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Jeffers V. Histone code: a common language and multiple dialects to meet the different developmental requirements of apicomplexan parasites. Curr Opin Microbiol 2024; 79:102472. [PMID: 38581913 PMCID: PMC11162943 DOI: 10.1016/j.mib.2024.102472] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 03/25/2024] [Accepted: 03/26/2024] [Indexed: 04/08/2024]
Abstract
Apicomplexan parasites have complex life cycles, often requiring transmission between two different hosts, facing periods of dormancy within the host or in the environment to maximize chances of transmission. To support survival in these different conditions, tightly regulated and correctly timed gene expression is critical. The modification of histones and nucleosome composition makes a significant contribution to this regulation, and as eukaryotes, the fundamental mechanisms underlying this process in apicomplexans are similar to those in model eukaryotic organisms. However, single-celled intracellular parasites face unique challenges, and regulation of gene expression at the epigenetic level provides tight control for responses that must often be rapid and robust. Here, we discuss the recent advances in understanding the dynamics of histone modifications across Apicomplexan life cycles and the molecular mechanisms that underlie epigenetic regulation of gene expression to promote parasite life cycle progression, dormancy, and transmission.
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Affiliation(s)
- Victoria Jeffers
- Molecular, Cellular and Biomedical Sciences, University of New Hampshire, Durham, NH, USA.
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2
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Angel SO, Vanagas L, Alonso AM. Mechanisms of adaptation and evolution in Toxoplasma gondii. Mol Biochem Parasitol 2024; 258:111615. [PMID: 38354788 DOI: 10.1016/j.molbiopara.2024.111615] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 12/28/2023] [Accepted: 02/06/2024] [Indexed: 02/16/2024]
Abstract
Toxoplasma has high host flexibility, infecting all nucleated cells of mammals and birds. This implies that during its infective process the parasite must constantly adapt to different environmental situations, which in turn leads to modifications in its metabolism, regulation of gene transcription, translation of mRNAs and stage specific factors. There are conserved pathways that support these adaptations, which we aim to elucidate in this review. We begin by exploring the widespread epigenetic mechanisms and transcription regulators, continue with the supportive role of Heat Shock Proteins (Hsp), the translation regulation, stress granules, and finish with the emergence of contingency genes in highly variable genomic domains, such as subtelomeres. Within epigenetics, the discovery of a new histone variant of the H2B family (H2B.Z), contributing to T. gondii virulence and differentiation, but also gene expression regulation and its association with the metabolic state of the parasite, is highlighted. Associated with the regulation of gene expression are transcription factors (TFs). An overview of the main findings on TF and development is presented. We also emphasize the role of Hsp90 and Tgj1 in T. gondii metabolic fitness and the regulation of protein translation. Translation regulation is also highlighted as a mechanism for adaptation to conditions encountered by the parasite as well as stress granules containing mRNA and proteins generated in the extracellular tachyzoite. Another important aspect in evolution and adaptability are the subtelomeres because of their high variability and gene duplication rate. Toxoplasma possess multigene families of membrane proteins and contingency genes that are associated with different metabolic stresses. Among them parasite differentiation and environmental stresses stand out, including those that lead tachyzoite to bradyzoite conversion. Finally, we are interested in positioning protozoa as valuable evolution models, focusing on research related to the Extended Evolutionary Synthesis, based on models recently generated, such as extracellular adaptation and ex vivo cyst recrudescence.
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Affiliation(s)
- Sergio O Angel
- Laboratorio de Parasitología Molecular, INTECH, CONICET-UNSAM, Av. Intendente Marino Km. 8.2, C.C 164, (B7130IIWA), Chascomús, Prov, Buenos Aires, Argentina.
| | - Laura Vanagas
- Laboratorio de Parasitología Molecular, INTECH, CONICET-UNSAM, Av. Intendente Marino Km. 8.2, C.C 164, (B7130IIWA), Chascomús, Prov, Buenos Aires, Argentina.
| | - Andres M Alonso
- Laboratorio de Parasitología Molecular, INTECH, CONICET-UNSAM, Av. Intendente Marino Km. 8.2, C.C 164, (B7130IIWA), Chascomús, Prov, Buenos Aires, Argentina.
