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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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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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Kieft R, Zhang Y, Yan H, Schmitz RJ, Sabatini R. Knockout of protein phosphatase 1 in Leishmania major reveals its role during RNA polymerase II transcription termination. Nucleic Acids Res 2023; 51:6208-6226. [PMID: 37194692 PMCID: PMC10325913 DOI: 10.1093/nar/gkad394] [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: 03/13/2023] [Revised: 04/26/2023] [Accepted: 05/04/2023] [Indexed: 05/18/2023] Open
Abstract
The genomes of kinetoplastids are organized into polycistronic transcription units that are flanked by a modified DNA base (base J, beta-D-glucosyl-hydroxymethyluracil). Previous work established a role of base J in promoting RNA polymerase II (Pol II) termination in Leishmania major and Trypanosoma brucei. We recently identified a PJW/PP1 complex in Leishmania containing a J-binding protein (JBP3), PP1 phosphatase 1, PP1 interactive-regulatory protein (PNUTS) and Wdr82. Analyses suggested the complex regulates transcription termination by recruitment to termination sites via JBP3-base J interactions and dephosphorylation of proteins, including Pol II, by PP1. However, we never addressed the role of PP1, the sole catalytic component, in Pol II transcription termination. We now demonstrate that deletion of the PP1 component of the PJW/PP1 complex in L. major, PP1-8e, leads to readthrough transcription at the 3'-end of polycistronic gene arrays. We show PP1-8e has in vitro phosphatase activity that is lost upon mutation of a key catalytic residue and associates with PNUTS via the conserved RVxF motif. Additionally, purified PJW complex with associated PP1-8e, but not complex lacking PP1-8e, led to dephosphorylation of Pol II, suggesting a direct role of PNUTS/PP1 holoenzymes in regulating transcription termination via dephosphorylating Pol II in the nucleus.
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Affiliation(s)
- Rudo Kieft
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA30602, USA
| | - Yang Zhang
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA30602, USA
| | - Haidong Yan
- Department of Genetics, University of Georgia, Athens, GA30602, USA
| | - Robert J Schmitz
- Department of Genetics, University of Georgia, Athens, GA30602, USA
| | - Robert Sabatini
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA30602, USA
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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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Abstract
Unlike most other eukaryotes, Leishmania and other trypanosomatid protozoa have largely eschewed transcriptional control of gene expression, relying instead on posttranscriptional regulation of mRNAs derived from polycistronic transcription units (PTUs). In these parasites, a novel modified nucleotide base (β-d-glucopyranosyloxymethyluracil) known as J plays a critical role in ensuring that transcription termination occurs only at the end of each PTU, rather than at the polyadenylation sites of individual genes. To further understand the biology of J-associated processes, we used tandem affinity purification (TAP) tagging and mass spectrometry to reveal proteins that interact with the glucosyltransferase performing the final step in J synthesis. These studies identified four proteins reminiscent of subunits in the PTW/PP1 complex that controls transcription termination in higher eukaryotes. Moreover, bioinformatic analyses identified the DNA-binding subunit of Leishmania PTW/PP1 as a novel J-binding protein (JBP3), which is also part of another complex containing proteins with domains suggestive of a role in chromatin modification/remodeling. Additionally, JBP3 associates (albeit transiently and/or indirectly) with the trypanosomatid equivalent of the PAF1 complex involved in the regulation of transcription in other eukaryotes. The downregulation of JBP3 expression levels in Leishmania resulted in a substantial increase in transcriptional readthrough at the 3′ end of most PTUs. We propose that JBP3 recruits one or more of these complexes to the J-containing regions at the end of PTUs, where they halt the progression of the RNA polymerase. This decoupling of transcription termination from the splicing of individual genes enables the parasites’ unique reliance on polycistronic transcription and posttranscriptional regulation of gene expression. IMPORTANCELeishmania parasites cause a variety of serious human diseases, with no effective vaccine and emerging resistance to current drug therapy. We have previously shown that a novel DNA base called J is critical for transcription termination at the ends of the polycistronic gene clusters that are a hallmark of Leishmania and related trypanosomatids. Here, we describe a new J-binding protein (JBP3) associated with three different protein complexes that are reminiscent of those involved in the control of transcription in other eukaryotes. However, the parasite complexes have been reprogrammed to regulate transcription and gene expression in trypanosomatids differently than in the mammalian hosts, providing new opportunities to develop novel chemotherapeutic treatments against these important pathogens.
