Abstract
Uridylation is a widespread modification destabilizing eukaryotic mRNAs. Yet, molecular mechanisms underlying TUTase-mediated mRNA degradation remain mostly unresolved. Here, we report that the Arabidopsis TUTase URT1 participates in a molecular network connecting several translational repressors/decapping activators. URT1 directly interacts with DECAPPING 5 (DCP5), the Arabidopsis ortholog of human LSM14 and yeast Scd6, and this interaction connects URT1 to additional decay factors like DDX6/Dhh1-like RNA helicases. Nanopore direct RNA sequencing reveals a global role of URT1 in shaping poly(A) tail length, notably by preventing the accumulation of excessively deadenylated mRNAs. Based on in vitro and in planta data, we propose a model that explains how URT1 could reduce the accumulation of oligo(A)-tailed mRNAs both by favoring their degradation and because 3’ terminal uridines intrinsically hinder deadenylation. Importantly, preventing the accumulation of excessively deadenylated mRNAs avoids the biogenesis of illegitimate siRNAs that silence endogenous mRNAs and perturb Arabidopsis growth and development.
Highlights
Uridylation is a widespread modification destabilizing eukaryotic mRNAs
We show that the Arabidopsis terminal uridylyltransferases (TUTases) URT1 is integrated in an interaction network comprising the deadenylation complex CCR4-NOT and other translation repressors/decapping activators, including DECAPPING 5 (DCP5), the plant ortholog of the translational inhibitor/decapping activator Scd[6] or LSM14A
The 764-long amino acid sequence of the Arabidopsis TUTase URT1 encoded by AT2G45620 can be divided in two regions discriminated by compositional biases and the presence of known domains (Fig. 1a)
Summary
Uridylation is a widespread modification destabilizing eukaryotic mRNAs. Yet, molecular mechanisms underlying TUTase-mediated mRNA degradation remain mostly unresolved. URT1 directly interacts with DECAPPING 5 (DCP5), the Arabidopsis ortholog of human LSM14 and yeast Scd[6], and this interaction connects URT1 to additional decay factors like DDX6/Dhh1-like RNA helicases. In fission yeast and human cultured cells, uridylation of short oligo(A) tails is proposed to favor the binding of the LSm1-7 complex, which recruits the decapping complex through the interaction with PAT1, and results in the degradation of the decapped mRNA by the 5′-3′ exoribonuclease 1 XRN1 (XRN4 in plants)[5,6,8,23]. We show that the Arabidopsis TUTase URT1 is integrated in an interaction network comprising the deadenylation complex CCR4-NOT and other translation repressors/decapping activators, including DCP5, the plant ortholog of the translational inhibitor/decapping activator Scd[6] or LSM14A. We show that in absence of URT1-mediated uridylation, excessively deadenylated mRNAs can become a source of spurious siRNAs that silence endogenous mRNAs, with a negative impact on plant fitness
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