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Kieft R, Reynolds D, Sabatini R. Epigenetic regulation of TERRA transcription and metacyclogenesis by base J in Leishmania major. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.27.601056. [PMID: 38979290 PMCID: PMC11230386 DOI: 10.1101/2024.06.27.601056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/10/2024]
Abstract
The hyper-modified DNA base J helps control termination of Pol II transcription at polycistronic transcription units (PTUs) in T. brucei and L. major , allowing epigenetic control of gene expression. The Telomere Repeat-containing RNA (TERRA) is synthesized in T. brucei by Pol I readthrough transcription of a telomeric PTU. While little is understood regarding TERRA synthesis and function, the hyper-modified DNA base J is highly enriched at telomeres in L. major promastigotes. We now show that TERRA is synthesized by Pol II in L. major and loss of base J leads to increased TERRA. For at least one site, the increased TERRA is by Pol II readthrough transcription from an adjacent PTU. Furthermore, Pol II readthrough defects and increased TERRA correlate with increased differentiation of promastigotes to the infectious metacyclic life stage and decreased cell viability. These results help explain the essential nature of base J in Leishmania and provide insight regarding epigenetic control of coding and non-coding RNA expression and parasite development during the life cycle of L. major .
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2
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de Vries I, Ammerlaan D, Heidebrecht T, Celie PH, Geerke DP, Joosten RP, Perrakis A. Distant sequence regions of JBP1 contribute to J-DNA binding. Life Sci Alliance 2023; 6:e202302150. [PMID: 37328191 PMCID: PMC10276184 DOI: 10.26508/lsa.202302150] [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: 05/11/2023] [Revised: 06/05/2023] [Accepted: 06/06/2023] [Indexed: 06/18/2023] Open
Abstract
Base-J (β-D-glucopyranosyloxymethyluracil) is a modified DNA nucleotide that replaces 1% of thymine in kinetoplastid flagellates. The biosynthesis and maintenance of base-J depends on the base-J-binding protein 1 (JBP1) that has a thymidine hydroxylase domain and a J-DNA-binding domain (JDBD). How the thymidine hydroxylase domain synergizes with the JDBD to hydroxylate thymine in specific genomic sites, maintaining base-J during semi-conservative DNA replication, remains unclear. Here, we present a crystal structure of the JDBD including a previously disordered DNA-contacting loop and use it as starting point for molecular dynamics simulations and computational docking studies to propose recognition models for JDBD binding to J-DNA. These models guided mutagenesis experiments, providing additional data for docking, which reveals a binding mode for JDBD onto J-DNA. This model, together with the crystallographic structure of the TET2 JBP1-homologue in complex with DNA and the AlphaFold model of full-length JBP1, allowed us to hypothesize that the flexible JBP1 N-terminus contributes to DNA-binding, which we confirmed experimentally. Α high-resolution JBP1:J-DNA complex, which must involve conformational changes, would however need to be determined experimentally to further understand this unique underlying molecular mechanism that ensures replication of epigenetic information.
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Affiliation(s)
- Ida de Vries
- Oncode Institute and Division of Biochemistry, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Danique Ammerlaan
- Oncode Institute and Division of Biochemistry, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Tatjana Heidebrecht
- Oncode Institute and Division of Biochemistry, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Patrick Hn Celie
- Oncode Institute and Division of Biochemistry, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Daan P Geerke
- Department of Chemistry and Pharmaceutical Sciences, Amsterdam Institute of Molecular and Life Sciences (AIMMS) and Amsterdam Center for Multiscale Modeling (ACMM), Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Robbie P Joosten
- Oncode Institute and Division of Biochemistry, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Anastassis Perrakis
- Oncode Institute and Division of Biochemistry, Netherlands Cancer Institute, Amsterdam, The Netherlands
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3
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Monti L, Di Antonio M. G-Quadruplexes as Key Transcriptional Regulators in Neglected Trypanosomatid Parasites. Chembiochem 2023; 24:e202300265. [PMID: 37146230 PMCID: PMC10946822 DOI: 10.1002/cbic.202300265] [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: 04/01/2023] [Revised: 05/04/2023] [Accepted: 05/05/2023] [Indexed: 05/07/2023]
Abstract
G-quadruplexes (G4s) are nucleic acid secondary structures that have been linked to the functional regulation of eukaryotic organisms. G4s have been extensively characterised in humans and emerging evidence suggests that they might also be biologically relevant for human pathogens. This indicates that G4s might represent a novel class of therapeutic targets for tackling infectious diseases. Bioinformatic studies revealed a high prevalence of putative quadruplex-forming sequences (PQSs) in the genome of protozoans, which highlights their potential roles in regulating vital processes of these parasites, including DNA transcription and replication. In this work, we focus on the neglected trypanosomatid parasites, Trypanosoma and Leishmania spp., which cause debilitating and deadly diseases across the poorest populations worldwide. We review three examples where G4-formation might be key to modulate transcriptional activity in trypanosomatids, providing an overview of experimental approaches that can be used to exploit the regulatory roles and relevance of these structures to fight parasitic infections.
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Affiliation(s)
- Ludovica Monti
- Chemistry Department, Imperial College LondonMolecular Sciences Research Hub82 Wood LaneW12 0BZLondonUK
| | - Marco Di Antonio
- Chemistry Department, Imperial College LondonMolecular Sciences Research Hub82 Wood LaneW12 0BZLondonUK
- The Francis Crick Institute1 Midland RoadNW1 1ATLondonUK
- The Institute of Chemical BiologyMolecular Sciences Research Hub82 Wood LaneW12 0BZLondonUK
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4
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Behind Base J: The Roles of JBP1 and JBP2 on Trypanosomatids. Pathogens 2023; 12:pathogens12030467. [PMID: 36986389 PMCID: PMC10057400 DOI: 10.3390/pathogens12030467] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Revised: 03/08/2023] [Accepted: 03/08/2023] [Indexed: 03/18/2023] Open
Abstract
β-D-glucopyranosyloxymethiluracil (Base J) is a modified thymidine base found in kinetoplastids and some related organisms. Interestingly, Base J distribution into the genome can vary depending on the organism and its life stage. Base J is reported to be found mostly at telomeric repeats, on inactive variant surface glycoproteins (VSG’s) expression sites (e.g., T. brucei), in RNA polymerase II termination sites and sub-telomeric regions (e.g., Leishmania). This hypermodified nucleotide is synthesized in two steps with the participation of two distinct thymidine hydroxylases, J-binding protein 1 and 2 (JBP1 and JBP2, respectively) and a β-glucosyl transferase. A third J-binding protein, named JBP3, was recently identified as part of a multimeric complex. Although its structural similarities with JBP1, it seems not to be involved in J biosynthesis but to play roles in gene expression regulation in trypanosomatids. Over the years, with the characterization of JBP1 and JBP2 mutant lines, Base J functions have been targeted and shone a light on that matter, showing genus-specific features. This review aims to explore Base J’s reported participation as a regulator of RNA polymerase II transcription termination and to summarize the functional and structural characteristics and similarities of the remarkable JBP proteins in pathogenic trypanosomatids.
