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Tavernelli LE, Alonso VL, Peña I, Rodríguez Araya E, Manarin R, Cantizani J, Martin J, Salamanca J, Bamborough P, Calderón F, Gabarro R, Serra E. Identification of novel bromodomain inhibitors of Trypanosoma cruzi bromodomain factor 2 ( TcBDF2) using a fluorescence polarization-based high-throughput assay. Antimicrob Agents Chemother 2024; 68:e0024324. [PMID: 39028190 PMCID: PMC11304739 DOI: 10.1128/aac.00243-24] [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: 02/15/2024] [Accepted: 06/30/2024] [Indexed: 07/20/2024] Open
Abstract
Bromodomains are structural folds present in all eukaryotic cells that bind to other proteins recognizing acetylated lysines. Most proteins with bromodomains are part of nuclear complexes that interact with acetylated histone residues and regulate DNA replication, transcription, and repair through chromatin structure remodeling. Bromodomain inhibitors are small molecules that bind to the hydrophobic pocket of bromodomains, interfering with the interaction with acetylated histones. Using a fluorescent probe, we have developed an assay to select inhibitors of the bromodomain factor 2 of Trypanosoma cruzi (TcBDF2) using fluorescence polarization. Initially, a library of 28,251 compounds was screened in an endpoint assay. The top 350-ranked compounds were further analyzed in a dose-response assay. From this analysis, seven compounds were obtained that had not been previously characterized as bromodomain inhibitors. Although these compounds did not exhibit significant trypanocidal activity, all showed bona fide interaction with TcBDF2 with dissociation constants between 1 and 3 µM validating these assays to search for bromodomain inhibitors.
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Affiliation(s)
- Luis E. Tavernelli
- Instituto de Biología Molecular y Celular de Rosario, CONICET, Rosario, Argentina
- GlaxoSmithKline Global Health, Madrid, Spain
| | - Victoria L. Alonso
- Instituto de Biología Molecular y Celular de Rosario, CONICET, Rosario, Argentina
- Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Imanol Peña
- GlaxoSmithKline Global Health, Madrid, Spain
| | - Elvio Rodríguez Araya
- Instituto de Biología Molecular y Celular de Rosario, CONICET, Rosario, Argentina
- Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Romina Manarin
- Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | | | | | | | - Paul Bamborough
- Molecular Design, GlaxoSmithKline, Stevenage, United Kingdom
| | | | | | - Esteban Serra
- Instituto de Biología Molecular y Celular de Rosario, CONICET, Rosario, Argentina
- Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
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2
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Kieft R, Yan H, Schmitz RJ, Sabatini R. Mono-allelic epigenetic regulation of bi-directional polycistronic transcription initiation by RNA Polymerase II in Trypanosoma brucei. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.21.600114. [PMID: 38948844 PMCID: PMC11213002 DOI: 10.1101/2024.06.21.600114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/02/2024]
Abstract
Unique for a eukaryote, protein-coding genes in trypanosomes are arranged in polycistronic units (PTUs). This genome arrangement has led to a model where Pol II transcription of PTUs is unregulated. The initial step in trypanosome lytic factor (TLF) mediated lysis of Trypanosoma brucei requires high affinity haptoglobin/hemoglobin receptor (HpHbR) binding. Here we demonstrate that by in vitro selection with TLF, resistance is obtained in a stepwise process correlating with loss of HpHbR expression at an allelic level. RNA-seq, Pol II ChIP and run-on analysis indicate HpHbR silencing is at the transcriptional level, where loss of Pol II binding at the promoter region specifically shuts down transcription of the HpHbR containing gene cluster and the adjacent opposing gene cluster. Reversible transcriptional silencing of the divergent PTUs correlates with DNA base J modification of the shared promoter region. Therefore, epigenetic mechanisms exist to regulate gene expression via Pol II transcription initiation of gene clusters in a mono-allelic fashion. These findings suggest epigenetic chromatin-based regulation of gene expression is deeply conserved among eukaryotes, including primitive eukaryotes that rely on polycistronic transcription.
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3
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Frisbie VS, Hashimoto H, Xie Y, De Luna Vitorino FN, Baeza J, Nguyen T, Yuan Z, Kiselar J, Garcia BA, Debler EW. Two DOT1 enzymes cooperatively mediate efficient ubiquitin-independent histone H3 lysine 76 tri-methylation in kinetoplastids. Nat Commun 2024; 15:2467. [PMID: 38503750 PMCID: PMC10951340 DOI: 10.1038/s41467-024-46637-6] [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: 08/04/2023] [Accepted: 03/04/2024] [Indexed: 03/21/2024] Open
Abstract
In higher eukaryotes, a single DOT1 histone H3 lysine 79 (H3K79) methyltransferase processively produces H3K79me2/me3 through histone H2B mono-ubiquitin interaction, while the kinetoplastid Trypanosoma brucei di-methyltransferase DOT1A and tri-methyltransferase DOT1B efficiently methylate the homologous H3K76 without H2B mono-ubiquitination. Based on structural and biochemical analyses of DOT1A, we identify key residues in the methyltransferase motifs VI and X for efficient ubiquitin-independent H3K76 methylation in kinetoplastids. Substitution of a basic to an acidic residue within motif VI (Gx6K) is essential to stabilize the DOT1A enzyme-substrate complex, while substitution of the motif X sequence VYGE by CAKS renders a rigid active-site loop flexible, implying a distinct mechanism of substrate recognition. We further reveal distinct methylation kinetics and substrate preferences of DOT1A (H3K76me0) and DOT1B (DOT1A products H3K76me1/me2) in vitro, determined by a Ser and Ala residue within motif IV, respectively, enabling DOT1A and DOT1B to mediate efficient H3K76 tri-methylation non-processively but cooperatively, and suggesting why kinetoplastids have evolved two DOT1 enzymes.
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Affiliation(s)
- Victoria S Frisbie
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, PA, USA
| | - Hideharu Hashimoto
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, PA, USA
| | - Yixuan Xie
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, USA
- Epigenetics Institute, Department of Biochemistry and Biophysics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Francisca N De Luna Vitorino
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, USA
| | - Josue Baeza
- Epigenetics Institute, Department of Biochemistry and Biophysics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Tam Nguyen
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, PA, USA
| | - Zhangerjiao Yuan
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, PA, USA
| | - Janna Kiselar
- Case Center for Proteomics and Bioinformatics, Department of Nutrition, Case Western Reserve University, School of Medicine, Cleveland, OH, USA
| | - Benjamin A Garcia
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, USA
- Epigenetics Institute, Department of Biochemistry and Biophysics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Erik W Debler
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, PA, USA.