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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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Sharma R, Terrão MC, Castro FF, Breitling R, Faça V, Oliveira EB, Cruz AK. Insights on a putative aminoacyl-tRNA-protein transferase of Leishmania major. PLoS One 2018; 13:e0203369. [PMID: 30208112 PMCID: PMC6135404 DOI: 10.1371/journal.pone.0203369] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Accepted: 08/20/2018] [Indexed: 11/29/2022] Open
Abstract
The N-end rule pathway leads to regulated proteolysis as an adaptive response to external stress and is ubiquitous from bacteria to mammals. In this study, we investigated a gene coding for a putative core enzyme of this post-translational regulatory pathway in Leishmania major, which may be crucial during cytodifferentiation and the environment adaptive responses of the parasite. Leucyl, phenylalanyl-tRNA protein transferase and arginyl-tRNA protein transferase are key components of this pathway in E. coli and eukaryotes, respectively. They catalyze the specific conjugation of leucine, phenylalanine or arginine to proteins containing exposed N-terminal amino acid residues, which are recognized by the machinery for the targeted proteolysis. Here, we characterized a conserved hypothetical protein coded by the LmjF.21.0725 gene in L. major. In silico analysis suggests that the LmjF.21.0725 protein is highly conserved among species of Leishmania and might belong to the Acyl CoA-N-acyltransferases (NAT) superfamily of proteins. Immunofluorescence cell imaging indicates that the cytosolic localization of the studied protein and the endogenous levels of the protein in promastigotes are barely detectable by western blotting assay. The knockout of the two alleles of LmjF.21.0725 by homologous recombination was only possible in the heterozygous transfectant expressing LmjF.21.0725 as a transgene from a plasmid. Moreover, the kinetics of loss of the plasmid in the absence of drug pressure suggests that maintenance of the gene is essential for promastigote survival. Here, evidence is provided that this putative aminoacyl tRNA-protein transferase is essential for parasite survival. The enzyme activity and corresponding post-translational regulatory pathway are yet to be investigated.
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Affiliation(s)
- Rohit Sharma
- Department of Cell and Molecular Biology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, SP, Brazil
| | - Monica Cristina Terrão
- Department of Cell and Molecular Biology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, SP, Brazil
| | - Felipe Freitas Castro
- Department of Cell and Molecular Biology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, SP, Brazil
| | | | - Vitor Faça
- Department of Biochemistry and Immunology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, SP, Brazil
| | - Eduardo Brandt Oliveira
- Department of Biochemistry and Immunology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, SP, Brazil
| | - Angela Kaysel Cruz
- Department of Cell and Molecular Biology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, SP, Brazil
- * E-mail:
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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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Reynolds DL, Hofmeister BT, Cliffe L, Siegel TN, Anderson BA, Beverley SM, Schmitz RJ, Sabatini R. Base J represses genes at the end of polycistronic gene clusters in Leishmania major by promoting RNAP II termination. Mol Microbiol 2016; 101:559-74. [PMID: 27125778 DOI: 10.1111/mmi.13408] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/27/2016] [Indexed: 12/27/2022]
Abstract
The genomes of kinetoplastids are organized into polycistronic gene clusters that are flanked by the modified DNA base J. Previous work has established a role of base J in promoting RNA polymerase II termination in Leishmania spp. where the loss of J leads to termination defects and transcription into adjacent gene clusters. It remains unclear whether these termination defects affect gene expression and whether read through transcription is detrimental to cell growth, thus explaining the essential nature of J. We now demonstrate that reduction of base J at specific sites within polycistronic gene clusters in L. major leads to read through transcription and increased expression of downstream genes in the cluster. Interestingly, subsequent transcription into the opposing polycistronic gene cluster does not lead to downregulation of sense mRNAs. These findings indicate a conserved role for J regulating transcription termination and expression of genes within polycistronic gene clusters in trypanosomatids. In contrast to the expectations often attributed to opposing transcription, the essential nature of J in Leishmania spp. is related to its role in gene repression rather than preventing transcriptional interference resulting from read through and dual strand transcription.
