A YTHDF-PABP Interaction is Required for M A-mediated Organogenesis in Plants

Overview

Journal EMBO Rep

Specialty Molecular Biology

Date 2023 Nov 27

PMID 38009565

Authors

Mathias Due Tankmar

Marlene Reichel

Laura Arribas-Hernandez

Peter Brodersen

Affiliations

Soon will be listed here.

Abstract

N6-methyladenosine (m A) in mRNA is key to eukaryotic gene regulation. Many m A functions involve RNA-binding proteins that recognize m A 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.

Citing Articles

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References

Worpenberg L, Paolantoni C, Longhi S, Mulorz M, Lence T, Wessels H . Ythdf is a N6-methyladenosine reader that modulates Fmr1 target mRNA selection and restricts axonal growth in Drosophila. EMBO J. 2021; 40(4):e104975. PMC: 7883056. DOI: 10.15252/embj.2020104975. View

Meszaros B, Erdos G, Dosztanyi Z . IUPred2A: context-dependent prediction of protein disorder as a function of redox state and protein binding. Nucleic Acids Res. 2018; 46(W1):W329-W337. PMC: 6030935. DOI: 10.1093/nar/gky384. View

Arribas-Hernandez L, Bressendorff S, Hansen M, Poulsen C, Erdmann S, Brodersen P . An mA-YTH Module Controls Developmental Timing and Morphogenesis in Arabidopsis. Plant Cell. 2018; 30(5):952-967. PMC: 6002192. DOI: 10.1105/tpc.17.00833. View

Zaccara S, Jaffrey S . A Unified Model for the Function of YTHDF Proteins in Regulating mA-Modified mRNA. Cell. 2020; 181(7):1582-1595.e18. PMC: 7508256. DOI: 10.1016/j.cell.2020.05.012. View

Bitinaite J, Nichols N . DNA cloning and engineering by uracil excision. Curr Protoc Mol Biol. 2009; Chapter 3:Unit 3.21. DOI: 10.1002/0471142727.mb0321s86. View

Dufresne P, Ubalijoro E, Fortin M, Laliberte J . Arabidopsis thaliana class II poly(A)-binding proteins are required for efficient multiplication of turnip mosaic virus. J Gen Virol. 2008; 89(Pt 9):2339-2348. DOI: 10.1099/vir.0.2008/002139-0. View

Xu C, Liu K, Ahmed H, Loppnau P, Schapira M, Min J . Structural Basis for the Discriminative Recognition of N6-Methyladenosine RNA by the Human YT521-B Homology Domain Family of Proteins. J Biol Chem. 2015; 290(41):24902-13. PMC: 4598999. DOI: 10.1074/jbc.M115.680389. View

Zhang Z, Theler D, Kaminska K, Hiller M, De La Grange P, Pudimat R . The YTH domain is a novel RNA binding domain. J Biol Chem. 2010; 285(19):14701-10. PMC: 2863249. DOI: 10.1074/jbc.M110.104711. View

Livingstone C, Barton G . Protein sequence alignments: a strategy for the hierarchical analysis of residue conservation. Comput Appl Biosci. 1993; 9(6):745-56. DOI: 10.1093/bioinformatics/9.6.745. View

10.

Wei L, Song P, Wang Y, Lu Z, Tang Q, Yu Q . The mA Reader ECT2 Controls Trichome Morphology by Affecting mRNA Stability in Arabidopsis. Plant Cell. 2018; 30(5):968-985. PMC: 6002187. DOI: 10.1105/tpc.17.00934. View

11.

Clough S, Bent A . Floral dip: a simplified method for Agrobacterium-mediated transformation of Arabidopsis thaliana. Plant J. 1999; 16(6):735-43. DOI: 10.1046/j.1365-313x.1998.00343.x. View

12.

Shen L, Liang Z, Gu X, Chen Y, Teo Z, Hou X . N(6)-Methyladenosine RNA Modification Regulates Shoot Stem Cell Fate in Arabidopsis. Dev Cell. 2016; 38(2):186-200. PMC: 6364302. DOI: 10.1016/j.devcel.2016.06.008. View

13.

Theler D, Dominguez C, Blatter M, Boudet J, Allain F . Solution structure of the YTH domain in complex with N6-methyladenosine RNA: a reader of methylated RNA. Nucleic Acids Res. 2014; 42(22):13911-9. PMC: 4267619. DOI: 10.1093/nar/gku1116. View

14.

Herzog V, Reichholf B, Neumann T, Rescheneder P, Bhat P, Burkard T . Thiol-linked alkylation of RNA to assess expression dynamics. Nat Methods. 2017; 14(12):1198-1204. PMC: 5712218. DOI: 10.1038/nmeth.4435. View

15.

Park O, Ha H, Lee Y, Boo S, Kwon D, Song H . Endoribonucleolytic Cleavage of mA-Containing RNAs by RNase P/MRP Complex. Mol Cell. 2019; 74(3):494-507.e8. DOI: 10.1016/j.molcel.2019.02.034. View

16.

Kolb A, Busby S, Buc H, Garges S, Adhya S . Transcriptional regulation by cAMP and its receptor protein. Annu Rev Biochem. 1993; 62:749-95. DOI: 10.1146/annurev.bi.62.070193.003533. View

17.

Vernon R, Chong P, Tsang B, Kim T, Bah A, Farber P . Pi-Pi contacts are an overlooked protein feature relevant to phase separation. Elife. 2018; 7. PMC: 5847340. DOI: 10.7554/eLife.31486. View

18.

Zhu T, Roundtree I, Wang P, Wang X, Wang L, Sun C . Crystal structure of the YTH domain of YTHDF2 reveals mechanism for recognition of N6-methyladenosine. Cell Res. 2014; 24(12):1493-6. PMC: 4260350. DOI: 10.1038/cr.2014.152. View

19.

Huber W, von Heydebreck A, Sultmann H, Poustka A, Vingron M . Variance stabilization applied to microarray data calibration and to the quantification of differential expression. Bioinformatics. 2002; 18 Suppl 1:S96-104. DOI: 10.1093/bioinformatics/18.suppl_1.s96. View

20.

Scutenaire J, Deragon J, Jean V, Benhamed M, Raynaud C, Favory J . The YTH Domain Protein ECT2 Is an mA Reader Required for Normal Trichome Branching in Arabidopsis. Plant Cell. 2018; 30(5):986-1005. PMC: 6002185. DOI: 10.1105/tpc.17.00854. View