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. 2023 Oct 3;12:e91997. doi: 10.7554/eLife.91997

Figure 4. Inter-species association mapping links METTL16 to 5’SS +4 sequence preference.

(A) Volcano plot showing the results of the PGLS analysis of the 5’SS +4 A to U ratio phenotype for orthogroups corresponding to known human splicing factors and METTL16. The magnitude and directionality of the model coefficients (x-axis) are used as a measure of effect size and direction of effect on phenotype, respectively. (B) Stacked histogram and traitgram showing the distribution of 5’SS +4 A to U ratio phenotypes for species which retain or lack a METTL16 ortholog. Ancestral loss events shown on the traitgram are estimated using Dollo parsimony. (C) Circular tree showing the full phylogenetic relationship between 240 Saccharomycotina species identified using Orthofinder. Bifurcations are colored by confidence, calculated using the number of single-locus gene trees that support the bifurcation in the Orthofinder STAG algorithm (Emms and Kelly, 2019; Emms and Kelly, 2018). Clades defined in Figure 2A have been colored accordingly. Stacked bar charts show the 5’SS +4 position nucleotide fractions of each species identified from conserved introns. Outer circles show the presence (black) or absence (grey) of an ortholog from the orthogroups representing METTL16 (inner ring) and SNRNP27K (outer ring), respectively.

Figure 4.

Figure 4—figure supplement 1. Structural analysis of METTL16 orthologs in the Saccharomycetaceae clade.

Figure 4—figure supplement 1.

(A) Superimposition of the structure of human METTL16 MTD (green) solved by X-ray crystallography (PDB: 6DU4) with the Alphafold2 predicted structures of the MTD domains of putative METTL16 orthologs from E. gossypii (pink), E. cymbalariae (orange), and Z. parabailli (blue). (B) Multiple sequence alignment showing the conservation of the catalytic NPPF motif of METTL6 in the putative orthologs from subgenera of Eremothecium and Zygosaccharomyces. Generated using Jalview (Procter et al., 2021) (C) Heatmap showing the pairwise TMscore of segmented domains from the Alphafold2 predictions of METTL16 orthologs from Eremothecium and Zygosaccharomyces species, with selected outgroups. The X-ray structures of human METTL16 MTD and VCR, and TUT1 KA-1 are included as positive controls. Domains are grouped into clusters (diagonal boxes) using the same color scheme as in Figure 1A.