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4
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Pal J, Sharma V, Khanna A, Saha S. The SET7 protein of Leishmania donovani moderates the parasite's response to a hostile oxidative environment. J Biol Chem 2024; 300:105720. [PMID: 38311179 PMCID: PMC10907163 DOI: 10.1016/j.jbc.2024.105720] [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: 11/17/2023] [Revised: 01/17/2024] [Accepted: 01/29/2024] [Indexed: 02/10/2024] Open
Abstract
SET domain proteins methylate specific lysines on proteins, triggering stimulation or repression of downstream processes. Twenty-nine SET domain proteins have been identified in Leishmania donovani through sequence annotations. This study initiates the first investigation into these proteins. We find LdSET7 is predominantly cytosolic. Although not essential, set7 deletion slows down promastigote growth and hypersensitizes the parasite to hydroxyurea-induced G1/S arrest. Intriguingly, set7-nulls survive more proficiently than set7+/+ parasites within host macrophages, suggesting that LdSET7 moderates parasite response to the inhospitable intracellular environment. set7-null in vitro promastigote cultures are highly tolerant to hydrogen peroxide (H2O2)-induced stress, reflected in their growth pattern, and no detectable DNA damage at H2O2 concentrations tested. This is linked to reactive oxygen species levels remaining virtually unperturbed in set7-nulls in response to H2O2 exposure, contrasting to increased reactive oxygen species in set7+/+ cells under similar conditions. In analyzing the cell's ability to scavenge hydroperoxides, we find peroxidase activity is not upregulated in response to H2O2 exposure in set7-nulls. Rather, constitutive basal levels of peroxidase activity are significantly higher in these cells, implicating this to be a factor contributing to the parasite's high tolerance to H2O2. Higher levels of peroxidase activity in set7-nulls are coupled to upregulation of tryparedoxin peroxidase transcripts. Rescue experiments using an LdSET7 mutant suggest that LdSET7 methylation activity is critical to the modulation of the cell's response to oxidative environment. Thus, LdSET7 tunes the parasite's behavior within host cells, enabling the establishment and persistence of infection without eradicating the host cell population it needs for survival.
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Affiliation(s)
- Jyoti Pal
- Department of Microbiology, University of Delhi South Campus, New Delhi, India
| | - Varshni Sharma
- Department of Microbiology, University of Delhi South Campus, New Delhi, India
| | - Arushi Khanna
- Department of Microbiology, University of Delhi South Campus, New Delhi, India
| | - Swati Saha
- Department of Microbiology, University of Delhi South Campus, New Delhi, India.
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5
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Gao J, Jishage M, Wang Y, Wang R, Chen M, Zhu Z, Zhang J, Diwu Y, Xu C, Liao S, Roeder RG, Tu X. Structural basis for evolutionarily conserved interactions between TFIIS and Paf1C. Int J Biol Macromol 2023; 253:126764. [PMID: 37696373 PMCID: PMC11164251 DOI: 10.1016/j.ijbiomac.2023.126764] [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: 04/22/2023] [Revised: 09/03/2023] [Accepted: 09/04/2023] [Indexed: 09/13/2023]
Abstract
The elongation factor TFIIS interacts with Paf1C complex to facilitate processive transcription by Pol II. We here determined the crystal structure of the trypanosoma TFIIS LW domain in a complex with the LFG motif of Leo1, as well as the structures of apo-form TFIIS LW domains from trypanosoma, yeast and human. We revealed that all three TFIIS LW domains possess a conserved hydrophobic core that mediates their interactions with Leo1. Intriguingly, the structural study revealed that trypanosoma Leo1 binding induces the TFIIS LW domain to undergo a conformational change reflected in the length and orientation of α6 helix that is absent in the yeast and human counterparts. These differences explain the higher binding affinity of the TFIIS LW domain interacting with Leo1 in trypanosoma than in yeast and human, and indicate species-specific variations in the interactions. Importantly, the interactions between the TFIIS LW domain and an LFG motif of Leo1 were found to be critical for TFIIS to anchor the entire Paf1C complex. Thus, in addition to revealing a detailed structural basis for the TFIIS-Paf1C interaction, our studies also shed light on the origin and evolution of the roles of TFIIS and Paf1C complex in regulation of transcription elongation.
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Affiliation(s)
- Jie Gao
- MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, Hefei National Research Center for Interdisciplinary Sciences at the Microscale, School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230022, PR China; Department of Ophthalmology, The Second Affiliated Hospital of Anhui Medical University, 678 Furong Road, Hefei, Anhui, PR China
| | - Miki Jishage
- Laboratory of Biochemistry and Molecular Biology, The Rockefeller University, New York, NY 10065, USA
| | - Yuzhu Wang
- MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, Hefei National Research Center for Interdisciplinary Sciences at the Microscale, School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230022, PR China
| | - Rui Wang
- MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, Hefei National Research Center for Interdisciplinary Sciences at the Microscale, School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230022, PR China; Department of Anthropotomy and Histoembryology, Medical College, Henan University of Science and Technology, Luoyang, Henan 471023, PR China
| | - Meng Chen
- MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, Hefei National Research Center for Interdisciplinary Sciences at the Microscale, School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230022, PR China
| | - Zhongliang Zhu
- MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, Hefei National Research Center for Interdisciplinary Sciences at the Microscale, School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230022, PR China
| | - Jiahai Zhang
- MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, Hefei National Research Center for Interdisciplinary Sciences at the Microscale, School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230022, PR China
| | - Yating Diwu
- MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, Hefei National Research Center for Interdisciplinary Sciences at the Microscale, School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230022, PR China
| | - Chao Xu
- MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, Hefei National Research Center for Interdisciplinary Sciences at the Microscale, School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230022, PR China
| | - Shanhui Liao
- MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, Hefei National Research Center for Interdisciplinary Sciences at the Microscale, School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230022, PR China.
| | - Robert G Roeder
- Laboratory of Biochemistry and Molecular Biology, The Rockefeller University, New York, NY 10065, USA.
| | - Xiaoming Tu
- MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, Hefei National Research Center for Interdisciplinary Sciences at the Microscale, School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230022, PR China.
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6
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Field MC. Deviating from the norm: Nuclear organisation in trypanosomes. Curr Opin Cell Biol 2023; 85:102234. [PMID: 37666024 DOI: 10.1016/j.ceb.2023.102234] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Revised: 08/10/2023] [Accepted: 08/10/2023] [Indexed: 09/06/2023]
Abstract
At first glance the nucleus is a highly conserved organelle. Overall nuclear morphology, the octagonal nuclear pore complex, the presence of peripheral heterochromatin and the nuclear envelope appear near constant features right down to the ultrastructural level. New work is revealing significant compositional divergence within these nuclear structures and their associated functions, likely reflecting adaptations and distinct mechanisms between eukaryotic lineages and especially the trypanosomatids. While many examples of mechanistic divergence currently lack obvious functional interpretations, these studies underscore the malleability of nuclear architecture. I will discuss some recent findings highlighting these facets within trypanosomes, together with the underlying evolutionary framework and make a call for the exploration of nuclear function in non-canonical experimental organisms.
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Affiliation(s)
- Mark C Field
- School of Life Sciences, University of Dundee, Dundee, UK; Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czechia.
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7
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Girasol MJ, Briggs EM, Marques CA, Batista JM, Beraldi D, Burchmore R, Lemgruber L, McCulloch R. Immunoprecipitation of RNA-DNA hybrid interacting proteins in Trypanosoma brucei reveals conserved and novel activities, including in the control of surface antigen expression needed for immune evasion by antigenic variation. Nucleic Acids Res 2023; 51:11123-11141. [PMID: 37843098 PMCID: PMC10639054 DOI: 10.1093/nar/gkad836] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Revised: 09/14/2023] [Accepted: 09/28/2023] [Indexed: 10/17/2023] Open
Abstract
RNA-DNA hybrids are epigenetic features of genomes that provide a diverse and growing range of activities. Understanding of these functions has been informed by characterising the proteins that interact with the hybrids, but all such analyses have so far focused on mammals, meaning it is unclear if a similar spectrum of RNA-DNA hybrid interactors is found in other eukaryotes. The African trypanosome is a single-cell eukaryotic parasite of the Discoba grouping and displays substantial divergence in several aspects of core biology from its mammalian host. Here, we show that DNA-RNA hybrid immunoprecipitation coupled with mass spectrometry recovers 602 putative interactors in T. brucei mammal- and insect-infective cells, some providing activities also found in mammals and some lineage-specific. We demonstrate that loss of three factors, two putative helicases and a RAD51 paralogue, alters T. brucei nuclear RNA-DNA hybrid and DNA damage levels. Moreover, loss of each factor affects the operation of the parasite immune survival mechanism of antigenic variation. Thus, our work reveals the broad range of activities contributed by RNA-DNA hybrids to T. brucei biology, including new functions in host immune evasion as well as activities likely fundamental to eukaryotic genome function.
