PXD036186-1

PXD036186 is an original dataset announced via ProteomeXchange.

Title	In situ analysis of osmolyte mechanisms of proteome thermal stabilisation
Description	Organisms across all kingdoms of life use small organic molecules called osmolytes to adapt to diverse environmental conditions and preserve viability. Osmolytes are thought to thermally stabilise proteins based on in vitro studies of a few purified proteins. The molecular mechanisms of osmolytes remain controversial and systematic global studies of osmolyte action within a complex cellular milieu are so far lacking. Here we present an in situ proteome-wide analysis of protein thermal stabilisation by osmolytes, covering all major classes of these molecules: trimethylamine N-oxide (TMAO), betaine, glycerol, proline, trehalose and glucose. Using a structural proteomics approach, we systematically probed the effects of osmolytes on protein thermal stability, native structures, and aggregation, thus revealing widespread mechanisms of osmolyte action, but also osmolyte- and protein- specific effects. All tested osmolytes stabilised the majority of the proteome. The stabilisation of most proteins could be explained by the preferential exclusion model, according to which osmolytes unfavourably interact with protein backbones thus promoting folded states. We also detected specific protein-osmolyte binding events which resulted in strong thermal stabilisation, although binding was not necessary for stabilisation. Aggregation of most proteins occurred at higher temperatures in the presence of osmolytes than in their absence. TMAO however promoted aggregation of small, unfolded proteins but also showed the strongest protein thermal stabilisation effects, which might reflect adaptation to the extreme living conditions of marine organisms that accumulate TMAO. Our global in situ analysis provides mechanistic insight into how osmolytes function within a complex biological matrix. Our data further provides a resource to guide the design or selection of stabilisers for protein-based drugs and the identification of conditions that increase thermotolerance of microorganisms in biotechnological applications.
HostingRepository	PRIDE
AnnounceDate	2024-08-10
AnnouncementXML	Submission_2024-08-09_18:13:49.074.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Monika Pepelnjak
SpeciesList	scientific name: Escherichia coli; NCBI TaxID: 562;
ModificationList	acetylated residue; iodoacetamide derivatized residue
Instrument	Orbitrap Eclipse; Orbitrap Fusion Lumos

Revision	Datetime	Status	ChangeLog Entry
0	2022-08-21 03:54:08	ID requested
⏵ 1	2024-08-09 18:13:49	announced
2	2024-10-22 06:54:08	announced	2024-10-22: Updated project metadata.

10.1038/s41589-024-01568-7;

Pepelnjak M, Velten B, N, ä, pflin N, von Rosen T, Palmiero UC, Ko JH, Maynard HD, Arosio P, Weber-Ban E, de Souza N, Huber W, Picotti P, In situ analysis of osmolyte mechanisms of proteome thermal stabilization. Nat Chem Biol, 20(8):1053-1065(2024) [pubmed]

submitter keyword: Osmolyte mechanisms, structural proteomics, stress adaptation, thermal stabilisation, aggregation

Paola Picotti
contact affiliation	Insitute of molecular systems biology, ETH Zurich, Switzerland
contact email	picotti@imsb.biol.ethz.ch
lab head
Monika Pepelnjak
contact affiliation	ETH Zurich
contact email	pepelnjak@imsb.biol.ethz.ch
dataset submitter

Dataset FTP location NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2024/08/PXD036186

PRIDE project URI

• PRIDE
  1. PXD036186
     1. Label: PRIDE project
     2. Name: In situ analysis of osmolyte mechanisms of proteome thermal stabilisation