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Affiliation(s)
- David L Reynolds
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia, 30602, USA
| | | | - Laura Cliffe
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia, 30602, USA
| | - T Nicolai Siegel
- Research Center for Infectious Diseases, University of Wuerzburg, Wuerzburg, 97080, Germany
| | - Britta A Anderson
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, 63110, USA
| | - Stephen M Beverley
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, 63110, USA
| | - Robert J Schmitz
- Department of Genetics, University of Georgia, Athens, Georgia, 30602, USA
| | - Robert Sabatini
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia, 30602, USA
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11
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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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12
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O’Neill EC, Trick M, Henrissat B, Field RA. Euglena in time: Evolution, control of central metabolic processes and multi-domain proteins in carbohydrate and natural product biochemistry. ACTA ACUST UNITED AC 2015. [DOI: 10.1016/j.pisc.2015.07.002] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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13
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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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Depletion of the RNA-binding protein RBP33 results in increased expression of silenced RNA polymerase II transcripts in Trypanosoma brucei. PLoS One 2014; 9:e107608. [PMID: 25215501 PMCID: PMC4162612 DOI: 10.1371/journal.pone.0107608] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2014] [Accepted: 08/18/2014] [Indexed: 12/30/2022] Open
Abstract
We have characterized the RNA-binding protein RBP33 in Trypanosoma brucei, and found that it localizes to the nucleus and is essential for viability. The subset of RNAs bound to RBP33 was determined by immunoprecipitation of ribonucleoprotein complexes followed by deep sequencing. Most RBP33-bound transcripts are predicted to be non-coding. Among these, over one-third are located close to the end of transcriptional units (TUs) or have an antisense orientation within a TU. Depletion of RBP33 resulted in an increase in the level of RNAs derived from regions that are normally silenced, such as strand-switch regions, retroposon and repeat sequences. Our work provides the first example of an RNA-binding protein involved in the regulation of gene silencing in trypanosomes.
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15
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Reynolds D, Cliffe L, Förstner KU, Hon CC, Siegel TN, Sabatini R. Regulation of transcription termination by glucosylated hydroxymethyluracil, base J, in Leishmania major and Trypanosoma brucei. Nucleic Acids Res 2014; 42:9717-29. [PMID: 25104019 PMCID: PMC4150806 DOI: 10.1093/nar/gku714] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Base J, β-d-glucosyl-hydroxymethyluracil, is an epigenetic modification of thymine in the nuclear DNA of flagellated protozoa of the order Kinetoplastida. J is enriched at sites involved in RNA polymerase (RNAP) II initiation and termination. Reduction of J in Leishmania tarentolae via growth in BrdU resulted in cell death and indicated a role of J in the regulation of RNAP II termination. To further explore J function in RNAP II termination among kinetoplastids and avoid indirect effects associated with BrdU toxicity and genetic deletions, we inhibited J synthesis in Leishmania major and Trypanosoma brucei using DMOG. Reduction of J in L. major resulted in genome-wide defects in transcription termination at the end of polycistronic gene clusters and the generation of antisense RNAs, without cell death. In contrast, loss of J in T. brucei did not lead to genome-wide termination defects; however, the loss of J at specific sites within polycistronic gene clusters led to altered transcription termination and increased expression of downstream genes. Thus, J regulation of RNAP II transcription termination genome-wide is restricted to Leishmania spp., while in T. brucei it regulates termination and gene expression at specific sites within polycistronic gene clusters.