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Kalamuddin M, Shakri AR, Wang C, Min H, Li X, Cui L, Miao J. MYST regulates DNA repair and forms a NuA4-like complex in the malaria parasite Plasmodium falciparum. mSphere 2024; 9:e0014024. [PMID: 38564734 PMCID: PMC11036802 DOI: 10.1128/msphere.00140-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2024] [Accepted: 03/13/2024] [Indexed: 04/04/2024] Open
Abstract
Histone lysine acetyltransferase MYST-associated NuA4 complex is conserved from yeast to humans and plays key roles in cell cycle regulation, gene transcription, and DNA replication/repair. Here, we identified a Plasmodium falciparum MYST-associated complex, PfNuA4, which contains 11 of the 13 conserved NuA4 subunits. Reciprocal pulldowns using PfEAF2, a shared component between the NuA4 and SWR1 complexes, not only confirmed the PfNuA4 complex but also identified the PfSWR1 complex, a histone remodeling complex, although their identities are low compared to the homologs in yeast or humans. Notably, both H2A.Z/H2B.Z were associated with the PfSWR1 complex, indicating that this complex is involved in the deposition of H2A.Z/H2B.Z, the variant histone pair that is enriched in the activated promoters. Overexpression of PfMYST resulted in earlier expression of genes involved in cell cycle regulation, DNA replication, and merozoite invasion, and upregulation of the genes related to antigenic variation and DNA repair. Consistently, PfMYST overexpression led to high basal phosphorylated PfH2A (γ-PfH2A), the mark of DNA double-strand breaks, and conferred protection against genotoxic agent methyl methanesulfonate (MMS), X-rays, and artemisinin, the first-line antimalarial drug. In contrast, the knockdown of PfMYST caused a delayed parasite recovery upon MMS treatment. MMS induced the gradual disappearance of PfMYST in the cytoplasm and concomitant accumulation of PfMYST in the nucleus, suggesting cytoplasm-nucleus shuttling of PfMYST. Meanwhile, PfMYST colocalized with the γ-PfH2A, indicating PfMYST was recruited to the DNA damage sites. Collectively, PfMYST plays critical roles in cell cycle regulation, gene transcription, and DNA replication/DNA repair in this low-branching parasitic protist.IMPORTANCEUnderstanding gene regulation and DNA repair in malaria parasites is critical for identifying targets for antimalarials. This study found PfNuA4, a PfMYST-associated, histone modifier complex, and PfSWR1, a chromatin remodeling complex in malaria parasite Plasmodium falciparum. These complexes are divergent due to the low identities compared to their homologs from yeast and humans. Furthermore, overexpression of PfMYST resulted in substantial transcriptomic changes, indicating that PfMYST is involved in regulating the cell cycle, antigenic variation, and DNA replication/repair. Consistently, PfMYST was found to protect against DNA damage caused by the genotoxic agent methyl methanesulfonate, X-rays, and artemisinin, the first-line antimalarial drug. Additionally, DNA damage led to the relocation of cytoplasmic PfMYST to the nucleus and colocalization of PfMYST with γ-PfH2A, the mark of DNA damage. In summary, this study demonstrated that the PfMYST complex has critical functions in regulating cell cycle, antigenic variation, and DNA replication/DNA repair in P. falciparum.
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Affiliation(s)
- Mohammad Kalamuddin
- Department of Internal Medicine, University of South Florida, Morsani College of Medicine, Tampa, Florida, USA
| | - Ahmad Rushdi Shakri
- Department of Internal Medicine, University of South Florida, Morsani College of Medicine, Tampa, Florida, USA
| | - Chengqi Wang
- Center for Global Health and Infectious Diseases Research, College of Public Health, University of South Florida, Tampa, Florida, USA
| | - Hui Min
- Department of Internal Medicine, University of South Florida, Morsani College of Medicine, Tampa, Florida, USA
| | - Xiaolian Li
- Department of Internal Medicine, University of South Florida, Morsani College of Medicine, Tampa, Florida, USA
| | - Liwang Cui
- Department of Internal Medicine, University of South Florida, Morsani College of Medicine, Tampa, Florida, USA
- Center for Global Health and Infectious Diseases Research, College of Public Health, University of South Florida, Tampa, Florida, USA
| | - Jun Miao
- Department of Internal Medicine, University of South Florida, Morsani College of Medicine, Tampa, Florida, USA
- Center for Global Health and Infectious Diseases Research, College of Public Health, University of South Florida, Tampa, Florida, USA
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Deng B, Vanagas L, Alonso AM, Angel SO. Proteomics Applications in Toxoplasma gondii: Unveiling the Host-Parasite Interactions and Therapeutic Target Discovery. Pathogens 2023; 13:33. [PMID: 38251340 PMCID: PMC10821451 DOI: 10.3390/pathogens13010033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Revised: 12/25/2023] [Accepted: 12/27/2023] [Indexed: 01/23/2024] Open
Abstract
Toxoplasma gondii, a protozoan parasite with the ability to infect various warm-blooded vertebrates, including humans, is the causative agent of toxoplasmosis. This infection poses significant risks, leading to severe complications in immunocompromised individuals and potentially affecting the fetus through congenital transmission. A comprehensive understanding of the intricate molecular interactions between T. gondii and its host is pivotal for the development of effective therapeutic strategies. This review emphasizes the crucial role of proteomics in T. gondii research, with a specific focus on host-parasite interactions, post-translational modifications (PTMs), PTM crosstalk, and ongoing efforts in drug discovery. Additionally, we provide an overview of recent advancements in proteomics techniques, encompassing interactome sample preparation methods such as BioID (BirA*-mediated proximity-dependent biotin identification), APEX (ascorbate peroxidase-mediated proximity labeling), and Y2H (yeast two hybrid), as well as various proteomics approaches, including single-cell analysis, DIA (data-independent acquisition), targeted, top-down, and plasma proteomics. Furthermore, we discuss bioinformatics and the integration of proteomics with other omics technologies, highlighting its potential in unraveling the intricate mechanisms of T. gondii pathogenesis and identifying novel therapeutic targets.
