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Nuclear Pore Complex Comes into Focus

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Image: Nuclear pores in the nuclear envelope, by Blausen.com staff (2014). "Medical gallery of Blausen Medical 2014". WikiJournal of Medicine 1 (2). DOI:10.15347/wjm/2014.010. ISSN 2002-4436., CC BY 3.0 , via Wikimedia Commons.

In the classic film Unlocking the Mystery of Life, the viewer goes on a voyage through a nuclear pore complex, the “gatekeeper for traffic in and out of the cell,” into the domain of DNA. The 2002-era animation was effective, but now scientists know much more about those portals. More recently, in 2017, the Walter and Eliza Hall Institute (WEHI) produced sharper animations of the cell nucleus with glimpses of the nuclear pore complexes (watch this one-minute animation to become familiar with the subject matter). 

Now, with super-resolution microscopy, details are becoming so clear, it’s like putting on bionic glasses. Biochemists are now reaching into the sub-nanometer scale — a feat unheard of just a couple of years ago. What are they seeing now that the nuclear pore complex is coming into sharp focus?

A Comprehensive Model

An open-access paper in Cell by Akey et al., “Comprehensive structure and functional adaptations of the yeast nuclear pore complex,” takes readers on a newly upgraded voyage through this multi-faceted authenticating gatekeeper. No fewer than 23 researchers from multiple leading institutions like Boston University, Baylor College of Medicine, UC San Diego, and Rockefeller University participated in the effort to produce a comprehensive model of one of the largest (~100 megadalton) and most complex molecular machines in the living cell.

Nuclear pore complexes (NPCs) mediate the nucleocytoplasmic transport of macromolecules. Here we provide a structure of the isolated yeast NPC in which the inner ring is resolved by cryo-EM at sub-nanometer resolution to show how flexible connectors tie together different structural and functional layers. These connectors may be targets for phosphorylation and regulated disassembly in cells with an open mitosis…. Cryo-electron tomography extended these studies, providing a model of the in situ NPC with a radially expanded inner ring. Our comprehensive model reveals features of the nuclear basket and central transporter, suggests a role for the lumenal Pom152 ring in restricting dilation, and highlights structural plasticity that may be required for transport. [Emphasis added.]

The NPC has 30 protein parts, most of them affectionately called Nups (nucleoporins). They form the shape of a circular basket through which traffic is directed in and out of the cell. This portal plays a vital role, authenticating every macromolecule going in and out of the nucleus and providing chaperone service to guide them to their destinations.      

Nuclear pore complexes (NPCs) are cylindrical assemblies with 8-fold symmetry that form a gateway in the nuclear envelope (NE) for the selective exchange of macromolecules between the cytoplasm and nucleus. These transport machines stabilize a pore in the NE, termed the pore membrane, and are key players in RNA processing and chromatin organization. Given this central role, it is not surprising that NPC defects are linked to many diseases and that nuclear transport is a target for therapeutics.

Success on Every Try

Another wonder about NPCs is how they quickly disassemble and reassemble during each cell division. There are about a thousand NPCs per vertebrate cell nucleus that participate in this operation, something like a scramble and regather formation by a marching band on the field. Think of the potential confusion when all the NPCs are doing it at the same moment. But they seem to succeed every time.

The team looked at NPCs in a “simple” yeast, which is about half the size of vertebrate NPCs. Even this smaller model has 550 protein parts! They took a “divide and conquer” approach to build a comprehensive model. Here are some highlights of the new view:

  • The basket moves! The inner ring can stretch inward and outward.
  • Parts interact with each other in complex ways.
  • The ring structures are anchored in the nuclear envelope.
  • Various Nups surround the central Transport Channel, like guards on duty watching every traveler entering and leaving.
  • A cell can have three or more different isoforms of NPCs on its nuclear membrane, which may have distinct roles.
  • “The NPC is a modular assembly with a ‘Lego’-like ability to have major scaffold elements added, reorganized, and/or removed.”

The diagrams are exquisite. Feast your eyes on these new detailed views. Watch some of the animations that show the structure from various angles as layers of parts are added. Who could not be impressed?

Many Open Questions Remain

The research team was primarily interested in solving the structure of the NPC but left many questions open about the machinery’s operation. Now that scientists can visualize the structure, exciting discoveries are bound to come, showing how the NPC authenticates traffic and transports molecules to their destinations. Hopefully both the structural and functional insights will lead to treatments for those afflicted with NPC defects.

It’s going to be awesome to build animations of the NPC in operation, and to find out how this comparatively large structure can quickly disassemble during cell division, duplicate all its parts, and then reassemble in the two daughter cells.

Intelligence Test

In standardized IQ tests, sometimes there are puzzles that require the student to circle the word in a group that doesn’t belong. Try that with these words: insight, architecture, transport, evolution, structure, function, machine. They are found in this sentence:

In this work, a multi-pronged approach has provided a comprehensive picture of the yeast NPC, generating insights into the architectural principles, evolutionary origins, and structure-function relationships of this transport machine.

Did any particular word stick out? If it was obvious, it’s a good sign of intelligence!