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Affiliation(s)
- David Reynolds
- Department of Biochemistry and Molecular Biology, University of Georgia, Davison Life Sciences Building, 120 Green Street, Athens, GA 30602-7229, USA
| | - Laura Cliffe
- Department of Biochemistry and Molecular Biology, University of Georgia, Davison Life Sciences Building, 120 Green Street, Athens, GA 30602-7229, USA
| | - Konrad U Förstner
- Core Unit Systems Medicine, University of Wuerzburg, Wuerzburg 97080, Germany
| | - Chung-Chau Hon
- Institut Pasteur, Unité Biologie Cellulaire du Parasitisme, Département Biologie cellulaire et infection, Paris 75015, France INSERM U786, Paris 75015, France
| | - T Nicolai Siegel
- Research Center for Infectious Diseases, University of Wuerzburg, Wuerzburg 97080, Germany
| | - Robert Sabatini
- Department of Biochemistry and Molecular Biology, University of Georgia, Davison Life Sciences Building, 120 Green Street, Athens, GA 30602-7229, USA
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16
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Maree JP, Patterton HG. The epigenome of Trypanosoma brucei: a regulatory interface to an unconventional transcriptional machine. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2014; 1839:743-50. [PMID: 24942804 DOI: 10.1016/j.bbagrm.2014.05.028] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2014] [Revised: 05/09/2014] [Accepted: 05/28/2014] [Indexed: 12/15/2022]
Abstract
The epigenome represents a major regulatory interface to the eukaryotic genome. Nucleosome positions, histone variants, histone modifications and chromatin associated proteins all play a role in the epigenetic regulation of DNA function. Trypanosomes, an ancient branch of the eukaryotic evolutionary lineage, exhibit some highly unusual transcriptional features, including the arrangement of functionally unrelated genes in large, polymerase II transcribed polycistronic transcription units, often exceeding hundreds of kilobases in size. It is generally believed that transcription initiation plays a minor role in regulating the transcript level of genes in trypanosomes, which are mainly regulated post-transcriptionally. Recent advances have revealed that epigenetic mechanisms play an essential role in the transcriptional regulation of Trypanosoma brucei. This suggested that the modulation of gene activity, particularly that of pol I transcribed genes, is, indeed, an important control mechanism, and that the epigenome is critical in regulating gene expression programs that allow the successful migration of this parasite between hosts, as well as the continuous evasion of the immune system in mammalian hosts. A wide range of epigenetic signals, readers, writers and erasers have been identified in trypanosomes, some of which have been mapped to essential genetic functions. Some epigenetic mechanisms have also been observed to be unique to trypanosomes. We review recent advances in our understanding of epigenetic control mechanisms in T. brucei, the causative agent of African sleeping sickness, and highlight the utility of epigenetic targets in the possible development of new therapies for human African trypanosomiasis.
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Affiliation(s)
- Johannes P Maree
- Advanced Biomolecular Research Cluster, University of the Free State, PO Box 339, Bloemfontein 9332, South Africa
| | - Hugh-G Patterton
- Advanced Biomolecular Research Cluster, University of the Free State, PO Box 339, Bloemfontein 9332, South Africa.
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17
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Bullard W, Lopes da Rosa-Spiegler J, Liu S, Wang Y, Sabatini R. Identification of the glucosyltransferase that converts hydroxymethyluracil to base J in the trypanosomatid genome. J Biol Chem 2014; 289:20273-82. [PMID: 24891501 DOI: 10.1074/jbc.m114.579821] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
O-linked glucosylation of thymine in DNA (base J) is an important regulatory epigenetic mark in trypanosomatids. β-d-glucopyranosyloxymethyluracil (base J) synthesis is initiated by the JBP1/2 enzymes that hydroxylate thymine, forming 5-hydroxymethyluracil (hmU). hmU is then glucosylated by a previously unknown glucosyltransferase. A recent computational screen identified a possible candidate for the base J-associated glucosyltransferase (JGT) in trypanosomatid genomes. We demonstrate that recombinant JGT utilizes uridine diphosphoglucose to transfer glucose to hmU in the context of dsDNA. Mutation of conserved residues typically involved in glucosyltransferase catalysis impairs DNA glucosylation in vitro. The deletion of both alleles of JGT from the genome of Trypanosoma brucei generates a cell line that completely lacks base J. Reintroduction of JGT in the JGT KO restores J synthesis. Ablation of JGT mRNA levels by RNAi leads to the sequential reduction in base J and increased levels of hmU that dissipate rapidly. The analysis of JGT function confirms the two-step J synthesis model and demonstrates that JGT is the only glucosyltransferase enzyme required for the second step of the pathway. Similar to the activity of the related Ten-Eleven Translocation (TET) family of dioxygenases on 5mC, our studies also suggest the ability of the base J-binding protein enzymes to catalyze iterative oxidation of thymine in trypanosome DNA. Here we discuss the regulation of hmU and base J formation in the trypanosome genome by JGT and base J-binding protein.