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Affiliation(s)
- Mark J Girasol
- University of Glasgow, College of Medical, Veterinary and Life Sciences, School of Infection and Immunity, Wellcome Centre for Integrative Parasitology, Glasgow, UK
- University of the Philippines Manila, College of Medicine, Manila, Philippines
| | - Emma M Briggs
- University of Glasgow, College of Medical, Veterinary and Life Sciences, School of Infection and Immunity, Wellcome Centre for Integrative Parasitology, Glasgow, UK
- University of Edinburgh, Institute for Immunology and Infection Research, School of Biological Sciences, Edinburgh, UK
| | - Catarina A Marques
- University of Glasgow, College of Medical, Veterinary and Life Sciences, School of Infection and Immunity, Wellcome Centre for Integrative Parasitology, Glasgow, UK
| | - José M Batista
- University of Glasgow, College of Medical, Veterinary and Life Sciences, School of Infection and Immunity, Wellcome Centre for Integrative Parasitology, Glasgow, UK
| | - Dario Beraldi
- University of Glasgow, College of Medical, Veterinary and Life Sciences, School of Infection and Immunity, Wellcome Centre for Integrative Parasitology, Glasgow, UK
| | - Richard Burchmore
- University of Glasgow, College of Medical, Veterinary and Life Sciences, School of Infection and Immunity, Wellcome Centre for Integrative Parasitology, Glasgow, UK
| | - Leandro Lemgruber
- University of Glasgow, College of Medical, Veterinary and Life Sciences, School of Infection and Immunity, Wellcome Centre for Integrative Parasitology, Glasgow, UK
| | - Richard McCulloch
- University of Glasgow, College of Medical, Veterinary and Life Sciences, School of Infection and Immunity, Wellcome Centre for Integrative Parasitology, Glasgow, UK
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8
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Russell C, Carter JL, Borgia JM, Bush J, Calderón F, Gabarró R, Conway SJ, Mottram JC, Wilkinson AJ, Jones NG. Bromodomain Factor 5 as a Target for Antileishmanial Drug Discovery. ACS Infect Dis 2023; 9:2340-2357. [PMID: 37906637 PMCID: PMC10644352 DOI: 10.1021/acsinfecdis.3c00431] [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: 08/22/2023] [Revised: 10/16/2023] [Accepted: 10/16/2023] [Indexed: 11/02/2023]
Abstract
Leishmaniases are a collection of neglected tropical diseases caused by kinetoplastid parasites in the genus Leishmania. Current chemotherapies are severely limited, and the need for new antileishmanials is of pressing international importance. Bromodomains are epigenetic reader domains that have shown promising therapeutic potential for cancer therapy and may also present an attractive target to treat parasitic diseases. Here, we investigate Leishmania donovani bromodomain factor 5 (LdBDF5) as a target for antileishmanial drug discovery. LdBDF5 contains a pair of bromodomains (BD5.1 and BD5.2) in an N-terminal tandem repeat. We purified recombinant bromodomains of L. donovani BDF5 and determined the structure of BD5.2 by X-ray crystallography. Using a histone peptide microarray and fluorescence polarization assay, we identified binding interactions of LdBDF5 bromodomains with acetylated peptides derived from histones H2B and H4. In orthogonal biophysical assays including thermal shift assays, fluorescence polarization, and NMR, we showed that BDF5 bromodomains bind to human bromodomain inhibitors SGC-CBP30, bromosporine, and I-BRD9; moreover, SGC-CBP30 exhibited activity against Leishmania promastigotes in cell viability assays. These findings exemplify the potential BDF5 holds as a possible drug target in Leishmania and provide a foundation for the future development of optimized antileishmanial compounds targeting this epigenetic reader protein.
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Affiliation(s)
- Catherine
N. Russell
- York
Structural Biology Laboratory and York Biomedical Research Institute,
Department of Chemistry, University of York, York YO10 5DD, U.K.
| | - Jennifer L. Carter
- Department
of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, U.K.
| | - Juliet M. Borgia
- York
Structural Biology Laboratory and York Biomedical Research Institute,
Department of Chemistry, University of York, York YO10 5DD, U.K.
| | - Jacob Bush
- GSK, Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, U.K.
| | | | | | - Stuart J. Conway
- Department
of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, U.K.
| | - Jeremy C. Mottram
- York
Biomedical Research Institute, Department of Biology, University of York, York YO10 5NG, U.K.
| | - Anthony J. Wilkinson
- York
Structural Biology Laboratory and York Biomedical Research Institute,
Department of Chemistry, University of York, York YO10 5DD, U.K.
| | - Nathaniel G. Jones
- York
Biomedical Research Institute, Department of Biology, University of York, York YO10 5NG, U.K.
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9
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Deák G, Wapenaar H, Sandoval G, Chen R, Taylor MRD, Burdett H, Watson J, Tuijtel M, Webb S, Wilson M. Histone divergence in trypanosomes results in unique alterations to nucleosome structure. Nucleic Acids Res 2023; 51:7882-7899. [PMID: 37427792 PMCID: PMC10450195 DOI: 10.1093/nar/gkad577] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Revised: 06/02/2023] [Accepted: 06/26/2023] [Indexed: 07/11/2023] Open
Abstract
Eukaryotes have a multitude of diverse mechanisms for organising and using their genomes, but the histones that make up chromatin are highly conserved. Unusually, histones from kinetoplastids are highly divergent. The structural and functional consequences of this variation are unknown. Here, we have biochemically and structurally characterised nucleosome core particles (NCPs) from the kinetoplastid parasite Trypanosoma brucei. A structure of the T. brucei NCP reveals that global histone architecture is conserved, but specific sequence alterations lead to distinct DNA and protein interaction interfaces. The T. brucei NCP is unstable and has weakened overall DNA binding. However, dramatic changes at the H2A-H2B interface introduce local reinforcement of DNA contacts. The T. brucei acidic patch has altered topology and is refractory to known binders, indicating that the nature of chromatin interactions in T. brucei may be unique. Overall, our results provide a detailed molecular basis for understanding evolutionary divergence in chromatin structure.
