The Yeast RNA Methylation Complex Consists of Conserved Yet Reconfigured Components with M6A-dependent and Independent Roles

Overview

Journal Elife

Specialty Biology

Date 2023 Jul 25

PMID 37490041

Authors

Imke Ensinck

Alexander Maman

Waleed S Albihlal

Michelangelo Lassandro

Giulia Salzano

Theodora Sideri

Steven A Howell

Enrica Calvani

Harshil Patel

Guy Bushkin

Markus Ralser

Ambrosius P Snijders

Mark Skehel

Ana Casanal

Schraga Schwartz

Folkert J van Werven

Affiliations

Soon will be listed here.

Abstract

-methyladenosine (m6A), the most abundant mRNA modification, is deposited in mammals/insects/plants by m6A methyltransferase complexes (MTC) comprising a catalytic subunit and at least five additional proteins. The yeast MTC is critical for meiosis and was known to comprise three proteins, of which two were conserved. We uncover three novel MTC components (Kar4/Ygl036w-Vir1/Dyn2). All MTC subunits, except for Dyn2, are essential for m6A deposition and have corresponding mammalian MTC orthologues. Unlike the mammalian bipartite MTC, the yeast MTC is unipartite, yet multifunctional. The mRNA interacting module, comprising Ime4, Mum2, Vir1, and Kar4, exerts the MTC's m6A-independent function, while Slz1 enables the MTC catalytic function in m6A deposition. Both functions are critical for meiotic progression. Kar4 also has a mechanistically separate role from the MTC during mating. The yeast MTC constituents play distinguishable m6A-dependent, MTC-dependent, and MTC-independent functions, highlighting their complexity and paving the path towards dissecting multi-layered MTC functions in mammals.

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References

Knuckles P, Lence T, Haussmann I, Jacob D, Kreim N, Carl S . Zc3h13/Flacc is required for adenosine methylation by bridging the mRNA-binding factor Rbm15/Spenito to the mA machinery component Wtap/Fl(2)d. Genes Dev. 2018; 32(5-6):415-429. PMC: 5900714. DOI: 10.1101/gad.309146.117. View

Kurihara L, Stewart B, Gammie A, Rose M . Kar4p, a karyogamy-specific component of the yeast pheromone response pathway. Mol Cell Biol. 1996; 16(8):3990-4002. PMC: 231395. DOI: 10.1128/MCB.16.8.3990. View

Yue Y, Liu J, Cui X, Cao J, Luo G, Zhang Z . VIRMA mediates preferential mA mRNA methylation in 3'UTR and near stop codon and associates with alternative polyadenylation. Cell Discov. 2018; 4:10. PMC: 5826926. DOI: 10.1038/s41421-018-0019-0. View

Wang Y, Li Y, Toth J, Petroski M, Zhang Z, Zhao J . N6-methyladenosine modification destabilizes developmental regulators in embryonic stem cells. Nat Cell Biol. 2014; 16(2):191-8. PMC: 4640932. DOI: 10.1038/ncb2902. View

Sledz P, Jinek M . Structural insights into the molecular mechanism of the m(6)A writer complex. Elife. 2016; 5. PMC: 5023411. DOI: 10.7554/eLife.18434. View

Wang P, Doxtader K, Nam Y . Structural Basis for Cooperative Function of Mettl3 and Mettl14 Methyltransferases. Mol Cell. 2016; 63(2):306-317. PMC: 4958592. DOI: 10.1016/j.molcel.2016.05.041. View

Ensinck I, Sideri T, Modic M, Capitanchik C, Vivori C, Toolan-Kerr P . m6A-ELISA, a simple method for quantifying -methyladenosine from mRNA populations. RNA. 2023; 29(5):705-712. PMC: 10159001. DOI: 10.1261/rna.079554.122. View

White J, Li Z, Sardana R, Bujnicki J, Marcotte E, Johnson A . Bud23 methylates G1575 of 18S rRNA and is required for efficient nuclear export of pre-40S subunits. Mol Cell Biol. 2008; 28(10):3151-61. PMC: 2423152. DOI: 10.1128/MCB.01674-07. View

Tam J, van Werven F . Regulated repression governs the cell fate promoter controlling yeast meiosis. Nat Commun. 2020; 11(1):2271. PMC: 7210989. DOI: 10.1038/s41467-020-16107-w. View

10.

Deutschbauer A, Williams R, Chu A, Davis R . Parallel phenotypic analysis of sporulation and postgermination growth in Saccharomyces cerevisiae. Proc Natl Acad Sci U S A. 2002; 99(24):15530-5. PMC: 137751. DOI: 10.1073/pnas.202604399. View

11.

Schwartz S, Agarwala S, Mumbach M, Jovanovic M, Mertins P, Shishkin A . High-resolution mapping reveals a conserved, widespread, dynamic mRNA methylation program in yeast meiosis. Cell. 2013; 155(6):1409-21. PMC: 3956118. DOI: 10.1016/j.cell.2013.10.047. View

12.

Wang Y, Zhang L, Ren H, Ma L, Guo J, Mao D . Role of Hakai in mA modification pathway in Drosophila. Nat Commun. 2021; 12(1):2159. PMC: 8041851. DOI: 10.1038/s41467-021-22424-5. View

13.

Lahav R, Gammie A, Tavazoie S, Rose M . Role of transcription factor Kar4 in regulating downstream events in the Saccharomyces cerevisiae pheromone response pathway. Mol Cell Biol. 2006; 27(3):818-29. PMC: 1800688. DOI: 10.1128/MCB.00439-06. View

14.

. UniProt: the Universal Protein Knowledgebase in 2023. Nucleic Acids Res. 2022; 51(D1):D523-D531. PMC: 9825514. DOI: 10.1093/nar/gkac1052. View

15.

Barbieri I, Tzelepis K, Pandolfini L, Shi J, Millan-Zambrano G, Robson S . Promoter-bound METTL3 maintains myeloid leukaemia by mA-dependent translation control. Nature. 2017; 552(7683):126-131. PMC: 6217924. DOI: 10.1038/nature24678. View

16.

Varier R, Sideri T, Capitanchik C, Manova Z, Calvani E, Rossi A . -methyladenosine (m6A) reader Pho92 is recruited co-transcriptionally and couples translation to mRNA decay to promote meiotic fitness in yeast. Elife. 2022; 11. PMC: 9731578. DOI: 10.7554/eLife.84034. View

17.

Sharma S, Yang J, Watzinger P, Kotter P, Entian K . Yeast Nop2 and Rcm1 methylate C2870 and C2278 of the 25S rRNA, respectively. Nucleic Acids Res. 2013; 41(19):9062-76. PMC: 3799443. DOI: 10.1093/nar/gkt679. View

18.

Longtine M, McKenzie 3rd A, DeMarini D, Shah N, Wach A, Brachat A . Additional modules for versatile and economical PCR-based gene deletion and modification in Saccharomyces cerevisiae. Yeast. 1998; 14(10):953-61. DOI: 10.1002/(SICI)1097-0061(199807)14:10<953::AID-YEA293>3.0.CO;2-U. View

19.

Agarwala S, Blitzblau H, Hochwagen A, Fink G . RNA methylation by the MIS complex regulates a cell fate decision in yeast. PLoS Genet. 2012; 8(6):e1002732. PMC: 3369947. DOI: 10.1371/journal.pgen.1002732. View

20.

Love M, Huber W, Anders S . Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 2014; 15(12):550. PMC: 4302049. DOI: 10.1186/s13059-014-0550-8. View