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

J Ignacio Gutierrez,Yonca Karadeniz,Gregory P Brittingham,Liam J Holt,Arnob Dutta,Craig L Peterson,Alex S Holehouse,Kathleen D Tran

doi:10.7554/elife.70344

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, 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.

Highlights

Biological processes are inherently sensitive to the solution environment in which they occur
Silver-stains of the untagged Snf5p and Western blotting of tandem affinity purification (TAP)-tagged SNF5 (Puig et al, 2001) strains showed that all SNF5 alleles were expressed at similar levels to wild-type both in glucose and upon carbon starvation (Figure 1 – figure supplement 7B). These results show that deletion of the SNF5 Q-rich low409 complexity sequences (QLCs) is distinct from total loss of the SNF5 gene and that this N-terminal sequence is important for efficient recovery from carbon starvation
This defect was far stronger in the ΔQsnf5 and HtoAsnf5 strains than in snf5Δ strains; snf5Δ strains did not completely repress ADH2 expression in glucose, and showed partial induction upon carbon starvation, while ΔQsnf5 strains tightly repressed ADH2 in glucose, but completely failed to induce expression upon starvation (Figure 1D). These results suggest a dual-role for SNF5 in ADH2 regulation, both contributing to strong repression in glucose, and robust induction upon carbon starvation

Summary

Introduction

Biological processes are inherently sensitive to the solution environment in which they occur. When cells are starved for carbon, these pumps are inactivated, leading to a rapid acidification of the intracellular space to pH ~ 6 (Kane, 1995; Orij et al, 2009) This decrease in intracellular pHi is crucial for viability upon carbon-starvation, and is thought to conserve energy, leading to storage of metabolic enzymes in filamentous assemblies (Petrovska et al, 2014), reduction of macromolecular diffusion (Joyner et al, 2016; Munder et al, 2016), decreased membrane biogenesis (Young et al, 2010) and possibly the non-covalent crosslinking of the cytoplasm into a solid-like material state (Joyner et al, 2016; Munder et al, 2016). We propose changes in histidine charge within QLCs as a mechanism to sense pH changes and instruct transcriptional reprograming during carbon starvation

Results

Discussion

Material and Methods