The exoribonuclease Dis3L2 defines a novel eukaryotic RNA degradation pathway

Abstract

The final step of cytoplasmic mRNA degradation proceeds in either a 5 0 -3 0 direction catalysed by Xrn1 or in a 3 0 -5 0 direction catalysed by the exosome. Dis3/Rrp44, an RNase II family protein, is the catalytic subunit of the exosome. In humans, there are three paralogues of this enzyme: DIS3, DIS3L, and DIS3L2. In this work, we identified a novel Schizosaccharomyces pombe exonuclease belonging to the conserved family of human DIS3L2 and plant SOV. Dis3L2 does not interact with the exosome components and localizes in the cytoplasm and in cytoplasmic foci, which are docked to P-bodies. Deletion of dis3l2 þ is synthetically lethal with xrn1D, while deletion of dis3l2 þ in an lsm1D background results in the accumulation of transcripts and slower mRNA degradation rates. Accumulated transcripts show enhanced uridylation and in vitro Dis3L2 displays a preference for uridylated substrates. Altogether, our results suggest that in S. pombe, and possibly in most other eukaryotes, Dis3L2 is an important factor in mRNA degradation. Therefore, this novel 3 0 -5 0 RNA decay pathway represents an alternative to degradation by Xrn1 and the exosome.

mRNA stability in the nucleus

“…Exosome is a conserved ~400-kD hetero-multimeric protein complex in eukaryotes, containing nine core components (named as Exo9) and acting as 3'-5' exoribonuclease and endoribonuclease in association with some cofactors (Mitchell et al, 1997;Hilleren et al, 2001;Houseley et al, 2006;Vanacova and Stefl, 2007). In eukaryotes, there are two general forms of exosomes: one is the cytoplasmic exosome that contains the nine-subunit core (Exo9) plus Rrp44p (named as Exo10), responsible for 3'-5' exoribonuclease and endoribonuclease activities; the other is the nuclear exosome that consists of Exo9 with Rrp44p and Rrp6p (named as Exo11) (Chen et al, 2001;Liu et al, 2006;Dziembowski et al, 2007;Tomecki et al, 2010;Malecki et al, 2013). Actually, in human cells, there are three Rrp44 homologs: DIS3 (named from yeast 'disjunction abnormal') that only shows exoribonuclease activity and predominantly locates in the nucleus; DIS3L that shows exo-and endoribonuclease activities in the cytoplasm-like yeast Rrp44p; and, DIS3L2 that does not interact with Exo9 but is involved in mRNA degradation in the cytoplasm (Tomecki et al, 2010;Malecki et al, 2013).…”

Functional characterization of a chr13q22.1 pancreatic cancer risk locus reveals long-range interaction and allele-specific effects onDIS3expression

“…Although these studies were not performed in human cells, the high conservation of DIS3 and of the exosome complex as a whole suggests that many of its broader functions are likely conserved (25,32,33). However, a key difference between yeast and humans in this regard is the presence of two DIS3 paralogs in humans, DIS3L and DIS3L2 (25,33,34).…”

“…However, a key difference between yeast and humans in this regard is the presence of two DIS3 paralogs in humans, DIS3L and DIS3L2 (25,33,34). Yeast DIS3 is localized to both the nucleus and cytoplasm.…”

The roles of the exoribonucleases DIS3L2 and XRN1 in human disease

“…DIS3L2 is a 3'-5' exoribonuclease which is conserved from bacteria to humans. It acts independently of the 3'-5' exoribonuclease-exosome complex and degrades non-coding RNAs as well as mRNAs [13,14]. In humans and the yeast S. pombe, this is often achieved by addition of a polyuridine (polyU) tract to the 3' end of the transcript which provides an ideal landing pad for DIS3L2 to initiate/reinitiate 3'-5' decay [14][15][16].…”

“…It acts independently of the 3'-5' exoribonuclease-exosome complex and degrades non-coding RNAs as well as mRNAs [13,14]. In humans and the yeast S. pombe, this is often achieved by addition of a polyuridine (polyU) tract to the 3' end of the transcript which provides an ideal landing pad for DIS3L2 to initiate/reinitiate 3'-5' decay [14][15][16]. As well as mRNAs, miRNAs such as pre-let-7 have been shown to be poly-uridylated and then degraded by DIS3L2 in human cells and mouse embryonic stem cells [17,18].…”