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Affiliation(s)
- Whitney Bullard
- From the Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia 30602 and
| | | | - Shuo Liu
- the Environmental Toxicology Graduate Program and
| | - Yinsheng Wang
- the Environmental Toxicology Graduate Program and Department of Chemistry, University of California, Riverside, California 92521
| | - Robert Sabatini
- From the Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia 30602 and
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18
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Abstract
SUMMARY Hsp90 (a.k.a. Hsp83) plays a significant role in the life cycle control of the protozoan parasite Leishmania donovani. Rather than protecting Leishmania spp. against adverse and stressful environs, Hsp90 is required for the maintenance of the motile, highly proliferative insect stage, the promastigote. However, Hsp90 is also essential for survival and proliferation of the intracellular mammalian stage, the amastigote. Moreover, recent evidence shows Hsp90 and other components of large multi-chaperone complexes as substrates of stage-specific protein phosphorylation pathways, and thus as likely effectors of the signal transduction pathways in Leishmania spp. Future efforts should be directed towards the identification of the protein kinases and the critical phosphorylation sites as targets for novel therapeutic approaches.
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19
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Anderson BA, Wong ILK, Baugh L, Ramasamy G, Myler PJ, Beverley SM. Kinetoplastid-specific histone variant functions are conserved in Leishmania major. Mol Biochem Parasitol 2013; 191:53-7. [PMID: 24080031 DOI: 10.1016/j.molbiopara.2013.09.005] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2013] [Revised: 09/16/2013] [Accepted: 09/18/2013] [Indexed: 01/08/2023]
Abstract
Regions of transcription initiation and termination in kinetoplastid protists lack known eukaryotic promoter and terminator elements, although epigenetic marks such as histone variants and the modified DNA base J have been localized to these regions in Trypanosoma brucei, Trypanosoma cruzi, and/or Leishmania major. Phenotypes of base J mutants vary significantly across trypanosomatids, implying divergence in the epigenetic networks governing transcription during evolution. Here, we demonstrate that the histone variants H2A.Z and H2B.V are essential in L. major using a powerful quantitative plasmid segregation-based test. In contrast, H3.V is not essential for viability or normal growth in Leishmania. Steady-state transcript levels and the efficiency of transcription termination at convergent strand switch regions (SSRs) in H3V-null parasites were comparable to WT parasites. Our genetic tests show a conservation of histone variant phenotypes between L. major and T. brucei, unlike the diversity of phenotypes associated with genetic manipulation of the DNA base J modification.
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Affiliation(s)
- Britta A Anderson
- Department of Molecular Microbiology, Washington University School of Medicine, Box 8230, 600 S. Euclid Avenue, St. Louis, MO 63110, USA
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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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In silico identification of conserved intercoding sequences in Leishmania genomes: Unraveling putative cis-regulatory elements. Mol Biochem Parasitol 2012; 183:140-50. [DOI: 10.1016/j.molbiopara.2012.02.009] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2011] [Revised: 02/16/2012] [Accepted: 02/17/2012] [Indexed: 01/21/2023]
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22
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Cliffe LJ, Hirsch G, Wang J, Ekanayake D, Bullard W, Hu M, Wang Y, Sabatini R. JBP1 and JBP2 proteins are Fe2+/2-oxoglutarate-dependent dioxygenases regulating hydroxylation of thymidine residues in trypanosome DNA. J Biol Chem 2012; 287:19886-95. [PMID: 22514282 DOI: 10.1074/jbc.m112.341974] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
