Abstract
Intracellular pathogens need to develop sophisticated mechanisms to survive and thrive in the hostile environment within host cells. Unicellular, eukaryotic parasites from the Apicomplexa phylum have become masters of manipulating their host cells, exploiting signaling, and metabolic pathways to hijack host gene expression to their own advantage. These intracellular parasites have developed a wide range of strategies that affect transcriptional machineries and epigenetic events in the host cell nucleus. In recent years, many laboratories have risen to the challenge of studying the epigenetics of host-pathogen interactions with the hope that unraveling the complexity of the mechanisms involved will provide important insights into parasitism and provide clues to fight infection. In this review, we survey some of these many strategies that Apicomplexan parasites employ to hijack their hosts, including inducing epigenetic enzymes, secreting epigenators into host cells, sequestering host signaling proteins, and co-opting non-coding RNAs to change gene and protein expression. We cite selected examples from the literature on Apicomplexa parasites (including Toxoplasma, Theileria, and Cryptosporidium) to highlight the success of these parasitic processes. We marvel at the effectiveness of the strategies that these pathogens have evolved and wonder what mysteries lie ahead in exploring the epigenetics of host–parasite interactions.
Similar content being viewed by others
References
Seeber F, Steinfelder S (2016) Recent advances in understanding apicomplexan parasites. F1000Res 5:1369
Cowman AF, Healer J, Marapana D, Marsh K (2016) Malaria: biology and disease. Cell. 167(3):610–624
Pasternak ND, Dzikowski R (2009) PfEMP1: an antigen that plays a key role in the pathogenicity and immune evasion of the malaria parasite Plasmodium falciparum. Int J Biochem Cell Biol 41(7):1463–1466
Hviid L, Jensen ATR (2015) PfEMP1 – a parasite protein family of key importance in Plasmodium falciparum malaria immunity and pathogenesis. Adv Parasitol 88:51–84
Hunter CA, Sibley LD (2012) Modulation of innate immunity by Toxoplasma gondii virulence effectors. Nat Rev Microbiol 10(11):766–778
Tretina K, Gotia HT, Mann DJ, Silva JC (2015) Theileria-transformed bovine leukocytes have cancer hallmarks. Trends Parasitol 31(7):306–314
Dobbelaere DA, Küenzi P (2004) The strategies of the Theileria parasite: a new twist in host–pathogen interactions. Curr Opin Immunol 16(4):524–530
Morisaki JH, Heuser JE, Sibley LD (1995) Invasion of Toxoplasma gondii occurs by active penetration of the host cell. J Cell Sci 108(Pt 6):2457–2464
Hakimi M-A, Bougdour A (2015) Toxoplasma’s ways of manipulating the host transcriptome via secreted effectors. Curr Opin Microbiol 26:24–31
Hakimi M-A, Olias P, Sibley LD (2017) Toxoplasma effectors targeting host signaling and transcription. Clin Microbiol Rev 30(3):615–645
Soldati D, Dubremetz JF, Lebrun M (2001) Microneme proteins: structural and functional requirements to promote adhesion and invasion by the apicomplexan parasite Toxoplasma gondii. Int J Parasitol 31(12):1293–1302
Cheeseman K, Weitzman JB (2015) Host-parasite interactions: an intimate epigenetic relationship. Cell Microbiol 17(8):1121–1132
Heussler VT, Rottenberg S, Schwab R, Küenzi P, Fernandez PC, McKellar S, Shiels B, Chen ZJ, Orth K, Wallach D, Dobbelaere DA (2002) Hijacking of host cell IKK signalosomes by the transforming parasite Theileria. Science. 298(5595):1033–1036
Certad G, Viscogliosi E, Chabé M, Cacciò SM (2017) Pathogenic mechanisms of Cryptosporidium and Giardia. Trends Parasitol 33(7):561–576
