Integrated structural analysis of the human nuclear pore complex scaffold

The nuclear pore complex (NPC) is a fundamental component of all eukaryotic cells that facilitates nucleocytoplasmic exchange of macromolecules. It is assembled from multiple copies of about 30 nucleoporins. Due to its size and complex composition, determining the structure of the NPC is an enormous challenge, and the overall architecture of the NPC scaffold remains elusive. In this study, we have used an integrated approach based on electron tomography, single-particle electron microscopy, and crosslinking mass spectrometry to determine the structure of a major scaffold motif of the human NPC, the Nup107 subcomplex, in both isolation and integrated into the NPC. We show that 32 copies of the Nup107 subcomplex assemble into two reticulated rings, one each at the cytoplasmic and nuclear face of the NPC. This arrangement may explain how changes of the diameter are realized that would accommodate transport of huge cargoes.

Molecular architecture of the inner ring scaffold of the human nuclear pore complex

Nuclear pore complexes (NPCs) are 110-megadalton assemblies that mediate nucleocytoplasmic transport. NPCs are built from multiple copies of ~30 different nucleoporins, and understanding how these nucleoporins assemble into the NPC scaffold imposes a formidable challenge. Recently, it has been shown how the Y complex, a prominent NPC module, forms the outer rings of the nuclear pore. However, the organization of the inner ring has remained unknown until now. We used molecular modeling combined with cross-linking mass spectrometry and cryo-electron tomography to obtain a composite structure of the inner ring. This architectural map explains the vast majority of the electron density of the scaffold. We conclude that despite obvious differences in morphology and composition, the higher-order structure of the inner and outer rings is unexpectedly similar.

Cellular apoptosis susceptibility (CAS) is linked to integrin β1 and required for tumor cell migration and invasion in hepatocellular carcinoma (HCC)

Importins and exportins represent an integral part of the nucleocytoplasmic transport machinery with fundamental importance for eukaryotic cell function. A variety of malignancies including hepatocellular carcinoma (HCC) show de-regulation of nuclear transport factors such as overexpression of the exportin Cellular Apoptosis Susceptibility (CAS). The functional implications of CAS in hepatocarcinogenesis remain, however, poorly understood. Here we integrated proteomics, transcriptomics and functional assays with patient data to further characterize the role of CAS in HCC. By analyzing ∼ 1700 proteins using quantitative mass spectrometry in HCC cells we found that CAS depletion by RNAi leads to de-regulation of integrins, particularly down-regulation of integrin β1. Consistent with this finding, CAS knockdown resulted in substantially reduced migration and invasion of HCC cell lines as analyzed by 2D ‘scratch’ and invasion chamber assays, respectively. Supporting the potential in vivo relevance, high expression levels of CAS in HCC tissue samples were associated with macroangioinvasion and poorer patient outcome. Our data suggest a previously unanticipated link between CAS and integrin signaling which correlates with an aggressive HCC phenotype.

Purification of Cdk-CyclinB-Kinase-Targeted Phosphopeptides from Nuclear Envelope

We describe a method for rapid identification of protein kinase substrates within the nuclear envelope. Open mitosis in higher eukaryotes is characterized by nuclear envelope breakdown (NEBD) concerted with disassembly of the nuclear lamina and dissociation of nuclear pore complexes (NPCs) into individual subcomplexes. Evidence indicates that reversible phosphorylation events largely drive this mitotic NEBD. These posttranslational modifications likely disrupt structurally significant interactions among nucleoporins (Nups), lamina and membrane proteins of the nuclear envelope (NE). It is therefore critical to determine when and where these substrates are phosphorylated. One likely regulator is the mitotic kinase: Cdk1-Cyclin B. We employed an "analog-sensitive" Cdk1 to bio-orthogonally and uniquely label its substrates in the NE with a phosphate analog tag. Subsequently, peptides covalently modified with the phosphate analogs are rapidly purified by a tag-specific covalent capture and release methodology. In this manner, we were able to confirm the identity of known Cdk1 targets in the NE and discover additional candidates for regulation by mitotic phosphorylation.

