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The Functional Relationship between the Nonsense-Mediated mRNA Decay Pathway and the Prematurely Terminating Ribosome

Serdar, Lucas D.
http://rave.ohiolink.edu/etdc/view?acc_num=case1554304118763865

Abstract Details

2019, Doctor of Philosophy, Case Western Reserve University, Biochemistry.
The fidelity of gene expression depends on quality control pathways that act to detect and resolve errors in the transmission of genetic information. Premature termination of translation at nonsense codons within mRNA open reading frames leads to the production of C-terminally truncated polypeptides with potentially deleterious functions in the cell. The nonsense-mediated mRNA decay (NMD) pathway is a conserved quality control pathway in eukaryotes that limits accumulation of these aberrant protein products by recognizing the nonsense-containing mRNA and targeting it to accelerated degradation. Recognition and rapid destabilization of NMD substrates requires a conserved machinery consisting of the proteins UPF1, UPF2, and UPF3. Recent transcriptome-wide studies have shown that the RNA helicase UPF1 associates with both nonsense-containing and normal mRNAs, suggesting that the mechanistic distinction between normal and aberrant mRNAs occurs after UPF1 associates with the transcript. To investigate the requirements for NMD at steps downstream of UPF1 association with mRNA, we applied tethered function analysis in yeast cells and found that destabilization of mRNAs by tethered UPF1 requires ATP hydrolysis by UPF1, and is enhanced by premature termination. Surprisingly, the activity of tethered UPF1 was robust upon inhibition of translation, and in cells lacking UPF2 and UPF3 Next, we provide evidence that ATP hydrolysis by UPF1 is required for efficient translation termination and ribosome release at a premature termination codon. Ribosome stalling at or near premature termination codons in UPF1 ATPase mutants impedes the progress of the exonuclease XRN1, leading to the accumulation of 3’ RNA decay fragments. We show also that the ability of UPF1 to impinge upon premature termination requires NMD co-factors UPF2 and UPF3. Unexpectedly, ribosome stalling in cells expressing ATPase-deficient UPF1 occurs at a position downstream of the premature stop codon. The position of stalling is dependent on the mRNA sequence downstream of the stop codon, and transit of ribosomes to these positions did not require ongoing polypeptide synthesis. Our results reveal that ATP hydrolysis by UPF1 modulates a functional interaction between the NMD machinery and terminating ribosomes necessary for targeting substrates to accelerated degradation.
Kristian Baker (Advisor)
Jo Ann Wise (Committee Chair)
Donny Licatalosi (Committee Member)
Derek Taylor (Committee Member)
147 p.
Molecular Biology
mRNA decay, NMD, UPF1, translation termination

Recommended Citations

Citations

  • Serdar, L. D. (2019). The Functional Relationship between the Nonsense-Mediated mRNA Decay Pathway and the Prematurely Terminating Ribosome [Doctoral dissertation, Case Western Reserve University]. OhioLINK Electronic Theses and Dissertations Center. http://rave.ohiolink.edu/etdc/view?acc_num=case1554304118763865

    APA Style (7th edition)

  • Serdar, Lucas. The Functional Relationship between the Nonsense-Mediated mRNA Decay Pathway and the Prematurely Terminating Ribosome. 2019. Case Western Reserve University, Doctoral dissertation. OhioLINK Electronic Theses and Dissertations Center, http://rave.ohiolink.edu/etdc/view?acc_num=case1554304118763865.

    MLA Style (8th edition)

  • Serdar, Lucas. "The Functional Relationship between the Nonsense-Mediated mRNA Decay Pathway and the Prematurely Terminating Ribosome." Doctoral dissertation, Case Western Reserve University, 2019. http://rave.ohiolink.edu/etdc/view?acc_num=case1554304118763865

    Chicago Manual of Style (17th edition)

case1554304118763865
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© 2019, all rights reserved.
This open access ETD is published by Case Western Reserve University School of Graduate Studies and OhioLINK.