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DNA methyltransferase (DNMT) associated proteins in human malaria parasite Plasmodium falciparum

ABSTRACT: This study identified Plasmodium falciparum DNA methyltransferase (DNMT)associated proteins in parasite cytosol and nucleus, including RNA binding proteins and AP2-domain containing proteins, indicating this protein is involved in RNA process and transctiptional regulation.

INSTRUMENT(S): Q Exactive

ORGANISM(S): Plasmodium Falciparum (isolate 3d7)

TISSUE(S): Single Nucleate Cell

DISEASE(S): Plasmodium Falciparum Malaria

SUBMITTER: JUN MIAO

LAB HEAD: Jun Miao

PROVIDER: PXD032860 | Pride | 2023-07-20

REPOSITORIES: Pride

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			Action	DRS
	20200810_3D7-TEV_Cy-1.raw	Raw
	20200810_3D7-TEV_Cy-1__F185738_.mzid.gz	Mzid
	20200810_3D7-TEV_Cy-1__F185738_.mzid_20200810_3D7-TEV_Cy-1__F185738_.MGF	Mzid
	20200810_3D7-TEV_Cy-2.raw	Raw
	20200810_3D7-TEV_Cy-2__F185739_.mzid.gz	Mzid

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1 - 5 of 41

Publications

Characterization of the dual role of Plasmodium falciparum DNA methyltransferase in regulating transcription and translation.

Lucky Amuza B AB Wang Chengqi C Li Xiaolian X Chim-Ong Anongruk A Adapa Swamy R SR Quinlivan Eoin P EP Jiang Rays R Cui Liwang L Miao Jun J

Nucleic acids research 20230501 8

DNA modifications are critical in fine-tuning the biological processes in model organisms. However, the presence of cytosine methylation (5mC) and the function of the putative DNA methyltransferase, PfDNMT2, in the human malaria pathogen, Plasmodium falciparum, remain controversial. Here, we revisited the 5mC in the parasite genome and the function of PfDNMT2. Low levels of genomic 5mC (0.1-0.2%) during asexual development were identified using a sensitive mass spectrometry procedure. Native PfD ...[more]

PMID: 37026483

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Interactome of PRMT5 in malaria parasite Plasmodium falciparum

Project description:Protein arginine methyltransferases (PRMTs) modify proteins that cause their functional change by modulating their localization and interactions with their partners, which controls their functions on cellular processes, such as transcription and signal transduction, DNA repair, and RNA processing. The majority of studies on PRMTs are focused on yeast and mammals. We characterize PfPRMT5, a type II PRMT, from the early eukaryote Plasmodium falciparum. PfPRMT5 contains the conserved domain structures of type II enzyme with a diverse long N-terminus. This study revealed that PfPRMT5 associated with other invasion related transcriptional regulators such as AP2-I and BDP1. Furthermore, PfPRMT5 was associated with RNA splicing machinery, indicating that PfPRMT5 plays a critical role in regulating invasion and harbors conserved function in RNA metabolism.

2023-06-28 | PXD032834 | Pride

Isolation of PfPuf3 protein complex and mass spectrometry (MS) analysis

Project description:Recent studies of the Puf family of RNA-binding proteins revealed that besides their traditional roles in translational regulation of mRNAs, some Puf proteins are also involved in ribosome biogenesis by binding rRNA. In this study, we report the role of a Puf-like protein (Puf3) in ribosome biogenesis in Plasmodium falciparum and Plasmodium yoelii. Secondary structure prediction suggested that the RNA-binding domain of Puf3 consists of 11 pumilio repeats, similar to human Puf-A/yeast Puf6, which is involved in ribosome biogenesis. Neither pfpuf3 nor pypuf3 could be genetically disrupted, suggesting they may be essential for the intraerythrocytic developmental cycle (IDC). A time-course study of PfPuf3 protein indicated that PfPuf3 was expressed during the entire IDC, with peak expression in early trophozoites. Cellular fractionation of PfPuf3 revealed that it is preferentially partitioned to the nuclear rather than the cytoplasmic fractions, which is consistent with a nuclear localization of PfPuf3::GFP and PyPuf3::GFP as seen by immunofluorescence. Further, we found PfPuf3 co-localized with a well-known nucleolus maker, PfNop1, demonstrating that PfPuf3 is a nucleolar protein. This localization is in contrast to the cytoplasmic localization of PfPuf1 and PfPuf2, but matches the localization of human Puf-A and yeast Puf6. Affinity purification of a C-terminal PTP-tagged variant of PfPuf3 revealed an association with 32 proteins associated with the 60S ribosome, and an enrichment of 28S rRNA and internal transcribed spacer 2. Taken together, these results demonstrate a nucleolar localization of PfPuf3 and suggest an essential function of PfPuf3 in ribosomal biogenesis.

