Insights into the conservation and diversification of the molecular functions of YTHDF proteins

Abstract

YT521-B homology (YTH) domain proteins act as readers of N6-methyladenosine (m6A), the most common internal covalent modification in eukaryotic mRNA. Members of the YTHDF subclade can determine properties of m6A-containing mRNAs in the cytoplasm of animal and plant cells. Vertebrates encode three YTHDF proteins, and whether they perform specialized or redundant molecular functions is currently debated. In land plants, the YTHDF clade has expanded from just one member in basal lineages to eleven so-called EVOLUTIONARILY CONSERVED C-TERMINAL REGION1-11 (ECT1-11) proteins in Arabidopsis thaliana, named after the conserved YTH domain found at the C-terminus following a long intrinsically disordered region (IDR) at the N-terminus. The origin and implications of YTHDF expansion in higher plants are not known, as it is unclear whether it involves acquisition of fundamentally different properties, in particular of their divergent IDRs. Here, we used the leaf formation defects in ect2/ect3/ect4 mutants to test whether the many Arabidopsis YTHDF proteins can perform the same function if expressed at similar levels in leaf primordia. We show that the ancestral molecular function of the m6A-YTHDF axis in land plants is conserved over YTHDF diversification, and currently present in all major clades of YTHDF proteins in flowering plants. Nevertheless, lineage-specific neo-functionalization of a few members also happened after late duplication events. ECT1, the closest homolog of ECT2/3/4, is one such divergent YTHDF protein. Accordingly, mutation of ECT1 does not aggravate the defective organogenesis of ect2/ect3/ect4 mutants, even though the four proteins are naturally expressed in the same population of primordial cells.

Plant YTHDF proteins are direct effectors of antiviral immunity against an N6‐methyladenosine‐containing RNA virus

“…ECT2 and ECT3 act redundantly as m 6 A readers to stimulate cellular proliferation in organ primordia, such that ect2/ect3 double mutants show delayed leaf and flower formation, slow root and stem growth, and aberrant leaf, flower, silique, and trichome morphology (Arribas‐Hernández et al , 2018 , 2020 , 2021b ). In nearly all cases, these phenotypes are exacerbated by additional mutation of ECT4 (Arribas‐Hernández et al , 2018 , 2020 ), and five additional Arabidopsis YTHDF proteins (ECT5, ECT6, ECT7, ECT8, ECT10) share the molecular functions of ECT2/3 required for primordial cell proliferation, as seen by complementation of ect2/ect3/ect4 phenotypes upon ectopic expression in the ECT2/3 expression domain (preprint: Flores‐Téllez et al , 2023 ). Stimulation of growth is a recurrent function of plant YTHDF proteins because similar roles have been found for rice and tomato YTHDF proteins (Ma et al , 2022 ; Yin et al , 2022 ), and because the sole YTHDF protein of the liverwort Marchantia polymorpha can replace ECT2/3 function when expressed in Arabidopsis (preprint: Flores‐Téllez et al , 2023 ).…”