Global Histone Analysis by Mass Spectrometry Reveals a High Content of Acetylated Lysine Residues in the Malaria Parasite <i>Plasmodium falciparum</i>

Trelle, Morten Beck; Salcedo-Amaya, Adriana M.; Cohen, Adrian; Stunnenberg, Hendrik G.; Jensen, Ole N.

doi:10.1021/pr9000898

Cited by 146 publications

(202 citation statements)

References 69 publications

(140 reference statements)

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“…For example, expression of variant surface antigen gene families (7) and ligands involved in parasite red blood cell (RBC) invasion (8) are controlled by histone acetylation and methylation marks. Apicomplexan parasites, including Plasmodium and Toxoplasma, possess orthologs to many chromatin remodeling proteins and enzymes responsible for histone modifications (9-11), and many conserved posttranslational modifications have been identified on P. falciparum histones (12). Genome-wide high-resolution ChIP-on-chip analysis revealed that the generally activating histone modifications trimethyl histone H3 lysine 4 (H3K4me3) and acetyl histone H3 lysine 9 (H3K9ac) are located throughout the parasite genome (13,14).…”

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confidence: 99%

Small-molecule histone methyltransferase inhibitors display rapid antimalarial activity against all blood stage forms inPlasmodium falciparum

Malmquist

Moss

Mécheri

et al. 2012

Proc. Natl. Acad. Sci. U.S.A.

118

112

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Epigenetic factors such as histone methylation control the developmental progression of malaria parasites during the complex life cycle in the human host. We investigated Plasmodium falciparum histone lysine methyltransferases as a potential target class for the development of novel antimalarials. We synthesized a compound library based upon a known specific inhibitor (BIX-01294) of the human G9a histone methyltransferase. Two compounds, BIX-01294 and its derivative TM2-115, inhibited P. falciparum 3D7 parasites in culture with IC 50 values of ∼100 nM, values at least 22-fold more potent than their apparent IC 50 toward two human cell lines and one mouse cell line. These compounds irreversibly arrested parasite growth at all stages of the intraerythrocytic life cycle. Decrease in parasite viability (>40%) was seen after a 3-h incubation with 1 µM BIX-01294 and resulted in complete parasite killing after a 12-h incubation. Additionally, mice with patent Plasmodium berghei ANKA strain infection treated with a single dose (40 mg/kg) of TM2-115 had 18-fold reduced parasitemia the following day. Importantly, treatment of P. falciparum parasites in culture with BIX-01294 or TM2-115 resulted in significant reductions in histone H3K4me3 levels in a concentration-dependent and exposure time-dependent manner. Together, these results suggest that BIX-01294 and TM2-115 inhibit malaria parasite histone methyltransferases, resulting in rapid and irreversible parasite death. Our data position histone lysine methyltransferases as a previously unrecognized target class, and BIX-01294 as a promising lead compound, in a presently unexploited avenue for antimalarial drug discovery targeting multiple life-cycle stages.chromatin | global health | chemical genetics M alaria continues to claim >1 million lives annually, particularly in the vulnerable populations of pregnant women and children <5 y of age (1, 2). Although artemisinin-based combination therapies have helped rescue the world's antimalarial armamentarium, the parasite's ability to develop resistance continues to outpace our ability to control this devastating disease (3). Effective malaria drug discovery efforts must therefore include both the development of improved antimalarials from existing compounds and the discovery of new parasite drug targets and novel small-molecule inhibitors.Epigenetic control of gene regulation in Plasmodium falciparum, the main causative agent of human malaria, has received considerable attention originally due to the apparent lack of recognizable transcription factors in the parasite genome (4). Although the recent discovery of a family of apicomplexan AP2 transcription factors (5, 6) has partly fulfilled the search for more traditional transcription factors, epigenetic gene regulation, particularly at the level of histone posttranslational modifications, has proven to play a significant role in P. falciparum virulence gene regulation. For example, expression of variant surface antigen gene families (7) and ligands involved in parasite red bl...

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confidence: 99%

Small-molecule histone methyltransferase inhibitors display rapid antimalarial activity against all blood stage forms inPlasmodium falciparum

Malmquist

Moss

Mécheri

et al. 2012

Proc. Natl. Acad. Sci. U.S.A.

118

112

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“…about 2% of the total protein-coding genes of P. falciparum). By contrast, only a few substrates for ubiquitylation have been identified in P. falciparum, including actin (12) and the histone protein H2B (13). The quickly reversible character of ubiquitylation (intervention of deubiquitinases) and the rapid degradation of polyubiquitylated proteins (proteasome) render the isolation and analysis of ubiquitylated proteins challenging.…”