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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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6
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Abstract
Telomeres are the ends of linear eukaryotic chromosomes facilitating the resolution of the ‘end replication and protection’ problems, associated with linearity. At the nucleotide level, telomeres typically represent stretches of tandemly arranged telomeric repeats, which vary in length and sequence among different groups of organisms. Recently, a composition of the telomere-associated protein complex has been scrutinized in Trypanosoma brucei. In this work, we subjected proteins from that list to a more detailed bioinformatic analysis and delineated a core set of 20 conserved proteins putatively associated with telomeres in trypanosomatids. Out of these, two proteins (Ku70 and Ku80) are conspicuously missing in representatives of the genus Blastocrithidia, yet telomeres in these species do not appear to be affected. In this work, based on the analysis of a large set of trypanosomatids widely different in their phylogenetic position and life strategies, we demonstrated that telomeres of trypanosomatids are diverse in length, even within groups of closely related species. Our analysis showed that the expression of two proteins predicted to be associated with telomeres (those encoding telomerase and telomere-associated hypothetical protein orthologous to Tb927.6.4330) may directly affect and account for the differences in telomere length within the species of the Leishmania mexicana complex.
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Morea EGO, Vasconcelos EJR, Alves CDS, Giorgio S, Myler PJ, Langoni H, Azzalin CM, Cano MIN. Exploring TERRA during Leishmania major developmental cycle and continuous in vitro passages. Int J Biol Macromol 2021; 174:573-586. [PMID: 33548324 DOI: 10.1016/j.ijbiomac.2021.01.192] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2020] [Revised: 01/25/2021] [Accepted: 01/28/2021] [Indexed: 12/22/2022]
Abstract
Telomeres from different eukaryotes, including trypanosomatids, are transcribed into TERRA noncoding RNAs, crucial in regulating chromatin deposition and telomere length. TERRA is transcribed from the C-rich subtelomeric strand towards the 3'-ends of the telomeric array. Using bioinformatics, we confirmed the presence of subtelomeric splice acceptor sites at all L. major chromosome ends. Splice leader sequences positioned 5' upstream of L. major chromosomes subtelomeres were then mapped using SL-RNA-Seq libraries constructed from three independent parasite life stages and helped confirm TERRA expression from several chromosomes ends. Northern blots and RT-qPCR validated the results showing that L. major TERRA is processed by trans-splicing and polyadenylation coupled reactions. The number of transcripts varied with the parasite's life stage and continuous passages, being more abundant in the infective forms. However, no putative subtelomeric promoters involved in TERRA's transcriptional regulation were detected. In contrast, the observed changes in parasite's telomere length during development, suggest that differences in telomeric base J levels may control TERRA transcription in L. major. Also, TERRA-R loops' detection, mainly in the infective forms, was suggestive of TERRA's involvement in telomere protection. Therefore, Leishmania TERRA shares conserved features with other eukaryotes and advances new telomere specific functions in a Public Health-impacting parasite.
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Affiliation(s)
- Edna Gicela Ortiz Morea
- Department of Chemical and Biological Sciences, Biosciences Institute, São Paulo State University, UNESP, Botucatu, São Paulo, Brazil
| | | | - Cristiane de Santis Alves
- Department of Chemical and Biological Sciences, Biosciences Institute, São Paulo State University, UNESP, Botucatu, São Paulo, Brazil
| | - Selma Giorgio
- Department of Animal Biology, Biology Institute, State University of Campinas, UNICAMP, Brazil
| | - Peter J Myler
- Department of Global Health and Department of Biomedical Informatics & Medical Education, University of Washington, Seattle, WA, United States of America
| | - Helio Langoni
- Department of Public Health, Veterinary Medical School, São Paulo State University, UNESP, Botucatu, São Paulo, Brazil
| | | | - Maria Isabel Nogueira Cano
- Department of Chemical and Biological Sciences, Biosciences Institute, São Paulo State University, UNESP, Botucatu, São Paulo, Brazil.
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Adamopoulos A, Heidebrecht T, Roosendaal J, Touw WG, Phan IQ, Beijnen J, Perrakis A. The domain architecture of the protozoan protein J-DNA-binding protein 1 suggests synergy between base J DNA binding and thymidine hydroxylase activity. J Biol Chem 2019; 294:12815-12825. [PMID: 31292194 DOI: 10.1074/jbc.ra119.007393] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Revised: 07/04/2019] [Indexed: 11/06/2022] Open
Abstract
J-DNA-binding protein 1 (JBP1) contributes to the biosynthesis and maintenance of base J (β-d-glucosyl-hydroxymethyluracil), an epigenetic modification of thymidine (T) confined to pathogenic protozoa such as Trypanosoma and Leishmania JBP1 has two known functional domains: an N-terminal T hydroxylase (TH) homologous to the 5-methylcytosine hydroxylase domain in TET proteins and a J-DNA-binding domain (JDBD) that resides in the middle of JBP1. Here, we show that removing JDBD from JBP1 results in a soluble protein (Δ-JDBD) with the N- and C-terminal regions tightly associated together in a well-ordered structure. We found that this Δ-JDBD domain retains TH activity in vitro but displays a 15-fold lower apparent rate of hydroxylation compared with JBP1. Small-angle X-ray scattering (SAXS) experiments on JBP1 and JDBD in the presence or absence of J-DNA and on Δ-JDBD enabled us to generate low-resolution three-dimensional models. We conclude that Δ-JDBD, and not the N-terminal region of JBP1 alone, is a distinct folding unit. Our SAXS-based model supports the notion that binding of JDBD specifically to J-DNA can facilitate T hydroxylation 12-14 bp downstream on the complementary strand of the J-recognition site. We postulate that insertion of the JDBD module into the Δ-JDBD scaffold during evolution provided a mechanism that synergized J recognition and T hydroxylation, ensuring inheritance of base J in specific sequence patterns following DNA replication in kinetoplastid parasites.
