المؤلفون: Govindaraju, Gayathri, Jabeena, CA., Sethumadhavan, Devadathan Valiyamangalath, Rajaram, Nivethika, Rajavelu, Arumugam

المصدر: BBA - Gene Regulatory Mechanisms; Oct2017, Vol. 1860 Issue 10, p1047-1057, 11p

مستخلص: In eukaryotes, cytosine methylation regulates diverse biological processes such as gene expression, development and maintenance of genomic integrity. However, cytosine methylation and its functions in pathogenic apicomplexan protozoans remain enigmatic. To address this, here we investigated the presence of cytosine methylation in the nucleic acids of the protozoan Plasmodium falciparum. Interestingly, P. falciparum has TRDMT1, a conserved homologue of DNA methyltransferase DNMT2. However, we found that TRDMT1 did not methylate DNA, in vitro . We demonstrate that TRDMT1 methylates cytosine in the endogenous aspartic acid tRNA of P. falciparum . Through RNA bisulfite sequencing, we mapped the position of 5-methyl cytosine in aspartic acid tRNA and found methylation only at C38 position. P. falciparum proteome has significantly higher aspartic acid content and a higher proportion of proteins with poly aspartic acid repeats than other apicomplexan pathogenic protozoans. Proteins with such repeats are functionally important, with significant roles in host-pathogen interactions. Therefore, TRDMT1 mediated C38 methylation of aspartic acid tRNA might play a critical role by translational regulation of important proteins and modulate the pathogenicity of the malarial parasite. [ABSTRACT FROM AUTHOR]

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المؤلفون: Sethumadhavan, Devadathan Valiyamangalath^1,2 (AUTHOR), Tiburcio, Marta³ (AUTHOR), Kanyal, Abhishek⁴ (AUTHOR), Jabeena, C.A.^1,2 (AUTHOR), Govindaraju, Gayathri^1,2 (AUTHOR), Karmodiya, Krishanpal⁴ (AUTHOR), Rajavelu, Arumugam^1,5 (AUTHOR) arumugam.rajavelu@iitm.ac.in

المصدر: Journal of Molecular Biology. Jun2022, Vol. 434 Issue 12, pN.PAG-N.PAG. 1p.

مستخلص: [Display omitted] • The human malaria parasite Plasmodium falciparum expresses virulence proteins on the surface of infected RBCs. • P. falciparum chromodomain containing protein (CDP) binds to the H3K9me3 mark. • Interaction of PfCDP – H3K9me3 suppresses the expression of subsets of RIFINs family proteins. • Deletion of PfCDP in P. falciparum upregulates the subsets of RIFINs expression and promotes the RBC resetting. Plasmodium falciparum expresses clonally variant proteins on the surface of infected erythrocytes to evade the host immune system. The clonally variant multigene families include var, rifin, and stevor, which express Erythrocyte Membrane Protein 1 (EMP1), Repetitive Interspersed Families of polypeptides (RIFINs), and Sub-telomeric Variable Open Reading frame (STEVOR) proteins, respectively. The rifins are the largest multigene family and are essentially involved in the RBC rosetting, the hallmark of severe malaria. The molecular regulators that control the RIFINs expression in Plasmodium spp. have not been reported so far. This study reports a chromodomain-containing protein (PfCDP) that binds to H3K9me3 modification on P. falciparum chromatin. Conditional deletion of the chromodomain (CD) gene in P. falciparum using an inducible DiCre-LoxP system leads to selective up-regulation of a subset of virulence genes, including rifins, a few var, and stevor genes. Further, we show that PfCDP conditional knockout (PfΔCDP) promotes RBC rosette formation. This study provides the first evidence of an epigenetic regulator mediated control on a subset of RIFINs expression and RBC rosetting by P. falciparum. [ABSTRACT FROM AUTHOR]

المؤلفون: Sethumadhavan, Devadathan Valiyamangalath, Govindaraju, Gayathri, Jabeena, C.A., Rajavelu, Arumugam

المصدر: BBA - Gene Regulatory Mechanisms; Oct2021, Vol. 1864 Issue 10, pN.PAG-N.PAG, 1p

مستخلص: The antigenic variation is an essential mechanism employed by the malaria parasite to establish a chronic infection in humans. Three major virulent proteins EMP1, RIFINs, and STEVOR have been implicated in contributing to the antigenic variation process and are encoded by multigene families in Plasmodium spp. The key virulence factor PfEMP1 is encoded by var genes, and it exhibits a mutually exclusive transcriptional switching between var genes, ensuring an individual parasite only transcribes a single var gene at a time. Expression of var genes is tightly regulated by two histone epigenetic methylation marks H3K36me3 and H3K9me3, of which the H3K36me3 mark is highly enriched on transcription start sites (TSSs) of suppressed var genes in P. falciparum. However, the mechanisms of H3K36me3 mark propagation on all the 59 var genes of P. falciparum are not known. Here, we have identified a PHD (Plant Homeodomain-like Domain) like domain present within the PfSET2 protein that specifically binds to the H3K36me2 mark, an intermediate product of the H3K36me3 mark formation on the nucleosome. Surprisingly, we have found that PHD - H3K36me2 interaction leads to stimulation of SET2 domain activity on the nucleosome substrates. The allosteric stimulation of the PfSET2 domain by PHD-like domain present within the same protein suggests a novel mechanism of H3K36me3 mark propagation on var genes of P. falciparum. This study proposes allosteric regulation of PfSET2 protein by H3K36me2 mark as an essential mechanism of var genes suppression to ensure successful antigenic variation by the malaria parasite. • Plasmodium falciparum virulence genes are tightly controlled by epigenetic mark H3K36me3. • Reporting a methyl-reader domain to H3K36me3 mark • Allosteric activation of PfSET2 domain methyltransferase activity by H3K36me2 mark • A novel mechanisms of H3K36me3 mark propagation on the var genes of P. falciparum [ABSTRACT FROM AUTHOR]

