Context-Dependent Dual Role of SKI8 Homologs in mRNA Synthesis and Turnover

Abstract

Eukaryotic mRNA transcription and turnover is controlled by an enzymatic machinery that includes RNA polymerase II and the 3′ to 5′ exosome. The activity of these protein complexes is modulated by additional factors, such as the nuclear RNA polymerase II-associated factor 1 (Paf1c) and the cytoplasmic Superkiller (SKI) complex, respectively. Their components are conserved across uni- as well as multi-cellular organisms, including yeast, Arabidopsis, and humans. Among them, SKI8 displays multiple facets on top of its cytoplasmic role in the SKI complex. For instance, nuclear yeast ScSKI8 has an additional function in meiotic recombination, whereas nuclear human hSKI8 (unlike ScSKI8) associates with Paf1c. The Arabidopsis SKI8 homolog VERNALIZATION INDEPENDENT 3 (VIP3) has been found in Paf1c as well; however, whether it also has a role in the SKI complex remains obscure so far. We found that transgenic VIP3-GFP, which complements a novel vip3 mutant allele, localizes to both nucleus and cytoplasm. Consistently, biochemical analyses suggest that VIP3–GFP associates with the SKI complex. A role of VIP3 in the turnover of nuclear encoded mRNAs is supported by random-primed RNA sequencing of wild-type and vip3 seedlings, which indicates mRNA stabilization in vip3. Another SKI subunit homolog mutant, ski2, displays a dwarf phenotype similar to vip3. However, unlike vip3, it displays neither early flowering nor flower development phenotypes, suggesting that the latter reflect VIP3's role in Paf1c. Surprisingly then, transgenic ScSKI8 rescued all aspects of the vip3 phenotype, suggesting that the dual role of SKI8 depends on species-specific cellular context. The production and turnover of messenger RNAs (mRNAs) are conserved processes in eukaryotes, from single-cell organisms to plants and mammals. To some degree, this is also true for modulators of these processes, such as the Paf1 and SKI complexes. One particular protein, SKI8, has been described to have a role in the SKI complex, which influences mRNA stability, both in yeast and in mammals. Moreover, in yeast SKI8 has an additional role in meiotic recombination, whereas in humans it influences mRNA production through association with the Paf1 complex. This functional divergence is commonly thought to arise from differences in protein sequence between the yeast and mammalian SKI8 homologs. Here we show that the conserved SKI8 homolog of the model plant Arabidopsis acts in the SKI complex as well as the Paf1 complex, similar to human. However, using an Arabidopsis ski8 mutant as a tool, we show that yeast SKI8 can fulfill all roles of Arabidopsis SKI8 if introduced into Arabidopsis cells. Thus, it appears that the functional divergence of SKI8 homologs might a priori be related to species-specific cellular context rather than divergence in protein sequence.