The TUTase URT1 connects decapping activators and prevents the accumulation of excessively deadenylated mRNAs to avoid siRNA biogenesis

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 including DECAPPING 5 (DCP5), the Arabidopsis ortholog of human LSM14 and yeast Scd6. A conserved Helical Leucine-rich Motif (HLM) within an intrinsically disordered region of URT1 binds to the LSm domain of DCP5. This interaction connects URT1 to additional decay factors like DDX6/Dhh1-like RNA helicases. The combination of in planta and in vitro analyses supports a model that explains how URT1 reduces the accumulation of oligo(A)-tailed mRNAs: first, by connecting decapping factors and second, because 3’ terminal uridines can intrinsically hinder deadenylation. Importantly, preventing the accumulation of excessively deadenylated mRNAs in Arabidopsis avoids the biogenesis of illegitimate siRNAs that silence endogenous mRNAs and perturb plant growth and development.

The mRNA‐binding proteome of a critical phase transition during Arabidopsis seed germination

“…The pPABP2-PABP2-RFP reporter lines in wild-type and hsp101 background were described in Merret et al (2017). The pUBQ-DCP5-GFP like was a kind gift from the laboratory of Scheer, Hélène (Scheer et al, 2021) while the hsp101 mutant and complementation line used for the germination phenotypes of Supporting Information Fig. S5 (see later) were a kind gift from Elizabeth Vierling (McLoughlin et al, 2019).…”

FRIENDLY (FMT) is an RNA binding protein associated with cytosolic ribosomes at the mitochondrial surface

“…To identify significantly affected proteins, a statistical analysis based on spectral counts was performed using a homemade R package (https://github.com/hzuber67/IPinquiry4) as described in (Scheer et al, 2021). To avoid too much bias, only proteins with a mean of at least 3 spectra in the most expressed condition were further considered.…”

Epigenetic management of self and non-self: lessons from 40 years of transgenic plants

“…Because RQC null alleles are embryolethal or die at a very early stage of development, a complete view of PCGs capable of producing siRNAs when RQC is impaired cannot be obtained using constitutive mutants. Analysis of mutants that partially impair RQC extended the list of siRNA-producing PCGs [50,[73][74][75]. Moreover, another category of siRNAs derived from PCGs was identified when plants are infected by viruses [76].…”

“…Étant donné que les allèles nuls RQC sont embryolétaux ou meurent à un stade très précoce du développement, il est impossible d'obtenir une vue complète des PCG capables de produire des siARN en utilisant des mutants totalement déficients pour le RQC. L'analyse de mutants qui altèrent partiellement le RQC a permis d'étendre la liste des PCG produisant des siARN [50,[73][74][75]. De plus, une autre catégorie de siARN dérivés des PCG a été identifiée lorsque les plantes sont infectées par des virus [76].…”