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Affiliation(s)
- Bin Deng
- Department of Biology and VBRN Proteomics Facility, University of Vermont, Burlington, VT 05405, USA
| | - Laura Vanagas
- Laboratorio de Parasitología Molecular, Instituto Tecnológico de Chascomús (CONICET-UNSAM), Chascomús 7130, Provincia de Buenos Aires, Argentina; (L.V.); (S.O.A.); (A.M.A.)
- Escuela de Bio y Nanotecnologías (UNSAM), 25 de Mayo y Francia. C.P., San Martín 1650, Provincia de Buenos Aires, Argentina
| | - Andres M. Alonso
- Laboratorio de Parasitología Molecular, Instituto Tecnológico de Chascomús (CONICET-UNSAM), Chascomús 7130, Provincia de Buenos Aires, Argentina; (L.V.); (S.O.A.); (A.M.A.)
- Escuela de Bio y Nanotecnologías (UNSAM), 25 de Mayo y Francia. C.P., San Martín 1650, Provincia de Buenos Aires, Argentina
| | - Sergio O. Angel
- Laboratorio de Parasitología Molecular, Instituto Tecnológico de Chascomús (CONICET-UNSAM), Chascomús 7130, Provincia de Buenos Aires, Argentina; (L.V.); (S.O.A.); (A.M.A.)
- Escuela de Bio y Nanotecnologías (UNSAM), 25 de Mayo y Francia. C.P., San Martín 1650, Provincia de Buenos Aires, Argentina
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5
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Azizan S, Selvarajah SA, Tang J, Jeninga MD, Schulz D, Pareek K, Herr T, Day KP, De Koning-Ward TF, Petter M, Duffy MF. The P. falciparum alternative histones Pf H2A.Z and Pf H2B.Z are dynamically acetylated and antagonized by PfSir2 histone deacetylases at heterochromatin boundaries. mBio 2023; 14:e0201423. [PMID: 37882786 PMCID: PMC10746207 DOI: 10.1128/mbio.02014-23] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Accepted: 09/18/2023] [Indexed: 10/27/2023] Open
Abstract
The Plasmodium falciparum alternative histones Pf H2A.Z and Pf H2B.Z are enriched in the same nucleosomes in intergenic euchromatin but depleted from heterochromatin. They occupy most promoters but are only dynamically associated with expression at var genes. In other organisms, acetylation of H2A.Z is important for its functions in gene expression and chromatin structure. Here, we show that acetylated Pf H2A.Z and Pf H2B.Z are dynamically associated with gene expression at promoters. In addition, acetylated Pf H2A.Z and Pf H2B.Z are antagonized by the sirtuin class III histone deacetylases (HDAC) PfSir2A and B at heterochromatin boundaries and encroach upon heterochromatin in parasites lacking PfSir2A or B. However, the majority of acetylated Pf H2A.Z and Pf H2B.Z are deacetylated by class I or II HDACs. Acetylated Pf H2A.Z and Pf H2B.Z are also dynamically associated with promoter activity of both canonical upstream var gene promoters and var gene introns. These findings suggest that both acetylated Pf H2A.Z and Pf H2B.Z play critical roles in gene expression and contribute to maintenance of chromatin structure at the boundaries of subtelomeric, facultative heterochromatin, critical for the variegated expression of genes that enable rapid adaptation to altered host environments.IMPORTANCEThe malaria parasite Plasmodium falciparum relies on variant expression of members of multi-gene families as a strategy for environmental adaptation to promote parasite survival and pathogenesis. These genes are located in transcriptionally silenced DNA regions. A limited number of these genes escape gene silencing, and switching between them confers variant fitness on parasite progeny. Here, we show that PfSir2 histone deacetylases antagonize DNA-interacting acetylated alternative histones at the boundaries between active and silent DNA. This finding implicates acetylated alternative histones in the mechanism regulating P. falciparum variant gene silencing and thus malaria pathogenesis. This work also revealed that acetylation of alternative histones at promoters is dynamically associated with promoter activity across the genome, implicating acetylation of alternative histones in gene regulation genome wide. Understanding mechanisms of gene regulation in P. falciparum may aid in the development of new therapeutic strategies for malaria, which killed 619,000 people in 2021.
