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

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YT521-B homology (YTH) domain proteins act as readers of N6-methyladenosine (m6A) in mRNA. Members of the YTHDF clade determine properties of m6A-containing mRNAs in the cytoplasm. Vertebrates encode three YTHDF proteins whose possible functional specialization is debated. In land plants, the YTHDF clade has expanded from 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 placed behind a long N-terminal intrinsically disordered region (IDR). ECT2, ECT3 and ECT4 show genetic redundancy in stimulation of primed stem cell division, but the origin and implications of YTHDF expansion in higher plants are unknown, as it is unclear whether it involves acquisition of fundamentally different molecular properties, in particular of their divergent IDRs. Here, we use functional complementation of ect2/ect3/ect4 mutants to test whether different YTHDF proteins can perform the same function when similarly expressed in leaf primordia. We show that stimulation of primordial cell division relies on an ancestral molecular function of the m6A-YTHDF axis in land plants that is present in bryophytes and is conserved over YTHDF diversification, as it appears in all major clades of YTHDF proteins in flowering plants. Importantly, although our results indicate that the YTH domains of all arabidopsis ECT proteins have m6A-binding capacity, lineage-specific neo-functionalization of ECT1, ECT9 and ECT11 happened after late duplication events, and involves altered properties of both the YTH domains, and, especially, of the IDRs. We also identify two biophysical properties recurrent in IDRs of YTHDF proteins able to complement ect2 ect3 ect4 mutants, a clear phase separation propensity and a charge distribution that creates electric dipoles. Human and fly YTHDFs do not have IDRs with this combination of properties and cannot replace ECT2/3/4 function in arabidopsis, perhaps suggesting different molecular activities of YTHDF proteins between major taxa.

OriginalsprogEngelsk
Artikelnummere1010980
TidsskriftPLOS Genetics
Vol/bind19
Udgave nummer10
Antal sider37
ISSN1553-7390
DOI
StatusUdgivet - 2023

Bibliografisk note

Funding Information:
Funding:ThisworkwassupportedbytheNovo NordiskFoundationthroughaHallas-Møller AscendingInvestigator2019grant (NNF19OC0054973)toP.B.andagranttoK.L.-L. viathePRISM(ProteinInteractionsandStabilityin MedicineandGenomics)center (NNF18OC0033950),bytheEuropeanMolecular BiologyOrganisationthroughalong-term fellowship(ALTF810-2022)toS.v.B.,bythe EuropeanResearchCouncilthroughaConsolidator grant(ERC-2016-CoG726417PATHORISC)toP. B.,andbytheIndependentResearchFund DenmarkthroughaResearchProject2grant (9040-00409B)toP.B.Thefundershadnorolein studydesign,datacollectionandanalysis,decision topublish,orpreparationofthemanuscript.The followingauthorsreceivedsalaryfromthefunders: M.D.T.(NovoNordiskFoundation,grant NNF19OC0054973);S.v.B.(NovoNordisk Foundation,grantNNF18OC0033950,and EuropeanMolecularBiologyOrganisation,grant ALTF810-2022);J.C.(NovoNordiskFoundation, grantNNF19OC0054973);L.A.-H.(European ResearchCouncilgrantERC-2016-CoG726417, IndependentResearchFundDenmark,grant9040-00409B,andNovoNordiskFoundation,grant NNF19OC0054973).

Funding Information:
This work was supported by the Novo Nordisk Foundation through a Hallas-Møller Ascending Investigator 2019 grant (NNF19OC0054973) to P.B. and a grant to K.L.-L. via the PRISM (Protein Interactions and Stability in Medicine and Genomics) center (NNF18OC0033950), by the European Molecular Biology Organisation through a long-term fellowship (ALTF 810-2022) to S.v.B., by the European Research Council through a Consolidator grant (ERC-2016-CoG 726417 PATHORISC) to P. B., and by the Independent Research Fund Denmark through a Research Project2 grant (9040-00409B) to P.B. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. The following authors received salary from the funders: M.D.T. (Novo Nordisk Foundation, grant NNF19OC0054973); S.v.B. (Novo Nordisk Foundation, grant NNF18OC0033950, and European Molecular Biology Organisation, grant ALTF 810-2022); J.C. (Novo Nordisk Foundation, grant NNF19OC0054973); L.A.-H. (European Research Council grant ERC-2016-CoG 726417, Independent Research Fund Denmark, grant 9040-00409B, and Novo Nordisk Foundation, grant NNF19OC0054973). We thank Lena Bjørn Johansson, Sergio D’Anna, Jakub Najbar and Tobias Lahti for technical assistance, Theo Bølsterli and his team for plant care, and the Danish National Life Science Supercomputing Center Computerome and the core facility for biocomputing at the Department of Biology (University of Copenhagen) for the use of computational resources. We acknowledge the constructive criticism of Rupert Fray as a reviewer on previous publications, as his suggestion to use the ect2/ect3/ect4 triple mutant phenotype to test ECT molecular function by systematic ectopic expression in the ECT2 expression domain inspired us to embark on the present project.

Publisher Copyright:
Copyright: © 2023 Flores-Téllez et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

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