{"database":"Pride","file_versions":[{"headers":{"Content-Type":["application/json"]},"body":{"files":{"Txt":["ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD059094/peptides.txt","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD059094/parameters.txt","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD059094/proteinGroups.txt","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD059094/mzRange.txt","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD059094/msScans.txt","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD059094/summary.txt","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD059094/msmsScans.txt","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD059094/Oxidation_M_Sites.txt","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD059094/allPeptides.txt","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD059094/modificationSpecificPeptides.txt","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD059094/msms.txt","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD059094/evidence.txt"],"Raw":["ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD059094/C3.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD059094/A1.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD059094/A3.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD059094/C2.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD059094/C1.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD059094/A2.raw"]},"type":"primary"},"statusCode":"OK","statusCodeValue":200}],"scores":null,"additional":{"labhead_mail":["marcellcrispim@gmail.com"],"submitter":["Ignasi Bofill Verdaguer"],"technology_type":["Data-dependent acquisition","Mass Spectrometry","Bottom-up proteomics"],"disease":["Plasmodium Falciparum Malaria"],"software":[""],"submitter_keywords":["Plasmodium falciparum","Prenol kinase","Malaria","Geranylgeraniol","Farnesol","Isoprenoid metabolism","Knockout"],"full_dataset_link":["https://www.ebi.ac.uk/pride/archive/projects/PXD059094"],"tissue":["Permanent Cell Line Cell","Cell Culture"],"sample_protocol":["Parasites transgenic P. falciparum parasites preserving the PfPolK gene (control; Sample A; x3 replicates) to parasites in which the gene was excised as explained elsewhere (Sample C; x3 replicates) (Crispim et al., 2024). 5 mL of synchronous cultures of P. falciparum at trophozoite-schizont stage were centrifuged in 1.5 mL microtubes at 2000 x g for 10 min, and parasites were obtained through saponin lysis (Christopher & Fulton, 1939). For this, cultures pellets were lysed with 1 mL 0.03 % saponin in PBS at 4 °C. Parasites were then centrifuged at 1,500 x g for 5 min at 4 °C and subsequently washed in PBS. Parasites were purified of lipids and other contaminants by SDS-PAGE. For this purpose, it was used 50 µg of parasite protein solubilized in Laemmli Buffer per sample, prepared as described before. Three replicates for each parasite strain extracts were loaded on a 10% SDS-PAGE and run for 1-2 cm. The gel bands containing all proteins were then excised and proteins were in-gel digested as previously described (Shevchenko et al. 2006). Briefly, gel bands were distained with 40% acetonitrile in 50 mM ammonium bicarbonate (AMBIC), were reduced with 10 mM 1,4-Dithiothreitol (DTT) in 50 mM AMBIC for for 45 min at 56°C, alkylated with 55 mM iodoacetamide in 50 mM AMBIC  30 min at room temperature, protected from light Protein was digested into peptides by trypsin (Promega) at 1:50 (w/w) at 37°C for 16 h. The reaction was stopped with trifluoroacetic acid (TFA) at a 1% final concentration. The peptides were extracted from gel using 40% acetonitrile and 0.1% TFA  and  were purified on a house made C18 stagetips (Thermo Scientific) (Gobom et al., 1999; Larsen et al., 2002). The peptides were dried under a vacuum centrifuge, and stored at −20 °C for further analysis. The samples analysis were performed at Biomass—Mass Spectrometry and Proteome Discovery Facility at Centro de Facilidades à Pesquisa (CEFAP-USP) of the Institute of Biomedical Sciences of the University of São Paulo, using an EASY-nano LC system (Thermo Scientific) coupled to a LTQ-Orbitrap Velos mass spectrometer (Thermo Scientific). Peptides were loaded into a C18 PicoFrit column (C18 PepMap, 75 µm id × 10 cm, 3.5 µm particle size, 100 Å pore size; New Objective, Ringoes, NJ, USA) and eluted at a flow rate of 300 nL/min using a linear gradient of 2–30% phase B (0.1% formic acid, 95% acetonitrile) for 105 min. Mass spectra were acquired in positive ionization mode using a data dependent acquisition method where the top 20 most intense precursor ions at MS1 spectra with charge-state ≥2, acquired at a 60,000 FWHM resolution, 400-1500 m/z mass range and a minimum threshold of 1x106 were selected to fragmentation using CID at 35 normalized collision energy, 10 ms activation time and 30 s of dynamic exclusion.   