Abstract A46: Cellular apoptosis susceptibility (CAS) regulates integrin-beta1 and is required for tumor cell migration and invasion in hepatocellular carcinoma (HCC)

Nuclear transport is an essential, highly selective process in eukaryotic cells which guarantees the bidirectional communication between the nucleus and the cytoplasm. Emerging evidence suggests that aberrant expression of nuclear transport factors may contribute to cancer formation and progression. We could recently show that the nuclear exporter Cellular apoptosis susceptibility (CAS) is overexpressed in hepatocellular carcinoma (HCC), the functional implications of which remain, however, not completely understood. Here, we integrated proteomics, transcriptomics and functional assays with patient data to further characterize the role of CAS in HCC. We found that CAS depletion in HCC cells led to deregulation of integrins, particularly integrin-beta1, and resulted in reduced cell migration and invasion. Moreover, we determined that high expression levels of CAS in HCC cases were associated with macroangioinvasion and poorer patient outcome. Our data indicate that CAS is linked to integrin signaling and correlates with an aggressive HCC phenotype.

Citation Format: Juliane Winkler, Carsten Sticht, Amanda DiGuilio, Eva Maria Eiteneuer, Kerstin Holzer, Stephanie Rössler, Norbert Gretz, Kai Breuhahn, Peter Schirmacher, Alessandro Ori, Stephan Singer. Cellular apoptosis susceptibility (CAS) regulates integrin-beta1 and is required for tumor cell migration and invasion in hepatocellular carcinoma (HCC). [abstract]. In: Proceedings of the Fourth AACR International Conference on Frontiers in Basic Cancer Research; 2015 Oct 23-26; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2016;76(3 Suppl):Abstract nr A46.

The discovery of a Werner Helicase Interacting Protein (WHIP) association with the nuclear pore complex

The gateway for molecular trafficking between the cytoplasm and the nucleus is the Nuclear Pore Complex (NPC). Through mass spectral analysis of the isolated Nuclear Pore Nup107-160 subcomplex, we discovered an in vivo interaction with Werner's Helicase Interacting Protein 1, (WRNIP1 or WHIP). WHIP was originally identified as a binding partner of Werner protein (WRN), which functions to maintain genome stability and is responsible for the progeria disease, Werner syndrome. We established the reciprocal isolation of Nup107 by alpha-WHIP. WHIP was found in purified Nuclear Envelope (NE) fractions treated with DNase/RNase/Heparin. We demonstrated by immunofluorescence microscopy that WHIP is located at the nuclear rim as well as punctate regions in the nuclear matrix. Ultimately, synchronized cells show a dynamic association between WHIP and the Nup107-160 subcomplex through the cell cycle without an interaction with WRN. We thus identify WHIP as a partner/component of the NE/NPC and set forth to investigate a role for the protein positioned at the NPC.

The prolyl isomerase FKBP11 is a secretory translocon accessory factor

Eukaryotic cells encode thousands of secretory and membrane proteins, many of which are cotranslationally translocated into the endoplasmic reticulum (ER). Nascent polypeptides entering the ER encounter a network of molecular chaperones and enzymes that facilitate their folding. A rate-limiting step for some proteins is the trans-to-cis isomerization of the peptide bond between proline and the residue preceding it. The human ER contains six prolyl isomerases, but the function, organization, and substrate range of these proteins is not clear. Here we show that the metazoan-specific, prolyl isomerase FKBP11 binds to ribosome-translocon complexes (RTCs) in the ER membrane, dependent on its single transmembrane domain and a conserved, positively charged region at its cytosolic C-terminus. High-throughput mRNA sequencing shows selective engagement with ribosomes synthesizing secretory and membrane proteins with long translocated segments, and functional analysis shows reduced stability of two such proteins, EpCAM and PTTG1IP, in cells depleted of FKBP11. We propose that FKBP11 is a translocon accessory factor that acts on a broad range of soluble secretory and transmembrane proteins during their synthesis at the ER.