PXD017122

PXD017122 is an original dataset announced via ProteomeXchange.

Title	An integrated model system to study biofilm-associated adaptation to antimicrobials and resistance evolution in Pseudomonas aeruginosa MPAO1
Description	Using an integrated model system for reproducible growth of biofilms, a JPIAMR-funded consortium of researchers* studied the expressed proteome of P. aeruginosa strain MPAO1 under i) planktonic growth, and ii) biofilm formation conditions. The model system included, as a first step, the sequencing and de novo assembly of the complete genome of this opportunistic human pathogen that belongs to the notorious group of Gram-negative ESKAPE pathogens. MPAO1 is also the parental strain for the widely used transposon (Tn) mutant library from the University of Washington. The complete MPAO1 genome sequence turned out to harbor several deletions and insertions compared to the PAO1-UW reference genome including numerous MPAO1-unique genes. As a second step in the model system, a biofilm flow cell based on poly (dimethylsiloxane) (PDMS) was designed to reproducibly study and identify known and novel genes related to biofilm growth and antibiotic resistance (ABR) from the Tn mutant collection. With the complete genome as optimal basis, publicly available TnSeq data were reanalyzed to identify known and novel essential genes. Furthermore, shotgun proteomics data was generated uncovering 1530 (planktonic) and 1728 (biofilm) expressed proteins, respectively, resulting in the identification of 1922 (33.1%) of the 5799 annotated P. aeruginosa MPAO1 proteins. They included proteins known to be differentially expressed during biofilm formation, and proteogenomic evidence for proteins uniquely encoded by MPAO1 as well as novel proteins.
HostingRepository	PRIDE
AnnounceDate	2021-09-09
AnnouncementXML	Submission_2021-09-08_18:05:14.977.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD017122
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Christian Ahrens
SpeciesList	scientific name: Pseudomonas aeruginosa; NCBI TaxID: 287;
ModificationList	monohydroxylated residue; acetylated residue; iodoacetamide derivatized residue
Instrument	Orbitrap Fusion Lumos

Revision	Datetime	Status	ChangeLog Entry
0	2020-01-15 05:36:20	ID requested
⏵ 1	2021-09-08 18:05:15	announced

Varadarajan AR, Allan RN, Valentin JDP, Casta, ñ, eda Ocampo OE, Somerville V, Pietsch F, Buhmann MT, West J, Skipp PJ, van der Mei HC, Ren Q, Schreiber F, Webb JS, Ahrens CH, An integrated model system to gain mechanistic insights into biofilm-associated antimicrobial resistance in Pseudomonas aeruginosa MPAO1. NPJ Biofilms Microbiomes, 6(1):46(2020) [pubmed]

curator keyword: Biological, Biomedical

submitter keyword: P. aeruginosa, strain MPAO1, genome sequencing, comparative genomics, transposon sequencing, biofilm, planktonic, shotgun proteomics, proteogenomics, flow chamber, antimicrobials, antibiotic resistance related proteins, colistin

Dr. Paul Skipp
contact affiliation	Associate Professor in Proteomics, Head of Proteomics, Centre for Proteomic Research, University of Southampton, UK
contact email	pjss@soton.ac.uk
lab head
Christian Ahrens
contact affiliation	Agroscope
contact email	christian.ahrens@agroscope.admin.ch
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/2021/09/PXD017122

PRIDE project URI

• PRIDE
  1. PXD017122
     1. Label: PRIDE project
     2. Name: An integrated model system to study biofilm-associated adaptation to antimicrobials and resistance evolution in Pseudomonas aeruginosa MPAO1