REFERENCES • Christophers, S. R., & Fulton, J. D. (1939). Experiments with isolated malaria parasites (Plasmodium knowlesi) free from red cells. Annals of Tropical Medicine & Parasitology, 33(2), 161-170. • Crispim M, Verdaguer IB, Hernández A, Kronenberger T, Fenollar À, Yamaguchi LF, Alberione MP, Ramirez M, de Oliveira SS, Katzin AM, Izquierdo L. Beyond the MEP Pathway: A novel kinase required for prenol utilization by malaria parasites. PLoS Pathog. 2024 Jan 26;20(1):e1011557. doi: 10.1371/journal.ppat.1011557. PMID: 38277417; PMCID: PMC10849223. • Gobom, J., Nordhoff, E., Mirgorodskaya, E., Ekman, R., and Roepstorff, P. (1999). Sample purification and preparation technique based on nano-scale reversed-phase columns for the sensitive analysis of complex peptide mixtures by matrix-assisted laser desorption/ionization mass spectrometry. J. Mass Spectrom. 34, 105–116. doi:10.1002/(sici)1096-9888(199902)34:2<105::aid-jms768>3.0.co;2-4 • Larsen, M. R., Cordwell, S. J., and Roepstorff, P. (2002). Graphite powder as an alternative or supplement to reversed-phase material for desalting and concentration of peptide mixtures prior to matrix-assisted laser desorption/ionization-mass spectrometry. Proteomics 29, 1277–1287. • Shevchenko, A., Tomas, H., Havlis, J., Olsen, J. V., & Mann, M. (2006). In-gel digestion for mass spectrometric characterization of proteins and proteomes. Nature protocols, 1(6), 2856–2860."],"repository":["Pride"],"quantification_method":[""],"modification":[""],"data_protocol":["Raw data were accessed in Xcalibur v.2.1 (Thermo Scientific) and data processing was performed using MaxQuant version 1.5.3.8 for protein identification and quantification, using Andromeda search engine against P. falciparum 3D7 strain database downloaded from PlasmoDB (https://plasmodb.org/plasmo/app, last accessed in April 2024). The protein expression data were processed using Perseus 2.0.7.0 computational platform (Tyanova et al., 2016). LFQ Intensities data were log2 transformed, protein reverse, contaminants were removed and the proteins data was filtered by at least two valid values in at least one experimental group. Imputation was performed where missing values were replaced by random values drawn from a normal distribution.  The analysis of protein abundance between the experiments was performed using two different statistical methodologies. The more restrictive method involved a paired Student t-test comparation between the experiments (with or without PfPolK preservation in parasites), using Benjamini-Hochberg FDR correction. Proteins with an FDR < 0.05 were considered regulated proteins. Alternatively, the less restrictive method involved a paired Student t-test, where proteins with a p-value < 0.05 were considered differentially abundant proteins. Hierarchical clustering analysis was performed after Z-score normalization. Gene Ontology Biological Process and Cell Component analysis were performed using the tools available on PlasmoDB (https://plasmodb.org/plasmo/app, last accessed in April 2024). Specifically, the PlasmoDB accession numbers were employed to find the GO terms of regulated/exclusive proteins. For this, it was performed a Gene Ontology Enrichment of biological processes, with evidence computed or curated, limiting to GO Slim terms (p-Value cutoff = 1). REFERENCES • Tyanova, S., Temu, T., Sinitcyn, P., Carlson, A., Hein, M. Y., Geiger, T., ... & Cox, J. (2016). The Perseus computational platform for comprehensive analysis of (prote) omics data. Nature methods, 13(9), 731-740."],"omics_type":["Proteomics"],"labhead":["Marcell Crispim"],"instrument_platform":[""],"labhead_affiliation":["Department of Clinical and Toxicological Analysis, Federal University of Alfenas, Brazil"],"submission_type":["PARTIAL"],"species":["Plasmodium Falciparum Nf54"],"submitter_mail":["ig_la123@hotmail.com"],"publication":["10.21203/RS.3.RS-6574048/V1"],"submitter_affiliation":["Institute of Biomedical