SWI/SNF senses carbon starvation with a pH-sensitive low-complexity sequence

Elife. 2022 Feb 7;11:e70344. doi: 10.7554/eLife.70344.


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, was 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 leads to conformational expansion, providing a potential biophysical mechanism for regulation of these interactions. Together, our results indicate that pH changes are a second messenger for transcriptional reprogramming during carbon starvation and that the SNF5 QLC acts as a pH sensor.

Keywords: S. cerevisiae; biochemistry; chemical biology; chromatin; chromosomes; gene expression; low-complexity sequences; pH; polyglutamine; transcription.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Carbon
  • Chromatin Assembly and Disassembly
  • Chromosomal Proteins, Non-Histone* / metabolism
  • Hydrogen-Ion Concentration
  • Saccharomyces cerevisiae / genetics
  • Saccharomyces cerevisiae / metabolism
  • Saccharomyces cerevisiae Proteins* / metabolism
  • Transcription Factors / metabolism


  • Chromosomal Proteins, Non-Histone
  • Saccharomyces cerevisiae Proteins
  • Transcription Factors
  • Carbon

Associated data

  • GEO/GSE174687