PPR polyadenylation factor defines mitochondrial mRNA identity and stability in trypanosomes. (7th July 2017)

• Record Type: Journal Article
• Authors: Zhang, Liye; Sement, Francois M; Suematsu, Takuma; Yu, Tian; Monti, Stefano; Huang, Lan; Aphasizhev, Ruslan; Aphasizheva, Inna
• Is Part Of: EMBO journal. Volume 36:Number 16(2017)
• Page Start: 2435
• Page End: 2454
• Publication Date: 2017-07-07
• Subjects: pentatricopeptide repeat -- polyadenylation -- RNA editing -- RNA stability -- Trypanosoma; Molecular biology -- Periodicals; 572.805
• DOI: 10.15252/embj.201796808
• Languages: English
• ISSNs: 0261-4189

Abstract

Abstract: In Trypanosoma brucei, most mitochondrial mRNAs undergo internal changes by RNA editing and 3′ end modifications. The temporally separated and functionally distinct modifications are manifested by adenylation prior to editing, and by post‐editing extension of a short A‐tail into a long A/U‐heteropolymer. The A‐tail stabilizes partially and fully edited mRNAs, while the A/U‐tail enables mRNA binding to the ribosome. Here, we identify an essential pentatricopeptide repeat‐containing RNA binding protein, kinetoplast polyadenylation factor 3 (KPAF3), and demonstrate its role in protecting pre‐mRNA against degradation by the processome. We show that KPAF3 recruits KPAP1 poly(A) polymerase to the 3′ terminus, thus leading to pre‐mRNA stabilization, or decay depending on the occurrence and extent of editing. In vitro, KPAF3 stimulates KPAP1 activity and inhibits mRNA uridylation by RET1 TUTase. Our findings indicate that KPAF3 selectively directs pre‐mRNA toward adenylation rather than uridylation, which is a default post‐trimming modification characteristic of ribosomal and guide RNAs. As a quality control mechanism, KPAF3 binding ensures that mRNAs entering the editing pathway are adenylated and, therefore, competent for post‐editing A/U‐tailing and translational activation. Synopsis: The length and composition of poly(A) tails regulates mRNA fate. This study identifies PPR‐domain protein KPAF3 in the mitochondrion of Trypanosoma brucei, and shows it to facilitate mRNA editing by controlling the 3′ modification state of specific RNAs. 3′–5′ trimming by the mitochondrial processome (MPsome) is the major processing pathway for primary mitochondrial transcripts. Sequence‐specific KPAF3 binding distinguishes pre‐mRNAs from rRNAs. KPAF3 protects mRNA against degradation by the MPsome. KPAF3 stimulates mRNA adenylation by KPAP1 and inhibits uridylation by RET1. Differential KPAF3 binding to pre‐edited mRNAs ensures that only adenylated mRNAs proceed to U‐insertion/deletion editing. Abstract : By controlling a switch between adenylation and uridylation of mitochondrial mRNAs, RNA‐binding protein KPAF3 illustrates how the nature of mRNA 3′ ends can serve as a checkpoint for RNA editing.