The pentatricopeptide repeat protein Rmd9 recognizes the dodecameric element in the 3′-UTRs of yeast mitochondrial mRNAs


Hillen HS, Markov DA, Wojtas ID, Hofmann KB, Lidschreiber M, Cowan AT, Jones JL, Temiakov D, Cramer P, Anikin M


Proceedings of the National Academy of Sciences of the United States of America


PNAS, Apr 2021, 118 (15) e2009329118.


Respiration-coupled ATP production yields most of the energy in eukaryotic cells and relies on the function of mitochondrial oxidative phosphorylation complexes. Biogenesis of these complexes involves both nuclear and mitochondrial genes, which must be coordinately expressed to assure stoichiometric assembly. The regulatory system that provides this coordination remains poorly understood. Here, we report on the function of a nuclear gene product Rmd9, a feasible component of such a system from yeast. We show that Rmd9 is the factor that binds to the dodecamer element present in mitochondrial mRNAs and provide structural insights into Rmd9-RNA interaction. Combined with previous genetic analyses, our results indicate that Rmd9 controls yeast mitochondrial gene expression by stabilizing and enabling the processing of the mitochondrial mRNAs.Stabilization of messenger RNA is an important step in posttranscriptional gene regulation. In the nucleus and cytoplasm of eukaryotic cells it is generally achieved by 5′ capping and 3′ polyadenylation, whereas additional mechanisms exist in bacteria and organelles. The mitochondrial mRNAs in the yeast Saccharomyces cerevisiae comprise a dodecamer sequence element that confers RNA stability and 3′-end processing via an unknown mechanism. Here, we isolated the protein that binds the dodecamer and identified it as Rmd9, a factor that is known to stabilize yeast mitochondrial RNA. We show that Rmd9 associates with mRNA around dodecamer elements in vivo and that recombinant Rmd9 specifically binds the element in vitro. The crystal structure of Rmd9 bound to its dodecamer target reveals that Rmd9 belongs to the family of pentatricopeptide (PPR) proteins and uses a previously unobserved mode of specific RNA recognition. Rmd9 protects RNA from degradation by the mitochondrial 3′-exoribonuclease complex mtEXO in vitro, indicating that recognition and binding of the dodecamer element by Rmd9 confers stability to yeast mitochondrial mRNAs.The PAR-CLIP RNA sequencing data have been deposited in the Gene Expression Omnibus (GEO) database (accession no. GSE139514). Atomic coordinates and structure factors of Rmd9-RNA16 and Rmd9-RNA20 complexes have been deposited in the Protein Data Bank, (PDB ID codes 7A9X and 7A9W, respectively).



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