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Affiliation(s)
- Gauri Deák
- Wellcome Centre for Cell Biology, University of Edinburgh, Michael Swann Building, Kings Buildings, Mayfield Road, Edinburgh EH9 3JR, UK
| | - Hannah Wapenaar
- Wellcome Centre for Cell Biology, University of Edinburgh, Michael Swann Building, Kings Buildings, Mayfield Road, Edinburgh EH9 3JR, UK
| | - Gorka Sandoval
- Wellcome Centre for Cell Biology, University of Edinburgh, Michael Swann Building, Kings Buildings, Mayfield Road, Edinburgh EH9 3JR, UK
| | - Ruofan Chen
- Wellcome Centre for Cell Biology, University of Edinburgh, Michael Swann Building, Kings Buildings, Mayfield Road, Edinburgh EH9 3JR, UK
| | - Mark R D Taylor
- Wellcome Centre for Cell Biology, University of Edinburgh, Michael Swann Building, Kings Buildings, Mayfield Road, Edinburgh EH9 3JR, UK
| | - Hayden Burdett
- Wellcome Centre for Cell Biology, University of Edinburgh, Michael Swann Building, Kings Buildings, Mayfield Road, Edinburgh EH9 3JR, UK
| | - James A Watson
- Wellcome Centre for Cell Biology, University of Edinburgh, Michael Swann Building, Kings Buildings, Mayfield Road, Edinburgh EH9 3JR, UK
| | - Maarten W Tuijtel
- Wellcome Centre for Cell Biology, University of Edinburgh, Michael Swann Building, Kings Buildings, Mayfield Road, Edinburgh EH9 3JR, UK
- Department of Molecular Sociology, Max Planck Institute of Biophysics, Max-von-Laue-Straße 3, 60438 Frankfurt am Main, Germany
| | - Shaun Webb
- Wellcome Centre for Cell Biology, University of Edinburgh, Michael Swann Building, Kings Buildings, Mayfield Road, Edinburgh EH9 3JR, UK
| | - Marcus D Wilson
- Wellcome Centre for Cell Biology, University of Edinburgh, Michael Swann Building, Kings Buildings, Mayfield Road, Edinburgh EH9 3JR, UK
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10
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Menezes AP, Murillo AM, de Castro CG, Bellini NK, Tosi LRO, Thiemann OH, Elias MC, Silber AM, da Cunha JPC. Navigating the boundaries between metabolism and epigenetics in trypanosomes. Trends Parasitol 2023; 39:682-695. [PMID: 37349193 DOI: 10.1016/j.pt.2023.05.010] [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: 02/15/2023] [Revised: 05/24/2023] [Accepted: 05/24/2023] [Indexed: 06/24/2023]
Abstract
Epigenetic marks enable cells to acquire new biological features that favor their adaptation to environmental changes. These marks are chemical modifications on chromatin-associated proteins and nucleic acids that lead to changes in the chromatin landscape and may eventually affect gene expression. The chemical tags of these epigenetic marks are comprised of intermediate cellular metabolites. The number of discovered associations between metabolism and epigenetics has increased, revealing how environment influences gene regulation and phenotype diversity. This connection is relevant to all organisms but underappreciated in digenetic parasites, which must adapt to different environments as they progress through their life cycles. This review speculates and proposes associations between epigenetics and metabolism in trypanosomes, which are protozoan parasites that cause human and livestock diseases.
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Affiliation(s)
- Ana Paula Menezes
- Laboratório de Ciclo Celular - Instituto Butantan, São Paulo-SP, Brazil; Centro de Toxinas, Resposta Imune e Sinalização Celular (CeTICS), Instituto Butantan, São Paulo, Brazil
| | - Ana Milena Murillo
- Laboratório de Bioquímica de Tryps - LabTryps, Departamento de Parasitologia, Universidade de São Paulo, São Paulo-SP, Brazil
| | - Camila Gachet de Castro
- Laboratório de Ciclo Celular - Instituto Butantan, São Paulo-SP, Brazil; Centro de Toxinas, Resposta Imune e Sinalização Celular (CeTICS), Instituto Butantan, São Paulo, Brazil
| | - Natalia Karla Bellini
- Laboratório de Ciclo Celular - Instituto Butantan, São Paulo-SP, Brazil; Centro de Toxinas, Resposta Imune e Sinalização Celular (CeTICS), Instituto Butantan, São Paulo, Brazil
| | | | | | - Maria Carolina Elias
- Laboratório de Ciclo Celular - Instituto Butantan, São Paulo-SP, Brazil; Centro de Toxinas, Resposta Imune e Sinalização Celular (CeTICS), Instituto Butantan, São Paulo, Brazil
| | - Ariel Mariano Silber
- Laboratório de Bioquímica de Tryps - LabTryps, Departamento de Parasitologia, Universidade de São Paulo, São Paulo-SP, Brazil.
| | - Julia Pinheiro Chagas da Cunha
- Laboratório de Ciclo Celular - Instituto Butantan, São Paulo-SP, Brazil; Centro de Toxinas, Resposta Imune e Sinalização Celular (CeTICS), Instituto Butantan, São Paulo, Brazil.
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11
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Ashby EC, Havens JL, Rollosson LM, Hardin J, Schulz D. Chemical Inhibition of Bromodomain Proteins in Insect-Stage African Trypanosomes Perturbs Silencing of the Variant Surface Glycoprotein Repertoire and Results in Widespread Changes in the Transcriptome. Microbiol Spectr 2023; 11:e0014723. [PMID: 37097159 PMCID: PMC10269879 DOI: 10.1128/spectrum.00147-23] [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: 02/23/2023] [Accepted: 04/04/2023] [Indexed: 04/26/2023] Open
Abstract
The eukaryotic protozoan parasite Trypanosoma brucei is transmitted by the tsetse fly to both humans and animals, where it causes a fatal disease called African trypanosomiasis. While the parasite lacks canonical DNA sequence-specific transcription factors, it does possess histones, histone modifications, and proteins that write, erase, and read histone marks. Chemical inhibition of chromatin-interacting bromodomain proteins has previously been shown to perturb bloodstream specific trypanosome processes, including silencing of the variant surface glycoprotein (VSG) genes and immune evasion. Transcriptomic changes that occur in bromodomain-inhibited bloodstream parasites mirror many of the changes that occur as parasites developmentally progress from the bloodstream to the insect stage. We performed transcriptome sequencing (RNA-seq) time courses to determine the effects of chemical bromodomain inhibition in insect-stage parasites using the compound I-BET151. We found that treatment with I-BET151 causes large changes in the transcriptome of insect-stage parasites and also perturbs silencing of VSG genes. The transcriptomes of bromodomain-inhibited parasites share some features with early metacyclic-stage parasites in the fly salivary gland, implicating bromodomain proteins as important for regulating transcript levels for developmentally relevant genes. However, the downregulation of surface procyclin protein that typically accompanies developmental progression is absent in bromodomain-inhibited insect-stage parasites. We conclude that chemical modulation of bromodomain proteins causes widespread transcriptomic changes in multiple trypanosome life cycle stages. Understanding the gene-regulatory processes that facilitate transcriptome remodeling in this highly diverged eukaryote may shed light on how these mechanisms evolved. IMPORTANCE The disease African trypanosomiasis imposes a severe human and economic burden for communities in sub-Saharan Africa. The parasite that causes the disease is transmitted to the bloodstream of a human or ungulate via the tsetse fly. Because the environments of the fly and the bloodstream differ, the parasite modulates the expression of its genes to accommodate two different lifestyles in these disparate niches. Perturbation of bromodomain proteins that interact with histone proteins around which DNA is wrapped (chromatin) causes profound changes in gene expression in bloodstream-stage parasites. This paper reports that gene expression is also affected by chemical bromodomain inhibition in insect-stage parasites but that the genes affected differ depending on life cycle stage. Because trypanosomes diverged early from model eukaryotes, an understanding of how trypanosomes regulate gene expression may lend insight into how gene-regulatory mechanisms evolved. This could also be leveraged to generate new therapeutic strategies.