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Affiliation(s)
- Suffian Azizan
- School of BioSciences, The University of Melbourne, Melbourne, Australia
- Bio21 Institute, Parkville, Victoria, Australia
| | - Shamista A. Selvarajah
- School of BioSciences, The University of Melbourne, Melbourne, Australia
- Bio21 Institute, Parkville, Victoria, Australia
| | - Jingyi Tang
- School of Medicine, Faculty of Health, Deakin University, Geelong Waurn Ponds Campus, Waurn Ponds, Australia
| | - Myriam D. Jeninga
- Universitätsklinikum Erlangen, Mikrobiologisches Institut – Klinische Mikrobiologie, Immunologie und Hygiene, Friedrich-Alexander-Universität (FAU) Erlangen-Nürnberg, Erlangen, Germany
| | | | - Kapil Pareek
- Universitätsklinikum Erlangen, Mikrobiologisches Institut – Klinische Mikrobiologie, Immunologie und Hygiene, Friedrich-Alexander-Universität (FAU) Erlangen-Nürnberg, Erlangen, Germany
| | - Tamara Herr
- Universitätsklinikum Erlangen, Mikrobiologisches Institut – Klinische Mikrobiologie, Immunologie und Hygiene, Friedrich-Alexander-Universität (FAU) Erlangen-Nürnberg, Erlangen, Germany
| | - Karen P. Day
- Bio21 Institute, Parkville, Victoria, Australia
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria, Australia
| | - Tania F. De Koning-Ward
- School of Medicine, Faculty of Health, Deakin University, Geelong Waurn Ponds Campus, Waurn Ponds, Australia
| | - Michaela Petter
- Universitätsklinikum Erlangen, Mikrobiologisches Institut – Klinische Mikrobiologie, Immunologie und Hygiene, Friedrich-Alexander-Universität (FAU) Erlangen-Nürnberg, Erlangen, Germany
| | - Michael F. Duffy
- Bio21 Institute, Parkville, Victoria, Australia
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria, Australia
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Vanagas L, Muñoz D, Cristaldi C, Ganuza A, Nájera R, Bonardi MC, Turowski VR, Guzman F, Deng B, Kim K, Sullivan WJ, Angel SO. Histone variant H2B.Z acetylation is necessary for maintenance of Toxoplasma gondii biological fitness. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2023; 1866:194943. [PMID: 37217032 PMCID: PMC10524646 DOI: 10.1016/j.bbagrm.2023.194943] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 05/15/2023] [Accepted: 05/16/2023] [Indexed: 05/24/2023]
Abstract
Through regulation of DNA packaging, histone proteins are fundamental to a wide array of biological processes. A variety of post-translational modifications (PTMs), including acetylation, constitute a proposed histone code that is interpreted by "reader" proteins to modulate chromatin structure. Canonical histones can be replaced with variant versions that add an additional layer of regulatory complexity. The protozoan parasite Toxoplasma gondii is unique among eukaryotes in possessing a novel variant of H2B designated H2B.Z. The combination of PTMs and the use of histone variants are important for gene regulation in T. gondii, offering new targets for drug development. In this work, T. gondii parasites were generated in which the 5 N-terminal acetylatable lysines in H2B.Z were mutated to either alanine (c-Myc-A) or arginine (c-Myc-R). The c-Myc-A mutant displayed no phenotype over than a mild defect in its ability to kill mice. The c-Myc-R mutant presented an impaired ability to grow and an increase in differentiation to latent bradyzoites. The c-Myc-R mutant was also more sensitive to DNA damage, displayed no virulence in mice, and provided protective immunity against future infection. While nucleosome composition was unaltered, key genes were abnormally expressed during in vitro bradyzoite differentiation. Our results show that regulation of the N-terminal positive charge patch of H2B.Z is important for these processes. We also show that acetylated N-terminal H2B.Z interacts with some unique proteins compared to its unacetylated counterpart; the acetylated peptide pulled down proteins associated with chromosome maintenance/segregation and cell cycle, suggesting a link between H2B.Z acetylation status and mitosis.
