PXD016863

PXD016863 is an original dataset announced via ProteomeXchange.

Title	Encystation deep proteome of Giardia duodenalis
Description	Background: Cyst formation in parasitic protist Giardia duodenalis is critical to its transmission. Proteomic data is essential for the system-level understanding of the molecular mechanisms managing stage transition from a flagellated, binucleate trophozoite to a tetra-nucleate cyst. The current encystation proteome quantifies 16% of predicted protein coding genes and lacks complete coverage of the developmental transition. Given recent gains in mass spectrometry instrumentation, we have generated significantly improved proteomes for Giardia across encystation, providing framework for transcriptome-proteome correlation drawing insights into molecular networks modulating encystation in Giardia. Results: We have reproducibly identified 3,796 (64.6% of Giardia proteins) and quantified 3,402 proteins (56.12 % of Giardia proteins), tripling the currently published encystation proteome coverage. This includes timepoints from standard trophozoite growth (TY), during low-bile encystation priming (LB), mid-encystation (EC), and enriched, mature cysts (C), making this the first proteome study across the entire encystation process. This is also the first proteome analysis of trophozoites during low bile priming prior to in vitro induction of encystation, and analysis of mature cyst proteomes. Almost 28% (1,102 proteins) of the proteome is differentially changed during encystation including within proteasomal machinery, metabolic pathways and lipid metabolism, indicating a multimodal regulation in encystation. To further understand novel observations in lipid metabolism, we used hidden markov model (HMM) based domain prediction strategies and i-Tasser based structural modelling to provide evidence for the presence of three families of lipid transporters (LTP’s) StARkin (steroidogenic acute regulatory protein–related lipid transfer), ORP/Osh (Oxysterol Binding protein related protein), GLTP (Glycosphingolipid transfer protein) in Giardia. Finally, we performed functional interaction studies using in silico docking of newly identified LTP’s with corresponding lipid ligands to validate their interaction. This identified a shift in lipid species dependency in Giardia as the parasite progress towards cyst formation.
HostingRepository	PRIDE
AnnounceDate	2023-11-14
AnnouncementXML	Submission_2023-11-14_08:50:30.376.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Samantha Emery
SpeciesList	scientific name: Giardia lamblia ATCC 50803; NCBI TaxID: 184922;
ModificationList	monohydroxylated residue; iodoacetamide derivatized residue
Instrument	LTQ Orbitrap Elite

Revision	Datetime	Status	ChangeLog Entry
0	2019-12-20 02:25:52	ID requested
1	2023-02-07 20:04:05	announced
⏵ 2	2023-11-14 08:50:30	announced	2023-11-14: Updated project metadata.

Dataset with its publication pending

submitter keyword: proteomics, deep proteome,Giardia, encystation

Aaron Jex
contact affiliation	Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia Faculty of Veterinary and Agricultural Science, University of Melbourne, Melbourne, Victoria, Australia
contact email	jex.a@wehi.edu.au
lab head
Samantha Emery
contact affiliation	Population Health and Immunity, Walter and Eliza Hall Institute of Medical Research
contact email	emery.s@wehi.edu.au
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/2023/02/PXD016863

PRIDE project URI

• PRIDE
  1. PXD016863
     1. Label: PRIDE project
     2. Name: Encystation deep proteome of Giardia duodenalis