Vir1p, the yeast homolog of virilizer, is required for mRNA m6A methylation and meiosis

Abstract

N6-Methyladenosine (m6A) is among the most abundant modifications of eukaryotic mRNAs. mRNA methylation regulates many biological processes including playing an essential role in meiosis. During meiosis in the budding yeast, Saccharomyces cerevisiae, m6A levels peak early, before the initiation of the meiotic divisions. High-throughput studies suggested, and this work confirms that the uncharacterized protein Ygl036wp interacts with Kar4p, a component of the mRNA m6A-methyltransferase complex. Protein structure programs predict that Ygl036wp folds like VIRMA/Virilizer/VIR, which is involved in mRNA m6A-methylation in higher eukaryotes. In addition, Ygl036wp contains conserved motifs shared with VIRMA/Virilizer/VIR. Accordingly, we propose the name VIR1 for budding yeast ortholog of VIRMA/Virilizer/VIR 1. Vir1p interacts with all other members of the yeast methyltransferase complex and is itself required for mRNA m6A methylation and meiosis. In the absence of Vir1p proteins comprising the methyltransferase complex become unstable, suggesting that Vir1p acts as a scaffold for the complex. The vir1Δ/Δ mutant is defective for premeiotic S-phase, which is suppressed by overexpression of the early meiotic transcription factor IME1; additional overexpression of the translational regulator RIM4 is required for sporulation. The vir1Δ/Δ mutant exhibits reduced levels of IME1 mRNA, as well as transcripts within Ime1p’s regulon. Suppression by IME1 revealed an additional defect in the expression of the middle meiotic transcription factor, Ndt80p (and genes in its regulon), which is rescued by overexpression of RIM4. Together, these data suggest that Vir1p is required for cells to initiate the meiotic program and for progression through the meiotic divisions and spore formation.

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.…”

“…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.…”

“…Briefly, Kar4 was identified as the METTL14 orthologue. Ygl036w was renamed to Vir1, because its sequence is orthologous to VIRMA/Virilizer (Ensinck et al, 2023; Park, Belnap, et al, 2023; Park, Sporer, et al, 2023). Both genes are essential for m6A deposition.…”

Rewiring of the phosphoproteome executes two meiotic divisions in budding yeast

“…S7B,C ; cluster 7). Some proteins involved in spore formation (Sps1, Sps22, Spr1) accumulated prematurely while the m6A methyltransferase complex component, Vir1, which is required for the initiation of the meiotic programme (Park et al, 2023 ), was elevated in spo13Δ cells (Appendix Fig. S7B,C ).…”

Rewiring of the phosphoproteome executes two meiotic divisions

“…Proteins that showed altered abundance in spo13Δ included key meiotic regulators Pds1 securin and Sgo1 which showed reduced and delayed accumulation in spo13Δ cells (Fig EV7B and C; cluster 7). Some proteins involved in spore formation (Sps1, Sps22, Spr1) accumulated prematurely while the m6A methyltransferase complex component, Vir1, which is required for the initiation of the meiotic programme (Park et al , 2023), was elevated in spo13Δ cells (Fig EV7B and C). Regulators Spo12 and Bud14 of the Cdc14 phosphatase, which is required for two meiotic divisions (Kocakaplan et al , 2021; Marston et al , 2003; Fox et al , 2017), were also deregulated in spo13Δ cells.…”