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Affiliation(s)
- Laura Vanagas
- Laboratorio de Parasitología Molecular, INTECH, CONICET-UNSAM, Av. Intendente Marino Km. 8.2, C.C 164, B7130IIWA, Chascomús, Prov. Buenos Aires, Argentina.
| | - Daniela Muñoz
- Laboratorio de Parasitología Molecular, INTECH, CONICET-UNSAM, Av. Intendente Marino Km. 8.2, C.C 164, B7130IIWA, Chascomús, Prov. Buenos Aires, Argentina
| | - Constanza Cristaldi
- Laboratorio de Parasitología Molecular, INTECH, CONICET-UNSAM, Av. Intendente Marino Km. 8.2, C.C 164, B7130IIWA, Chascomús, Prov. Buenos Aires, Argentina
| | - Agustina Ganuza
- Laboratorio de Parasitología Molecular, INTECH, CONICET-UNSAM, Av. Intendente Marino Km. 8.2, C.C 164, B7130IIWA, Chascomús, Prov. Buenos Aires, Argentina
| | - Rosario Nájera
- Laboratorio de Parasitología Molecular, INTECH, CONICET-UNSAM, Av. Intendente Marino Km. 8.2, C.C 164, B7130IIWA, Chascomús, Prov. Buenos Aires, Argentina
| | - Mabel C Bonardi
- Laboratorio de Parasitología Molecular, INTECH, CONICET-UNSAM, Av. Intendente Marino Km. 8.2, C.C 164, B7130IIWA, Chascomús, Prov. Buenos Aires, Argentina
| | - Valeria R Turowski
- Laboratorio de Bioquímica y Biología Celular de Parásitos, INTECH, CONICET-UNSAM, Av. Intendente Marino Km. 8.2, C.C 164, B7130IIWA Chascomús, Prov. Buenos Aires, Argentina
| | - Fanny Guzman
- Núcleo de Biotecnología Curauma, Pontificia Universidad Católica de Valparaiso, Av. Universidad 330 Curauma, Valparaiso, Chile
| | - Bin Deng
- Department of Biology and VBRN, University of Vermont, VT, USA
| | - Kami Kim
- Department of Internal Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA
| | - William J Sullivan
- Department of Pharmacology and Toxicology, Indiana School of Medicine, Indianapolis, IN 46202, USA
| | - Sergio O Angel
- Laboratorio de Parasitología Molecular, INTECH, CONICET-UNSAM, Av. Intendente Marino Km. 8.2, C.C 164, B7130IIWA, Chascomús, Prov. Buenos Aires, Argentina.
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7
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Singh P, Lonardi S, Liang Q, Vydyam P, Khabirova E, Fang T, Gihaz S, Thekkiniath J, Munshi M, Abel S, Ciampossin L, Batugedara G, Gupta M, Lu XM, Lenz T, Chakravarty S, Cornillot E, Hu Y, Ma W, Gonzalez LM, Sánchez S, Estrada K, Sánchez-Flores A, Montero E, Harb OS, Le Roch KG, Mamoun CB. Babesia duncani multi-omics identifies virulence factors and drug targets. Nat Microbiol 2023; 8:845-859. [PMID: 37055610 PMCID: PMC10159843 DOI: 10.1038/s41564-023-01360-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Accepted: 03/14/2023] [Indexed: 04/15/2023]
Abstract
Babesiosis is a malaria-like disease in humans and animals that is caused by Babesia species, which are tick-transmitted apicomplexan pathogens. Babesia duncani causes severe to lethal infection in humans, but despite the risk that this parasite poses as an emerging pathogen, little is known about its biology, metabolic requirements or pathogenesis. Unlike other apicomplexan parasites that infect red blood cells, B. duncani can be continuously cultured in vitro in human erythrocytes and can infect mice resulting in fulminant babesiosis and death. We report comprehensive, detailed molecular, genomic, transcriptomic and epigenetic analyses to gain insights into the biology of B. duncani. We completed the assembly, 3D structure and annotation of its nuclear genome, and analysed its transcriptomic and epigenetics profiles during its asexual life cycle stages in human erythrocytes. We used RNA-seq data to produce an atlas of parasite metabolism during its intraerythrocytic life cycle. Characterization of the B. duncani genome, epigenome and transcriptome identified classes of candidate virulence factors, antigens for diagnosis of active infection and several attractive drug targets. Furthermore, metabolic reconstitutions from genome annotation and in vitro efficacy studies identified antifolates, pyrimethamine and WR-99210 as potent inhibitors of B. duncani to establish a pipeline of small molecules that could be developed as effective therapies for the treatment of human babesiosis.
