PXD044412-1

PXD044412 is an original dataset announced via ProteomeXchange.

Title	Metabolite interactions in the bacterial Calvin cycle and implications for flux regulation
Description	Metabolite-level regulation of enzyme activity is important for microbes to cope with environmental shifts. Knowledge of such regulations can also guide strain engineering to improve industrial phenotypes. Recently developed chemoproteomics workflows allow for genome-wide detection of metabolite-protein interactions that may regulate pathway activity. We applied limited proteolysis small molecule mapping (LiP-SMap) to identify and compare metabolite-protein interactions in the proteomes of two cyanobacteria and two lithoautotrophic bacteria that fix CO2 using the Calvin cycle. Clustering analysis of the hundreds of detected interactions showed that some metabolites interacted in a species-specific manner, such as interactions of glucose-6-phosphate in Cupriavidus necator and of glyoxylate in Synechocystis sp.sp PCC 6803. These are interpreted in light of the different central carbon conversion pathways present. Metabolites interacting with the Calvin cycle enzymes fructose-1,6/sedoheptulose-1,7-bisphosphatase (F/SBPase) and transketolase were tested for effects on catalytic activity in vitro. The Calvin cycle intermediate glyceraldehyde-3-phosphate activated both Synechocystis and Cupriavidus F/SBPase, which suggests a feed-forward activation of the cycle in both photoautotrophs and chemolithoautotrophs. In contrast to the stimulating effect in reduced conditions, glyceraldehyde-3-phosphate inactivated the Synechocystis F/SBPase in oxidized conditions by accelerating protein aggregation. Thus, metabolite-level regulation of the Calvin cycle is more prevalent than previously appreciated and may act in addition to redox regulation.
HostingRepository	PRIDE
AnnounceDate	2023-09-06
AnnouncementXML	Submission_2023-09-06_08:48:03.450.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	EmilSporre
SpeciesList	scientific name: Hydrogenophaga pseudoflava; NCBI TaxID: 47421; scientific name: Synechocystis sp. (strain PCC 6803 / Kazusa); NCBI TaxID: 1111708; scientific name: Synechococcus elongatus (strain PCC 7942) (Anacystis nidulans R2); NCBI TaxID: 1140; scientific name: Bacteria; NCBI TaxID: NCBITaxon:2; scientific name: Cupriavidus necator (strain ATCC 17699 / H16 / DSM 428 / Stanier 337) (Ralstonia eutropha); NCBI TaxID: 381666;
ModificationList	acetylated residue; monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Q Exactive HF

Revision	Datetime	Status	ChangeLog Entry
0	2023-08-07 07:57:39	ID requested
⏵ 1	2023-09-06 08:48:03	announced
2	2024-10-22 06:02:44	announced	2024-10-22: Updated project metadata.

Dataset with its publication pending

submitter keyword: Cupriavidus necator, cyanobacteria, prosit, Synechococcus sp. PCC7942, interaction proteomics, encyclopeDIA, Hydrogenophaga pseudoflava, LiP-SMap, carbon fixation, Synechocystis sp. PCC6803, Ralstonia eutropha

Elton PaulHudson
contact affiliation	Head of the Department of Protein Science, Division of Systems Biology at the Royal Institute of Technology (KTH), Stockholm, Sweden
contact email	paul.hudson@scilifelab.se
lab head
EmilSporre
contact affiliation	Royal Institute of Technology (KTH)
contact email	emil.sporre@scilifelab.se
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/2023/08/PXD044412

PRIDE project URI

• PRIDE
  1. PXD044412
     1. Label: PRIDE project
     2. Name: Metabolite interactions in the bacterial Calvin cycle and implications for flux regulation