Rph1/KDM4 mediates nutrient-limitation signaling that leads to the transcriptional induction of autophagy

Curr Biol. 2015 Mar 2;25(5):546-55. doi: 10.1016/j.cub.2014.12.049. Epub 2015 Feb 5.


Background: Autophagy is a conserved process mediating vacuolar degradation and recycling. Autophagy is highly upregulated upon various stresses and is essential for cell survival in deleterious conditions. Autophagy defects are associated with severe pathologies, whereas unchecked autophagy activity causes cell death. Therefore, to support proper cellular homeostasis, the induction and amplitude of autophagy activity have to be finely regulated. Transcriptional control is a critical, yet largely unexplored, aspect of autophagy regulation. In particular, little is known about the signaling pathways modulating the expression of autophagy-related genes, and only a few transcriptional regulators have been identified as contributing in the control of this process.

Results: We identified Rph1 as a negative regulator of the transcription of several ATG genes and a repressor of autophagy induction. Rph1 is a histone demethylase protein, but it regulates autophagy independently of its demethylase activity. Rim15 mediates the phosphorylation of Rph1 upon nitrogen starvation, which causes an inhibition of its function. Preventing Rph1 phosphorylation or overexpressing the protein causes a severe block in autophagy induction. A similar function of Rph1/KDM4 is seen in mammalian cells, indicating that this process is highly conserved.

Conclusion: Rph1 maintains autophagy at a low level in nutrient-rich conditions; upon nutrient limitation, the inhibition of its activity is a prerequisite to the induction of ATG gene transcription and autophagy.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Autophagy / genetics
  • Autophagy / physiology*
  • Blotting, Western
  • Cell Culture Techniques
  • Cell Survival / physiology
  • Gene Expression Regulation / physiology*
  • HeLa Cells
  • Histone Demethylases / antagonists & inhibitors
  • Histone Demethylases / metabolism*
  • Humans
  • Jumonji Domain-Containing Histone Demethylases / antagonists & inhibitors
  • Jumonji Domain-Containing Histone Demethylases / metabolism*
  • Microscopy, Electron, Transmission
  • Nitrogen / deficiency
  • Phosphorylation
  • Real-Time Polymerase Chain Reaction
  • Repressor Proteins / antagonists & inhibitors
  • Repressor Proteins / metabolism*
  • Saccharomyces cerevisiae
  • Saccharomyces cerevisiae Proteins / antagonists & inhibitors
  • Saccharomyces cerevisiae Proteins / metabolism*
  • Signal Transduction / physiology*


  • RPH1 protein, S cerevisiae
  • Repressor Proteins
  • Saccharomyces cerevisiae Proteins
  • Histone Demethylases
  • Jumonji Domain-Containing Histone Demethylases
  • KDM4A protein, human
  • Nitrogen