A deep proteomics perspective on CRM1-mediated nuclear export and nucleocytoplasmic partitioning.

Dirk Görlich,Kuan Ting Pan,Samir Karaca,Christof Lenz,Koray Kırlı,Henning Urlaub,Matthias Samwer,Heinz Jürgen Dehne

doi:10.7554/elife.11466

Abstract

CRM1 is a highly conserved, RanGTPase-driven exportin that carries proteins and RNPs from the nucleus to the cytoplasm. We now explored the cargo-spectrum of CRM1 in depth and identified surprisingly large numbers, namely >700 export substrates from the yeast S. cerevisiae, ≈1000 from Xenopus oocytes and >1050 from human cells. In addition, we quantified the partitioning of ≈5000 unique proteins between nucleus and cytoplasm of Xenopus oocytes. The data suggest new CRM1 functions in spatial control of vesicle coat-assembly, centrosomes, autophagy, peroxisome biogenesis, cytoskeleton, ribosome maturation, translation, mRNA degradation, and more generally in precluding a potentially detrimental action of cytoplasmic pathways within the nuclear interior. There are also numerous new instances where CRM1 appears to act in regulatory circuits. Altogether, our dataset allows unprecedented insights into the nucleocytoplasmic organisation of eukaryotic cells, into the contributions of an exceedingly promiscuous exportin and it provides a new basis for NES prediction.

Highlights

The nuclear envelope (NE) separates the cell nucleus from the cytoplasm
Nuclear proteins, which are not firmly associated with solid structures like chromatin, will leak out and contaminate the cytoplasmic fraction—just as the nuclear fraction will be contaminated by cytoplasmic components
The nucleocytoplasmic distribution of a given protein or protein complex in these cells should be solely determined by its passive diffusion properties and by their potential to access active nuclear import and/or export pathways

Summary

Introduction

The nuclear envelope (NE) separates the cell nucleus from the cytoplasm. its lipid bilayers are impermeable for macromolecules, embedded nuclear pore complexes (NPCs) allow an exchange of material between these compartments (Feldherr, 1962). On the other end of the distribution, we identified »700 proteins in Xenopus, »900 in human and »600 in yeast, which were strongly selected against in the ‘CRM1+RanGTP’-bound fractions (Supplementary files 2–4, Figure 3).

Results

Conclusion