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Affiliation(s)
- Athanassios Adamopoulos
- Department of Biochemistry, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
| | - Tatjana Heidebrecht
- Department of Biochemistry, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
| | - Jeroen Roosendaal
- Department of Clinical Pharmacology, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
| | - Wouter G Touw
- Department of Biochemistry, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
| | - Isabelle Q Phan
- Seattle Structural Genomics Center for Infectious Disease, Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, Washington 98109
| | - Jos Beijnen
- Department of Clinical Pharmacology, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
| | - Anastassis Perrakis
- Department of Biochemistry, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
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9
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Hofer A, Liu ZJ, Balasubramanian S. Detection, Structure and Function of Modified DNA Bases. J Am Chem Soc 2019; 141:6420-6429. [DOI: 10.1021/jacs.9b01915] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Alexandre Hofer
- Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom
| | - Zheng J. Liu
- Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom
| | - Shankar Balasubramanian
- Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom
- Cancer Research
UK Cambridge Institute, University of Cambridge, Cambridge CB2 0RE, United Kingdom
- School of Clinical Medicine, University of Cambridge, Cambridge CB2 0SP, United Kingdom
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10
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Ahmadian S, Eslami G, Fatahi A, Hosseini SS, Vakili M, Ajamein Fahadan V, Elloumi M. J- binding protein 1 and J- binding protein 2 expression in clinical Leishmania major no response-antimonial isolates. J Parasit Dis 2018; 43:39-45. [PMID: 30956444 DOI: 10.1007/s12639-018-1052-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2018] [Accepted: 11/07/2018] [Indexed: 12/12/2022] Open
Abstract
Cutaneous leishmaniasis (CL) is a major disease in many parts of the world. Since no vaccine has been developed, treatment is the best way to control it. In most areas, antimonial resistance whose mechanisms have not been completely understood has been reported. The main aim of this study is gene expression assessing of J-binging protein 1 and J-binding protein 2 in clinical Leishmania major isolates. The patients with CL from central and north Iran were considered for this study. The samples were transferred in RNAlater solution and stored in - 20 °C. RNA extraction and cDNA synthesis were performed. The gene expression analysis was done with SYBR Green real-time PCR using ∆∆CT. Written informed consent forms were filled out by patients, and then, information forms were filled out based on the Helsinki Declaration. Statistical analysis was done with SPSS (16.0; SPSS Inc, Chicago) using independent t test, Shapiro-Wilk, and Pearson's and Spearman's rank correlation coefficients. P ≤ 0.05 was considered significant. The gene expression of JBP1 and JBP2 had no relation with sex and age. The JBP1 gene expression was high in sensitive isolates obtained from north of the country. The JBP2 gene expression was significant in sensitive and no response-antimonial isolates from the north, but no significant differences were detected in sensitive and resistant isolates from central Iran. Differential gene expression of JBP1 and JBP2 in various clinical resistances isolates in different geographical areas shows multifactorial ways of developing resistance in different isolates.
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Affiliation(s)
- Salman Ahmadian
- 1Research Center for Food Hygiene and Safety, Shahid Sadoughi University of Medical Sciences, Yazd, Iran
- 2Department of Parasitology and Mycology, Faculty of Medicine, Shahid Sadoughi University of Medical Sciences, Yazd, Iran
| | - Gilda Eslami
- 1Research Center for Food Hygiene and Safety, Shahid Sadoughi University of Medical Sciences, Yazd, Iran
- 2Department of Parasitology and Mycology, Faculty of Medicine, Shahid Sadoughi University of Medical Sciences, Yazd, Iran
| | - Ali Fatahi
- 2Department of Parasitology and Mycology, Faculty of Medicine, Shahid Sadoughi University of Medical Sciences, Yazd, Iran
| | - Saeede Sadat Hosseini
- 1Research Center for Food Hygiene and Safety, Shahid Sadoughi University of Medical Sciences, Yazd, Iran
| | - Mahmoud Vakili
- 3Department of Community and Preventive Medicine, Faculty of Medicine, Shahid Sadoughi University of Medical Sciences, Yazd, Iran
| | - Vahid Ajamein Fahadan
- 1Research Center for Food Hygiene and Safety, Shahid Sadoughi University of Medical Sciences, Yazd, Iran
- 2Department of Parasitology and Mycology, Faculty of Medicine, Shahid Sadoughi University of Medical Sciences, Yazd, Iran
| | - Mourad Elloumi
- 4Laboratory of Technologies of Information and Communication and Electrical Engineering (LaTICE), University of Tunis, Tunis, Tunisia
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van Beusekom B, Heidebrecht T, Adamopoulos A, Fish A, Pardon E, Steyaert J, Joosten RP, Perrakis A. Characterization and structure determination of a llama-derived nanobody targeting the J-base binding protein 1. Acta Crystallogr F Struct Biol Commun 2018; 74:690-695. [PMID: 30387773 PMCID: PMC6213982 DOI: 10.1107/s2053230x18010282] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Accepted: 07/16/2018] [Indexed: 01/06/2023] Open
Abstract
J-base binding protein 1 (JBP1) contributes to the biosynthesis and maintenance of base J (β-D-glucosylhydroxymethyluracil), a modification of thymidine confined to some protozoa. Camelid (llama) single-domain antibody fragments (nanobodies) targeting JBP1 were produced for use as crystallization chaperones. Surface plasmon resonance screening identified Nb6 as a strong binder, recognizing JBP1 with a 1:1 stoichiometry and high affinity (Kd = 30 nM). Crystallization trials of JBP1 in complex with Nb6 yielded crystals that diffracted to 1.47 Å resolution. However, the dimensions of the asymmetric unit and molecular replacement with a nanobody structure clearly showed that the crystals of the expected complex with JBP1 were of the nanobody alone. Nb6 crystallizes in space group P31 with two molecules in the asymmetric unit; its crystal structure was refined to a final resolution of 1.64 Å. Ensemble refinement suggests that in the ligand-free state one of the complementarity-determining regions (CDRs) is flexible, while the other two adopt well defined conformations.
