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Article: Chromodomain protein interacts with H3K9me3 and controls RBC rosette formation by regulating the expression of a subset of RIFINs in the malaria parasite

Valiyamangalath Sethumadhavan, Devadathan / Tiburcio, Marta / Kanyal, Abhishek / Jabeena, C.A. / Govindaraju, Gayathri / Karmodiya, Krishanpal / Rajavelu, Arumugam

Journal of molecular biology. 2022 Apr. 17,

2022

Abstract: Plasmodium falciparum expresses clonally variant proteins on the surface of infected erythrocytes to evade the host immune system. The clonally variant multigene families includevar, rifin, andstevor, which express Erythrocyte Membrane Protein 1 (EMP1), ... ...

Abstract	Plasmodium falciparum expresses clonally variant proteins on the surface of infected erythrocytes to evade the host immune system. The clonally variant multigene families includevar, rifin, andstevor, 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 inPlasmodium 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. falciparumusingan inducible DiCre-LoxP system leads to selective up-regulation of a subset of virulence genes, including rifins, a fewvar,andstevorgenes. 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 byP. falciparum.
Keywords	Plasmodium falciparum ; chromatin ; epigenetics ; erythrocyte membrane ; erythrocytes ; immune system ; malaria ; membrane proteins ; molecular biology ; multigene family ; open reading frames ; parasites ; polypeptides ; virulence
Language	English
Dates of publication	2022-0417
Publishing place	Elsevier Ltd
Document type	Article
Note	Pre-press version
ZDB-ID	80229-3
ISSN	1089-8638 ; 0022-2836
ISSN (online)	1089-8638
ISSN	0022-2836
DOI	10.1016/j.jmb.2022.167601
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Plasmodium falciparum SET2 domain is allosterically regulated by its PHD-like domain to methylate at H3K36.

Sethumadhavan, Devadathan Valiyamangalath / Govindaraju, Gayathri / Jabeena, C A / Rajavelu, Arumugam

Biochimica et biophysica acta. Gene regulatory mechanisms

2021 Volume 1864, Issue 10, Page(s) 194744

Abstract: 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 ... ...

Abstract	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.
MeSH term(s)	Allosteric Regulation ; Histone Code ; Histone-Lysine N-Methyltransferase/chemistry ; Histone-Lysine N-Methyltransferase/metabolism ; Histones/metabolism ; Methylation ; Nucleosomes/enzymology ; Plasmodium falciparum/enzymology ; Protein Domains ; Protozoan Proteins/chemistry ; Protozoan Proteins/metabolism
Chemical Substances	Histones ; Nucleosomes ; Protozoan Proteins ; Histone-Lysine N-Methyltransferase (EC 2.1.1.43)
Language	English
Publishing date	2021-08-11
Publishing country	Netherlands
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2918786-2
ISSN	1876-4320 ; 1874-9399
ISSN (online)	1876-4320
ISSN	1874-9399
DOI	10.1016/j.bbagrm.2021.194744
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Article ; Online: Correction to: N

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

Epigenetics & chromatin

2020 Volume 13, Issue 1, Page(s) 36

Abstract: An amendment to this paper has been published and can be accessed via the original article. ...

Abstract	An amendment to this paper has been published and can be accessed via the original article.
Keywords	covid19
Language	English
Publishing date	2020-09-22
Publishing country	England
Document type	Published Erratum
ZDB-ID	2462129-8
ISSN	1756-8935 ; 1756-8935
ISSN (online)	1756-8935
ISSN	1756-8935
DOI	10.1186/s13072-020-00357-5
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Article ; Online: The severity of SARS-CoV-2 infection is dictated by host factors? Epigenetic perspectives.

Sethumadhavan, Devadathan Valiyamangalath / Jabeena, C A / Govindaraju, Gayathri / Soman, Aparna / Rajavelu, Arumugam

Current research in microbial sciences

2021 Volume 2, Page(s) 100079

Abstract: The emergence of COVID-19, caused by SARS-CoV-2 poses a significant threat to humans as it is highly contagious with increasing mortality. There exists a high degree of heterogeneity in the mortality rates of COVID-19 across the globe. There are multiple ...

