Layers of regulation of cell-cycle gene expression in the budding yeastSaccharomyces cerevisiae

Abstract

In the budding yeast Saccharomyces cerevisiae, transcription factors (TFs) regulate the periodic expression of many genes during the cell cycle, including gene products required for progression through cell-cycle events. Experimental evidence coupled with quantitative models suggests that a network of interconnected TFs is capable of regulating periodic genes over the cell cycle. Importantly, these dynamical models were built on transcriptomics data and assumed that TF protein levels and activity are directly correlated with mRNA abundance. To ask whether TF transcripts match protein expression levels as cells progress through the cell cycle, we applied a multiplexed targeted mass spectrometry approach (parallel reaction monitoring) to synchronized populations of cells. We found that protein expression of many TFs and cell-cycle regulators closely followed their respective mRNA transcript dynamics in cycling wild-type cells. Discordant mRNA/protein expression dynamics was also observed for a subset of cell-cycle TFs and for proteins targeted for degradation by E3 ubiquitin ligase complexes such as SCF (Skp1/Cul1/F-box) and APC/C (anaphase-promoting complex/cyclosome). We further profiled mutant cells lacking B-type cyclin/CDK activity ( clb1-6) where oscillations in ubiquitin ligase activity, cyclin/CDKs, and cell-cycle progression are halted. We found that a number of proteins were no longer periodically degraded in clb1-6 mutants compared with wild type, highlighting the importance of posttranscriptional regulation. Finally, the TF complexes responsible for activating G1/S transcription (SBF and MBF) were more constitutively expressed at the protein level than at periodic mRNA expression levels in both wild-type and mutant cells. This comprehensive investigation of cell-cycle regulators reveals that multiple layers of regulation (transcription, protein stability, and proteasome targeting) affect protein expression dynamics during the cell cycle.

Building blocks are synthesized on demand during the yeast cell cycle

“…S5C). In a recent study by Kelliher et al (14), for some cell cyclerelated genes, protein abundance also did not reflect periodic mRNA behavior. This included SWI6, which here is also found to have significantly periodic mRNA (P ≤ 0.001) and, as previously found, could not be identified as periodic at the protein level (P = 0.297), nor were any periodic changes found for its protein phosphorylation state either.…”

Conservation of dynamic characteristics of transcriptional regulatory elements in periodic biological processes

“…MCM1 is the only core TF to not rank in the top 70 TFs in at least one of the two S. cerevisiae datasets using DL × JTK (Table S1). However, MCM1 acts in complex with other rhythmically-expressed genes like NDD1 [40, 41], so it can still be part of a highly periodic TF complex without itself exhibiting highly periodic signatures in transcript abundance. It is enticing to imagine there may be other features captured in the gene or protein expression profiles, as well as features not related to gene expression, such as sequence-based and protein interaction features that could be used to more accurately capture all core genes, including those identified in TF complexes.…”

Activation of the Anaphase Promoting Complex reverses multiple drug resistant cancer

“…This is controlled by transcripton factors that are themselves cell cycle regulated by the APC, such as FOXM1 [56]. The mRNAs encoding many APC substrates in yeast are also cell cycle regulated, with synthesis of their corresponding proteins peaking following the mRNA expression peak [75][76][77]. In fact, transcription factors that transcribe yeast APC substrates, such as Fkh1 [29] and Ndd1 [78], are targeted by the APC, thereby creating feedforward loops.…”