Clough B, Frickel E-M (2017) The Toxoplasma parasitophorous vacuole: an evolving host–parasite frontier. Trends Parasitol 33(6):473–488
Robert McMaster W, Morrison CJ, Kobor MS (2016) Epigenetics: a new model for intracellular parasite–host cell regulation. Trends Parasitol 32(7):515–521
Silmon de Monerri NC, Kim K (2014) Pathogens hijack the epigenome. Am J Pathol 184(4):897–911
Kouzarides T (2007) Chromatin modifications and their function. Cell. 128(4):693–705
Deaton AM, Bird A (2011) CpG islands and the regulation of transcription. Genes Dev 25(10):1010–1022
Huang H, Weng H, Chen J (2019) The biogenesis and precise control of RNA m6A methylation. Trends Genet 36(1):44–52
Baumgarten S, Bryant JM, Sinha A, Reyser T, Preiser PR, Dedon PC, Scherf A (2019) Transcriptome-wide dynamics of extensive m6A mRNA methylation during Plasmodium falciparum blood-stage development. Nat Microbiol 4(12):2246–2259
Hattman S (2005) DNA-[adenine] methylation in lower eukaryotes. Biochem. 70(5):550–558
Tessarz P, Kouzarides T (2014) Histone core modifications regulating nucleosome structure and dynamics. Nat Rev Mol Cell Biol 15(11):703–708
Sindikubwabo F, Ding S, Hussain T, Ortet P, Barakat M et al (2017) Modifications at K31 on the lateral surface of histone H4 contribute to genome structure and expression in apicomplexan parasites. Elife. 6. pii: e29391
Bannister AJ, Kouzarides T (2011) Regulation of chromatin by histone modifications. Cell Res 21(3):381–395
Carlson SM, Gozani O (2016) Nonhistone lysine methylation in the regulation of cancer pathways. Cold Spring Harb Perspect Med 6(11):a026435
Dillon SC, Zhang X, Trievel RC, Cheng X (2005) The SET-domain protein superfamily: protein lysine methyltransferases. Genome Biol 6(8):227
Wu Z, Connolly J, Biggar KK (2017) Beyond histones - the expanding roles of protein lysine methylation. FEBS J 284(17):2732–2744
Wei J-W, Huang K, Yang C, Kang C-S (2017) Non-coding RNAs as regulators in epigenetics. Oncol Rep 37(1):3–9
Bierne H, Cossart P (2012) When bacteria target the nucleus: the emerging family of nucleomodulins. Cell Microbiol 14(5):622–633
Weitzman MD, Weitzman JB (2014) What’s the damage? The impact of pathogens on pathways that maintain host genome integrity. Cell Host Microbe 15(3):283–294
Somerville RPTT, Adamson RE, Brown CGDD, Hall FR (1998) Metastasis of Theileria annulata macroschizont-infected cells in scid mice is mediated by matrix metalloproteinases. Parasitology. 116(3):S0031182097002151
Cock-Rada AM, Medjkane S, Janski N, Yousfi N, Perichon M, Chaussepied M, Chluba J, Langsley G, Weitzman JB (2012) SMYD3 promotes cancer invasion by epigenetic upregulation of the metalloproteinase MMP-9. Cancer Res 72(3):810–820
Bougdour A, Durandau E, Brenier-Pinchart MP, Ortet P, Barakat M, Kieffer S, Curt-Varesano A, Curt-Bertini RL, Bastien O, Coute Y, Pelloux H, Hakimi MA (2013) Host cell subversion by Toxoplasma GRA16, an exported dense granule protein that targets the host cell nucleus and alters gene expression. Cell Host Microbe 13(4):489–500
Braun L, Brenier-Pinchart M-P, Hammoudi P-M, Cannella D, Kieffer-Jaquinod S et al (2019) The Toxoplasma effector TEEGR promotes parasite persistence by modulating NF-κB signalling via EZH2. Nat Microbiol 4(7):1208–1220
Kuzmichev A, Nishioka K, Erdjument-Bromage H, Tempst P, Reinberg D (2002) Histone methyltransferase activity associated with a human multiprotein complex containing the enhancer of Zeste protein. Genes Dev 16(22):2893–2905
Bierne H, Tham TN, Batsche E, Dumay A, Leguillou M, Kernéis-Golsteyn S, Regnault B, Seeler JS, Muchardt C, Feunteun J, Cossart P (2009) Human BAHD1 promotes heterochromatic gene silencing. Proc Natl Acad Sci U S A 106(33):13826–13831
