The Lsm1-7 complex marginally affects unstable mRNA degradation in yeast

Like-SM proteins (Lsm) assemble into heptameric complexes that are conserved in eukaryotes. The Lsm2-8 complex is involved in the nuclear maturation of spliceosomal U6 snRNA, whereas the Lsm1-7/Pat1 complex associates with mRNA decapping complexes in the cytoplasm. A proposed role of Lsm1-7 is to recruit the decapping machinery to unstable mRNA that are rapidly deadenylated. However, the impact of deadenylation on RNA stability has been challenged by recent studies in yeast and other organisms. To investigate the dynamics of the Lsm1-7 in recruiting the decapping enzyme Dcp2 we used stable isotope labeling with aminoacids in cell culture (SILAC) combined with affinity purifications and mass spectrometry for Lsm1 and Dcp1. These experiments identified a slow dynamics of protein exchange between Dcp2 or Pby1 when bound by Dcp1 and a similarly slow exchange between the Lsm components of the Lsm1-7 complex, with faster exchange rates for other components of these complexes. To evaluate the potential role of Lsm1 in the degradation of unstable transcripts, we investigated the effects on mRNA of a rapid depletion of Lsm1 in an inducible degron system. Lsm1 depletion led to an increase in the abundance of transcripts that have been previously identified as stablised in the absence of LSM1. However, depletion of Lsm1 also led to a modest increase in the levels of nonsense-mediated mRNA decay (NMD) substrates, similar to the expected results of a minor decapping defect. Altogether, our results suggest that Lsm1-7 is required for the normal function of the decapping complex on specific transcripts, including NMD substrates, although its impact on RNA degradation, in particular for unstable mRNA, is very limited.