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Affiliation(s)
- Ethan C. Ashby
- Department of Biology, Harvey Mudd College, Claremont, California, USA
| | | | | | - Johanna Hardin
- Department of Mathematics and Statistics, Pomona College, Claremont, California, USA
| | - Danae Schulz
- Department of Biology, Harvey Mudd College, Claremont, California, USA
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12
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Rodriguez Araya E, Merli ML, Cribb P, de Souza VC, Serra E. Deciphering Divergent Trypanosomatid Nuclear Complexes by Analyzing Interactomic Datasets with AlphaFold2 and Genetic Approaches. ACS Infect Dis 2023; 9:1267-1282. [PMID: 37167453 DOI: 10.1021/acsinfecdis.3c00148] [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] [Indexed: 05/13/2023]
Abstract
Acetylation signaling pathways in trypanosomatids, a group of early branching organisms, are poorly understood due to highly divergent protein sequences. To overcome this challenge, we used interactomic datasets and AlphaFold2 (AF2)-multimer to predict direct interactions and validated them using yeast two and three-hybrid assays. We focused on MORF4 related gene (MRG) domain-containing proteins and their interactions, typically found in histone acetyltransferase/deacetylase complexes. The results identified a structurally conserved complex, TcTINTIN, which is orthologous to human and yeast trimer independent of NuA4 for transcription interaction (TINTIN) complexes; and another trimeric complex involving an MRG domain, only seen in trypanosomatids. The identification of a key component of TcTINTIN, TcMRGBP, would not have been possible through traditional homology-based methods. We also conducted molecular dynamics simulations, revealing a conformational change that potentially affects its affinity for TcBDF6. The study also revealed a novel way in which an MRG domain participates in simultaneous interactions with two MRG binding proteins binding two different surfaces, a phenomenon not previously reported. Overall, this study demonstrates the potential of using AF2-processed interactomic datasets to identify protein complexes in deeply branched eukaryotes, which can be challenging to study based on sequence similarity. The findings provide new insights into the acetylation signaling pathways in trypanosomatids, specifically highlighting the importance of MRG domain-containing proteins in forming complexes, which may have important implications for understanding the biology of these organisms and developing new therapeutics. On the other hand, our validation of AF2 models for the determination of multiprotein complexes illuminates the power of using such artificial intelligence-derived tools in the future development of biology.
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Affiliation(s)
- Elvio Rodriguez Araya
- Instituto de Biología Molecular y Celular de Rosario, CONICET, Suipacha 590, CP2000 Rosario, Argentina
- Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, CP2000 Rosario, Argentina
| | - Marcelo L Merli
- Instituto de Biología Molecular y Celular de Rosario, CONICET, Suipacha 590, CP2000 Rosario, Argentina
- Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, CP2000 Rosario, Argentina
| | - Pamela Cribb
- Instituto de Biología Molecular y Celular de Rosario, CONICET, Suipacha 590, CP2000 Rosario, Argentina
- Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, CP2000 Rosario, Argentina
| | | | - Esteban Serra
- Instituto de Biología Molecular y Celular de Rosario, CONICET, Suipacha 590, CP2000 Rosario, Argentina
- Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, CP2000 Rosario, Argentina
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13
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Yang L, Zhang X, Zhang J, Tu X. 1H, 13C and 15N resonance assignments of TbBDF5-bromo1 domain from Trypanosoma brucei. BIOMOLECULAR NMR ASSIGNMENTS 2022; 16:253-255. [PMID: 35652998 DOI: 10.1007/s12104-022-10088-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Accepted: 05/05/2022] [Indexed: 06/15/2023]
Abstract
1H, 13C and 15N resonance assignments are presented for the first bromo domain of TbBDF5 (TbBDF5-bromo1) from Trypanosoma brucei. TbBDF5 is localized in the nucleus and plays a potential role in transcription regulation. Bromo domains can recognize acetylated histone through a conserved binding pocket. Here we report the NMR resonance assignments of TbBDF5-bromo1 domain for further studies of the relationship between its structure and function.
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Affiliation(s)
- Li Yang
- MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, School of Life Sciences, University of Science and Technology of China, Hefei, 230027, Anhui, China
| | - Xiaole Zhang
- MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, School of Life Sciences, University of Science and Technology of China, Hefei, 230027, Anhui, China
| | - Jiahai Zhang
- MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, School of Life Sciences, University of Science and Technology of China, Hefei, 230027, Anhui, China.
| | - Xiaoming Tu
- MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, School of Life Sciences, University of Science and Technology of China, Hefei, 230027, Anhui, China.
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14
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Maree JP, Tvardovskiy A, Ravnsborg T, Jensen ON, Rudenko G, Patterton HG. Trypanosoma brucei histones are heavily modified with combinatorial post-translational modifications and mark Pol II transcription start regions with hyperacetylated H2A. Nucleic Acids Res 2022; 50:9705-9723. [PMID: 36095123 PMCID: PMC9508842 DOI: 10.1093/nar/gkac759] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Revised: 08/09/2022] [Accepted: 08/30/2022] [Indexed: 11/12/2022] Open
Abstract
Trypanosomes diverged from the main eukaryotic lineage about 600 million years ago, and display some unusual genomic and epigenetic properties that provide valuable insight into the early processes employed by eukaryotic ancestors to regulate chromatin-mediated functions. We analysed Trypanosoma brucei core histones by high mass accuracy middle-down mass spectrometry to map core histone post-translational modifications (PTMs) and elucidate cis-histone combinatorial PTMs (cPTMs). T. brucei histones are heavily modified and display intricate cPTMs patterns, with numerous hypermodified cPTMs that could contribute to the formation of non-repressive euchromatic states. The Trypanosoma brucei H2A C-terminal tail is hyperacetylated, containing up to five acetylated lysine residues. MNase-ChIP-seq revealed a striking enrichment of hyperacetylated H2A at Pol II transcription start regions, and showed that H2A histones that are hyperacetylated in different combinations localised to different genomic regions, suggesting distinct epigenetic functions. Our genomics and proteomics data provide insight into the complex epigenetic mechanisms used by this parasite to regulate a genome that lacks the transcriptional control mechanisms found in later-branched eukaryotes. The findings further demonstrate the complexity of epigenetic mechanisms that were probably shared with the last eukaryotic common ancestor.