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confidence: 99%

Unraveling the Ubiquitome of the Human Malaria Parasite

Ponts

Saraf

Chung

et al. 2011

Journal of Biological Chemistry

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Malaria is one of the deadliest infectious diseases worldwide. The most severe form is caused by the eukaryotic protozoan parasite Plasmodium falciparum. Recent studies have highlighted the importance of post-translational regulations for the parasite's progression throughout its life cycle, protein ubiquitylation being certainly one of the most abundant. The specificity of its components and the wide range of biological processes in which it is involved make the ubiquitylation pathway a promising source of suitable targets for anti-malarial drug development. Here, we combined immunofluorescent microscopy, biochemical assays, in silico prediction, and mass spectrometry analysis using the multidimensional protein identification technology, or MudPIT, to describe the P. falciparum ubiquitome. We found that ubiquitin conjugates are detected at every morphological stage of the parasite erythrocytic cycle. Furthermore, we detected that more than half of the parasite's proteome represents possible targets for ubiquitylation, especially proteins found to be present at the most replicative stage of the asexual cycle, the trophozoite stage. A large proportion of ubiquitin conjugates were also detected at the schizont stage, consistent with a cell activity slowdown to prepare for merozoite differentiation and invasion. Finally, for the first time in the human malaria parasite, our results strongly indicate the presence of heterologous mixed conjugations, SUMO/UB. This discovery suggests that sumoylated proteins may be regulated by ubiquitylation in P. falciparum. Altogether, our results present the first stepping stone toward a better understanding of ubiquitylation and its role(s) in the biology of the human malaria parasite.

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“…The detection and identification of methylated peptides can be validated by the observation of these characteristic marker ions or neutral loss, particularly in the cases that the MS/MS fragmentation patterns are insufficient to determine the nature of the modification. 137,138 In addition to the validation of sequencing data, the marker ions can also be utilized in the discovery of methylated peptides. In "immonium ion scanning" method, modified peptides can be specifically selected by monitoring their characteristic immonium ion(s) using tandem mass spectrometers, such as triple quadrupole instruments.…”

Section: A Ms Methods For the Detection And Site Mapping Of Histone mentioning

confidence: 99%

“…137,138 Fragmentation of trimethylated peptides usually generates a neutral loss of trimethyl amine at 59 Da whereas an acetylated peptide produces an ammonium ion at 126 Da during collision induced dissociation. 135 A recent example reported by Trelle and coworkers reveals the distinction of H3K9 acetylation and H3K9 trimethylation in P. falciparum.…”

Section: A Ms Methods For the Detection And Site Mapping Of Histone mentioning

confidence: 99%

“…135 A recent example reported by Trelle and coworkers reveals the distinction of H3K9 acetylation and H3K9 trimethylation in P. falciparum. 138 The sequence of the peptide, K 3Me STAGK Ac APR, was determined by the complete y-ion series in its MS/MS spectrum. The presence of a trimethylated N-terminal lysine in the peptide is validated by the observation of an almost complete series of fragments corresponding to neutral loss of trimethylamine (59 Da) from b-ions (a series of N-terminal fragments produced in MS/MS) ( Figure 6).…”

Section: A Ms Methods For the Detection And Site Mapping Of Histone mentioning

confidence: 99%

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Chemical and biochemical approaches in the study of histone methylation and demethylation

Luo

Wang

et al. 2010

Med. Res. Rev.

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Histone methylation represents one of the most critical epigenetic events in DNA function regulation in eukaryotic organisms. Classic molecular biology and genetics tools provide significant knowledge about mechanisms and physiological roles of histone methyltransferases and demethylases in various cellular processes. In addition to this stream line, development and application of chemistry and chemistry-related techniques are increasingly involved in biological study, and provide information otherwise difficulty to obtain by standard molecular biology methods. Herein, we review recent achievements and progress in developing and applying chemical and biochemical approaches in the study of histone methylation, including chromatin immunoprecipitation (ChIP), chemical ligation, mass spectrometry (MS), biochemical assays, and inhibitor development. These technological advances allow histone methylation to be studied from genome-wide level to molecular and atomic levels. With ChIP technology, information can be obtained about precise mapping of histone methylation patterns at specific promoters, genes or other genomic regions. MS is particularly useful in detecting and analyzing methylation marks in histone and nonhistone protein substrates. Chemical approaches that permit site-specific incorporation of methyl groups into histone proteins greatly facilitate the investigation of the biological impacts of methylation at individual modification sites. Discovery and design of selective organic inhibitors of histone methyltransferases and demethylases provide chemical probes to interrogate methylation-mediated cellular pathways. Overall, these chemistry-related technological advances have greatly improved our understanding of the biological functions of histone methylation in normal physiology and diseased states, and also are of great potential to translate basic epigenetics research into diagnostic and therapeutic application in the clinic.

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Global Histone Analysis by Mass Spectrometry Reveals a High Content of Acetylated Lysine Residues in the Malaria Parasite Plasmodium falciparum

Cited by 146 publications

References 69 publications

Small-molecule histone methyltransferase inhibitors display rapid antimalarial activity against all blood stage forms inPlasmodium falciparum

Small-molecule histone methyltransferase inhibitors display rapid antimalarial activity against all blood stage forms inPlasmodium falciparum

Unraveling the Ubiquitome of the Human Malaria Parasite

Chemical and biochemical approaches in the study of histone methylation and demethylation

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