PXD021237

PXD021237 is an original dataset announced via ProteomeXchange.

Title	Proteomic characterization of the Pseudomonas sp. strain phDV1 response to monocyclic aromatic compounds
Description	The degradation of aromatic compounds comprises an important step in the removal of pollutants and re-utilization of plastics and other non-biological polymers. Here we set out to study Pseudomonas sp. strain phDV1, a gram-negative bacterium that was selected for its ability to degrade aromatic compounds. In order to understand how the aromatic compounds and their degradation products are reintroduced in the metabolism of the bacteria and the systematic/metabolic response of the bacterium to the new carbon source, the proteome of this strain was analysed in the presence of succinate, phenol and o-, m-, p-cresol as sole carbon source. We then applied label-free quantitative proteomics to monitor overall proteome remodeling during metabolic adaptation to different carbon sources. As a reference proteome, we grew the bacteria in succinate and then compared the respective proteomes of bacteria grown on phenol and different cresols. In total, we identified 2295 proteins; 1908 proteins were used for quantification between different growth conditions. We found that 70, 100, 150 and 155 proteins were significantly differentially expressed in cells were grown in phenol, o-, m- and p-cresol-containing medium, respectively. The carbon source affected the synthesis of enzymes related to aromatic compound degradation, and in particular, the enzyme involved in the meta-pathway of monocyclic aromatic compounds degradation. In addition, proteins involved in the production of polyhydroxyalkanoate (PHA), an attractive biomaterial, showed higher expression levels in the presence of monocyclic aromatic compounds.Our results provide for the first time comprehensive information on the proteome response of this strain to monocyclic aromatic compounds.
HostingRepository	PRIDE
AnnounceDate	2020-10-22
AnnouncementXML	Submission_2020-11-09_04:40:00.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Julian Langer
SpeciesList	scientific name: Pseudomonas sp. phDV1; NCBI TaxID: 253237;
ModificationList	monohydroxylated residue; iodoacetamide derivatized residue
Instrument	impact II

Revision	Datetime	Status	ChangeLog Entry
0	2020-09-01 00:36:42	ID requested
1	2020-10-22 05:33:29	announced
⏵ 2	2020-11-09 04:40:01	announced	2020-11-09: Updated publication reference for PubMed record(s): 33108051.

Lyratzakis A, Valsamidis G, Kanavaki I, Nikolaki A, Rupprecht F, Langer JD, Tsiotis G, Proteomic Characterization of the Pseudomonas sp. Strain phDV1 Response to Monocyclic Aromatic Compounds. Proteomics, 21(2):e2000003(2021) [pubmed]

submitter keyword: Pseudomonas, aromatic degradation, phenol, cresol

Julian Langer
contact affiliation	Proteomics and Mass Spectrometry lab Max Planck Institute of Biophysics Max Planck Institute for Brain Research Max von Laue Strasse 3/4 60438 Frankfurt am Main Germany
contact email	julian.langer@biophys.mpg.de
lab head
Julian Langer
contact affiliation	MPIs for Biophysics and Brain Research
contact email	julian.langer@biophys.mpg.de
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD021237
     1. Label: PRIDE project
     2. Name: Proteomic characterization of the Pseudomonas sp. strain phDV1 response to monocyclic aromatic compounds