Figure 2.

Model of interactions between the exosome and helicase-containing cofactors: threading in tandem? Nucleus (left): In preparation for degradation by the nuclear exosome, structured substrates are unwound by the DExH-box helicase Mtr4 and threaded into the exosome central channel. Route I (Mtr4 alone, black arrows): If the RNA substrate contains a sufficiently long 3′ overhang of approximately 5–6 nt (I), Mtr4 can bind and act on its own. It is currently unclear whether Mtr4 associates with the exosome prior to RNA binding (Ia) or whether unwinding by Mtr4 requires the presence of the exosome in vivo(Ib). Route II (TRAMP complex, green arrows): Substrates with shorter 3′ extensions (II) are targets for the TRAMP complex and are bound by Air1 or Air2 and oligoadenylated by the poly(A) polymerase Trf4 or Trf5 (IIa) until a minimal binding site for Mtr4 is generated (IIb). Mtr4 is believed to loosely associate with the remaining components of the TRAMP complex on structured substrates. This association becomes more stable when the oligo(A) tails added by Trf4 or Trf5 reach the optimum of 5–6 nt, at which point Mtr4 binding inhibits further oligoadenylation (IIc). Mtr4 functions better on short 3′ extensions, so TRAMP favors the production of substrates that are optimal for unwinding. Consistent with this functional interplay between polymerase and helicase activities, in vivo crosslinking of RNA to Trf4 revealed the predominance of very short oligo(A) tails (A_1–5) on TRAMP substrates. Cytoplasm (right): Analogous to the Trf4/5–Air1/2–Mtr4 polyadenylation (TRAMP) complex in the nucleus, the DExH box helicase Ski2 in the cytoplasmic Ski2/3/8 complex is believed to prepare exosome substrates for threading. An additional factor, Ski7, is related to translation-associated GTPases and may aid in recruitment of Ski2/3/8 and the exosome to ribosomes. DExH, subgroup of helicase protein family; Ski, superkiller; A, adenosine; Rrp6*, exosome binding fragment of Rrp6.