PXD023389

PXD023389 is an original dataset announced via ProteomeXchange.

Title	GCN5 associated complex in human malaria Plasmodium falciparum
Description	The histone acetyltransferase (HAT) GCN5-associated SAGA complex is evolutionarily conserved from yeast to human and functions as a general transcription co-activator in global gene regulation. To study GCN5 associated complex in human malaria parasite Plasmodium falciparum, PfGCN5 was tagged with PTP tag for a tandem affinity purification (TAP). We performed the TAP procedure using nuclear extracts from synchronized trophozoites of the PfGCN5::PTP parasite, which was followed by liquid chromatography and tandem mass spectrometry (LC-MS/MS) for accurate protein identification. The MS data were subjected to Significance Analysis of INTeractome (SAINT) using a threshold of probability above 94% and false discovery rate (FDR) below 1% (Teo et al., 2014). Nine proteins were identified as core components of PfGCN5 complex including a plant apetela2 (AP2)-domain transcription factor (PF3D7_0802100), three hypothetical proteins with unknown function (PF3D7_1019700, PF3D7_1364400 and PF3D7_1402800) and two PHD domain containing proteins (PF3D7_1008100 and PF3D7_1433400, named as PfPHD1 and PfPHD2). Among them, only PfGCN5 and PfADA2 are known as the components of SAGA complex, indicating PfGCN5 complex is highly divergent from SAGA complex. To confirm the subunits identified by TAP, PfPHD1 and PF3D7_1019700 were tagged with C-myc and GFP tag, respectively. Immuno-precipitations (IPs) from parasites with PfPHD1-myc and PF3D7_1019700-GFP were conducted with myc- or GFP-trap beads followed by LC-MS/MS. Indeed, the core complex were identified by these reciprocal pulldowns. To study the function of PfGCN5 complex, Bromodomain (BrD) in PfGCN5 and PHD in PfPHD1 at the C-termini of PfGCN5 and PfPHD1 were deleted and meanwhile tag the C-termini of these truncated proteins with a GFP tag for sorting parasites with truncated PfGCN5 or PfPHD1. The parasite lines with these deletions grew significantly slower with substantial defect in merozoite invasion. IPs by GFP-trap beads from these parasites were performed to reveal the integrity of PfGCN5 complex after domain deletion. IPs with the PfGCN5-∆BrD::GFP parasites confidently purified the nine core subunits of the PfGCN5 complex, suggesting the deletion of the BrD from PfGCN5 did not affect the integrity of the complex, whereas only four major components of the PfGCN5 complex (PfGCN5, PfADA2, PfPHD1, and PF3D7_1402800) were detected from the PfPHD1-∆PHD::GFP parasites. Collectively, the PfGCN5 complex represents a novel HAT complex with a unique subunit composition including the AP2 transcription factor, which signifies a new paradigm for targeting the co-activator complex to regulate general and parasite-specific cellular processes in this low-branching parasitic protist.
HostingRepository	PRIDE
AnnounceDate	2021-08-06
AnnouncementXML	Submission_2021-08-06_00:53:00.215.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD023389
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	JUN MIAO
SpeciesList	scientific name: Plasmodium falciparum 3D7; NCBI TaxID: 36329;
ModificationList	No PTMs are included in the dataset
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2021-01-04 03:59:44	ID requested
⏵ 1	2021-08-06 00:53:00	announced

Dataset with its publication pending

submitter keyword: GCN5, Malaria, Plasmodium falciparum

Jun Miao
contact affiliation	Internal Medicine Morsani College of Medicine University of South Florida
contact email	jmiao1@usf.edu
lab head
JUN MIAO
contact affiliation	University of Sourth Florida
contact email	jmiao1@usf.edu
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD023389
     1. Label: PRIDE project
     2. Name: GCN5 associated complex in human malaria Plasmodium falciparum