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Affiliation(s)
- Pallavi Singh
- Department of Internal Medicine, Section of Infectious Diseases, Yale School of Medicine, New Haven, CT, USA
| | - Stefano Lonardi
- Department of Computer Science and Engineering, University of California, Riverside, CA, USA.
| | - Qihua Liang
- Department of Computer Science and Engineering, University of California, Riverside, CA, USA
| | - Pratap Vydyam
- Department of Internal Medicine, Section of Infectious Diseases, Yale School of Medicine, New Haven, CT, USA
| | | | - Tiffany Fang
- Department of Internal Medicine, Section of Infectious Diseases, Yale School of Medicine, New Haven, CT, USA
| | - Shalev Gihaz
- Department of Internal Medicine, Section of Infectious Diseases, Yale School of Medicine, New Haven, CT, USA
| | - Jose Thekkiniath
- Department of Internal Medicine, Section of Infectious Diseases, Yale School of Medicine, New Haven, CT, USA
| | - Muhammad Munshi
- Department of Internal Medicine, Section of Infectious Diseases, Yale School of Medicine, New Haven, CT, USA
| | - Steven Abel
- Department of Molecular, Cell and Systems Biology, University of California, Riverside, CA, USA
| | - Loic Ciampossin
- Department of Molecular, Cell and Systems Biology, University of California, Riverside, CA, USA
| | - Gayani Batugedara
- Department of Molecular, Cell and Systems Biology, University of California, Riverside, CA, USA
| | - Mohit Gupta
- Department of Molecular, Cell and Systems Biology, University of California, Riverside, CA, USA
| | - Xueqing Maggie Lu
- Department of Molecular, Cell and Systems Biology, University of California, Riverside, CA, USA
| | - Todd Lenz
- Department of Molecular, Cell and Systems Biology, University of California, Riverside, CA, USA
| | - Sakshar Chakravarty
- Department of Computer Science and Engineering, University of California, Riverside, CA, USA
| | - Emmanuel Cornillot
- Institut de Biologie Computationnelle (IBC), and Institut de Recherche en Cancérologie de Montpellier (IRCM - INSERM U1194), Institut régional du Cancer Montpellier (ICM) and Université de Montpellier, Montpellier, France
| | - Yangyang Hu
- Department of Computer Science and Engineering, University of California, Riverside, CA, USA
| | - Wenxiu Ma
- Department of Statistics, University of California, Riverside, CA, USA
| | - Luis Miguel Gonzalez
- Parasitology Reference and Research Laboratory, National Centre for Microbiology, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
| | - Sergio Sánchez
- Reference and Research Laboratory on Food and Waterborne Bacterial Infections, National Centre for Microbiology, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
| | - Karel Estrada
- Unidad Universitaria de Secuenciación Masiva y Bioinformática, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, México
| | - Alejandro Sánchez-Flores
- Unidad Universitaria de Secuenciación Masiva y Bioinformática, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, México
| | - Estrella Montero
- Parasitology Reference and Research Laboratory, National Centre for Microbiology, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
| | - Omar S Harb
- Department of Biology, University of Pennsylvania, Philadelphia, PA, USA
| | - Karine G Le Roch
- Department of Molecular, Cell and Systems Biology, University of California, Riverside, CA, USA.
| | - Choukri Ben Mamoun
- Department of Internal Medicine, Section of Infectious Diseases, Yale School of Medicine, New Haven, CT, USA.
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Vanagas L, Muñoz D, Cristaldi C, Ganuza A, Nájera R, Bonardi MC, Turowski VR, Guzman F, Deng B, Kim K, Sullivan WJ, Angel SO. Histone variant H2B.Z acetylation is necessary for maintenance of Toxoplasma gondii biological fitness. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.14.528480. [PMID: 36824796 PMCID: PMC9949044 DOI: 10.1101/2023.02.14.528480] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/16/2023]
Abstract
Through regulation of DNA packaging, histone proteins are fundamental to a wide array of biological processes. A variety of post-translational modifications (PTMs), including acetylation, constitute a proposed histone code that is interpreted by "reader" proteins to modulate chromatin structure. Canonical histones can be replaced with variant versions that add an additional layer of regulatory complexity. The protozoan parasite Toxoplasma gondii is unique among eukaryotes in possessing a novel variant of H2B designated H2B.Z. The combination of PTMs and the use of histone variants is important for gene regulation in T. gondii, offering new targets for drug development. In this work, T. gondii parasites were generated in which the 5 N-terminal acetylatable lysines in H2B.Z were mutated to either alanine (c-Myc-A) or arginine (c-Myc-R). c-Myc-A mutant only displayed a mild effect in its ability to kill mice. c-Myc-R mutant presented an impaired ability to grow and an increase in differentiation to latent bradyzoites. This mutant line was also more sensitive to DNA damage, displayed no virulence in mice, and provided protective immunity against future infection. While nucleosome composition was unaltered, key genes were abnormally expressed during in vitro bradyzoite differentiation. Our results show that the N-terminal positive charge patch of H2B.Z is important for these procceses. Pull down assays with acetylated N-terminal H2B.Z peptide and unacetylated one retrieved common and differential interactors. Acetylated peptide pulled down proteins associated with chromosome maintenance/segregation and cell cycle, opening the question of a possible link between H2B.Z acetylation status and mitosis.
