Aerobic reactions are essential to sustain plant growth and development. Impaired oxygen availability due to excessive water availability, e.g., during waterlogging or flooding, reduces plant productivity and survival. Consequently, plants monitor oxygen availability to adjust growth and metabolism accordingly. Despite the identification of central components in hypoxia adaptation in recent years, molecular pathways involved in the very early activation of low-oxygen responses are insufficiently understood and prolonged periods of stress will have detrimental effects on plant yield and survival.

A cell harbors several organelles, including the endoplasmic reticulum (ER), which is a large dynamic tubular structure that surrounds the cellular nucleus and is involved in  protein synthesis and lipid metabolism. The researchers characterized three ER-anchored Arabidopsis ANAC transcription factors, namely ANAC013, ANAC016, and ANAC017, which bind to the promoters of a subset of hypoxia core genes (HCGs) and activate their expression. Upon hypoxia, nuclear ANAC013 associates with the promoters of multiple HCGs.

It was found that a dormant transcription factor (ANAC013) bound to the ER membrane is released upon low-oxygen stress through proteolytic cleavage of its anchoring domain. Subsequently, the activated ANAC013 protein travels to the nucleus to initiate transcriptional reprogramming to induce adaptive responses.

“Not only did we identify the transcription factor responsible for this initial reprogramming, but also the protease, i.e, the enzyme capable of cutting proteins, that releases ANAC013 from the ER membrane”, says the author. The protease belongs to a class of so-called rhomboid proteases that are present in almost all species to regulate cellular processes. However, substrates for these proteases were not reported in plants previously, indicating the novelty of the uncovered mechanism in our work.

In addition, the researchers were able to demonstrate that cleavage of ANAC013 by the rhomboid protease relies on a mitochondrial-derived signal. “We expect that exploring the molecular nature of the upstream signal will be of extreme interest for understanding organellar communication. Moreover, as the newly identified module consisting of the ANAC013 factor and its processing protease is highly conserved in plants, we envisage that the obtained results can be translated to crops to improve their waterlogging tolerance”, says the the senior author.

https://www.pnas.org/doi/10.1073/pnas.2221308120