The Exosome Cofactor Rrp47 Is Critical for the Stability and Normal Expression of Its Associated Exoribonuclease Rrp6 in Saccharomyces cerevisiae

Abstract

Rrp6 is a conserved catalytic subunit of the eukaryotic nuclear exosome ribonuclease complex that functions in the productive 3’ end maturation of stable RNAs, the degradation of transiently expressed noncoding transcripts and in discard pathways that eradicate the cell of incorrectly processed or assembled RNAs. The function of Rrp6 in these pathways is at least partially dependent upon its interaction with a small nuclear protein called Rrp47/Lrp1, but the underlying mechanism(s) by which Rrp47 functions in concert with Rrp6 are not established. Previous work on yeast grown in rich medium has suggested that Rrp6 expression is not markedly reduced in strains lacking Rrp47. Here we show that Rrp6 expression in rrp47∆ mutants is substantially reduced during growth in minimal medium through effects on both transcript levels and protein stability. Exogenous expression of Rrp6 enables normal levels to be attained in rrp47∆ mutants. Strikingly, exogenous expression of Rrp6 suppresses many, but not all, of the RNA processing and maturation defects observed in an rrp47∆ mutant and complements the synthetic lethality of rrp47∆ mpp6∆ and rrp47∆ rex1∆ double mutants. Increased Rrp6 expression in the resultant rrp47∆ rex1∆ double mutant suppresses the defect in the 3’ maturation of box C/D snoRNAs. In contrast, increased Rrp6 expression in the rrp47∆ mpp6∆ double mutant diminishes the block in the turnover of CUTs and in the degradation of the substrates of RNA discard pathways. These results demonstrate that a principal function of Rrp47 is to facilitate appropriate expression levels of Rrp6 and support the conclusion that the Rrp6/Rrp47 complex and Rex1 provide redundant exonuclease activities for the 3’ end maturation of box C/D snoRNAs.

Perturbation of mRNP biogenesis reveals a dynamic landscape of the Rrp6-dependent surveillance machinery trafficking along the yeast genome

“…By monitoring the rescue of the PMA1 mRNA level in different deletion strains, we showed that the targeting and degradation of Rho-induced aberrant mRNPs by Rrp6 is stimulated by the cofactors Rrp47 and Mpp6 as well as the TRAMP complex [13]. An interesting finding made in those studies, which was also reported by others [14][15][16], is that Rrp47 plays an important role in a mutual protein stabilization with Rrp6, highlighting a close physical association between the two protein partners [16]. In effect, removal of one partner by gene deletion induces a depletion of the other partner by more than 90% [13].…”

Stress-induced nuclear depletion of Entamoeba histolytica 3′-5′ exoribonuclease EhRrp6 and its role in growth and erythrophagocytosis

“…Although CSL4 is essential in yeast, mutant strains with truncated versions that lack NTD or S1 domain are viable, and the zinc-ribbon domain is not essential in vivo. In addition it has been shown that Csl4 is not stably associated with exosomes in vitro (61). Absence of csl4 has also been reported in another protozoan parasite, Giardia lamblia (37), and may be a more common feature in early eukaryotic evolution.…”

The RNA Exosome Channeling and Direct Access Conformations Have Distinct In Vivo Functions

“…This predicts that the rrp44-da mutation may show genetic interactions with mutations of nuclear RNA exosome cofactors, such as Rrp6. Rrp6 is an additional exonuclease that associates with the RNA exosome in the nucleus, but also has non-catalytic roles including mediating interactions with additional cofactors such as Rrp47 and Mtr4 (Butler and Mitchell, 2011; Feigenbutz et al, 2013; Schuch et al, 2014). As expected, the rrp44-da mutation shows a synthetic growth defect with rrp6Δ (Figure 3B) confirming that the Rrp44 da conformation is important for the nuclear functions of the RNA exosome.…”