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Affiliation(s)
- Bart van Beusekom
- Department of Biochemistry, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
| | - Tatjana Heidebrecht
- Department of Biochemistry, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
| | - Athanassios Adamopoulos
- Department of Biochemistry, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
| | - Alexander Fish
- Department of Biochemistry, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
| | - Els Pardon
- VIB–VUB Center for Structural Biology, VIB, Pleinlaan 2, 1050 Brussels, Belgium
- Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium
| | - Jan Steyaert
- VIB–VUB Center for Structural Biology, VIB, Pleinlaan 2, 1050 Brussels, Belgium
- Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium
| | - Robbie P. Joosten
- Department of Biochemistry, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
| | - Anastassis Perrakis
- Department of Biochemistry, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
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12
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Martínez-Calvillo S, Romero-Meza G, Vizuet-de-Rueda JC, Florencio-Martínez LE, Manning-Cela R, Nepomuceno-Mejía T. Epigenetic Regulation of Transcription in Trypanosomatid Protozoa. Curr Genomics 2018; 19:140-149. [PMID: 29491742 PMCID: PMC5814962 DOI: 10.2174/1389202918666170911163517] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2017] [Revised: 02/13/2017] [Accepted: 04/18/2017] [Indexed: 12/15/2022] Open
Abstract
The Trypanosomatid family includes flagellated parasites that cause fatal human diseases. Remarkably, protein-coding genes in these organisms are positioned in long tandem arrays that are transcribed polycistronically. However, the knowledge about regulation of transcription initiation and termination in trypanosomatids is scarce. The importance of epigenetic regulation in these processes has become evident in the last years, as distinctive histone modifications and histone variants have been found in transcription initiation and termination regions. Moreover, multiple chromatin-related proteins have been identified and characterized in trypanosomatids, including histone-modifying enzymes, effector complexes, chromatin-remodelling enzymes and histone chaperones. Notably, base J, a modified thymine residue present in the nuclear DNA of trypanosomatids, has been implicated in transcriptional regulation. Here we review the current knowledge on epigenetic control of transcription by all three RNA polymerases in this group of early-diverged eukaryotes.
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Affiliation(s)
- Santiago Martínez-Calvillo
- Unidad de Biomedicina, Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México. Av. de los Barrios 1, Col. Los Reyes Iztacala, Tlalnepantla, Edo. de México, CP 54090, México
| | - Gabriela Romero-Meza
- Unidad de Biomedicina, Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México. Av. de los Barrios 1, Col. Los Reyes Iztacala, Tlalnepantla, Edo. de México, CP 54090, México
| | - Juan C. Vizuet-de-Rueda
- Unidad de Biomedicina, Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México. Av. de los Barrios 1, Col. Los Reyes Iztacala, Tlalnepantla, Edo. de México, CP 54090, México
| | - Luis E. Florencio-Martínez
- Unidad de Biomedicina, Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México. Av. de los Barrios 1, Col. Los Reyes Iztacala, Tlalnepantla, Edo. de México, CP 54090, México
| | - Rebeca Manning-Cela
- Departamento de Biomedicina Molecular, Centro de Investigación y de Estudios Avanzados del IPN, Av. IPN 2508, México, D.F., CP 07360, México
| | - Tomás Nepomuceno-Mejía
- Unidad de Biomedicina, Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México. Av. de los Barrios 1, Col. Los Reyes Iztacala, Tlalnepantla, Edo. de México, CP 54090, México
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13
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Kawasaki F, Murat P, Li Z, Santner T, Balasubramanian S. Synthesis and biophysical analysis of modified thymine-containing DNA oligonucleotides. Chem Commun (Camb) 2017; 53:1389-1392. [PMID: 28074944 PMCID: PMC5759927 DOI: 10.1039/c6cc08670e] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
We report the synthesis of a 5-formyl-2'-deoxyuridine (5fU) phosphoramidite and the preparation of oligonucleotides comprising all known, naturally observed eukaryotic thymidine modifications. Biophysical characterization of the synthetic oligonucleotides indicates that 5fU, but not the other T-derivatives, can alter DNA structures.
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Affiliation(s)
- F Kawasaki
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK.
| | - P Murat
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK.
| | - Z Li
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK.
| | - T Santner
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK.
