophagy’ pathway in yeast and mammalian systems through which parts or whole stress granules are degraded. Whether this occurs in plants has not been investigated.

A connection between hypoxia-induced stress granules and autophagy comes from the A. thaliana hypoxia-induced calcium-sensor protein CALMODULIN LIKE 38 (CML38), which localizes to stress granules. The CML38 homolog in tobacco, Regulator of gene silencing calmodulin, interacts with the cytoplasmic granule protein SUPPRESSOR OF GENE SILENCING 3 (SGS3) and targets it for degradation via autophagy. Based on this, an investigation into hypoxia-induced stress granule regulation by CML38 was performed.

The data presented here show that stress granules are dynamically regulated during hypoxia stress and aerobic recovery via two phases of autophagy that require CML38 and the AAA ATPase CELL DIVISION CYCLE 48 (CDC48). CML38 is essential for selective autophagy of stress granules during sustained hypoxia, and cml38 mutants show disorganized stress granule morphology during extended hypoxia, suggesting a role in stress granule maintenance and autophagy. Upon the return of aerobic conditions, intracellular calcium and CML38 are necessary for stress granule disassembly and turnover, and for the aerobic burst of autophagy. cml38 mutants lose these responses and have sustained autophagosome accumulation during reoxygenation recovery.

Further, it is shown here that SGS3 is a CML38-binding protein, and that SGS3 and CML38 co-localize within hypoxia-induced stress granule-like structures. Hypoxia-induced SGS3 granules are degraded by autophagy, which requires both CML38 and CDC48A. CML38 was also shown to interact with CDC48A, and CML38 recruits CDC48A to CML38 granules in planta. Together, this work demonstrates SGS3 and stress granules are subject to degradation during hypoxia by CML38 through a CDC48-dependent granulophagy mechanism.

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