The Nuclear Proteome of a Vertebrate

ABSTRACT: Despite the nucleus’ central role in multi-cellular biology, it is still poorly understood how the cell’s proteome is partitioned between the nucleus and cytoplasm. This is mostly due to the difficulty of separating the nuclear and cytoplasmic contents and the challenge to comprehensively measure relative protein abundance. Here, we quantify the nucleocytoplasmic distribution for more than 9000 proteins of the Xenopus laevis oocyte, with two different methods of quantitative proteomics. We find a trimodal distribution, with most proteins localizing exclusively to either the nucleus or the cytoplasm, and where a third subset is equidistributed. By measuring the physiological protein size in undiluted cell lysate we show that nearly all partitioned proteins behave according to a molecular weight larger than ~100kDa, while physiologically smaller proteins are typically equipartitioned. To investigate the role of nuclear export on segregation of nuclear and cytoplasmic contents, we followed nucleocytoplasmic protein localization upon inhibition of the nuclear export receptor Exportin 1 with Leptomycin B (LMB). After 24h of perturbation only a small subset of proteins relocated significantly towards the nucleus suggesting that protein assembly and passive retention, rather than active nuclear transport , are primarily responsible for the maintenance of nuclear composition. Among the proteins that respond to LMB we find a significant overrepresentation of kinases, suggesting an intriguing explanation for the efficacy of Exportin 1 inhibitors in the treatment of various cancers. Thus, we present the first resource for the quantitative nucleocytoplasmic partitioning of a proteome, measure its dynamics upon perturbation, shed new light on the mechanisms of subcellular protein localization, and suggest novel mechanisms of action for promising cancer therapeutics.

INSTRUMENT(S): Q Exactive

ORGANISM(S): Xenopus Laevis (african Clawed Frog)

TISSUE(S): Oocyte

SUBMITTER: Martin Wuehr  

LAB HEAD: Steven Gygi

PROVIDER: PXD001297 | Pride | 2015-09-17

REPOSITORIES: Pride