Abstract	The emergence of COVID-19, caused by SARS-CoV-2 poses a significant threat to humans as it is highly contagious with increasing mortality. There exists a high degree of heterogeneity in the mortality rates of COVID-19 across the globe. There are multiple speculations on the varying degree of mortality. Still, all the clinical reports have indicated that preexisting chronic diseases like hypertension, diabetes, chronic obstructive pulmonary disease (COPD), kidney disorders, and cardiovascular diseases are associated with the increased risk for high mortality in SARS-CoV-2 infected patients. It is worth noting that host factors, mainly epigenetic factors could play a significant role in deciding the outcome of COVID-19 diseases. Over the recent years, it is evident that chronic diseases are developed due to altered epigenome that includes a selective loss/gain of DNA and histone methylation on the chromatin of the cells. Since, there is a high positive correlation between chronic diseases and elevated mortality due to SARS-CoV-2, in this review; we discuss the overall picture of the aberrant epigenome map in varying chronic ailments and its implications in COVID-19 disease severity and high mortality.
Language	English
Publishing date	2021-10-27
Publishing country	Netherlands
Document type	Journal Article ; Review
ISSN	2666-5174
ISSN (online)	2666-5174
DOI	10.1016/j.crmicr.2021.100079
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Article ; Online: Chromodomain Protein Interacts with H3K9me3 and Controls RBC Rosette Formation by Regulating the Expression of a Subset of RIFINs in the Malaria Parasite.

Sethumadhavan, Devadathan Valiyamangalath / Tiburcio, Marta / Kanyal, Abhishek / Jabeena, C A / Govindaraju, Gayathri / Karmodiya, Krishanpal / Rajavelu, Arumugam

Journal of molecular biology

2022 Volume 434, Issue 12, Page(s) 167601

Abstract: 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), ...

Abstract	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.
MeSH term(s)	Animals ; Epigenesis, Genetic ; Erythrocytes/immunology ; Erythrocytes/parasitology ; Gene Deletion ; Histones/metabolism ; Malaria, Falciparum/parasitology ; Multigene Family ; Plasmodium falciparum/genetics ; Plasmodium falciparum/pathogenicity ; Protozoan Proteins/genetics ; Protozoan Proteins/metabolism ; Rosette Formation ; Virulence/genetics
Chemical Substances	Histones ; Protozoan Proteins
Language	English
Publishing date	2022-04-20
Publishing country	Netherlands
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	80229-3
ISSN	1089-8638 ; 0022-2836
ISSN (online)	1089-8638
ISSN	0022-2836
DOI	10.1016/j.jmb.2022.167601
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: N

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

Epigenetics & chromatin

2020 Volume 13, Issue 1, Page(s) 33

Abstract: 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 N: Results: Using sequence analysis, we computationally ... ...

Abstract	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 N 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.
MeSH term(s)	Adenosine/analogs & derivatives ; Adenosine/metabolism ; Epigenesis, Genetic ; Plasmodium falciparum/genetics ; Plasmodium falciparum/metabolism ; Protozoan Proteins/genetics ; Protozoan Proteins/metabolism ; RNA Processing, Post-Transcriptional ; RNA, Messenger/genetics ; RNA, Messenger/metabolism
Chemical Substances	Protozoan Proteins ; RNA, Messenger ; N-methyladenosine (CLE6G00625) ; Adenosine (K72T3FS567)
Language	English
Publishing date	2020-08-31
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2462129-8
ISSN	1756-8935 ; 1756-8935
ISSN (online)	1756-8935
ISSN	1756-8935
DOI	10.1186/s13072-020-00355-7
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Article ; Online: Dynamic association of the H3K64 trimethylation mark with genes encoding exported proteins in Plasmodium falciparum.

