PXD022356

PXD022356 is an original dataset announced via ProteomeXchange.

Title	Mycoplasma pneumoniae processes functionally diverse proteins (N-Terminiome & Surfaceome)
Description	Mycoplasma pneumoniae is a significant cause of pneumonia, particularly in children, the elderly and the immunocompromised, and post infection sequelae affecting organ sites distant to the respiratory tract are common. It is also a model pathogen where extensive ‘omics’ studies have been conducted to gain insight into how minimal genome self-replicating organisms function. Here we conducted an N-terminome study to determine which proteins are targets of processing events in M. pneumoniae. We identified 6,973 unique N-terminal peptides that mapped to 391 (56%) predicted M. pneumoniae proteins. True N-terminal sequences beginning with the initiating methionine (iMet) residue from the predicted Open Reading Frame (ORF) were identified for 163 proteins. Nearly half (317; 46%) of the ORFS derived from M. pneumoniae strain M129 are post-translationally modified, presumably by proteolytic processing, because dimethyl labelled neo-N-termini were characterised that mapped beyond the predicted N-terminus. An analysis of the N-terminome describes endoproteolytic processing events which predominately target negatively charged residues in P1′ (D and E) with lysine or serine/alanine in P2′ and P3′ positions. Surfaceome studies identified 160 proteins (23% of the proteome) to be exposed on the extracellular surface of M. pneumoniae. The two orthogonal methodologies used to characterise the surfaceome each identified the same 116 proteins, a 72% (116/160) overlap. Apart from lipoproteins, transporters, and adhesins, 93/160 (58%) of the surface proteins lack signal peptides and have well characterised, canonical functions in the cell. Mycoplasma pneumoniae culture conditions The M. pneumoniae (strain M129) cells were cultured in modified Hayflick’s medium at 37 °C in tissue culture flasks using established culture conditions63. Modified Hayflick’s medium contained 21 g PPLO broth base without crystal violet, 5 g of D-glucose, 4 mL of 0.5% phenol red, 100 mL of liquid yeast extract (150 g/L), 200 mL heat-inactivated horse serum (56 °C, 30 min) supplemented with 1 g ampicillin (Sigma, A5354, St. Louis, MO, USA) per litre. M. pneumoniae cells were harvested at mid-log phase by washing adherant cells 3 times with PBS and collected using cell scaping.
HostingRepository	PRIDE
AnnounceDate	2021-05-01
AnnouncementXML	Submission_2021-05-02_23:16:09.171.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Joel Steele
SpeciesList	scientific name: Mycoplasma pneumoniae; NCBI TaxID: 2104; scientific name: Mycoplasma pneumoniae M129; NCBI TaxID: 272634;
ModificationList	S-carboxamidoethyl-L-cysteine; monohydroxylated residue; alpha-amino dimethylated residue; deamidated residue
Instrument	QSTAR; TripleTOF 5600; Q Exactive Plus

Revision	Datetime	Status	ChangeLog Entry
0	2020-11-04 08:20:18	ID requested
1	2021-05-01 06:59:47	announced
⏵ 2	2021-05-02 23:16:10	announced	2021-05-03: Updated publication reference for PubMed record(s): 33762641.

Berry IJ, Widjaja M, Jarocki VM, Steele JR, Padula MP, Djordjevic SP, Protein cleavage influences surface protein presentation in Mycoplasma pneumoniae. Sci Rep, 11(1):6743(2021) [pubmed]

submitter keyword: Mycoplasma, pneumonia, N-Terminiome, Surfaceome, Affinity

Professor Steven Djordjevic
contact affiliation	ithree institute, University of Technology Sydney, PO Box 123, Broadway, NSW, 2007, Australia
contact email	Steven.Djordjevic@uts.edu.au
lab head
Joel Steele
contact affiliation	University of Technology Sydney
contact email	joel.r.steele@gmail.com
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/2021/05/PXD022356

PRIDE project URI

• PRIDE
  1. PXD022356
     1. Label: PRIDE project
     2. Name: Mycoplasma pneumoniae processes functionally diverse proteins (N-Terminiome & Surfaceome)