Lebreton A, Lakisic G, Job V, Fritsch L, Tham TN et al (2011) A bacterial protein targets the BAHD1 chromatin complex to stimulate type III interferon response. Science 331(6022):1319–1321
Gay G, Braun L, Brenier-Pinchart M-P, Vollaire J, Josserand V et al (2016) Toxoplasma gondii TgIST co-opts host chromatin repressors dampening STAT1-dependent gene regulation and IFN-γ–mediated host defenses. J Exp Med 213(9):1779–1798
Olias P, Etheridge RD, Zhang Y, Holtzman MJ, Sibley LD (2016) Toxoplasma effector recruits the Mi-2/NuRD complex to repress STAT1 transcription and block IFN-γ-dependent gene expression. Cell Host Microbe 20(1):72–82
Denslow SA, Wade PA (2007) The human Mi-2/NuRD complex and gene regulation. Oncogene. 26(37):5433–5438
Tong JK, Hassig CA, Schnitzler GR, Kingston RE, Schreiber SL (1998) Chromatin deacetylation by an ATP-dependent nucleosome remodelling complex. Nature. 395(6705):917–921
Braun L, Brenier-Pinchart MP, Yogavel M, Curt-Varesano A, Curt-Bertini RL, Hussain T, Kieffer-Jaquinod S, Coute Y, Pelloux H, Tardieux I, Sharma A, Belrhali H, Bougdour A, Hakimi MA (2013) A Toxoplasma dense granule protein, GRA24, modulates the early immune response to infection by promoting a direct and sustained host p38 MAPK activation. J Exp Med 210(10):2071–2086
Pellegrini E, Palencia A, Braun L, Kapp U, Bougdour A, Belrhali H, Bowler MW, Hakimi MA (2017) Structural basis for the subversion of MAP kinase signaling by an intrinsically disordered parasite secreted agonist. Structure. 25(1):16–26
Dessauge F, Lizundia R, Baumgartner M, Chaussepied M, Langsley G (2005) Taking the Myc is bad for Theileria. Trends Parasitol 21(8):377–385
Marsolier J, Perichon M, DeBarry JD, Villoutreix BO, Chluba J, Lopez T, Garrido C, Zhou XZ, Lu KP, Fritsch L, Ait-Si-Ali S, Mhadhbi M, Medjkane S, Weitzman JB (2015) Theileria parasites secrete a prolyl isomerase to maintain host leukocyte transformation. Nature. 520(7547):378–382
Marsolier J, Perichon M, Weitzman JB, Medjkane S (2019) Secreted parasite Pin1 isomerase stabilizes host PKM2 to reprogram host cell metabolism. Commun Biol 2(1):152
Zurawski DV, Mumy KL, Faherty CS, McCormick BA, Maurelli AT (2009) Shigella flexneri type III secretion system effectors OspB and OspF target the nucleus to downregulate the host inflammatory response via interactions with retinoblastoma protein. Mol Microbiol 71(2):350–368
Bierne H, Hamon M, Cossart P (2012) Epigenetics and bacterial infections. Cold Spring Harb Perspect Med 2(12):a010272–a010272
Rolando M, Sanulli S, Rusniok C, Gomez-Valero L, Bertholet C, Sahr T, Margueron R, Buchrieser C (2013) Legionella pneumophila effector RomA uniquely modifies host chromatin to repress gene expression and promote intracellular bacterial replication. Cell Host Microbe 13(4):395–405
Pennini ME, Perrinet S, Dautry-Varsat A, Subtil A (2010) Histone methylation by NUE, a novel nuclear effector of the intracellular pathogen Chlamydia trachomatis. PLoS Pathog 6(7):1–12
Ming Z, Gong A-Y, Wang Y, Zhang X-T, Li M et al (2018) Involvement of Cryptosporidium parvum Cdg7_FLc_1000 RNA in the attenuation of intestinal epithelial cell migration via trans-suppression of host cell SMPD3. J Infect Dis 217(1):122–133
Ming Z, Gong AY, Wang Y, Zhang XT, Li M, Li Y, Pang J, Dong S, Strauss-Soukup JK, Chen XM (2018) Trans-suppression of host CDH3 and LOXL4 genes during Cryptosporidium parvum infection involves nuclear delivery of parasite Cdg7_FLc_1000 RNA. Int J Parasitol 48(6):423–431