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المؤلفون: Govindaraju, Gayathri, Kadumuri, Rajashekar Varma, Sethumadhavan, Devadathan Valiyamangalath, Jabeena, C. A., Chavali, Sreenivas, Rajavelu, Arumugam

المصدر: Epigenetics & Chromatin; 8/31/2020, Vol. 13 Issue 1, pN.PAG-N.PAG, 1p

مصطلحات موضوعية: PLASMODIUM falciparum, PROTEIN domains, PLASMODIUM, MESSENGER RNA, MOLECULAR dynamics, METHYLATION

مستخلص: Background: Plasmodium falciparum exhibits high translational plasticity during its development in RBCs, yet the regulation at the post-transcriptional level is not well understood. The N⁶-methyl adenosine (m6A) is an important epigenetic modification primarily present on mRNA that controls the levels of transcripts and efficiency of translation in eukaryotes. Recently, the dynamics of m6A on mRNAs at all three developmental stages of P. falciparum in RBCs have been profiled; however, the proteins that regulate the m6A containing mRNAs in the parasites are unknown. Results: Using sequence analysis, we computationally identified that the P. falciparum genome encodes two putative YTH (YT521-B Homology) domain-containing proteins, which could potentially bind to m6A containing mRNA. We developed a modified methylated RNA immunoprecipitation (MeRIP) assay using PfYTH2 and find that it binds selectively to m6A containing transcripts. The PfYTH2 has a conserved aromatic amino acid cage that forms the methyl-binding pocket. Through site-directed mutagenesis experiments and molecular dynamics simulations, we show that F98 residue is important for m6A binding on mRNA. Fluorescence depolarization assay confirmed that PfYTH2 binds to methylated RNA oligos with high affinity. Further, MeRIP sequencing data revealed that PfYTH2 has more permissive sequence specificity on target m6A containing mRNA than other known eukaryotic YTH proteins. Taken together, here we identify and characterize PfYTH2 as the major protein that could regulate m6A containing transcripts in P. falciparum. Conclusion: Plasmodium spp. lost the canonical m6A-specific demethylases in their genomes, however, the YTH domain-containing proteins seem to be retained. This study presents a possibility that the YTH proteins are involved in post-transcriptional control in P. falciparum, and might orchestrate the translation of mRNA in various developmental stages of P. falciparum. This is perhaps the first characterization of the methyl-reading function of YTH protein in any parasites. [ABSTRACT FROM AUTHOR]

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المؤلفون: Jabeena, C. A.^1,2, Govindaraju, Gayathri^1,2, Rawat, Mukul³, Gopi, Soundhararajan⁴, Sethumadhavan, Devadathan Valiyamangalath^1,2, Jaleel, Abdul⁵, Sasankan, Dhakshmi¹, Karmodiya, Krishanpal³, Rajavelu, Arumugam¹ arajavelu@rgcb.res.in

المصدر: Journal of Biological Chemistry. Jan-Jun2021, Vol. 296, p1-18. 18p.

مصطلحات موضوعية: *PLASMODIUM falciparum, *REGULATOR genes, *GENE expression, *PROTEINS, *GENE families, *IMMUNOPRECIPITATION, *MALARIA

مستخلص: Epigenetic modifications have emerged as critical regulators of virulence genes and stage-specific gene expression in Plasmodium falciparum. However, the specific roles of histone core epigenetic modifications in regulating the stage-specific gene expression are not well understood. In this study, we report an unconventional trimethylation at lysine 64 on histone 3 (H3K64me3) and characterize its functional relevance in P. falciparum. We show that PfSET4 and PfSET5 proteins of P. falciparum methylate H3K64 and that they prefer the nucleosome as a substrate over free histone 3 proteins. Structural analysis of PfSET5 revealed that it interacts with the nucleosome as a dimer. The H3K64me3 mark is dynamic, being enriched in the ring and trophozoite stages and drastically reduced in the schizont stages. Stage-specific global chromatin immunoprecipitation -sequencing analysis of the H3K64me3 mark revealed the selective enrichment of this methyl mark on the genes of exported family proteins in the ring and trophozoite stages and a significant reduction of the same in the schizont stages. Collectively, our data identify a novel epigenetic mark that is associated with the subset of genes encoding for exported proteins, which may regulate their expression in different stages of P. falciparum. [ABSTRACT FROM AUTHOR]