| | - S Balasubramanian
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK. and Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK and School of Clinical Medicine, University of Cambridge, Cambridge CB2 0SP, UK
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14
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Laffitte MCN, Leprohon P, Hainse M, Légaré D, Masson JY, Ouellette M. Chromosomal Translocations in the Parasite Leishmania by a MRE11/RAD50-Independent Microhomology-Mediated End Joining Mechanism. PLoS Genet 2016; 12:e1006117. [PMID: 27314941 PMCID: PMC4912120 DOI: 10.1371/journal.pgen.1006117] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2015] [Accepted: 05/20/2016] [Indexed: 01/15/2023] Open
Abstract
The parasite Leishmania often relies on gene rearrangements to survive stressful environments. However, safeguarding a minimum level of genome integrity is important for cell survival. We hypothesized that maintenance of genomic integrity in Leishmania would imply a leading role of the MRE11 and RAD50 proteins considering their role in DNA repair, chromosomal organization and protection of chromosomes ends in other organisms. Attempts to generate RAD50 null mutants in a wild-type background failed and we provide evidence that this gene is essential. Remarkably, inactivation of RAD50 was possible in a MRE11 null mutant that we had previously generated, providing good evidence that RAD50 may be dispensable in the absence of MRE11. Inactivation of the MRE11 and RAD50 genes led to a decreased frequency of homologous recombination and analysis of the null mutants by whole genome sequencing revealed several chromosomal translocations. Sequencing of the junction between translocated chromosomes highlighted microhomology sequences at the level of breakpoint regions. Sequencing data also showed a decreased coverage at subtelomeric locations in many chromosomes in the MRE11-/-RAD50-/- parasites. This study demonstrates an MRE11-independent microhomology-mediated end-joining mechanism and a prominent role for MRE11 and RAD50 in the maintenance of genomic integrity. Moreover, we suggest the possible involvement of RAD50 in subtelomeric regions stability. The parasite Leishmania relies on gene rearrangements to survive stressful conditions. However, maintaining a minimum level of genomic integrity is crucial for cell survival. Studies in other organisms have provided evidence that the DNA repair proteins MRE11 and RAD50 are involved in chromosomes organization, protection of chromosomes ends and therefore in the maintenance of genomic integrity. In this manuscript, we present the conditional inactivation of the Leishmania infantum RAD50 gene that was only possible in MRE11 deficient cells and suggest the genetic background is crucial for RAD50 inactivation. We demonstrate the occurrence of chromosomal translocations in the MRE11 and RAD50 deficient cells and described a MRE11-independent microhomology-mediated end-joining mechanism at the level of translocation breakpoints. We also suggest a possible involvement of RAD50 in subtelomeric regions stability. Our results highlight that both MRE11 and RAD50 are important for the maintenance of genomic integrity in Leishmania.
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Affiliation(s)
| | - Philippe Leprohon
- Centre de Recherche en Infectiologie, CRCHU de Québec, Québec City, Québec, Canada
| | - Maripier Hainse
- Genome Stability Laboratory, CRCHU de Québec, Pavillon HDQ Oncology axis, Québec City, Québec, Canada
| | - Danielle Légaré
- Centre de Recherche en Infectiologie, CRCHU de Québec, Québec City, Québec, Canada
| | - Jean-Yves Masson
- Genome Stability Laboratory, CRCHU de Québec, Pavillon HDQ Oncology axis, Québec City, Québec, Canada
- Department of Molecular Biology, Medical Biochemistry and Pathology, Centre de recherche sur le Cancer, Université Laval, Québec City, Québec, Canada
| | - Marc Ouellette
- Centre de Recherche en Infectiologie, CRCHU de Québec, Québec City, Québec, Canada
- * E-mail:
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15
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Borst P. Maxi-circles, glycosomes, gene transposition, expression sites, transsplicing, transferrin receptors and base J. Mol Biochem Parasitol 2016; 205:39-52. [DOI: 10.1016/j.molbiopara.2016.03.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2016] [Revised: 03/22/2016] [Accepted: 03/22/2016] [Indexed: 01/05/2023]
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16
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Genest PA, Baugh L, Taipale A, Zhao W, Jan S, van Luenen HGAM, Korlach J, Clark T, Luong K, Boitano M, Turner S, Myler PJ, Borst P. Defining the sequence requirements for the positioning of base J in DNA using SMRT sequencing. Nucleic Acids Res 2015; 43:2102-15. [PMID: 25662217 PMCID: PMC4344527 DOI: 10.1093/nar/gkv095] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Base J (β-D-glucosyl-hydroxymethyluracil) replaces 1% of T in the Leishmania genome and is only found in telomeric repeats (99%) and in regions where transcription starts and stops. This highly restricted distribution must be co-determined by the thymidine hydroxylases (JBP1 and JBP2) that catalyze the initial step in J synthesis. To determine the DNA sequences recognized by JBP1/2, we used SMRT sequencing of DNA segments inserted into plasmids grown in Leishmania tarentolae. We show that SMRT sequencing recognizes base J in DNA. Leishmania DNA segments that normally contain J also picked up J when present in the plasmid, whereas control sequences did not. Even a segment of only 10 telomeric (GGGTTA) repeats was modified in the plasmid. We show that J modification usually occurs at pairs of Ts on opposite DNA strands, separated by 12 nucleotides. Modifications occur near G-rich sequences capable of forming G-quadruplexes and JBP2 is needed, as it does not occur in JBP2-null cells. We propose a model whereby de novo J insertion is mediated by JBP2. JBP1 then binds to J and hydroxylates another T 13 bp downstream (but not upstream) on the complementary strand, allowing JBP1 to maintain existing J following DNA replication.