Sciences of the University of São Paulo"],"submitter_country":["Brazil"],"additional_accession":[]},"is_claimable":false,"name":"Comparative proteomic analysis of Plasmodium falciparum parasites with and without the prenol kinase-encoding gene (knockout parasites)","description":"The methylerythritol 4-phosphate (MEP) pathway, essential for producing isoprenoids in Plasmodium parasites. The key isoprenoids produced by the MEP pathway are farnesyl and geranylgeranyl pyrophosphates (FPP and GGPP), vital for protein isoprenylation, ubiquinone, and dolichol biosynthesis. In vitro studies have demonstrated that prenols, like farnesol (FOH) and geranylgeraniol (GGOH), can temporarily circumvent the MEP pathway, rescuing parasites from MEP inhibitors (Crispim et al., 2024). It was identified a gene in the genome of P. falciparum, encoding a transmembrane prenol kinase (PolK) involved in the salvage of FOH and GGOH. The enzyme was expressed in Saccharomyces cerevisiae, and its FOH/GGOH kinase activities were experimentally validated. Furthermore, conditional knockout parasites (Δ-PolK) were created to investigate the biological importance of the FOH/GGOH salvage pathway. Δ-PolK parasites were viable but displayed increased susceptibility to fosmidomycin. Their sensitivity to MEP inhibitors could not be rescued by adding prenols. We decided to explore the biological role of PolK through proteomics. To this end, we compared proteomic profiles between transgenic P. falciparum parasites preserving the PfPolK gene (control) to parasites in which the gene was excised as explained elsewhere (Crispim et al., 2024). Proteomic analysis was performed with three replicates of each sample (parasites preserving or not PfPolK) and it was identified 442 proteins in control parasites compared to 439 in PfPolK knockout parasites. Of these, 24 proteins were only present in parasites lacking PfPolK compared to the control, which had 27 exclusive proteins found. Pyruvate kinase II (PF3D7_1037100) was exclusively detected in parasites lacking PfPolK, and not in control parasites. Paired t-test between groups using Benjamini-Hochberg-based FDR correction (FDR < 0.05) led to the identification of regulated proteins. Molecular deletion of PfPolK upregulated the expression of 37 proteins and downregulated 12, compared to control parasites. Most regulated proteins are enzymes, especially those related to the following GO terms: carbohydrate metabolic process (GO:0005975), nucleobase-containing small molecule metabolic process (GO:0055086), cellular amino acid metabolic process (GO:0006520), carbohydrate derivative metabolic process (GO:1901135), tRNA metabolic process (GO:0006399), protein catabolic process (GO:0030163). The excision of PfPolK upregulated the expression of proliferating cell nuclear antigen 1 (PCNA, PF3D7_1361900), several tRNA ligases (e.g.: leucine--tRNA ligase, PF3D7_0622800; cysteine--tRNA ligase, PF3D7_1015200), as well as several enzymes related to oxidative stress defense (e.g.: glutathione S-transferase, PF3D7_1419300 thioredoxin 1, PF3D7_1457200 )  and proteostasis (e.g.: heat shock protein 110, PF3D7_0708800; Hsp70/Hsp90 organizing protein, PF3D7_1434300), together with some enzymes related to protein catabolism (e.g.: plasmepsin III, PF3D7_1408100; aminopeptidase P, PF3D7_1454400). The excision of PfPolK make no detectable or downregulated Ras-related protein Rab-2 (PF3D7_1231100) and merozoite surface protein 1 and 2 (PF3D7_0930300 and PF3D7_0206800, respectively) which are prenylated/glycosylated proteins which may been affected of some dysregulation of the isoprenoid pathway. Contradictorily, parasites lacking PfPolK showed an upregulation of HAD-2 (PF3D7_1226300) along with several glycolytic enzymes or glucose metabolism-related enzymes, including hexokinase (PF3D7_0624000), fructose-bisphosphate aldolase (PF3D7_1444800), enolase (PF3D7_1015900), and the glycolytic pyruvate kinase type I (PF3D7_0626800) and inositol-3-phosphate synthase (PF3D7_0511800).  REFERENCES • Crispim M, Verdaguer IB, Hernández A, Kronenberger T, Fenollar À, Yamaguchi LF, Alberione MP, Ramirez M, de Oliveira SS, Katzin AM, Izquierdo L. Beyond the MEP Pathway: A novel kinase required for prenol utilization by malaria parasites. PLoS Pathog. 2024 Jan 26;20(1):e1011557. doi: 10.1371/journal.ppat.1011557. PMID: 38277417; PMCID: 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