Advanced Photon Source

An Office of Science National User Facility

Unfolding the Mystery of the Nuclear Pore Complex

Share

Unfolding the Mystery of the Nuclear Pore ComplexThe nuclear pore complex (NPC) is a large protein complex within the nuclear envelope—the double membrane that surrounds the nucleus in eukaryotic cells. It plays a central role in the transport of macromolecules across the nuclear envelope, and is therefore indispensable for cell function. Until recently, details about the structure of the NPC have been lacking. With this in mind, researchers performed studies to examine the architecture of the complex in fungi, using synchrotron x-rays from three U.S. Department of Energy light sources, including the Advanced Photon Source (APS) at Argonne. They solved the crystal structure of the coat nucleoporin complex (CNC), which comprises the outer ring of the pore, and the structure of the inner ring complex (IRC) which forms the central transport channel and diffusion barrier of the NPC. The results of these studies have important implications for understanding the architecture of the NPC and the mechanisms involved in its transport function, as well as their application to the development of potential therapies for disorders caused by NPC dysfunction.

Eukaryotic organisms are organisms in which the cells contain a defined nucleus. Surrounding the nucleus is a double-layered membrane known as the nuclear envelope, one of the functions of which is to protect the DNA inside the nucleus. Within the nuclear envelope, NPCs function as gatekeepers to allow the transport of select molecules in both directions between the cytoplasm and nucleus. In this way, NPCs play a key role in cell survival by regulating the flow of genetic information from DNA to RNA to protein.

However, despite more than 65 years of research, the structure of the NPC has remained poorly understood. With this in mind, the researchers in these studies, from the California Institute of Technology, The University of Chicago, and Heidelberg University used x-ray diffraction data collected at the National Institute of General Medical Sciences and National Cancer Institute (GM/CA-XSD) 23-ID-D beamline of the APS, at beamline BL12-2 of the Stanford Synchrotron Radiation Source (SSRL), and at the Advanced Light Source (ALS) beamline 8.2.1 to investigate the architecture of NPC building blocks from fungal organisms. The APS, SSRL, and ALS are Office of Science user facilities.

Initially, the Hoelz group from the California Institute of Technology and Kossiakoff group from The University of Chicago solved the crystal structure of the CNC (Fig. 1). The CNC is one of the main complexes in the NPC. The researchers demonstrated that the isolated CNC consists of a curved Y-shape structure. In addition, they identified how the individual coat nucleoporin proteins interact at the molecular level at the central junction of the three arms of the Y. Multiple CNC copies form the outer rings of the nuclear pore by intertwining together in a layer, which is curved to allow the CNC to fit around the curved nuclear envelope pores. Moreover, the researchers showed that the yeast CNC structure is able to unambiguously fit inside the human NPC cryoelectron tomographic reconstruction, demonstrating its precise organization into two 16-membered CNC rings on the nuclear and cytoplasmic sides of nuclear envelope pores. This illustrates significant similarities between NPCs in the two organisms, suggesting that the structure of the NPC has been highly conserved during evolution, and emphasizes the importance of this structure to cell function.

Subsequently, joined by the Hurt group from Heidelberg University (Germany), they also investigated the IRC that recruits the channel nucleoporin heterotrimer (CNT) — an assembly of 3 specific nucleoporin proteins — which forms the central transport channel and diffusion barrier of the NPC. Previously, scientists had assumed that the CNT was able to alter its three-dimensional shape and that rearrangements lead to a substantial expansion of the NPC’s central transport channel to allow large assemblies to pass through. However, in this study the researchers solved the crystal structure of the intact CNT bound to its NPC recruitment binding partner Nic96 (Fig. 1) and determined it to be a defined state that is recognized by Nic96. Thanks to additional experiments in yeast, they were further able to show that Nic96 is the only CNT recruitment site in the intact NPC. This nucleoporin is essential for CNT recruitment by recognizing its unique 3-dimensional shape. Moreover, the interaction of Nic96 with another protein Nup192 was shown to be critical to correctly position the channel within the inner ring scaffold.

The results of these studies represent a significant advance in the understanding of the structure of the NPC and have the potential to guide future work in the discovery and development of therapeutic agents for disorders—including certain types of cancer and neurodegenerative diseases—that are associated with NPC dysfunction.

