SWI/SNF senses carbon starvation with a pH-sensitive low complexity sequence
Abstract
It is increasingly appreciated that intracellular pH changes are important biological signals. This motivates the elucidation of molecular mechanisms of pH-sensing. We determined that a nucleocytoplasmic pH oscillation was required for the transcriptional response to carbon starvation in Saccharomyces cerevisiae. The SWI/SNF chromatin remodeling complex is a key mediator of this transcriptional response. A glutamine-rich low complexity domain (QLC) in the SNF5 subunit of this complex, and histidines within this sequence, were required for efficient transcriptional reprogramming. Furthermore, the SNF5 QLC mediated pH-dependent recruitment of SWI/SNF to an acidic transcription factor in a reconstituted nucleosome remodeling assay. Simulations showed that protonation of histidines within the SNF5 QLC lead to conformational expansion, providing a potential biophysical mechanism for regulation of these interactions. Together, our results indicate that that pH changes are a second messenger for transcriptional reprogramming during carbon starvation, and that the SNF5 QLC acts as a pH-sensor.
Data availability
Simulation code and details can be found at:https://github.com/holehouse-lab/supportingdata/tree/master/2021/Gutierrez_QLC_2021RNA-seq R-code can be found at:https://github.com/gbritt/SWI_SNF_pH_Sensor_RNASeqRNA-seq datasets are depositied at GEO accession number GSE174687https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE174687
-
SWI/SNF senses carbon starvation with a pH-sensitive low complexity sequenceNCBI Gene Expression Omnibus, GSE174687.
Article and author information
Author details
Funding
Becas Chile
- J Ignacio Gutierrez
National Science Foundation (Graduate Research Fellows Program)
- Gregory P Brittingham
Pershing Square Sohn Cancer Research Award
- Liam J Holt
National Cancer Institute (R37 CA240765)
- Liam J Holt
National Institute of General Medical Sciences (R01 GM132447)
- Liam J Holt
American Cancer Society Cornelia T. Bailey Foundation Research Scholar Grant (RSG-19-073-01-TBE)
- Liam J Holt
The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.
Copyright
© 2022, Gutierrez et al.
This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.
Metrics
-
- 2,809
- views
-
- 418
- downloads
-
- 29
- citations
Views, downloads and citations are aggregated across all versions of this paper published by eLife.