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Affiliation(s)
- Laura Vanagas
- Laboratorio de Parasitología Molecular, INTECH, CONICET-UNSAM, Av. Intendente Marino Km. 8.2, C.C 164, (B7130IIWA), Chascomús, Prov. Buenos Aires, Argentina
| | - Daniela Muñoz
- Laboratorio de Parasitología Molecular, INTECH, CONICET-UNSAM, Av. Intendente Marino Km. 8.2, C.C 164, (B7130IIWA), Chascomús, Prov. Buenos Aires, Argentina
| | - Constanza Cristaldi
- Laboratorio de Parasitología Molecular, INTECH, CONICET-UNSAM, Av. Intendente Marino Km. 8.2, C.C 164, (B7130IIWA), Chascomús, Prov. Buenos Aires, Argentina
| | - Agustina Ganuza
- Laboratorio de Parasitología Molecular, INTECH, CONICET-UNSAM, Av. Intendente Marino Km. 8.2, C.C 164, (B7130IIWA), Chascomús, Prov. Buenos Aires, Argentina
| | - Rosario Nájera
- Laboratorio de Parasitología Molecular, INTECH, CONICET-UNSAM, Av. Intendente Marino Km. 8.2, C.C 164, (B7130IIWA), Chascomús, Prov. Buenos Aires, Argentina
| | - Mabel C. Bonardi
- Laboratorio de Parasitología Molecular, INTECH, CONICET-UNSAM, Av. Intendente Marino Km. 8.2, C.C 164, (B7130IIWA), Chascomús, Prov. Buenos Aires, Argentina
| | - Valeria R. Turowski
- Laboratorio de Bioquímica y Biología Celular de Parásitos, INTECH, CONICET-UNSAM, Av. Intendente Marino Km. 8.2, C.C 164, (B7130IIWA), Chascomús, Prov. Buenos Aires, Argentina
| | - Fanny Guzman
- Núcleo de Biotecnología Curauma, Pontificia Universidad Católica de Valparaiso. Av. Universidad 330 Curauma, Valparaiso
| | - Bin Deng
- Department of Biology and VBRN, University of Vermont, Vermont, USA
| | - Kami Kim
- Department of Internal Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL 33612
| | - William J. Sullivan
- Department of Pharmacology and Toxicology, Indiana School of Medicine, Indianapolis, Indiana 46202, USA
| | - Sergio O. Angel
- Laboratorio de Parasitología Molecular, INTECH, CONICET-UNSAM, Av. Intendente Marino Km. 8.2, C.C 164, (B7130IIWA), Chascomús, Prov. Buenos Aires, Argentina
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Previously Unidentified Histone H1-Like Protein Is Involved in Cell Division and Ribosome Biosynthesis in Toxoplasma gondii. mSphere 2022; 7:e0040322. [PMID: 36468865 PMCID: PMC9769792 DOI: 10.1128/msphere.00403-22] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Chromatin dynamics can regulate all DNA-dependent processes. Access to DNA within chromatin is orchestrated mainly by histones and their posttranslational modifications (PTMs). Like other eukaryotes, the apicomplexan parasite Toxoplasma gondii encodes four canonical histones and five histone variants. In contrast, the linker histone (H1) has never been identified in apicomplexan parasites. In other eukaryotes, histone H1 compacts the chromatin by linking the nucleosome and increasing the DNA compaction. H1 is a multifunctional protein and can be involved in different steps of DNA metabolism or associated with protein complexes related to distinct biological processes. We have identified a novel protein in T. gondii ("TgH1-like") that, although lacking the globular domain of mammalian H1, is remarkably like the H1-like proteins of bacteria and trypanosomatids. Our results demonstrate that TgH1-like is a nuclear protein associated with chromatin and other histones. Curiously, TgH1-like is also in the nucleolus and associated with ribosomal proteins, indicating a versatile function in this parasite. Although knockout of the tgh1-like gene does not affect the cell cycle, it causes endopolygeny and asynchronous division. Interestingly, mutation of posttranslationally modified amino acids results in defects in cell division like those in the Δtgh1-like mutant, showing that these sites are important for protein function. Furthermore, in the bradyzoite stage, this protein is expressed only in dividing parasites, reinforcing its importance in cell division. Indeed, the absence of TgH1-like decreases compaction of peripheral chromatin, confirming its role in the chromatin modulation in T. gondii. IMPORTANCE Histone H1, or linker histone, is an important protein that binds to the nucleosome, aiding chromatin compaction. Here, we characterize for the first time a linker histone in T. gondii, named TgH1-like. It is a small and basic protein that corresponds only to the C-terminal portion of the human H1 but is similar to histone H1 from trypanosomatids and bacteria. TgH1-like is located in the nucleus, interacts with nucleosome histones, and acts in chromatin structure and cell division. Our findings show for the first time the presence of a histone H1 protein in an apicomplexan parasite and will provide new insights into cell division and chromatin dynamics in T. gondii and related parasites.