— Nicola Parry

See: Tobias Stuwe1, Ana R. Correia1, Daniel H. Lin1, Marcin Paduch2, Vincent T. Lu2, Anthony A. Kossiakoff2, and André Hoelz1*, “Architecture of the nuclear pore complex coat,” Science 347(6226), 1148 (6 March 2015). DOI: 10.1126/science.aaa4136

Author affiliations: 1California Institute of Technology, 2TheUniversity of Chicago

Correspondence: *hoelz@caltech.edu

T.S. was supported by a Postdoctoral Fellowship of the Deutsche Forschungsgemeinschaft. D.H.L. was supported by a NIH Research Service Award (5 T32 GM07616). A.A.K. was supported by NIH awards U01 GM094588 and U54 GM087519 and by Searle Funds at The Chicago Community Trust. A.H. was supported by Caltech startup funds, the Albert Wyrick V Scholar Award of the V Foundation for Cancer Research, the 54th Mallinckrodt Scholar Award of the Edward Mallinckrodt Jr. Foundation, and a Kimmel Scholar Award of the Sidney Kimmel Foundation for Cancer Research. GM/CA-XSD was funded in whole or in part with federal funds from the National Cancer Institute (ACB-12002) and the National Institute of General Medical Sciences (AGM-12006). This research used resources of the Advanced Photon Source, a U.S. Department of Energy Office of Science User Facility operated for the U.S. Department of Energy Office of Science by Argonne National Laboratory under Contract No. DE-AC02-06CH11357.

and

See: Tobias Stuwe1, Christopher J. Bley1, Karsten Thierbach1, Stefan Petrovic1, Sandra Schilbach1, Daniel J. Mayo1, Thibaud Perriches1, Emily J. Rundlet1, Young E. Jeon1, Leslie N. Collins1, Ferdinand M. Huber1, Daniel H. Lin1, Marcin Paduch2, Akiko Koide2, Vincent Lu2, Jessica Fischer3, Ed Hurt3, Shohei Koide2, Anthony A. Kossiakoff2, and André Hoelz1*, “Architecture of the fungal nuclear pore inner ring complex,” Science 350(6256), 56 (2 October 2015). DOI: 10.1126/science.aac9176

Author affiliations: 1California Institute of Technology, 2The University of Chicago, 3Heidelberg University

Correspondence: *hoelz@caltech.edu

T.S. was supported by a Postdoctoral Fellowship of the Deutsche Forschungsgemeinschaft. S.P. and D.H.L are Amgen Graduate Fellows, supported through the Caltech-Amgen Research Collaboration. F.M.H. was supported by a Ph.D. student fellowship of the Boehringer Ingelheim Fonds. S.K. was supported by NIH Awards R01-GM090324 and U54-GM087519 and by the University of Chicago Comprehensive Cancer Center (P30-CA014599). A.A.K. was supported by NIH awards U01-GM094588 and U54-GM087519 and by Searle Funds at The Chicago Community Trust. A.H. was supported by Caltech startup funds, the Albert Wyrick V Scholar Award of the V Foundation for Cancer Research, the 54th Mallinckrodt Scholar Award of the Edward Mallinckrodt Jr. Foundation, a Kimmel Scholar Award of the Sidney Kimmel Foundation for Cancer Research, a Camille-Dreyfus Teacher Scholar Award of The Camille and Henry Dreyfus Foundation, and NIH grant R01-GM111461. GM/CA-XSD was funded in whole or in part with federal funds from the National Cancer Institute (ACB-12002) and the National Institute of General Medical Sciences (AGM-12006). This research used resources of the Advanced Photon Source, a U.S. Department of Energy Office of Science User Facility operated for the U.S. Department of Energy Office of Science by Argonne National Laboratory under Contract No. DE-AC02-06CH11357.

Argonne National Laboratory seeks solutions to pressing national problems in science and technology. The nation’s first national laboratory, Argonne conducts leading-edge basic and applied scientific research in virtually every scientific discipline. Argonne researchers work closely with researchers from hundreds of companies, universities, and federal, state and municipal agencies to help them solve their specific problems, advance America’s scientific leadership and prepare the nation for a better future. With employees from more than 60 nations, Argonne is managed by UChicago Argonne, LLC for the U.S. Department of Energy’s Office of Science.

The U.S. Department of Energy’s Office of Science is the single largest supporter of basic research in the physical sciences in the United States and is working to address some of the most pressing challenges of our time. For more information, visit the Office of Science website.

Published Date: 
03.17.2016