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Affiliation(s)
- Johannes P Maree
- Department of Biochemistry, Stellenbosch University, Stellenbosch 7600, South Africa
| | - Andrey Tvardovskiy
- Department of Biochemistry and Molecular Biology, VILLUM Center for Bioanalytical Sciences, and Center for Epigenetics, University of Southern Denmark, Odense M DK-5230, Denmark
| | - Tina Ravnsborg
- Department of Biochemistry and Molecular Biology, VILLUM Center for Bioanalytical Sciences, and Center for Epigenetics, University of Southern Denmark, Odense M DK-5230, Denmark
| | - Ole N Jensen
- Department of Biochemistry and Molecular Biology, VILLUM Center for Bioanalytical Sciences, and Center for Epigenetics, University of Southern Denmark, Odense M DK-5230, Denmark
| | - Gloria Rudenko
- Department of Life Sciences, Imperial College London, London SW7 2AZ, UK
| | - Hugh-G Patterton
- Center for Bioinformatics and Computational Biology, Stellenbosch University, Stellenbosch 7600, South Africa
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15
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Bromodomain factor 5 is an essential regulator of transcription in Leishmania. Nat Commun 2022; 13:4071. [PMID: 35831302 PMCID: PMC9279504 DOI: 10.1038/s41467-022-31742-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Accepted: 06/30/2022] [Indexed: 11/23/2022] Open
Abstract
Leishmania are unicellular parasites that cause human and animal diseases. Like other kinetoplastids, they possess large transcriptional start regions (TSRs) which are defined by histone variants and histone lysine acetylation. Cellular interpretation of these chromatin marks is not well understood. Eight bromodomain factors, the reader modules for acetyl-lysine, are found across Leishmania genomes. Using L. mexicana, Cas9-driven gene deletions indicate that BDF1–5 are essential for promastigotes. Dimerisable, split Cre recombinase (DiCre)-inducible gene deletion of BDF5 show it is essential for both promastigotes and murine infection. ChIP-seq identifies BDF5 as enriched at TSRs. XL-BioID proximity proteomics shows the BDF5 landscape is enriched for BDFs, HAT2, proteins involved in transcriptional activity, and RNA processing; revealing a Conserved Regulators of Kinetoplastid Transcription (CRKT) Complex. Inducible deletion of BDF5 causes global reduction in RNA polymerase II transcription. Our results indicate the requirement of Leishmania to interpret histone acetylation marks through the bromodomain-enriched CRKT complex for normal gene expression and cellular viability. Leishmania use large (5–10 kb) transcriptional start regions, where the chromatin is highly enriched for acetylated histones, to drive the expression of polycistronic gene arrays. Here the authors show bromodomain-containing protein BDF5 is enriched at transcriptional start sites and its depletion leads to cell death in vitro and in murine infections, and they identify its interactors.
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16
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Ashby E, Paddock L, Betts HL, Liao J, Miller G, Porter A, Rollosson LM, Saada C, Tang E, Wade SJ, Hardin J, Schulz D. Genomic Occupancy of the Bromodomain Protein Bdf3 Is Dynamic during Differentiation of African Trypanosomes from Bloodstream to Procyclic Forms. mSphere 2022; 7:e0002322. [PMID: 35642518 PMCID: PMC9241505 DOI: 10.1128/msphere.00023-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Accepted: 05/05/2022] [Indexed: 12/05/2022] Open
Abstract
Trypanosoma brucei, the causative agent of human and animal African trypanosomiasis, cycles between a mammalian host and a tsetse fly vector. The parasite undergoes huge changes in morphology and metabolism during adaptation to each host environment. These changes are reflected in the different transcriptomes of parasites living in each host. However, it remains unclear whether chromatin-interacting proteins help mediate these changes. Bromodomain proteins localize to transcription start sites in bloodstream parasites, but whether the localization of bromodomain proteins changes as parasites differentiate from bloodstream to insect stages remains unknown. To address this question, we performed cleavage under target and release using nuclease (CUT&RUN) against bromodomain protein 3 (Bdf3) in parasites differentiating from bloodstream to insect forms. We found that Bdf3 occupancy at most loci increased at 3 h following onset of differentiation and decreased thereafter. A number of sites with increased bromodomain protein occupancy lie proximal to genes with altered transcript levels during differentiation, such as procyclins, procyclin-associated genes, and invariant surface glycoproteins. Most Bdf3-occupied sites are observed throughout differentiation. However, one site appears de novo during differentiation and lies proximal to the procyclin gene locus housing genes essential for remodeling surface proteins following transition to the insect stage. These studies indicate that occupancy of chromatin-interacting proteins is dynamic during life cycle stage transitions and provide the groundwork for future studies on the effects of changes in bromodomain protein occupancy. Additionally, the adaptation of CUT&RUN for Trypanosoma brucei provides other researchers with an alternative to chromatin immunoprecipitation (ChIP). IMPORTANCE The parasite Trypanosoma brucei is the causative agent of human and animal African trypanosomiasis (sleeping sickness). Trypanosomiasis, which affects humans and cattle, is fatal if untreated. Existing drugs have significant side effects. Thus, these parasites impose a significant human and economic burden in sub-Saharan Africa, where trypanosomiasis is endemic. T. brucei cycles between the mammalian host and a tsetse fly vector, and parasites undergo huge changes in morphology and metabolism to adapt to different hosts. Here, we show that DNA-interacting bromodomain protein 3 (Bdf3) shows changes in occupancy at its binding sites as parasites transition from the bloodstream to the insect stage. Additionally, a new binding site appears near the locus responsible for remodeling of parasite surface proteins during transition to the insect stage. Understanding the mechanisms behind host adaptation is important for understanding the life cycle of the parasite.
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Affiliation(s)
- Ethan Ashby
- Department of Mathematics and Statistics, Pomona College, Claremont, California, USA
| | - Lucinda Paddock
- Department of Biology, Harvey Mudd College, Claremont, California, USA
| | - Hannah L. Betts
- Department of Biology, Harvey Mudd College, Claremont, California, USA
| | - Jingwen Liao
- Department of Biology, Harvey Mudd College, Claremont, California, USA
| | - Geneva Miller
- Department of Biology, Harvey Mudd College, Claremont, California, USA
| | - Anya Porter
- Department of Biology, Harvey Mudd College, Claremont, California, USA
| | | | - Carrie Saada
- Department of Biology, Harvey Mudd College, Claremont, California, USA
| | - Eric Tang
- Department of Biology, Harvey Mudd College, Claremont, California, USA
| | - Serenity J. Wade
- Department of Biology, Harvey Mudd College, Claremont, California, USA
| | - Johanna Hardin
- Department of Mathematics and Statistics, Pomona College, Claremont, California, USA
| | - Danae Schulz
- Department of Biology, Harvey Mudd College, Claremont, California, USA
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17
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A novel SNF2 ATPase complex in Trypanosoma brucei with a role in H2A.Z-mediated chromatin remodelling. PLoS Pathog 2022; 18:e1010514. [PMID: 35675371 PMCID: PMC9236257 DOI: 10.1371/journal.ppat.1010514] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Revised: 06/27/2022] [Accepted: 04/08/2022] [Indexed: 11/25/2022] Open
Abstract
A cascade of histone acetylation events with subsequent incorporation of a histone H2A variant plays an essential part in transcription regulation in various model organisms. A key player in this cascade is the chromatin remodelling complex SWR1, which replaces the canonical histone H2A with its variant H2A.Z. Transcriptional regulation of polycistronic transcription units in the unicellular parasite Trypanosoma brucei has been shown to be highly dependent on acetylation of H2A.Z, which is mediated by the histone-acetyltransferase HAT2. The chromatin remodelling complex which mediates H2A.Z incorporation is not known and an SWR1 orthologue in trypanosomes has not yet been reported. In this study, we identified and characterised an SWR1-like remodeller complex in T. brucei that is responsible for Pol II-dependent transcriptional regulation. Bioinformatic analysis of potential SNF2 DEAD/Box helicases, the key component of SWR1 complexes, identified a 1211 amino acids-long protein that exhibits key structural characteristics of the SWR1 subfamily. Systematic protein-protein interaction analysis revealed the existence of a novel complex exhibiting key features of an SWR1-like chromatin remodeller. RNAi-mediated depletion of the ATPase subunit of this complex resulted in a significant reduction of H2A.Z incorporation at transcription start sites and a subsequent decrease of steady-state mRNA levels. Furthermore, depletion of SWR1 and RNA-polymerase II (Pol II) caused massive chromatin condensation. The potential function of several proteins associated with the SWR1-like complex and with HAT2, the key factor of H2A.Z incorporation, is discussed. Trypanosoma brucei is the causative agent of African trypanosomiasis (sleeping sickness) in humans and nagana in cattle. Its unusual genomic organisation featuring large polycistronic units requires a general mechanism of transcription initiation, because individual gene promoters are mostly absent. Despite the fact that the histone variant H2A.Z has previously been identified as a key player of transcription regulation, the complex responsible for correct H2A.Z incorporation at transcription start sites (TSS) remains elusive. In other eukaryotes, SWR1, a SNF2 ATPase-associated chromatin remodelling complex, is responsible for correct incorporation of this histone variant. This study identified a SWR1-like complex in T. brucei. Depletion of the SNF2 ATPase resulted in a reduction of H2A.Z incorporation at the TSS and decreased steady-state mRNA levels accompanied by chromatin condensation. In addition to the SWR1-like complex, we also identified a trypanosome-specific HAT2 complex that includes the histone acetyltransferases HAT2, a key player in the H2A.Z incorporation process. This complex has a trypanosome-specific composition that is different from the NuA4/TIP60 complex in Saccharomyces cerevisiae.