Wang Y, Gong A-Y, Ma S, Chen X, Strauss-Soukup JK, Chen X-M (2017) Delivery of parasite Cdg7_Flc_0990 RNA transcript into intestinal epithelial cells during Cryptosporidium parvum infection suppresses host cell gene transcription through epigenetic mechanisms. Cell Microbiol 19(11):e12760
Tachibana M, Sugimoto K, Fukushima T, Shinkai Y (2001) SET domain-containing protein, G9a, is a novel lysine-preferring mammalian histone methyltransferase with hyperactivity and specific selectivity to Lysines 9 and 27 of Histone H3. J Biol Chem 276(27):25309–25317
Menard KL, Haskins BE, Denkers EY (2019) Impact of Toxoplasma gondii infection on host non-coding RNA responses. Front Cell Infect Microbiol 9:132
Marsolier J, Pineau S, Medjkane S, Perichon M, Yin Q, Flemington E, Weitzman MD, Weitzman JB (2013) OncomiR addiction is generated by a miR-155 feedback loop in Theileria-transformed leukocytes. PLoS Pathog 9(4):e1003222
Haidar M, Rchiad Z, Ansari HR, Ben-Rached F, Tajeri S et al (2018) miR-126-5p by direct targeting of JNK-interacting protein-2 (JIP-2) plays a key role in Theileria-infected macrophage virulence. PLoS Pathog 14(3):e1006942
Cai Y, Chen H, Mo X, Tang Y, Xu X, Zhang A, Lun Z, Lu F, Wang Y, Shen J (2014) Toxoplasma gondii inhibits apoptosis via a novel STAT3-miR-17-92-Bim pathway in macrophages. Cell Signal 26(6):1204–1212
Cannella D, Brenier-Pinchart MP, Braun L, vanRooyen JM, Bougdour A et al (2014) MiR-146a and miR-155 delineate a microRNA fingerprint associated with toxoplasma persistence in the host brain. Cell Rep 6(5):928–937
Husmann D, Gozani O (2019) Histone lysine methyltransferases in biology and disease. Nat Struct Mol Biol 26(10):880–889
Morera L, Lübbert M, Jung M (2016) Targeting histone methyltransferases and demethylases in clinical trials for cancer therapy. Clin Epigenetics 8(1):57
Copeland RA (2018) Protein methyltransferase inhibitors as precision cancer therapeutics: a decade of discovery. Philos Trans R Soc Lond Ser B Biol Sci 373(1748). pii: 20170080
Shiels BR, McKellar S, Katzer F, Lyons K, Kinnaird J et al (2004) A Theileria annulata DNA binding protein localized to the host cell nucleus alters the phenotype of a bovine macrophage cell line. Eukaryot Cell 3(2):495–505
Xu T, Ping J, Yu Y, Yu F, Yu Y et al (2010) Revealing parasite influence in metabolic pathways in Apicomplexa infected patients. BMC Bioinformatics. 2010 Dec 14;11 Suppl 11:S13
Acknowledgments
JBW is a senior member of the Institut Universitaire de France (IUF). We thanks members of the Weitzman lab and members of the UMR7216 for helpful discussions.
Funding
The work in our lab is supported by the LabEx “Who Am I?” #ANR-11-LABX-0071, and the Université de Paris IdEx #ANR-18-IDEX-0001 funded by the French Government through its “Investments for the Future” program, the Agence Nationale de la Recherche (ANR PATHO-METHYLOME #ANR-15-CE12-0020), and the Plan Cancer “Epigénétique et cancer” 2015 (PARA-CAN #PARA-15-RCA).
Author information
Authors and Affiliations
Corresponding author
Ethics declarations
Conflict of interest
The authors declare that they have no conflict of interest.
Additional information
This article is a contribution to the special issue on Infection-induced epigenetic changes and the pathogenesis of diseases - Guest Editor: Nicole Fischer
Publisher’s note
Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
Rights and permissions
About this article
Cite this article
Villares, M., Berthelet, J. & Weitzman, J.B. The clever strategies used by intracellular parasites to hijack host gene expression. Semin Immunopathol 42, 215–226 (2020). https://doi.org/10.1007/s00281-020-00779-z
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s00281-020-00779-z