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Affiliation(s)
- Paul-Andre Genest
- Division of Molecular Oncology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
| | - Loren Baugh
- Seattle Biomedical Research Institute, 307 Westlake Avenue, Seattle, WA 98109-5219, USA
| | - Alex Taipale
- Seattle Biomedical Research Institute, 307 Westlake Avenue, Seattle, WA 98109-5219, USA
| | - Wanqi Zhao
- Division of Molecular Oncology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
| | - Sabrina Jan
- Division of Molecular Oncology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
| | - Henri G A M van Luenen
- Division of Molecular Oncology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
| | - Jonas Korlach
- Pacific Biosciences, 1380 Willow Road, Menlo Park, CA 94025, USA
| | - Tyson Clark
- Pacific Biosciences, 1380 Willow Road, Menlo Park, CA 94025, USA
| | - Khai Luong
- Pacific Biosciences, 1380 Willow Road, Menlo Park, CA 94025, USA
| | - Matthew Boitano
- Pacific Biosciences, 1380 Willow Road, Menlo Park, CA 94025, USA
| | - Steve Turner
- Pacific Biosciences, 1380 Willow Road, Menlo Park, CA 94025, USA
| | - Peter J Myler
- Seattle Biomedical Research Institute, 307 Westlake Avenue, Seattle, WA 98109-5219, USA Department of Biomedical Informatics and Medical Education, University of Washington, Seattle, WA 98195, USA Department of Global Health, University of Washington, Seattle, WA 98195, USA
| | - Piet Borst
- Division of Molecular Oncology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
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17
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Liu S, Ji D, Cliffe L, Bullard W, Sabatini R, Wang Y. Quantitative mass spectrometry-based analysis of β-D-glucosyl-5-hydroxymethyluracil in genomic DNA of Trypanosoma brucei. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2014; 25:1763-1770. [PMID: 25078157 PMCID: PMC4163122 DOI: 10.1007/s13361-014-0960-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2014] [Revised: 07/01/2014] [Accepted: 07/02/2014] [Indexed: 06/03/2023]
Abstract
β-D-glucosyl-5-hydroxymethyluracil (base J) is a hyper-modified nucleobase found in the nuclear DNA of kinetoplastid parasites. With replacement of a fraction of thymine in DNA, J is localized primarily in telomeric regions of all organisms carrying this modified base. The biosynthesis of J occurs in two putative steps: first, a specific thymine in DNA is recognized and converted into 5-hydroxymethyluracil (5-HmU) by J-binding proteins (JBP1 and JBP2); a glucosyl transferase (GT) subsequently glucosylates the 5-HmU to yield J. Although several recent studies revealed the roles of internal J in regulating transcription in kinetoplastids, functions of telomeric J and proteins involved in J synthesis remain elusive. Assessing the functions of base J and understanding fully its biosynthesis necessitate the measurement of its level in cells and organisms. In this study, we reported a reversed-phase HPLC coupled with tandem mass spectrometry (LC-MS/MS) method, together with the use of a surrogate internal standard (β-D-glucosyl-5-hydroxymethyl-2'-deoxycytidine, 5-gHmdC), for the accurate detection of β-D-glucosyl-5-hydroxymethyl-2'-deoxyuridine (dJ) in Trypanosoma brucei DNA. For comparison, we also measured the level of the precursor for dJ synthesis [i.e. 5-hydroxymethyl-2'-deoxyuridine (5-HmdU)]. We found that base J was not detectable in the JBP-null cells whereas it replaced approximately 0.5% thymine in wild-type cells, which was accompanied with a markedly decreased level of 5-HmdU in JBP1/JBP2-null strain relative to the wild-type strain. These results provided direct evidence supporting that JBP proteins play an important role in oxidizing thymidine to form 5-HmdU, which facilitated the generation of dJ. This is the first report about the application of LC-MS/MS for the quantification of base J. The analytical method built a solid foundation for dissecting the molecular mechanisms of J biosynthesis and assessing the biological functions of base J in the future.ᅟ
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Affiliation(s)
- Shuo Liu
- Environmental Toxicology Graduate Program, University of California, Riverside, CA 92521, USA
| | - Debin Ji
- Department of Chemistry, University of California, Riverside, CA 92521, USA
| | - Laura Cliffe
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia 30602, USA
| | - Whitney Bullard
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia 30602, USA
| | - Robert Sabatini
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia 30602, USA
| | - Yinsheng Wang
- Environmental Toxicology Graduate Program, University of California, Riverside, CA 92521, USA
- Department of Chemistry, University of California, Riverside, CA 92521, USA
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18
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Sekar A, Merritt C, Baugh L, Stuart K, Myler PJ. Tb927.10.6900 encodes the glucosyltransferase involved in synthesis of base J in Trypanosoma brucei. Mol Biochem Parasitol 2014; 196:9-11. [PMID: 25064607 DOI: 10.1016/j.molbiopara.2014.07.005] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2014] [Revised: 07/11/2014] [Accepted: 07/14/2014] [Indexed: 01/28/2023]
Abstract
Base J is a DNA modification found in the genome of Trypanosoma brucei and all other kinetoplastids analyzed, where it replaces a small fraction of Ts, mainly in telomeric and chromosome-internal transcription initiation and termination regions. The synthesis of base J is a two-step process whereby a specific T is converted to HOMedU (hydroxymethyldeoxyuridine) and subsequently glucosylated to generate J. The thymidine hydroxylases (JPB1 and JBP2) that catalyze the first step have been characterized, but the identity of the glucosyltransferase catalyzing the second step has proven elusive. Recent bioinformatic analysis by Iyer et al. (Nucleic Acids Res 2013;41:7635) suggested that Tb927.10.6900 encodes the glucosyltransferase (HmdUGT) responsible for converting HOMedU to J in T. brucei. We now present experimental evidence to validate this hypothesis; null mutants of Tb927.10.6900 are unable to synthesize base J. Orthologues from related kinetoplastids show only modest conservation, with several insertion sequences found in those from Leishmania and related genera.
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Affiliation(s)
- Aarthi Sekar
- Seattle Biomedical Research Institute, 307 Westlake Avenue N., Seattle WA 98109-5219, USA
| | - Christopher Merritt
- Seattle Biomedical Research Institute, 307 Westlake Avenue N., Seattle WA 98109-5219, USA
| | - Loren Baugh
- Seattle Biomedical Research Institute, 307 Westlake Avenue N., Seattle WA 98109-5219, USA
| | - Kenneth Stuart
- Seattle Biomedical Research Institute, 307 Westlake Avenue N., Seattle WA 98109-5219, USA; Department of Global Health, University of Washington, Seattle, WA 98195, USA
| | - Peter J Myler
- Seattle Biomedical Research Institute, 307 Westlake Avenue N., Seattle WA 98109-5219, USA; Department of Biomedical Informatics & Medical Education, Seattle, WA 98195, USA; Department of Global Health, University of Washington, Seattle, WA 98195, USA.