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18
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Pezza A, Tavernelli LE, Alonso VL, Perdomo V, Gabarro R, Prinjha R, Rodríguez Araya E, Rioja I, Docampo R, Calderón F, Martin J, Serra E. Essential Bromodomain TcBDF2 as a Drug Target against Chagas Disease. ACS Infect Dis 2022; 8:1062-1074. [PMID: 35482332 DOI: 10.1021/acsinfecdis.2c00057] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Trypanosoma cruzi is a unicellular parasite that causes Chagas disease, which is endemic in the American continent but also worldwide, distributed by migratory movements. A striking feature of trypanosomatids is the polycistronic transcription associated with post-transcriptional mechanisms that regulate the levels of translatable mRNA. In this context, epigenetic regulatory mechanisms have been revealed to be of great importance, since they are the only ones that would control the access of RNA polymerases to chromatin. Bromodomains are epigenetic protein readers that recognize and specifically bind to acetylated lysine residues, mostly at histone proteins. There are seven coding sequences for BD-containing proteins in trypanosomatids, named TcBDF1 to TcBDF7, and a putative new protein containing a bromodomain was recently described. Using the Tet-regulated overexpression plasmid pTcINDEX-GW and CRISPR/Cas9 genome editing, we were able to demonstrate the essentiality of TcBDF2 in T. cruzi. This bromodomain is located in the nucleus, through a bipartite nuclear localization signal. TcBDF2 was shown to be important for host cell invasion, amastigote replication, and differentiation from amastigotes to trypomastigotes. Overexpression of TcBDF2 diminished epimastigote replication. Also, some processes involved in pathogenesis were altered in these parasites, such as infection of mammalian cells, replication of amastigotes, and the number of trypomastigotes released from host cells. In in vitro studies, TcBDF2 was also able to bind inhibitors showing a specificity profile different from that of the previously characterized TcBDF3. These results point to TcBDF2 as a druggable target against T. cruzi.
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Affiliation(s)
- Alejandro Pezza
- Instituto de Biología Molecular y Celular de Rosario, CONICET, 2000 Rosario, Santa Fe, Argentina
| | - Luis E. Tavernelli
- Instituto de Biología Molecular y Celular de Rosario, CONICET, 2000 Rosario, Santa Fe, Argentina
| | - Victoria L. Alonso
- Instituto de Biología Molecular y Celular de Rosario, CONICET, 2000 Rosario, Santa Fe, Argentina
- Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, 2000 Rosario, Santa Fe, Argentina
| | - Virginia Perdomo
- Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, 2000 Rosario, Santa Fe, Argentina
| | - Raquel Gabarro
- GlaxoSmithKline Global Health, Tres Cantos, 28760 Madrid, Spain
| | - Rab Prinjha
- Immunology Research Unit, Research, R&D GlaxoSmithKline, Gunnels Wood Road, Stevenage, Herts SG1 2NY, U.K
| | - Elvio Rodríguez Araya
- Instituto de Biología Molecular y Celular de Rosario, CONICET, 2000 Rosario, Santa Fe, Argentina
- Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, 2000 Rosario, Santa Fe, Argentina
| | - Inmaculada Rioja
- Immunology Research Unit, Research, R&D GlaxoSmithKline, Gunnels Wood Road, Stevenage, Herts SG1 2NY, U.K
| | - Roberto Docampo
- Department of Cellular Biology and Center for Tropical and Global Emerging Diseases, University of Georgia, Athens, Georgia30602, United States
| | - Felix Calderón
- GlaxoSmithKline Global Health, Tres Cantos, 28760 Madrid, Spain
| | - Julio Martin
- GlaxoSmithKline Global Health, Tres Cantos, 28760 Madrid, Spain
| | - Esteban Serra
- Instituto de Biología Molecular y Celular de Rosario, CONICET, 2000 Rosario, Santa Fe, Argentina
- Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, 2000 Rosario, Santa Fe, Argentina
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19
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Kovářová J, Novotná M, Faria J, Rico E, Wallace C, Zoltner M, Field MC, Horn D. CRISPR/Cas9-based precision tagging of essential genes in bloodstream form African trypanosomes. Mol Biochem Parasitol 2022; 249:111476. [DOI: 10.1016/j.molbiopara.2022.111476] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 03/28/2022] [Accepted: 03/30/2022] [Indexed: 12/27/2022]
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20
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Ishii M, Akiyoshi B. Plasticity in centromere organization and kinetochore composition: Lessons from diversity. Curr Opin Cell Biol 2022; 74:47-54. [PMID: 35108654 PMCID: PMC9089191 DOI: 10.1016/j.ceb.2021.12.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2021] [Revised: 12/27/2021] [Accepted: 12/29/2021] [Indexed: 11/16/2022]
Abstract
Kinetochores are the macromolecular protein complexes that govern chromosome movement by binding spindle microtubules during mitosis and meiosis. Centromeres are the specific chromosomal regions that serve as the platform on which kinetochores assemble. Despite their essentiality for proper chromosome segregation, the size and organization of centromeres vary dramatically between species, while different compositions of kinetochores are found among eukaryotes. Here we discuss recent progress in understanding centromeres and kinetochores in non-traditional model eukaryotes. We specifically focus on select lineages (holocentric insects, early diverging fungi, and kinetoplastids) that lack CENP-A, a centromere-specific histone H3 variant that is critical for kinetochore specification and assembly in many eukaryotes. We also highlight some organisms that might have hitherto unknown types of kinetochore proteins.
