The yeast RNA methylation complex consists of conserved yet reconfigured components with m6A-dependent and independent roles

Abstract

N6-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 orthologs. 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 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.

Budding yeast as an ideal model for elucidating the role of N6‐methyladenosine in regulating gene expression

“…Recent works showed that the yeast MTC contains three additional subunits (Kar4, Ygl036w/Vir1 and Dyn2). Furthermore, the new analysis showed that the yeast MTC is much more conserved than previously anticipated (Ensinck et al, 2023; Park, Belnap, et al, 2023; Park, Sporer, et al, 2023). Briefly, Kar4 was identified as the METTL14 orthologue.…”

“…Budding yeast was one of the first models used to show that m6A has an important function (Bodi et al, 2010; Clancy, 2002). The IME4 gene (Inducer of Meiosis 4), which encodes the sole m6A methyltransferase in budding yeast and is orthologous to METTL3 in humans, is not essential for viability and acts specifically in the early phases of meiosis (Agarwala et al, 2012; Ensinck et al, 2023; Schwartz et al, 2013). The tight regulation of m6A deposition during early meiosis in budding yeast contrasts that in higher eukaryotes, where m6A is constitutively and by default deposited (Dominissini et al, 2012; Uzonyi et al, 2023).…”

“…However, in other common lab strain backgrounds, for example, S288C and Σ1278b, IME4 is required for meiosis and spore formation (Clancy, 2002; Hongay et al, 2006; Shah et al, 1992). Cells that harbour the catalytically inactive Ime4 ( IME4 CD ) display a much milder meiotic phenotype indicating that Ime4 possesses an important noncatalytic function in meiosis (Agarwala et al, 2012; Bushkin et al, 2019; Ensinck et al, 2023; Park, Belnap, et al, 2023). Two additional proteins, Mum2 and Slz1, were identified to interact with Ime4.…”

“…The colour matching subunits are orthologs of each other. The mammalian MTC has the MAC and MACOM composition, while the yeast MTC is likely a single complex (Ensinck et al, 2023). (b) Composition of the MTC required for m6A deposition (m6A‐dependent) and for m6A‐independent functions.…”

“…In budding yeast, Saccharomyces cerevisiae , the m6A mark is specifically deposited on mRNA during early phases of meiosis where it is important for meiotic progression (Agarwala et al, 2012; Ensinck et al, 2023; Schwartz et al, 2013) (Figure 1). The yeast methyltransferase complex (MTC) that deposits the m6A modification on mRNAs and the YTH domain‐containing protein, Mrb1/Pho92, that associates with m6A are highly conserved.…”