Up-frameshift protein interactions in translation termination and nonsense-mediated mRNA decay

In eukaryotes, gene expression is highly regulated involving multistep pathways in which mRNA plays a crucial role. Cells have evolved surveillance mechanisms able to detect and degrade defective transcripts.

Nonsense-mediated mRNA decay (NMD) is a mRNA surveillance mechanism which detects faulty mRNAs with premature termination codons (PTCs) and targets these transcripts to decay.

By modulating the expression of physiological mRNAs, NMD acts as a post-transcriptional regulator controlling important cellular processes in development, stress response, immunity and neuronal differentiation.

NMD is of medical importance because mutations or copy number variations of the NMD factors are implicated in human neurological disorders, intellectual disability, schizophrenia, autism, immune diseases and cancer.

The mammalian NMD machinery comprises the proteins UPF1, UPF2, and UPF3B, eukaryotic release factors (eRF1 and eRF3a), SMG1 kinase and SMG5-9.

Recently UPF3B was found to have a role in translation termination at a premature stop codon, interacting directly with the ribosome, release factors and UPF1, requiring modification of prevalent NMD models.

To understand the molecular mechanisms of UPF3B and its role in NMD, this proposal aims to determine the molecular architecture of UPF3B in complex with UPF1, ribosome and mRNA. Furthermore, I will explore the role of the helicase and ubiquitin ligase activities of UPF1 in NMD and protein decay.

I will use biochemistry, biophysics, X-ray crystallography and cryo-electron microscopy to identify the UPF3B domains involved in the recognition of NMD substrates and to investigate how UPF3B binding to the UPF1-RNA complex helps trigger mRNA decay.

Such information will shed light on how translation termination and assembly of the NMD machinery are coordinated and therefore will be of key importance for the future development of therapeutic approaches for the future development of therapeutic approaches for NMD- related diseases.