Jabeena, C A / Govindaraju, Gayathri / Rawat, Mukul / Gopi, Soundhararajan / Sethumadhavan, Devadathan Valiyamangalath / Jaleel, Abdul / Sasankan, Dhakshmi / Karmodiya, Krishanpal / Rajavelu, Arumugam

The Journal of biological chemistry

2021 Volume 296, Page(s) 100614

Abstract: 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 ... ...

Abstract	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.
MeSH term(s)	DNA Methylation ; Erythrocytes/parasitology ; Histone Code ; Histones/chemistry ; Histones/genetics ; Histones/metabolism ; Humans ; Lysine/chemistry ; Lysine/genetics ; Lysine/metabolism ; Malaria, Falciparum/genetics ; Malaria, Falciparum/metabolism ; Malaria, Falciparum/parasitology ; Nucleosomes/parasitology ; Plasmodium falciparum/genetics ; Plasmodium falciparum/growth & development ; Plasmodium falciparum/metabolism ; Protozoan Proteins/genetics ; Protozoan Proteins/metabolism
Chemical Substances	Histones ; Nucleosomes ; Protozoan Proteins ; Lysine (K3Z4F929H6)
Language	English
Publishing date	2021-04-09
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2997-x
ISSN	1083-351X ; 0021-9258
ISSN (online)	1083-351X
ISSN	0021-9258
DOI	10.1016/j.jbc.2021.100614
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Article: Correction to: N6Adenosine methylation on mRNA is recognized by YTH2 domain protein of human malaria parasite Plasmodium falciparum

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

Epigenetics Chromatin

Abstract: An amendment to this paper has been published and can be accessed via the original article. ...

Abstract	An amendment to this paper has been published and can be accessed via the original article.
Keywords	covid19
Publisher	WHO
Document type	Article
Note	WHO #Covidence: #32962747
Database	COVID19

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Article: DNA methyltransferase homologue TRDMT1 in Plasmodium falciparum specifically methylates endogenous aspartic acid tRNA.

Govindaraju, Gayathri / Jabeena, C A / Sethumadhavan, Devadathan Valiyamangalath / Rajaram, Nivethika / Rajavelu, Arumugam

Biochimica et biophysica acta. Gene regulatory mechanisms

2017 Volume 1860, Issue 10, Page(s) 1047–1057

Abstract: 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. ... ...

Abstract	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.
MeSH term(s)	DNA (Cytosine-5-)-Methyltransferases/chemistry ; DNA (Cytosine-5-)-Methyltransferases/genetics ; DNA (Cytosine-5-)-Methyltransferases/metabolism ; Methylation ; Plasmodium falciparum/enzymology ; RNA, Protozoan/chemistry ; RNA, Protozoan/genetics ; RNA, Protozoan/metabolism ; RNA, Transfer, Asp/chemistry ; RNA, Transfer, Asp/genetics ; RNA, Transfer, Asp/metabolism
Chemical Substances	RNA, Protozoan ; RNA, Transfer, Asp ; DNA (Cytosine-5-)-Methyltransferases (EC 2.1.1.37)
Language	English
Publishing date	2017-08-26
Publishing country	Netherlands
Document type	Journal Article ; Research Support, N.I.H., Intramural ; Research Support, Non-U.S. Gov't
ZDB-ID	60-7
ISSN	1879-2596 ; 1879-260X ; 1872-8006 ; 1879-2642 ; 1879-2618 ; 1879-2650 ; 1874-9399 ; 0006-3002 ; 0005-2728 ; 0005-2736 ; 0304-4165 ; 0167-4838 ; 1388-1981 ; 0167-4889 ; 0167-4781 ; 0304-419X ; 1570-9639 ; 0925-4439
ISSN (online)	1879-2596 ; 1879-260X ; 1872-8006 ; 1879-2642 ; 1879-2618 ; 1879-2650
ISSN	1874-9399 ; 0006-3002 ; 0005-2728 ; 0005-2736 ; 0304-4165 ; 0167-4838 ; 1388-1981 ; 0167-4889 ; 0167-4781 ; 0304-419X ; 1570-9639 ; 0925-4439
DOI	10.1016/j.bbagrm.2017.08.003
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