SMG5-SMG7 authorize nonsense-mediated mRNA decay by enabling SMG6 endonucleolytic activity

Abstract

Eukaryotic gene expression is constantly controlled by the translation-coupled nonsense-mediated mRNA decay (NMD) pathway. Aberrant translation termination leads to NMD activation, resulting in phosphorylation of the central NMD factor UPF1 and robust clearance of NMD targets via two seemingly independent and redundant mRNA degradation branches. Here, we uncover that the loss of the first SMG5-SMG7-dependent pathway also inactivates the second SMG6-dependent branch, indicating an unexpected functional connection between the final NMD steps. Transcriptome-wide analyses of SMG5-SMG7-depleted cells confirm exhaustive NMD inhibition resulting in massive transcriptomic alterations. Intriguingly, we find that the functionally underestimated SMG5 can substitute the role of SMG7 and individually activate NMD. Furthermore, the presence of either SMG5 or SMG7 is sufficient to support SMG6-mediated endonucleolysis of NMD targets. Our data support an improved model for NMD execution that features two-factor authentication involving UPF1 phosphorylation and SMG5-SMG7 recruitment to access SMG6 activity.

NMD is required for timely cell fate transitions by fine-tuning gene expression and regulating translation

“…The relatively weaker phenotype in Smg7 KOs is consistent with recent reports that SMG5 can compensate for the loss of SMG7 and that the presence of either SMG5 or SMG7 is sufficient to support SMG6-mediated endonucleolytic decay of NMD targets (Boehm et al 2021). Notably, our observations of a weak Smg7 KO phenotype without impact on cell proliferation and cell fitness are distinct from those recently made in HEK293 cells (Boehm et al 2021) but are in accordance with the observation that Smg6 depletion results in stronger NMD defects than Smg7 deficiency (Colombo et al 2017). It remains unclear whether the differences in cell fitness are due to distinct roles of Smg7 between mice and humans or between ESCs, somatic cells, and established immortalized human cell lines.…”

Translational repression of NMD targets by GIGYF2 and EIF4E2

“…Intriguingly, spliceostatin A treatment also led to an increase in the association of SMG1 with GIGYF2, even more so than UPF1 and almost all other RBPs (Fig 6E). This result is consistent with the idea that GIGYF2 is directly associated with mRNAs in the process of being recognized for NMD, since SMG1 is thought to only transiently interact with NMD targets [25,34,107]. Given this result and the epistasis that we observed between SMG1i treatment and GIGYF2•EIF4E2 knockout, we asked whether the UPF1-GIGYF2•EIF4E2 interaction depended on the phosphorylation state of UPF1.…”

Modulation of RNA binding properties of the RNA helicase UPF1 by its activator UPF2

“…Additionally, both phosphorylated and unphosphorylated UPF1 interact with the endonuclease SMG6 and phosphorylated UPF1 also engages the SMG5/SMG7 heterodimer, which in turn bridges the target mRNP to the deadenylation machinery (Okada-Katsuhata, Yamashita et al 2012, Loh, Jonas et al 2013, Chakrabarti, Bonneau et al 2014, Nicholson, Josi et al 2014). The involvement of SMG6 in NMD depends both on UPF1 as well as binding of SMG5/SMG7 to phospho-UPF1, indicating a complex interplay of interactions at work in this pathway (Boehm, Kueckelmann et al 2021). It therefore appears intuitive that many of these interactions must be short-lived in order to facilitate progression of NMD and efficient degradation of the nonsense mRNA.…”