Published April 11, 2024 | Version v1
Journal article Open

An adaptive biomolecular condensation response is conserved across environmentally divergent species

Description

Cells must sense and respond to sudden maladaptive environmental changes—stresses—to survive and thrive. Across eukaryotes, stresses such as heat shock trigger conserved responses: growth arrest, a specific transcriptional response, and biomolecular condensation of protein and mRNA into structures known as stress granules under severe stress. The composition, formation mechanism, adaptive significance, and even evolutionary conservation of these condensed structures remain enigmatic. Here we provide a remarkable view into stress-triggered condensation, its evolutionary conservation and tuning, and its integration into other well-studied aspects of the stress response. Using three morphologically near-identical budding yeast species adapted to different thermal environments and diverged by up to 100 million years, we show that proteome-scale biomolecular condensation is tuned to species-specific thermal niches, closely tracking corresponding growth and transcriptional responses. In each species, poly(A)-binding protein—a core marker of stress granules—condenses in isolation at species-specific temperatures, with conserved molecular features and conformational changes modulating condensation. From the ecological to the molecular scale, our results reveal previously unappreciated levels of evolutionary selection in the eukaryotic stress response, while establishing a rich, tractable system for further inquiry.

Data availability

The yeast proteome is available from Saccharomyces Genome Database http://sgd-archive.yeastgenome.org/sequence/S288C_reference/orf_protein/. Sequencing data have been deposited in GEO under accession code GSE234499. The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifiers PXD044702 and PXD044970. Raw and processed flow cytometry data, HDX-MS data, growth data, TSP-LC-MS/MS data, imaging data, and DLS data to reproduce all figures have been deposited to Dryad (https://doi.org/10.5061/dryad.w3r2280w6) or GitHub (https://github.com/drummondlab/conservation-of-condensation-2024). Source data are provided with this paper.

Code to reproduce all figures has been deposited on GitHub (https://github.com/drummondlab/conservation-of-condensation-2024).

Files

Adaptive-biomolecular-condensation-response-is-conserved-across-environmentally-divergent-species.pdf

Additional details

Identifiers

DOI
10.1038/s41467-024-47355-9
Other
oai:uchicago.tind.io:11548

Funding

National Institutes of Health
GM144278
National Institutes of Health
GM127406
National Institutes of Health
R01 GM055694
National Institutes of Health
R35 GM14833
National Institutes of Health
T32 GM007197-43
National Institutes of Health
F31 ES032337-01
National Institutes of Health
F30 ES032665
National Institutes of Health
T32 GM007281-45
National Institutes of Health
F30 ES035279-01
Frank Family Fellowship
Dr. Kenneth S. Polonsky Fellowship
National Science Foundation
OMA-2121044
Neubauer Family Foundation
Helen Hay Whitney Foundation

UChicago Information

Division(s)
Biological Sciences Division, Pritzker School of Molecular Engineering
Department(s)
Biochemistry and Molecular Biology, Biophysical Sciences, Genetics, Genomics, and Systems Biology, Medicine
Center(s) or Institute(s)
Institute for Biophysical Dynamics