A YTHDF–PABP interaction is required for m6A‐mediated organogenesis in plants

• Published in: EMBO reports 2023-12, Vol.24 (12), p.n/a
• Main Authors: Due Tankmar, Mathias, Reichel, Marlene, Arribas‐Hernández, Laura, Brodersen, Peter
• Format: Article
• Language: English
• Subjects: Amino acids; Arabidopsis; Cell division; ECT2; Gene expression; Gene regulation; Genes; Genetic control; Homology; IDR; Leaves; m6A; mRNA; Mutants; N6-methyladenosine; Organogenesis; PABP; Phase separation; Plants; Polyadenine; Primordia; Proteins; RNA modification; RNA-binding protein; Stimulation; Tyrosine
• ISSN: 1469-221X; 1469-3178
• DOI: 10.15252/embr.202357741

N6‐methyladenosine (m6A) in mRNA is key to eukaryotic gene regulation. Many m6A functions involve RNA‐binding proteins that recognize m6A via a YT521‐B Homology (YTH) domain. YTH domain proteins contain long intrinsically disordered regions (IDRs) that may mediate phase separation and interaction with protein partners, but whose precise biochemical functions remain largely unknown. The Arabidopsis thaliana YTH domain proteins ECT2, ECT3, and ECT4 accelerate organogenesis through stimulation of cell division in organ primordia. Here, we use ECT2 to reveal molecular underpinnings of this function. We show that stimulation of leaf formation requires the long N‐terminal IDR, and we identify two short IDR elements required for ECT2‐mediated organogenesis. Of these two, a 19‐amino acid region containing a tyrosine‐rich motif conserved in both plant and metazoan YTHDF proteins is necessary for binding to the major cytoplasmic poly(A)‐binding proteins PAB2, PAB4, and PAB8. Remarkably, overexpression of PAB4 in leaf primordia partially rescues the delayed leaf formation in ect2 ect3 ect4 mutants, suggesting that the ECT2‐PAB2/4/8 interaction on target mRNAs of organogenesis‐related genes may overcome limiting PAB concentrations in primordial cells. Synopsis An interaction between m6A‐binding YTHDF proteins and cytoplasmic poly(A)‐binding proteins promotes leaf formation. It is mediated by a short motif conserved across plant and animal YTHDF proteins, suggesting an effector function of m6A readers shared between animals and plants. The intrinsically disordered region of the plant YTHDF protein ECT2 contains a tyrosine‐rich short linear motif (SLiM) required for interaction with the cytoplasmic poly(A)‐binding proteins PAB2, PAB4, and PAB8. This tyrosine‐rich SLiM is required for ECT2‐mediated leaf formation and is deeply conserved in plant and animal YTHDF proteins. Overexpression of the cytoplasmic poly(A)‐binding protein PAB4 in leaf primordia partially rescues the leaf formation defects in mutants carrying knockouts in major YTHDF‐encoding genes. An interaction between m6A‐binding YTHDF proteins and cytoplasmic poly(A)‐binding proteins promotes leaf formation. It is mediated by a short motif conserved across plant and animal YTHDF proteins, suggesting an effector function of m6A readers shared between animals and plants.