PXD019952

PXD019952 is an original dataset announced via ProteomeXchange.

Title	Unravelling metabolic cross-feeding in a yeast-bacteria community using 13C proteomics
Description	Cross-feeding is fundamental to the diversity and function of microbial communities. However, identification of cross-fed metabolites is often challenging due to the universality of metabolic and biosynthetic intermediates. Here, we use 13C isotope tracing in peptides to elucidate cross-fed metabolites in cocultures of Saccharomyces cerevisiae and Lactococcus lactis. The community was grown on lactose as the main carbon source with either glucose or galactose fraction of the molecule labelled with 13C. Data analysis allowing for the possible mass-shifts yielded hundreds of peptides for which we could assign both species identity and labelling degree. The labelling pattern showed that the yeast utilized galactose and, to a lesser extent, lactic acid shared by L. lactis as carbon sources. While the yeast provided essential amino acids to the bacterium as expected, the data also uncovered a complex pattern of amino acid exchange. The identity of the cross-fed metabolites was further supported by metabolite labelling in the co-culture supernatant, and by diminished fitness of a galactose-negative yeast mutant in the community. Together, our results demonstrate the utility of 13C-based proteomics for uncovering microbial interactions.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_05:42:00.956.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD019952
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Christoniki Maga-Nteve
SpeciesList	scientific name: Saccharomyces cerevisiae (Baker's yeast); NCBI TaxID: 4932;
ModificationList	monohydroxylated residue; iodoacetamide derivatized residue
Instrument	LTQ Orbitrap Velos

Revision	Datetime	Status	ChangeLog Entry
0	2020-06-22 07:53:49	ID requested
1	2023-02-07 05:59:25	announced
2	2023-11-14 08:51:08	announced	2023-11-14: Updated project metadata.
⏵ 3	2024-10-22 05:42:01	announced	2024-10-22: Updated project metadata.

10.6019/PXD019952;

10.15252/MSB.202211501;

submitter keyword: protein stable-isotope labeling (protein-SIP), cross-feeding, synthetic community,: microbial interaction

Kiran Raosaheb Patil
contact affiliation	Group Leader, Structural and Computational Biology Unit, European Molecular Biology Laboratory Director of Research, MRC Toxicology Unit, University of Cambridge
contact email	kiran.patil@embl.de
lab head
Christoniki Maga-Nteve
contact affiliation	EMBL
contact email	christoniki.maga@embl.de
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/2023/02/PXD019952

PRIDE project URI

• PRIDE
  1. PXD019952
     1. Label: PRIDE project
     2. Name: Unravelling metabolic cross-feeding in a yeast-bacteria community using 13C proteomics