Abstract
The RNA exosome is a key 3’−5’ exoribonuclease with an evolutionarily conserved structure and function. Its cytosolic functions require the co-factors SKI7 and the Ski complex. Here we demonstrate by co-purification experiments that the ARM-repeat protein RESURRECTION1 (RST1) and RST1 INTERACTING PROTEIN (RIPR) connect the cytosolic Arabidopsis RNA exosome to the Ski complex. rst1 and ripr mutants accumulate RNA quality control siRNAs (rqc-siRNAs) produced by the post-transcriptional gene silencing (PTGS) machinery when mRNA degradation is compromised. The small RNA populations observed in rst1 and ripr mutants are also detected in mutants lacking the RRP45B/CER7 core exosome subunit. Thus, molecular and genetic evidence supports a physical and functional link between RST1, RIPR and the RNA exosome. Our data reveal the existence of additional cytosolic exosome co-factors besides the known Ski subunits. RST1 is not restricted to plants, as homologues with a similar domain architecture but unknown function exist in animals, including humans.
Highlights
The RNA exosome is a key 3’−5’ exoribonuclease with an evolutionarily conserved structure and function
The wax-deficient phenotype of rrp45b/cer[7] mutants is suppressed by mutations in genes encoding RNA silencing factors, such as RDR1, RDR6, AGO1, SUPPRESSOR OF GENE SILENCING 3 (SGS3) and DCL450,51. This and the identification of small RNAs accumulating in cer[7] mutants revealed that the wax deficiency observed in cer[7] plants is due to post-transcriptional silencing of CER3 mRNAs50,51, encoding a protein that together with the aldehyde decarbonylase CER1 catalyses the synthesis of very long-chain (VLC) alkanes from VLC acyl-CoAs52,53. These results demonstrated that the RNA exosome contributes to the degradation of the CER3 mRNA and that the wax-deficient phenotype of cer[7] mutants is a consequence of the established link between RNA degradation and silencing pathways[50,51,54]
To investigate whether the wax deficiency of rst[1] plants is linked to compromised degradation of the CER3 mRNA as reported in cer[7] mutants[49], we compared the stems of wild-type and mutant plants grown under identical conditions
Summary
The RNA exosome is a key 3’−5’ exoribonuclease with an evolutionarily conserved structure and function. This unique phosphorolytic activity of plant Exo[9] acts in combination with the hydrolytic activities provided by RRP6 and DIS310 Another exception among RNA exosomes is the association of human Exo[9] with functionally distinct DIS3L and DIS3 proteins, only the latter of which is conserved in yeast and plants[6,11]. They include the TRAMP (TRF4AIR1-MTR4 polyadenylation) complexes[20,21,22] in both baker’s yeast and humans, the human PAXT (polyA tail exosome targeting) complex[23], the (nuclear exosome targeting) complexes that differ slightly in humans and plants[24,25] and the MTREC (Mtr4-like 1 (Mtl1)-Red1-core) complex in fission yeast[26,27] These MTR4 containing complexes assist the exosome in nuclear RNA surveillance by targeting various RNA substrates, including precursors of ribosomal and other non-coding RNAs, spurious transcripts generated by pervasive transcription and untimely, superfluous or misprocessed mRNAs21,24,25,27–32.
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