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19
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Lu L, Zhu C, Xia B, Yi C. Oxidative Demethylation of DNA and RNA Mediated by Non-Heme Iron-Dependent Dioxygenases. Chem Asian J 2014; 9:2018-29. [DOI: 10.1002/asia.201402148] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2014] [Indexed: 11/10/2022]
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20
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van Luenen HGAM, Farris C, Jan S, Genest PA, Tripathi P, Velds A, Kerkhoven RM, Nieuwland M, Haydock A, Ramasamy G, Vainio S, Heidebrecht T, Perrakis A, Pagie L, van Steensel B, Myler PJ, Borst P. Glucosylated hydroxymethyluracil, DNA base J, prevents transcriptional readthrough in Leishmania. Cell 2012; 150:909-21. [PMID: 22939620 DOI: 10.1016/j.cell.2012.07.030] [Citation(s) in RCA: 115] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2011] [Revised: 05/16/2012] [Accepted: 07/25/2012] [Indexed: 12/25/2022]
Abstract
Some Ts in nuclear DNA of trypanosomes and Leishmania are hydroxylated and glucosylated to yield base J (β-D-glucosyl-hydroxymethyluracil). In Leishmania, about 99% of J is located in telomeric repeats. We show here that most of the remaining J is located at chromosome-internal RNA polymerase II termination sites. This internal J and telomeric J can be reduced by a knockout of J-binding protein 2 (JBP2), an enzyme involved in the first step of J biosynthesis. J levels are further reduced by growing Leishmania JBP2 knockout cells in BrdU-containing medium, resulting in cell death. The loss of internal J in JBP2 knockout cells is accompanied by massive readthrough at RNA polymerase II termination sites. The readthrough varies between transcription units but may extend over 100 kb. We conclude that J is required for proper transcription termination and infer that the absence of internal J kills Leishmania by massive readthrough of transcriptional stops.
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Affiliation(s)
- Henri G A M van Luenen
- Division of Molecular Biology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
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21
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Korlach J, Turner SW. Going beyond five bases in DNA sequencing. Curr Opin Struct Biol 2012; 22:251-61. [PMID: 22575758 DOI: 10.1016/j.sbi.2012.04.002] [Citation(s) in RCA: 106] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2012] [Revised: 04/16/2012] [Accepted: 04/16/2012] [Indexed: 12/01/2022]
Abstract
DNA sequencing has provided a wealth of information about biological systems, but thus far has focused on the four canonical bases, and 5-methylcytosine through comparison of the genomic DNA sequence to a transformed four-base sequence obtained after treatment with bisulfite. However, numerous other chemical modifications to the nucleotides are known to control fundamental life functions, influence virulence of pathogens, and are associated with many diseases. These modifications cannot be accessed with traditional sequencing methods. In this opinion, we highlight several emerging single-molecule sequencing techniques that have the potential to directly detect many types of DNA modifications as an integral part of the sequencing protocol.
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Affiliation(s)
- Jonas Korlach
- Pacific Biosciences, 1380 Willow Road, Menlo Park, CA 94025, United States.
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22
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Heidebrecht T, Christodoulou E, Chalmers MJ, Jan S, Ter Riet B, Grover RK, Joosten RP, Littler D, van Luenen H, Griffin PR, Wentworth P, Borst P, Perrakis A. The structural basis for recognition of base J containing DNA by a novel DNA binding domain in JBP1. Nucleic Acids Res 2011; 39:5715-28. [PMID: 21415010 PMCID: PMC3141245 DOI: 10.1093/nar/gkr125] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The J-binding protein 1 (JBP1) is essential for biosynthesis and maintenance of DNA base-J (β-d-glucosyl-hydroxymethyluracil). Base-J and JBP1 are confined to some pathogenic protozoa and are absent from higher eukaryotes, prokaryotes and viruses. We show that JBP1 recognizes J-containing DNA (J-DNA) through a 160-residue domain, DB-JBP1, with 10 000-fold preference over normal DNA. The crystal structure of DB-JBP1 revealed a helix-turn-helix variant fold, a 'helical bouquet' with a 'ribbon' helix encompassing the amino acids responsible for DNA binding. Mutation of a single residue (Asp525) in the ribbon helix abrogates specificity toward J-DNA. The same mutation renders JBP1 unable to rescue the targeted deletion of endogenous JBP1 genes in Leishmania and changes its distribution in the nucleus. Based on mutational analysis and hydrogen/deuterium-exchange mass-spectrometry data, a model of JBP1 bound to J-DNA was constructed and validated by small-angle X-ray scattering data. Our results open new possibilities for targeted prevention of J-DNA recognition as a therapeutic intervention for parasitic diseases.
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Affiliation(s)
- Tatjana Heidebrecht
- Division of Biochemistry, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
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23
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Cliffe LJ, Siegel TN, Marshall M, Cross GAM, Sabatini R. Two thymidine hydroxylases differentially regulate the formation of glucosylated DNA at regions flanking polymerase II polycistronic transcription units throughout the genome of Trypanosoma brucei. Nucleic Acids Res 2010; 38:3923-35. [PMID: 20215442 PMCID: PMC2896530 DOI: 10.1093/nar/gkq146] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Base J is a hypermodified DNA base localized primarily to telomeric regions of the genome of Trypanosoma brucei. We have previously characterized two thymidine-hydroxylases (TH), JBP1 and JBP2, which regulate J-biosynthesis. JBP2 is a chromatin re-modeling protein that induces de novo J-synthesis, allowing JBP1, a J-DNA binding protein, to stimulate additional J-synthesis. Here, we show that both JBP2 and JBP1 are capable of stimulating de novo J-synthesis. We localized the JBP1- and JBP2-stimulated J by anti-J immunoprecipitation and high-throughput sequencing. This genome-wide analysis revealed an enrichment of base J at regions flanking polymerase II polycistronic transcription units (Pol II PTUs) throughout the T. brucei genome. Chromosome-internal J deposition is primarily mediated by JBP1, whereas JBP2-stimulated J deposition at the telomeric regions. However, the maintenance of J at JBP1-specific regions is dependent on JBP2 SWI/SNF and TH activity. That similar regions of Leishmania major also contain base J highlights the functional importance of the modified base at Pol II PTUs within members of the kinetoplastid family. The regulation of J synthesis/localization by two THs and potential biological function of J in regulating kinetoplastid gene expression is discussed.
