Context dependent splicing functions of Bud31/Ycr063w define its role in budding and cell cycle progression

► Yeast BUD31 is non-essential but bud31Δ cells have budding defects. ► Bud31 is required for G1–S cell cycle transition and not other regulatory events. ► Efficient pre-mRNA splicing of some transcripts like SRC1 and ARP2 requires Bud31. ► Bud31 allows alternative 5′ splice-site use to create the two normal SRC1 isoforms. ► BUD31 and PRP17 have non-redundant functions in cell cycle and splicing. The yeast Bud31 protein, a Prp19 complex (NTC) member, aids spliceosome assembly and thus promotes efficient pre-mRNA splicing. The bud31 null cells show mild budding abnormalities at optimal growth temperatures and, at higher temperatures, have growth defects with aberrant budding. Here we have assessed cell cycle transitions which require Bud31. We find Bud31 facilitates passage through G1–S regulatory point (Start) but is not needed for G2-M transition or for exit from mitosis. To co-relate Bud31 functions in cell division with splicing, we studied the splicing status of transcripts that encode proteins involved in budding. We find Bud31 promotes efficient splicing of only some of these pre-mRNAs, for example, ARP2 and SRC1. Wild type cells have a long and a short isoform of SRC1 mRNA and protein, out of which the shorter mRNA splice variant is predominant. bud31Δ cells show inefficient SRC1 splicing and entirely lack the shorter SRC1 spliced mRNA isoform. Yeast PRP17, another NTC sub-complex member, is also required for G1–S and G2-M cell cycle transitions. We examined genetic interactions between BUD31 and PRP17. While both factors were needed for efficient cell cycle dependent gene expression, our data indicate that distinct pre-mRNAs depend on each of these non-essential splicing factors.