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Affiliation(s)
- Midori Ishii
- Department of Biochemistry, University of Oxford, UK
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21
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Zhang J, Sun Y, Zheng J. The State of Art of Extracellular Traps in Protozoan Infections (Review). Front Immunol 2022; 12:770246. [PMID: 34970259 PMCID: PMC8712655 DOI: 10.3389/fimmu.2021.770246] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Accepted: 11/29/2021] [Indexed: 11/25/2022] Open
Abstract
Protozoan parasite infection causes severe diseases in humans and animals, leading to tremendous economic and medical pressure. Natural immunity is the first line of defence against parasitic infection. Currently, the role of natural host immunity in combatting parasitic infection is unclear, so further research on natural host immunity against parasites will provide a theoretical basis for the prevention and treatment of related parasitic diseases. Extracellular traps (ETs) are an important natural mechanism of immunity involving resistance to pathogens. When immune cells such as neutrophils and macrophages are stimulated by external pathogens, they release a fibrous network structure, consisting mainly of DNA and protein, that can capture and kill a variety of extracellular pathogenic microorganisms. In this review, we discuss the relevant recently reported data on ET formation induced by protozoan parasite infection, including the molecular mechanisms involved, and discuss the role of ETs in the occurrence and development of parasitic diseases.
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Affiliation(s)
- Jing Zhang
- Intensive Care Unit, First Hospital of Jilin University, Changchun, China.,Department of Pathogenobiology, College of Basic Medical Sciences, Jilin University, Changchun, China
| | - Ying Sun
- Department of Respiratory and Critical Care Medicine, First Hospital of Jilin University, Changchun, China
| | - Jingtong Zheng
- Department of Pathogenobiology, College of Basic Medical Sciences, Jilin University, Changchun, China
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22
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Staneva DP, Bresson S, Auchynnikava T, Spanos C, Rappsilber J, Jeyaprakash AA, Tollervey D, Matthews KR, Allshire RC. The SPARC complex defines RNAPII promoters in Trypanosoma brucei. eLife 2022; 11:83135. [PMID: 36169304 PMCID: PMC9566855 DOI: 10.7554/elife.83135] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Accepted: 09/27/2022] [Indexed: 11/15/2022] Open
Abstract
Kinetoplastids are a highly divergent lineage of eukaryotes with unusual mechanisms for regulating gene expression. We previously surveyed 65 putative chromatin factors in the kinetoplastid Trypanosoma brucei. Our analyses revealed that the predicted histone methyltransferase SET27 and the Chromodomain protein CRD1 are tightly concentrated at RNAPII transcription start regions (TSRs). Here, we report that SET27 and CRD1, together with four previously uncharacterized constituents, form the SET27 promoter-associated regulatory complex (SPARC), which is specifically enriched at TSRs. SET27 loss leads to aberrant RNAPII recruitment to promoter sites, accumulation of polyadenylated transcripts upstream of normal transcription start sites, and conversion of some normally unidirectional promoters to bidirectional promoters. Transcriptome analysis in the absence of SET27 revealed upregulated mRNA expression in the vicinity of SPARC peaks within the main body of chromosomes in addition to derepression of genes encoding variant surface glycoproteins (VSGs) located in subtelomeric regions. These analyses uncover a novel chromatin-associated complex required to establish accurate promoter position and directionality.
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Affiliation(s)
- Desislava P Staneva
- Wellcome Centre for Cell Biology, University of EdinburghEdinburghUnited Kingdom,Institute of Immunology and Infection Biology, School of Biological Sciences, University of EdinburghEdinburghUnited Kingdom
| | - Stefan Bresson
- Wellcome Centre for Cell Biology, University of EdinburghEdinburghUnited Kingdom
| | | | - Christos Spanos
- Wellcome Centre for Cell Biology, University of EdinburghEdinburghUnited Kingdom
| | - Juri Rappsilber
- Wellcome Centre for Cell Biology, University of EdinburghEdinburghUnited Kingdom,Institute of Biotechnology, Technische UniversitätBerlinGermany
| | | | - David Tollervey
- Wellcome Centre for Cell Biology, University of EdinburghEdinburghUnited Kingdom
| | - Keith R Matthews
- Institute of Immunology and Infection Biology, School of Biological Sciences, University of EdinburghEdinburghUnited Kingdom
| | - Robin C Allshire
- Wellcome Centre for Cell Biology, University of EdinburghEdinburghUnited Kingdom
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Abstract
Protozoan parasites continue to cause a significant health and economic burden worldwide. As infectious organisms, they pose unique and difficult challenges due to a level of conservation of critical eukaryotic cellular pathways with their hosts. Gene regulation has been pinpointed as an essential pathway with enough divergence to warrant investigation into therapeutically targeting. Examination of human parasites such as Plasmodium falciparum, Toxoplasma gondii, and kinetoplastids have revealed that epigenetic mechanisms play a key role in their gene regulation. The enzymes involved in adding and removing epigenetic posttranslational modifications (PTMs) have historically been the focus of study. However, the reader proteins that recognize and bind PTMs, initiating recruitment of chromatin-modifying and transcription complexes, are now being realized for their critical role in regulation and their potential as drug targets. In this review, we highlight the current knowledge on epigenetic reader proteins in model parasitic protozoa, focusing on the histone acyl- and methyl-reading domains. With this knowledge base, we compare differences between medically relevant parasites, discuss conceivable functions of these understudied proteins, indicate gaps in knowledge, and provide current progress in drug development.
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Affiliation(s)
- Krista Fleck
- Molecular, Cellular and Biomedical Sciences, University of New Hampshire, Durham, New Hampshire, United States of America
| | - Malorie Nitz
- Molecular, Cellular and Biomedical Sciences, University of New Hampshire, Durham, New Hampshire, United States of America
| | - Victoria Jeffers
- Molecular, Cellular and Biomedical Sciences, University of New Hampshire, Durham, New Hampshire, United States of America
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24
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Kim HS. Genetic Interaction Between Site-Specific Epigenetic Marks and Roles of H4v in Transcription Termination in Trypanosoma brucei. Front Cell Dev Biol 2021; 9:744878. [PMID: 34722526 PMCID: PMC8551723 DOI: 10.3389/fcell.2021.744878] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Accepted: 09/15/2021] [Indexed: 11/13/2022] Open
Abstract
In Trypanosoma brucei, genes are assembled in polycistronic transcription units (PTUs). Boundaries of PTUs are designated transcription start sites and transcription termination sites (TTSs). Messenger RNAs are generated by trans-splicing and polyadenylation of precursor RNAs, and regulatory information in the 3' un-translated region (UTR), rather than promoter activity/sequence-specific transcription factors, controls mRNA levels. Given this peculiar genome structure, special strategies must be utilized to control transcription in T. brucei. TTSs are deposition sites for three non-essential chromatin factors-two of non-canonical histone variants (H3v and H4v) and a DNA modification (base J, which is a hydroxyl-glucosyl dT). This association generated the hypothesis that these three chromatin marks define a transcription termination site in T. brucei. Using a panel of null mutants lacking H3v, H4v, and base J, here I show that H4v is a major sign for transcription termination at TTSs. While having a secondary function at TTSs, H3v is important for monoallelic transcription of telomeric antigen genes. The simultaneous absence of both histone variants leads to proliferation and replication defects, which are exacerbated by the J absence, accompanied by accumulation of sub-G1 population. Thus, I propose that the coordinated actions of H3v, H4v, and J provide compensatory mechanisms for each other in chromatin organization, transcription, replication, and cell-cycle progression.
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Affiliation(s)
- Hee-Sook Kim
- Public Health Research Institute, New Jersey Medical School, Rutgers, The State University of New Jersey, Newark, NJ, United States
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