Pulsatile Dynamics in the Yeast Proteome
The activation of transcription factors in response to environmental conditions is fundamental to cellular regulation. Recent work has revealed that some transcription factors are activated in stochastic pulses of nuclear localization, rather than at a constant level, even in a constant environment. In such cases, signals control the mean activity of the transcription factor by modulating the frequency, duration, or amplitude of these pulses. Although specific pulsatile transcription factors have been identified in diverse cell types, it has remained unclear how prevalent pulsing is within the cell, how variable pulsing behaviors are between genes, and whether pulsing is specific to transcriptional regulators or is employed more broadly. To address these issues, we performed a proteome-wide movie-based screen to systematically identify localization-based pulsing behaviors in Saccharomyces cerevisiae. The screen examined all genes in a previously developed fluorescent protein fusion library of 4,159 strains in multiple media conditions. This approach revealed stochastic pulsing in ten proteins, all transcription factors. In each case, pulse dynamics were heterogeneous and unsynchronized among cells in clonal populations. Pulsing is the only dynamic localization behavior that we observed, and it tends to occur in pairs of paralogous and redundant proteins. Taken together, these results suggest that pulsatile dynamics play a pervasive role in yeast and may be similarly prevalent in other eukaryotic species.
Additional Information© 2014 Elsevier Ltd. Received: April 19, 2014; Revised: July 23, 2014; Accepted: July 28, 2014; Published: September 11, 2014. We thank T.F. Chou for initial assistance in obtaining and culturing the yeast GFP library collection. We thank A. Moses, J.G. Ojálvo, and P. Swain for comments on the manuscript and acknowledge NIH grants P50 GM068763 and R01 GM079771B for funding. Author Contributions: C.K.D., L.C., and M.B.E. conceived and designed the screen. C.K.D, L.C., and K.R conducted and analyzed the screen. Y.L. conducted and analyzed the two-color experiments. C.K.D., L.C., and M.B.E. wrote the manuscript with help from Y.L and K.R.
Accepted Version - nihms627456.pdf
Supplemental Material - mmc1.pdf
Supplemental Material - mmc2.xlsx
Supplemental Material - mmc3.xlsx
Supplemental Material - mmc4.xls
Supplemental Material - mmc5.mp4