Yeast poly(A)-binding protein (Pab1) controls translation initiation in vivo primarily by blocking mRNA decapping and decay

Poly(A)-binding protein (Pab1 in yeast) is involved in mRNA decay and translation initiation, but its molecular functions are incompletely understood. In this study, we employed a comprehensive multiomics strategy encompassing Ribosome profiling, spike-in normalized RNA-seq, SMPAT-seq, and CAGE-seq to gain mechanistic insight into Pab1's role in Saccharomyces cerevisiae. We found that auxin-induced degradation of Pab1 reduced bulk mRNA and polysome abundance in a manner suppressed by deleting the catalytic subunit of decapping enzyme (dcp2Δ), demonstrating that enhanced decapping/degradation is the major driver of reduced mRNA abundance and protein synthesis at limiting Pab1 levels. An increased median poly(A) tail length conferred by Pab1 depletion was also nullified by dcp2Δ, suggesting that mRNA isoforms with shorter tails are preferentially decapped/degraded at limiting Pab1. In contrast to findings on mammalian cells, the translational efficiencies (TEs) of many mRNAs were altered by Pab1 depletion; however, these changes were broadly diminished by dcp2∆, suggesting that reduced mRNA abundance is a major driver of translational reprogramming at limiting Pab1. Thus, assembly of the closed-loop mRNP via PABP-eIF4G interaction appears to be dispensable for normal translation of most yeast mRNAs in vivo at normal mRNA levels. Interestingly, histone mRNAs and proteins are preferentially diminished on Pab1 depletion dependent on Dcp2, accompanied by activation of internal cryptic promoters in the manner expected for reduced nucleosome occupancies, revealing a new layer of post-transcriptional control of histone gene expression. This study includes total 62 samples, 18 for ribosome profiling and 18 for total RNA-sequencing from triplicates cultures of WT, WT+NAA, pab1-AID, pab1-AID+NAA, dcp2∆+NAA and dcp2∆pab1-AID+NAA. Additionally, 12 samples for SMPAT-Seq using the same total RNA from WT+NAA, pab1-AID+NAA, dcp2∆+NAA and dcp2∆pab1-AID+NAA in triplicates. Additionally, the same total RNA in triplicates for WT+NAA, pab1-AID+NAA (6 samples) and total RNA in duplicates from spt6-1004, isogenic SPT6 WT, set1∆set1∆ and isogenic SET1SET2 WT (8 samples) were subjected to CAGE-sequencing. The strains WT, pab1-AID, dcp2∆ and dcp2∆pab1-AID were grown in YPD either with 1mM KOH or 1mM of 1-Napthaleneacetic acid (NAA) at 30ºC for 6h. The strains spt6-1004 mutant and isogenic WT, were cultured in SC medium at 30°C and shifted to 39°C for 90 min before harvesting. For set1∆set2∆ mutant and isogenic WT strain BY4741, cells were cultured in SC medium at 30°C