The Nuclear Proteome of a Vertebrate

The composition of the nucleoplasm determines the behavior of key processes such as transcription, yet there is still no reliable and quantitative resource of nuclear proteins. Furthermore, it is still unclear how the distinct nuclear and cytoplasmic compositions are maintained. To describe the nuclear proteome quantitatively, we isolated the large nuclei of frog oocytes via microdissection and measured the nucleocytoplasmic partitioning of ∼9,000 proteins by mass spectrometry. Most proteins localize entirely to either nucleus or cytoplasm; only ∼17% partition equally. A protein’s native size in a complex, but not polypeptide molecular weight, is predictive of localization: partitioned proteins exhibit native sizes larger than ∼100 kDa, whereas natively smaller proteins are equidistributed. To evaluate the role of nuclear export in maintaining localization, we inhibited Exportin 1. This resulted in the expected re-localization of proteins toward the nucleus, but only 3% of the proteome was affected. Thus, complex assembly and passive retention, rather than continuous active transport, is the dominant mechanism for the maintenance of nuclear and cytoplasmic proteomes. [Display omitted] •Nucleocytoplasmic partitioning was quantified for 9,000 proteins in Xenopus oocytes•Partitioned proteins have a native molecular weight larger than ∼100 kDa•Only a small fraction of proteins respond to Exportin 1 inhibition•Passive retention is the dominant mechanism for the maintenance of the nuclear proteome Wühr et al. quantify the nucleocytoplasmic partitioning for ∼9,000 proteins in the Xenopus oocyte. Most proteins localize almost exclusively to nucleus or cytoplasm. Proteome-wide analysis of native protein size reveals that the distinct composition of nucleus and cytoplasm is primarily maintained by retention of proteins in large complexes.