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’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.

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

“…An earlier study showed that disruption of SLZ1 decreased m6A by 80% (Agarwala et al, 2012). However, a recent study reported that no m6A levels were detected across different phases of early meiosis in slz1Δ cells (Ensinck et al, 2023). It is worth noting that slz1Δ cells also display a mild meiotic phenotype comparable to that of IME4 CD .…”

“…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;. Two additional proteins, Mum2 and Slz1, were identified to interact with Ime4.…”

“…Interestingly, the noncatalytic function of the MTC is of greater importance for progression into meiosis than the catalytic function (Ensinck et al, 2023).…”

“…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.…”

“…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 (m6Adependent) and for m6A-independent functions.…”