SWI/SNF senses carbon starvation with a pH-sensitive low complexity sequence
- Weill Cornell Medical College, United States
- New York University Langone Health, United States
- University of Massachusetts Medical School, United States
- University of Rhode Island, United States
- Washington University in St. Louis, United States
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
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SWI/SNF senses carbon starvation with a pH-sensitive low complexity sequenceNCBI Gene Expression Omnibus, GSE174687.
Article and author information
Author details
J Ignacio Gutierrez
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.
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SWI/SNF senses carbon starvation with a pH-sensitive low complexity sequence
eLife 11:e70344.
https://doi.org/10.7554/eLife.70344
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