PXD015800 is an
original dataset announced via ProteomeXchange.
Dataset Summary
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 |
Dataset History
Revision | Datetime | Status | ChangeLog Entry |
0 | 2019-10-14 02:04:12 | ID requested | |
⏵ 1 | 2020-06-07 22:58:36 | announced | |
Publication List
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] |
Keyword List
submitter keyword: Mycoplasma pneumoniae, Mycoplamsa agalactiae |
Contact List
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 | |
Full Dataset Link List
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 |
Repository Record List
[ + ]
[ - ]
- PRIDE
- PXD015800
- Label: PRIDE project
- Name: Mycoplasma pneuminiae and Mycoplasma agalactiae Proteomics