PXD015800

PXD015800 is an original dataset announced via ProteomeXchange.

Title	Mycoplasma pneuminiae and Mycoplasma agalactiae Proteomics
Description	During evolution, each bacterial strain shapes its metabolism in order to colonise a diversity of niches. Unraveling the biochemical reactions underlying bacteria metabolism is important for biotechnological purposes and for understanding relationships within a complex microbiome as well as the microbiome’s connection with its host. Here we propose a new approach to identifying active metabolic pathways, by integrating essentiality analysis and protein abundance. As an example, we used two bacterial species (Mycoplasma pneumoniae and Mycoplasma agalactiae) that share a high gene similarity yet show significant metabolic differences. After integrating all available metabolic knowledge about their enzymes, metabolites and reactions, we built detailed metabolic maps of their carbon metabolism. We determined the carbon sources that allow growth in M. agalactiae (as known for M. pneumoniae) and introduced glucose-dependent growth in M. agalactiae. By analyzing gene essentiality and performing quantitative proteomics, we could predict the active metabolic pathways and directionalities for the sugar, phospholipids, DNA/RNA precursors, glycoproteins, and glycolipids metabolism of these two bacteria. Comparison between predicted and experimentally determined active pathways shows an excellent agreement. Thus, protein essentiality profiling using transposon sequencing analysis combined with quantitative proteomics and metabolic maps could be used to determine and engineer metabolic fluxes.
HostingRepository	PRIDE
AnnounceDate	2020-06-08
AnnouncementXML	Submission_2020-06-07_22:58:35.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Samuel Miravet Verde
SpeciesList	scientific name: Mycoplasma pneumoniae M129; NCBI TaxID: 272634; scientific name: Mycoplasma agalactiae; NCBI TaxID: 2110;
ModificationList	No PTMs are included in the dataset
Instrument	LTQ Orbitrap Velos

Revision	Datetime	Status	ChangeLog Entry
0	2019-10-14 02:04:12	ID requested
⏵ 1	2020-06-07 22:58:36	announced

Montero-Blay A, Pi, ñ, ero-Lambea C, Miravet-Verde S, Lluch-Senar M, Serrano L, Inferring Active Metabolic Pathways from Proteomics and Essentiality Data. Cell Rep, 31(9):107722(2020) [pubmed]

submitter keyword: Mycoplasma pneumoniae, Mycoplamsa agalactiae

Luis Serrano
contact affiliation	Design of Biological Systems Lab, Centre for Genomic Regulation
contact email	luis.serrano@crg.eu
lab head
Samuel Miravet Verde
contact affiliation	Centre for Genomic Regulation
contact email	samuel.miravet@crg.eu
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/2020/06/PXD015800

PRIDE project URI

• PRIDE
  1. PXD015800
     1. Label: PRIDE project
     2. Name: Mycoplasma pneuminiae and Mycoplasma agalactiae Proteomics