PXD045993

PXD045993 is an original dataset announced via ProteomeXchange.

Title	Comprehensive proteomics analysis of polyhydroxyalkanoate (PHA) biology in Pseudomonas putida KT2440: the outer membrane lipoprotein OprL is a newly identified phasin Dataset 3
Description	Pseudomonas putida KT2440 is an important bioplastic-producing industrial microorganism capable of synthesizing the polymeric carbon-rich storage material, polyhydroxyalkanoate (PHA). PHA is sequestered in discrete PHA granules, or carbonosomes, and accumulates under conditions of stress, for example low levels of available nitrogen. The pha locus responsible for PHA metabolism encodes both anabolic and catabolic enzymes, a transcription factor, and carbonosome-localized proteins termed phasins. The functions of phasins are incompletely understood but genetic disruption of their function causes PHA-related phenotypes. To improve our understanding of these proteins, we investigated the PHA pathways of P.putida KT2440 using three types of experiment. First, we profiled cells grown in nitrogen-limited and nitrogen-excess media using global expression proteomics, identifying sets of proteins found to co-ordinately increase or decrease within clustered pathway. Next, we analysed the protein composition of isolated carbonosomes, identifying two new putative components. We carried out physical interaction screens focused on PHA-related proteins, generating a protein-protein network comprising 434 connected proteins. Finally, we confirmed that the outer membrane protein OprL (the Pal component of the Pal-Tol system) localizes to the carbonosome and shows a PHA-related phenotype, and therefore is a novel phasin. The combined datasets represent a valuable overview of the protein components of the PHA system in P.putida highlighting the complex nature of regulatory interactions responsive to nutrient stress.
HostingRepository	PRIDE
AnnounceDate	2024-06-16
AnnouncementXML	Submission_2024-06-15_23:18:35.320.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Eugene Dillon
SpeciesList	scientific name: Pseudomonas putida KT2440; NCBI TaxID: 160488;
ModificationList	acetylated residue; monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2023-10-09 05:59:28	ID requested
⏵ 1	2024-06-15 23:18:36	announced

10.1016/j.mcpro.2024.100765;

Kelly S, Tham JL, McKeever K, Dillon E, O'Connell D, Scholz D, Simpson JC, O'Connor K, Narancic T, Cagney G, Comprehensive Proteomics Analysis of Polyhydroxyalkanoate (PHA) Biology in Pseudomonas putida KT2440: The Outer Membrane Lipoprotein OprL is a Newly Identified Phasin. Mol Cell Proteomics, 23(5):100765(2024) [pubmed]

submitter keyword: proteomics, pseudomonas putida,bioplastics

Gerard Cagney
contact affiliation	School of Biomolecular and Biomedical Science, University College Dublin, Belfield, Dublin 4, Ireland
contact email	gerard.cagney@ucd.ie
lab head
Eugene Dillon
contact affiliation	UCD
contact email	eugene.dillon@ucd.ie
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/2024/06/PXD045993

PRIDE project URI

• PRIDE
  1. PXD045993
     1. Label: PRIDE project
     2. Name: Comprehensive proteomics analysis of polyhydroxyalkanoate (PHA) biology in Pseudomonas putida KT2440: the outer membrane lipoprotein OprL is a newly identified phasin Dataset 3