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TitleMolecular mechanisms governing the formation of distinct Upf1-containing complexes in yeast.
Journal, issue, pagesCell Rep, Vol. 44, Issue 10, Page 116415, Year 2025
Publish dateOct 10, 2025
AuthorsIuliia Iermak / Nicole R Wilson Eisele / Katharina Kurscheidt / Matina-Jasemi Loukeri / Jérôme Basquin / Fabien Bonneau / Lukas M Langer / Achim Keidel / Elena Conti /
PubMed AbstractUpf1 is a master regulator of nonsense-mediated mRNA decay (NMD), an mRNA surveillance and degradation pathway conserved from yeast to human. In Saccharomyces cerevisiae, Upf1 exists in two distinct ...Upf1 is a master regulator of nonsense-mediated mRNA decay (NMD), an mRNA surveillance and degradation pathway conserved from yeast to human. In Saccharomyces cerevisiae, Upf1 exists in two distinct complexes with factors that mediate NMD activation or 5'-3' mRNA degradation. We combined endogenous purifications and biochemical reconstitutions of yeast Upf1 complexes with structural analyses and biochemical assays to elucidate the molecular mechanisms driving the organization of the Upf1-5'-3' and Upf1-2-3 complexes. We show that yeast Upf1 is in a constitutive complex, whereby its CH, RecA, and C-terminal domains interact with the mRNA decapping factor Dcp2, NMD-associated proteins Nmd4 and Ebs1, and the 5'-3' exoribonuclease Xrn1, respectively. Together, the interacting surfaces and closed conformation of Upf1 in the Upf1-5'-3' complex sterically obstruct the binding of Upf2-3. Our work points to a major restructuring upon recruitment of these factors during NMD and provides insights into evolutionary divergence amongst species.
External linksCell Rep / PubMed:41076630
MethodsEM (single particle)
Resolution3.6 Å
Structure data

53032

9qdq

EMDB-53032, PDB-9qdq:
Cryo-EM structure of Upf1-Nmd4-Ebs1 in complex with RNA
Method: EM (single particle) / Resolution: 3.6 Å

Source
  • saccharomyces cerevisiae (brewer's yeast)
KeywordsRNA BINDING PROTEIN / helicase / Nonsense-mediated decay

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