Ice2 promotes ER membrane biogenesis in yeast by inhibiting the conserved lipin phosphatase complex

Abstract Cells dynamically adapt organelle size to current physiological demand. Organelle growth requires membrane biogenesis and therefore needs to be coordinated with lipid metabolism. The endoplasmic reticulum (ER) can undergo massive expansion, but the underlying regulatory mechanisms are largely unclear. Here, we describe a genetic screen for factors involved in ER membrane expansion in budding yeast and identify the ER transmembrane protein Ice2 as a strong hit. We show that Ice2 promotes ER membrane biogenesis by opposing the phosphatidic acid phosphatase Pah1, called lipin in metazoa. Specifically, Ice2 inhibits the conserved Nem1‐Spo7 complex and thus suppresses the dephosphorylation and activation of Pah1. Furthermore, Ice2 cooperates with the transcriptional regulation of lipid synthesis genes and helps to maintain cell homeostasis during ER stress. These findings establish the control of the lipin phosphatase complex as an important mechanism for regulating ER membrane biogenesis.

A C B Figure EV2. Deletion of ICE2 impairs UPR signaling during ER stress.

A
Flow cytometric measurements of GFP levels of WT and Dice2 cells containing the transcriptional UPR reporter (SSY2306, 2312). Cells were treated with 1 lg/ml tunicamycin for the times indicated. Data were normalized to untreated WT cells. Mean + s.e.m., n = 3 biological replicates. Asterisks indicate statistical significance compared with the corresponding value in WT cells, as judged by a two-tailed Student's t-test assuming equal variance. An exception was the test against the normalized value for WT cells, for which a two-tailed Student's t-test with unequal variance was applied. **P < 0.01; n.s., not significant. B, C Flow cytometric measurements of GFP levels of WT and Dice2 cells containing the HAC1 mRNA splicing reporter (SSY2309, 2313). Cells were treated with 8 mM DTT (B) or 1 lg/ml tunicamycin (C) for the times indicated. Data were normalized to untreated WT cells. Mean + s.e.m., n = 3 biological replicates. Asterisks indicate statistical significance compared with the corresponding value in WT cells, as judged by a two-tailed Student's t-test assuming equal variance. Exceptions were the tests against the normalized values for WT cells, for which a two-tailed Student's t-test with unequal variance was applied. *P < 0.05; **P < 0.01; n.s., not significant.
Source data are available online for this figure.  Figure EV3. Absence of lipid droplets has no effect on ER expansion in WT or Δice2 cells.
Source data are available online for this figure.  Figure EV4. Abundance of Ice2, Spo7, and Nem1.
Source data are available online for this figure. Western blot of HA from WT and Δice2 cells in which PAH1 was replaced with PAH1-HA or pah1(7A)-HA as indicated (SSY2841, SSY2842, SSY2970).
Source data are available online for this figure.