2018-03-12 | PXD007978 | Pride

mRNAs associated with EIF4E1 and EIF4E6 in Trypanosoma brucei

Project description:Trypanosomes expressing PTP-tagged EIF4E1 (PCF) or EIF4E6 (BSF) were used. The PTP-tagged proteins were purified on IgG columns, then eluted with TEV protease.

2021-05-22 | E-MTAB-10453 | biostudies-arrayexpress

The human nuclear exosome targeting complex is loaded onto newly synthesized RNA to direct early ribonucleolysis

Project description:Individual-nucleotide resolution UV-crosslinking and immunoprecipitation (iCLIP) followed by high-throughput sequencing of RBM7-associated transcripts. Note: these data relate to Figure 1, 2, 3, 4, 5 and 6 in Lubas, Andersen et al., Cell Reports 2014 RBM7-associated transcripts

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ChIP-Seq of Myf5, MyoD, Snai1, HDAC1, HDAC2, E47 and empty vector controls in mouse skeletal myoblasts or myotubes

Project description:In skeletal myogenesis, the transcription factor MyoD activates distinct transcriptional programs in progenitors compared to terminally differentiated cells. Using ChIP-seq and gene expression analyses, we show that in primary myoblasts, Snail-HDAC1/2 repressive complex bind and exclude MyoD from its targets. Notably, Snail binds E-box motifs that are G/C-rich in their central dinucleotides, and such sites are almost exclusively associated with genes expressed during differentiation. By contrast, Snail does not bind the A/T-rich E-boxes associated with MyoD targets in myoblasts. Thus, Snai1-HDAC1/2 prevents MyoD occupancy on differentiation-specific regulatory elements and the change from Snail- to MyoD-binding often results in enhancer switching during differentiation. Furthermore, we show that a regulatory network involving Myogenic Regulatory Factors (MRFs), Snail/2, miR-30a and miR-206 acts as a molecular switch that controls entry into myogenic differentiation. Together, these results reveal a regulatory paradigm that directs distinct gene expression programs in progenitors versus terminally differentiated cells. Genome wide binding sites of various transcription factors and chromatin modifiers in muscle cells

2012-07-04 | E-GEOD-24852 | biostudies-arrayexpress

Enhancer-bound LDB1 Regulates a Corticotrope Promoter Pausing Repression Program [ChIP-seq]

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2015-02-03 | E-GEOD-64483 | biostudies-arrayexpress

SUMO targets the APC/C in a phosphorylation-dependent manner to regulate transition from metaphase to anaphase

Project description:Signal transduction by Small Ubiquitin-like Modifier (SUMO) regulates a myriad of nuclear processes. Here, we report on the role of SUMO in mitosis in human cell lines. Knocking down the SUMO conjugation machinery resulted in a delay in mitosis and defects in mitotic chromosome separation. Searching for relevant SUMOylated proteins in mitosis, we identified the APC/C complex, a master regulator of metaphase to anaphase transition, as a SUMO target. The APC4 subunit is the major SUMO target in the complex, containing SUMO acceptor lysines at positions 772 and 798. SUMOylation increased APC/C ubiquitylation activity towards a subset of its targets, including the newly identified target KIF18B. Intriguingly, SUMOylation of APC/C was regulated by casein kinase driven phosphorylation of serines at positions 777 and 779. Combined, our findings demonstrate the importance of SUMO signal transduction for genome integrity during mitotic progression and reveal a triad of PTMs, cooperating to drive mitosis.

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Interacting partners of Trypanosoma brucei EIF4E2

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2022-10-18 | PXD033511 | Pride

Snail regulates MyoD binding-site occupancy to direct enhancer switching and differentiation-specific transcription in myogenesis

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