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Affiliation(s)
- Laura J Cliffe
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, USA
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24
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Vainio S, Genest PA, ter Riet B, van Luenen H, Borst P. Evidence that J-binding protein 2 is a thymidine hydroxylase catalyzing the first step in the biosynthesis of DNA base J. Mol Biochem Parasitol 2008; 164:157-61. [PMID: 19114062 DOI: 10.1016/j.molbiopara.2008.12.001] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2008] [Revised: 11/10/2008] [Accepted: 12/03/2008] [Indexed: 01/22/2023]
Abstract
The genomic DNA of kinetoplastid parasites contains a unique modified base, beta-d-glucosyl-hydroxymethyluracil or base J. We recently reported that two proteins, called J-binding protein (JBP) 1 and 2, which regulate the levels of J in the genome, display features of the family of Fe(II)-2-oxoglutarate dependent dioxygenases and are likely to be the enzymes catalyzing the first step in J biosynthesis. In this study, we examine the effects of replacing the four conserved residues critical for the activity of this class of enzymes on the function of Leishmania tarentolae JBP2. The results show that each of these four residues is indispensable for the ability of JBP2 to stimulate J synthesis, while mutating non-conserved residues has no consequences. We conclude that JBP2, like JBP1, is in all probability a thymidine hydroxylase involved in the biosynthesis of base J.
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Affiliation(s)
- Saara Vainio
- The Netherlands Cancer Institute, Plesmanlaan 121, Amsterdam, The Netherlands
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25
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Abstract
In 1993, a new base, beta-d-glucopyranosyloxymethyluracil (base J), was identified in the nuclear DNA of Trypanosoma brucei. Base J is the first hypermodified base found in eukaryotic DNA. It is present in all kinetoplastid flagellates analyzed and some unicellular flagellates closely related to trypanosomatids, but it has not been found in other protozoa or in metazoa. J is invariably present in the telomeric repeats of all organisms analyzed. Whereas in Leishmania nearly all J is telomeric, there are other repetitive DNA sequences containing J in T. brucei and T. cruzi, and most J is outside telomeres in Euglena. The biosynthesis of J occurs in two steps: First, a specific thymidine in DNA is converted into hydroxymethyldeoxyuridine (HOMedU), and then this HOMedU is glycosylated to form J. This review discusses the identification and localization of base J in the genome of kinetoplastids, the enzymes involved in J biosynthesis, possible biological functions of J, and J as a potential target for chemotherapy of diseases caused by kinetoplastids.
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Affiliation(s)
- Piet Borst
- Center of Biomedical Genetics, Division of Molecular Biology, The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands.
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26
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Harony H, Ankri S. What do unicellular organisms teach us about DNA methylation? Trends Parasitol 2008; 24:205-9. [PMID: 18403268 DOI: 10.1016/j.pt.2008.02.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2007] [Revised: 02/01/2008] [Accepted: 02/08/2008] [Indexed: 10/22/2022]
Abstract
DNA methylation is an epigenetic hallmark that has been studied intensively in mammals and plants. However, knowledge of this phenomenon in unicellular organisms is scanty. Examining epigenetic regulation, and more specifically DNA methylation, in these organisms represents a unique opportunity to better understand their biology. The determination of their methylation status is often complicated by the presence of several differentiation stages in their life cycle. This article focuses on some recent advances that have revealed the unexpected nature of the epigenetic determinants present in protozoa. The role of the enigmatic DNA methyltransferase Dnmt2 in unicellular organisms is discussed.
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Affiliation(s)
- Hala Harony
- Department of Microbiology, Ruth and Bruce Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, the Rappaport Institute, 31096 Haifa, Israel
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27
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Lopez-Rubio JJ, Riviere L, Scherf A. Shared epigenetic mechanisms control virulence factors in protozoan parasites. Curr Opin Microbiol 2007; 10:560-8. [PMID: 18024150 DOI: 10.1016/j.mib.2007.10.003] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2007] [Revised: 10/04/2007] [Accepted: 10/04/2007] [Indexed: 11/19/2022]
Abstract
Protozoan pathogens have evolved countermeasures to avoid immune clearance and prolong the period of infection in their vertebrate hosts. The type and degree of immune escape strategies depends on the in vivo 'lifestyle' the pathogen has adopted. Here we describe how parasites use different strategies to coordinate their expression of phenotypic variation, which is used in many cases to fool the immune system, or to successfully invade new host cells. Recent insights using modern molecular biology techniques show that this is achieved via a coordinated manner of action of different epigenetic factors such as histone marks, subnuclear localization, or novel unknown mechanism(s). This emerging field may have an enormous impact on disease therapy.
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Affiliation(s)
- Jose Juan Lopez-Rubio
- Unité de Biologie des Interactions Hôte-Parasite, CNRS-URA 2581, Institut Pasteur, Paris, France
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28
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Ekanayake DK, Cipriano MJ, Sabatini R. Telomeric co-localization of the modified base J and contingency genes in the protozoan parasite Trypanosoma cruzi. Nucleic Acids Res 2007; 35:6367-77. [PMID: 17881368 PMCID: PMC2095807 DOI: 10.1093/nar/gkm693] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2007] [Revised: 08/14/2007] [Accepted: 08/22/2007] [Indexed: 12/20/2022] Open
Abstract
Base J or beta-d-glucosylhydroxymethyluracil is a modification of thymine residues within the genome of kinetoplastid parasites. In organisms known to contain the modified base, J is located mainly within the telomeric repeats. However, in Trypanosoma brucei, a small fraction of J is also located within the silent subtelomeric variant surface glycoprotein (VSG) gene expression sites, but not in the active expression site, suggesting a role for J in regulating telomeric genes involved in pathogenesis. With the identification of surface glycoprotein genes adjacent to telomeres in the South American Trypanosome, Trypanosoma cruzi, we became interested in the telomeric distribution of base J. Analysis of J and telomeric repeat sequences by J immunoblots and Southern blots following DNA digestion, reveals approximately 25% of J outside the telomeric repeat sequences. Moreover, the analysis of DNA sequences immunoprecipitated with J antiserum, localized J within subtelomeric regions rich in life-stage-specific surface glycoprotein genes involved in pathogenesis. Interestingly, the pattern of J within these regions is developmentally regulated. These studies provide a framework to characterize the role of base J in the regulation of telomeric gene expression/diversity in T. cruzi.
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Affiliation(s)
| | | | - Robert Sabatini
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, USA
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