PXD001219

PXD001219 is an original dataset announced via ProteomeXchange.

Title	Proteomics analysis of Pseudomonas putida F1: From Early-Exponential to Late-Stationary
Description	The genus Pseudomonas is a very versatile and heterogeneous group whose members regularly serve as model system of various applications. These include pathogens and rhizospheric strains as well as organisms with exceptional broad substrate ranges. Nevertheless, when it comes to physiological adaptation due to cell density and growth, on transcript- or proteome level, our knowledge is rather limited. The few existing studies so far focused mainly on B. subtilis and E. coli. In this study Pseudomonas putida F1, a model for the degradation of aromatic compounds, and its adaptation to stationary growth was investigated by label-free proteome quantification. The data unveiled that entrance to the stationary phase does not involve an abrupt switch within the P. putida F1 proteome, but is rather an ongoing adaptation which starts during exponential growth which is illustrated by principle component and functional enrichment analysis. These changes were especially metabolic adaptations, which involved a clear increase in amino acid degradation capabilities and a loss of transcription as well as translation capacity. The final entrance to the stationary phase was accompanied by increased oxidative stress protection, although the stress and stationary sigma factor RpoS increased in abundance already during mid-exponential growth. Finally, the data supports previous observations that phenylacetic acid concentrations might play an important role in growth and pathogenicity regulation within Pseudomonades.
HostingRepository	PRIDE
AnnounceDate	2015-07-24
AnnouncementXML	Submission_2015-07-24_08:59:51.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Florian-Alexander Herbst
SpeciesList	scientific name: Pseudomonas putida (strain F1 / ATCC 700007); NCBI TaxID: 351746;
ModificationList	iodoacetamide derivatized residue
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2014-08-12 06:41:51	ID requested
⏵ 1	2015-07-24 08:59:52	announced

Herbst FA, Danielsen HN, Wimmer R, Nielsen PH, Dueholm MS, Label-free quantification reveals major proteomic changes in Pseudomonas putida F1 during the exponential growth phase. Proteomics, 15(18):3244-52(2015) [pubmed]

curator keyword: Biological

submitter keyword: Pseudomonas, growth, microbial proteomics, RpoS, exponential, stationary

Per Halkjær Nielsen
contact affiliation	Head of Center for Microbial Communities | Department of Biotechnology, Chemistry and Environmental Engineering Aalborg University | Sohngaardsholmsvej 49 | 9000 Aalborg | Denmark
contact email	phn@bio.aau.dk
lab head
Florian-Alexander Herbst
contact affiliation	Aalborg University
contact email	fah@bio.aau.dk
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD001219
     1. Label: PRIDE project
     2. Name: Proteomics analysis of Pseudomonas putida F1: From Early-Exponential to Late-Stationary