New insights into how endoplasmic reticulum and lysosomes coordinate protein production

Janelia researchers have uncovered a novel way that two of the structures inside cells-the endoplasmic reticulum (ER) and lysosomes-coordinate the production of proteins, highlighting how interactions between organelles are important for regulating cellular processes. 

Inside every eukaryotic cell lies a vast and dynamic network known as the ER. Stretching through the cytoplasm, this intricate continuum of tubules, junctions, and cisternal sheets is not a passive scaffold but a hub of biosynthetic activity. The ER's surfaces pulse with ribosomes-molecular structures that translate mRNAs that encode secretory and membrane proteins, which together represent nearly one-third of the human proteome.

Unlike mRNAs in the cell's cytoplasm, these secretome mRNAs must coordinate translation, translocation, and folding in real time. The moment elongation falters or misfolding begins, the cell responds swiftly, activating stress pathways that reshape translation.

This complexity has led scientists to wonder if the ER might be architecturally tuned to enable such precision.

Now, Janelia researchers led by Heejun Choi, a research scientist in the Lippincott-Schwartz Lab, have brought this idea into focus.

By tracing individual secretome mRNAs in living cells using single-molecule imaging, the researchers found that translation was far from random. Instead, it occurred at select ER subdomains. These were marked by the protein Lunapark, which stabilizes ER junctions where tubules meet, and in territories adjoining lysosomes-cellular organelles that store and release amino acids that make up proteins.

The new research found that when Lunapark was depleted, these translation hot spots faded, ribosomes dispersed, and protein synthesis waned. Strikingly, they found that translation was restored by ISRIB, which inhibits stress-induced translational arrest through the eIF2 pathway, hinting that Lunapark's influence operates through a stress-sensitive mechanism.

Even more unexpected was the contribution of lysosomes. During amino acid starvation, translation activity near lysosomes intensified, as though lysosomal signals were locally amplifying protein synthesis. Neutralizing lysosomal acidity abolished this surge, revealing that the organelle has a regulatory influence on nearby ER translation.

Together, these observations reveal a novel, finely tuned partnership between the ER and lysosomes, linking nutrient sensing and stress signaling directly to the sites of protein biogenesis. In this view, Lunapark's shaping of ER junctions and the metabolic signaling of lysosomes interlace to choreograph when and where secretory and membrane proteins are made.