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Ulahannan N, Cutler R, Doña-Termine R, Simões-Pires CA, Wijetunga NA, Croken MM, Johnston AD, Kong Y, Maqbool SB, Suzuki M, Greally JM. Genomic insights into host and parasite interactions during intracellular infection by Toxoplasma gondii. PLoS One 2022; 17:e0275226. [PMID: 36178892 PMCID: PMC9524707 DOI: 10.1371/journal.pone.0275226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Accepted: 08/02/2022] [Indexed: 11/18/2022] Open
Abstract
To gain insights into the molecular interactions of an intracellular pathogen and its host cell, we studied the gene expression and chromatin states of human fibroblasts infected with the Apicomplexan parasite Toxoplasma gondii. We show a striking activation of host cell genes that regulate a number of cellular processes, some of which are protective of the host cell, others likely to be advantageous to the pathogen. The simultaneous capture of host and parasite genomic information allowed us to gain insights into the regulation of the T. gondii genome. We show how chromatin accessibility and transcriptional profiling together permit novel annotation of the parasite's genome, including more accurate mapping of known genes and the identification of new genes and cis-regulatory elements. Motif analysis reveals not only the known T. gondii AP2 transcription factor-binding site but also a previously-undiscovered candidate TATA box-containing motif at one-quarter of promoters. By inferring the transcription factor and upstream cell signaling responses involved in the host cell, we can use genomic information to gain insights into T. gondii's perturbation of host cell physiology. Our resulting model builds on previously-described human host cell signalling responses to T. gondii infection, linked to induction of specific transcription factors, some of which appear to be solely protective of the host cell, others of which appear to be co-opted by the pathogen to enhance its own survival.
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Affiliation(s)
- Netha Ulahannan
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, United States of America
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY, United States of America
| | - Ronald Cutler
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, United States of America
| | - Reanna Doña-Termine
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, United States of America
| | - Claudia A. Simões-Pires
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, United States of America
| | - N. Ari Wijetunga
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY, United States of America
| | - Matthew McKnight Croken
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY, United States of America
| | - Andrew D. Johnston
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, United States of America
| | - Yu Kong
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, United States of America
| | - Shahina B. Maqbool
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, United States of America
| | - Masako Suzuki
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, United States of America
| | - John M. Greally
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, United States of America
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Architecture, Chromatin and Gene Organization of Toxoplasma gondii Subtelomeres. EPIGENOMES 2022; 6:epigenomes6030029. [PMID: 36135316 PMCID: PMC9498087 DOI: 10.3390/epigenomes6030029] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 09/05/2022] [Accepted: 09/08/2022] [Indexed: 11/17/2022] Open
Abstract
Subtelomeres (ST) are chromosome regions that separate telomeres from euchromatin and play relevant roles in various biological processes of the cell. While their functions are conserved, ST structure and genetic compositions are unique to each species. This study aims to identify and characterize the subtelomeric regions of the 13 Toxoplasma gondii chromosomes of the Me49 strain. Here, STs were defined at chromosome ends based on poor gene density. The length of STs ranges from 8.1 to 232.4 kbp, with a gene density of 0.049 genes/kbp, lower than the Me49 genome (0.15 kbp). Chromatin organization showed that H3K9me3, H2A.X, and H3.3 are highly enriched near telomeres and the 5′ end of silenced genes, decaying in intensity towards euchromatin. H3K4me3 and H2A.Z/H2B.Z are shown to be enriched in the 5′ end of the ST genes. Satellite DNA was detected in almost all STs, mainly the sat350 family and a novel satellite named sat240. Beyond the STs, only short dispersed fragments of sat240 and sat350 were found. Within STs, there were 12 functional annotated genes, 59 with unknown functions (Hypothetical proteins), 15 from multigene FamB, and 13 from multigene family FamC. Some genes presented low interstrain synteny associated with the presence of satellite DNA. Orthologues of FamB and FamC were also detected in Neospora caninum and Hammondia hammondi. A re-analysis of previous transcriptomic data indicated that ST gene expression is strongly linked to the adaptation to different situations such as extracellular passage (evolve and resequencing study) and changes in metabolism (lack of acetyl-CoA cofactor). In conclusion, the ST region of the T. gondii chromosomes was defined, the STs genes were determined, and it was possible to associate them with high interstrain plasticity and a role in the adaptability of T. gondii to environmental changes.
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