Biochemical and structural investigation of UPF1 function in eukaryotic mRNA turnover pathways

• Applicant: Professorin Sutapa Chakrabarti, Ph.D.
• Subject Area: General Genetics and Functional Genome Biology ; Biochemistry ; Structural Biology
• Term: from 2015 to 2019
• Project identifier: Deutsche Forschungsgemeinschaft (DFG) - Project number 269535551

This research proposal aims to dissect the role of the ATP-dependent RNA helicase UPF1 in cellular mRNA turnover pathways using a biochemical and structural (X-ray crystallography) approach. The degradation of mRNA is an important step in post-transcriptional gene regulation as it serves to regulate not only the level, but also the quality, of gene expression. As such, pathways of mRNA decay are implicated in several inflammatory and autoimmune disorders, as well as in genetic disorders that arise from aberrations in mRNA transcripts. Although there exist distinct pathways for the regulation mRNA levels (mRNA turnover) and mRNA quality control (mRNA surveillance), certain protein factors, such as UPF1, have been found to be involved in both kinds of degradation pathways. UPF1 was originally identified as a key component of the nonsense mediated mRNA decay (NMD) pathway, which is a surveillance pathway that degrades mRNA transcripts containing a premature stop codon. Subsequent studies showed that UPF1 can also act in conjunction with other RNA-binding proteins to regulate levels of specific target mRNAs. Although the mechanism and regulation of UPF1 in NMD is very well understood, little is known about its molecular mechanisms in mRNA turnover pathways. To this end, I will focus on two pathways of mRNA turnover that are mediated by UPF1: histone mRNA degradation and Staufen-mediated mRNA decay (SMD). Degradation of histone mRNA and SMD are mediated by the RNA binding proteins SLBP and Staufen respectively. These partner proteins recruit UPF1 in a translation termination-dependent manner to the 3'-UTR of the target mRNA. Localization of UPF1 to the 3'-UTR of the mRNA subsequently triggers degradation. Understanding how UPF1 is recruited by these RNA-binding proteins and dissecting its function in these pathways will elucidate its role in cellular mRNA turnover. This will enable us to generate a comprehensive model for UPF1 function (both in mRNA surveillance and mRNA turnover) and provide insight into the cross-talk between different mRNA degradation pathways in the eukaryotic cell. The proposed research will also be a distinct step towards viewing mRNA decay as a global phenomenon, rather than as individual linear pathways, and will enhance our knowledge of the regulation of disease-causing genes and of post-transcriptional gene regulation in general.

• DFG Programme: Research Grants