. The hexameric PH-ring and cap constitute the core of all eukaryotic exosomes, representing the degradation chamber and the substrate recognition region, respectively. The barrel-like structure of the exosome evolved to restrict substrate access and prevent indiscriminate degradation. The chamber contains two openings: a PH pore in the hexameric PH-ring (close to the active site) and the smaller S1 pore composed of the S1 domains in the cap.
The cap regulates and restricts entry to the degradation chamber, interacting with the RNA substrate and feeding it through the narrow S1 pore into the degradation chamber. The cap contains S1, KH and zinc-ribbon domains, which are organised to form an inner zone of S1 domains, and a peripheral zone of KH and zinc-ribbon domains. The inner S1 zone is responsible for the regulation of RNA entry through the S1 pore to the degradation chamber. The function of the peripheral zone is less clear, but it might be involved in substrate specificity and/or the binding of species-specific cofactors (KH and zinc-ribbon domains are involved in protein-protein and protein-nucleic acid interactions).
Only one, fully unfolded RNA with no secondary structure will fit through the S1 pore. However, RNA substrates are rarely unstructured, therefore, before they can enter the exosome they must first be unfolded and any bound proteins must be removed. In yeast, this RNA processing is accomplished by SKI and TRAMP complexes, which act as activators to provide the exosome with unstructured RNA substrates.
The SKI (superkiller) complex is a central component of the cytoplasmic 3’-5’ degradation pathway, which is involved in quality control of mRNAs. The SKI complex contains Ski2, a helicases enzyme required for the unfolding of mRNA substrates.
The TRAMP complex is involved with nuclear exosomes. It can polyadenylate nuclear RNA targets such as rRNA and snoRNA, tagging them for exosome degradation by making them suitable for the initial threading into the degradation chamber. The TRAMP complex contains Mtr4, a helicase enzyme required for unfolding of RNA substrates.
The size of the RNA substrate is also important, as it needs to be at least ten nucleotides long to form a stable association with the active Rrp41/rRp45 dimer of the hexameric PH-ring.
Sometimes, only the partial degradation of an RNA substrate is required, such as during the processing of rRNAs. The presence of stable secondary structures in the RNA, or the attachment of proteins, can be used to halt the degradation process at a specific point. Structural features vary widely among different RNAs, and these features may influence the way a particular RNA is processed or degraded.
Exosomes process (trim) or degrade RNA using inorganic phosphate as a nucleophile, adding it across the phosphodiester bond between the end two nucleotides in order to release ribonucleoside 5’-diphosphate (rNDP) from the 3’ end of the RNA substrate. The activie site is located at the end of an internal groove that extends from the central channel towards the outside of the ring, the only access to the active site being from the capped S1 pore. The central cavity of the degradation chamber can trap the substrate to prevent its release between consecutive rounds of cleavage.