Nuclear export dynamics of RNA-protein complexes

Abstract

The central dogma of molecular biology - DNA makes RNA makes proteins - is a flow of information that in eukaryotes encounters a physical barrier: the nuclear envelope, which encapsulates, organizes and protects the genome. Nuclear-pore complexes, embedded in the nuclear envelope, regulate the passage of molecules to and from the nucleus, including the poorly understood process of the export of RNAs from the nucleus. Recent imaging approaches focusing on single molecules have provided unexpected insight into this crucial step in the information flow. This review addresses the latest studies of RNA export and presents some models for how this complex process may work.

Figure 1. Nuclear-pore complex basic structure and function

A schematic representation of the NPC. Major structural elements are indicated. The cytoplasmic and nuclear extensions of the vertebrate NPC’s periphery are indicated on the cytoplasmic surface as Nup214 and Nup358, which carry factors that aid the egress of cargo such as ribonucleoproteins (RNPs) from the NPC, and on the nuclear surface as TPR (translocated promoter region), the nuclear-basket filament protein that carries factors aiding late RNP processing steps and the first stages of RNP export. See text for more details.

Figure 2. Modes of transport

Various models for how the FG Nups mediate the selective barrier function of the NPC are shown. The detailed distribution of FG repeat domains is not illustrated here. a, FG Nups polymerize into a gel through which transport receptors pass by binding to the FG Nups and dissolving the crosslinks. b, The FG repeat filaments diffuse around their tether, and other molecules are excluded from this region. Transport factors pass through by binding to the FG Nups^,. The FG Nups might also act as a molecular brush that collapses once transport receptors have bound other molecules. c, FG Nups collapse after binding by transport factors to form a layer along the walls of the channel. This layer is impenetrable to inert molecules but permeable to transport factors. Inert macromolecules are able to pass through the central channel only. d, FG Nups form two categories of disordered filaments: collapsed coils, which are gel-like; and extended coils, which are brush-like. Transport factors can pass through both configurations, but macromolecules are excluded. An argument can also be made (not shown) that the central channel in vivo will always be permeated with transport receptors, loaded or unloaded with cargo, resulting in a highly crowded environment. This could have a profound influence on the physical state of the FG Nups^,.

Figure 3. Transport of cargoes

The challenges faced by the NPC in transporting cargoes of different sizes are shown. Small cargoes are easily accounted for by all existing models (see Fig. 2), but large cargoes raise issues for the functionality of the NPC. a, Small cargoes are usually single proteins. They attach to karyopherins, which carry the cargo through the NPC by interacting with the FG Nups. No large-scale displacement of the FG Nups is necessary, and the cargo–karyopherin complexes can be transported bidirectionally. b, Large cargoes and RNPs are usually multiprotein complexes that contain several transport factors. Large cargoes displace the FG Nups and sterically hinder other transport. c, An mRNP is exported as a ‘string of beads’, in which each ‘bead’ behaves as a large cargo. Multiple accessory factors aid in the processing of the mRNP at both the nuclear basket and the cytoplasmic filaments.

Figure 4. Imaging of NPC transport events one molecule at a time

a, By localizing cargo relative to the NPC, spatially resolved binding sites can be recorded along the transport axis of the NPC. The histogram represents data on β-actin mRNA transport. The zero position (dotted line) is determined by localizing the position that POM121 is fused to a fluorescent marker. The two peaks, one on the nuclear surface and one on the cytoplasmic surface of the NPC, are interpreted as docking and release sites. b, An image series from a single mRNP export event showing β-actin mRNA (green) traversing the NPC (red). After docking in the nucleoplasm (Nux) in frame 1, the mRNA (arrows) is repeatedly observed along the NPC until, in frame 8, it reaches the cytoplasm (Cyto). The positions are super-registered to the NPC signal and contribute to the data in a. c, An artist’s impression of a large cargo (green) docking and transiting through the NPC (red). Up to a certain size limit (see text), large cargoes dock to the NPC, transit through the central channel relatively fast, then linger before release. The docking and release steps allow remodelling and/or reorientation of large cargoes. Artwork by Tremani, TU Delft.