We have recently demonstrated that O-linked glucosylation of thymine in trypanosome DNA (base J) regulates polymerase II transcription initiation. In vivo analysis has indicated that base J synthesis is initiated by the hydroxylation of thymidine by proteins (JBP1 and JBP2) homologous to the Fe(2+)/2-oxoglutarate (2-OG)-dependent dioxygenase superfamily where hydroxylation is driven by the oxidative decarboxylation of 2-OG, forming succinate and CO(2). However, no direct evidence for hydroxylase activity has been reported for the JBP proteins. We now demonstrate recombinant JBP1 hydroxylates thymine specifically in the context of dsDNA in a Fe(2+)-, 2-OG-, and O(2)-dependent manner. Under anaerobic conditions, the addition of Fe(2+) to JBP1/2-OG results in the formation of a broad absorption spectrum centered at 530 nm attributed to metal chelation of 2-OG bound to JBP, a spectroscopic signature of Fe(2+)/2-OG-dependent dioxygenases. The N-terminal thymidine hydroxylase domain of JBP1 is sufficient for full activity and mutation of residues involved in coordinating Fe(2+) inhibit iron binding and thymidine hydroxylation. Hydroxylation in vitro and J synthesis in vivo is inhibited by known inhibitors of Fe(2+)/2-OG-dependent dioxygenases. The data clearly demonstrate the JBP enzymes are dioxygenases acting directly on dsDNA, confirming the two-step J synthesis model. Growth of trypanosomes in hypoxic conditions decreases JBP1 and -2 activity, resulting in reduced levels of J and changes in parasite virulence previously characterized in the JBP KO. The influence of environment upon J biosynthesis via oxygen-sensitive regulation of JBP1/2 has exciting implications for the regulation of gene expression and parasite adaptation to different host niches.
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Affiliation(s)
- Laura J Cliffe
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia 30602-7229, USA
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23
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Leishmania donovani HslV does not interact stably with HslU proteins. Int J Parasitol 2012; 42:329-39. [PMID: 22370310 DOI: 10.1016/j.ijpara.2012.01.008] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2011] [Revised: 01/10/2012] [Accepted: 01/16/2012] [Indexed: 11/21/2022]
Abstract
Genes for HslVU-type peptidases are found in bacteria and in a few select Eukaryota, among those such important pathogens as Plasmodium spp. and Leishmania spp. In this study, we performed replacements of all three HslV/HslU gene homologues and found one of those, HslV, to be essential for Leishmania donovani viability. The Leishmania HslV gene can also partially relieve the thermosensitive phenotype of a combined HslVU/Lon/ClpXP knockout mutant of Escherichia coli, indicating a conserved function. However, we found that the role and function of the two Leishmania HslU genes has diverged since neither of those interacts stably with HslV. The latter forms a dodecameric complex by itself and shows a punctate distribution. We conclude that whilst the basic function of HslV may be conserved in Leishmania, its organisation and interaction with its canonical complex partner HslU is not. Nevertheless, given the absence of HslV from the proteome of mammals and its essential role in Leishmania viability, HslV is a promising target for intervention.
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24
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Mukherjee A, Langston LD, Ouellette M. Intrachromosomal tandem duplication and repeat expansion during attempts to inactivate the subtelomeric essential gene GSH1 in Leishmania. Nucleic Acids Res 2011; 39:7499-511. [PMID: 21693561 PMCID: PMC3177219 DOI: 10.1093/nar/gkr494] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Gamma-glutamylcysteine synthetase encoded by GSH1 is the rate-limiting enzyme in the biosynthesis of glutathione and trypanothione in Leishmania. Attempts to generate GSH1 null mutants by gene disruption failed in Leishmania infantum. Removal of even a single allele invariably led to the generation of an extra copy of GSH1, maintaining two intact wild-type alleles. In the second and even third round of inactivation, the markers integrated at the homologous locus but always preserved two intact copies of GSH1. We probed into the mechanism of GSH1 duplication. GSH1 is subtelomeric on chromosome 18 and Southern blot analysis indicated that a 10-kb fragment flanked by 466-bp direct repeated sequences was duplicated in tandem on the same chromosomal allele each time GSH1 was targeted. Polymerase chain reaction analysis and sequencing confirmed the generation of novel junctions created at the level of the 466-bp repeats consequent to locus duplication. In loss of heterozygosity attempts, the same repeated sequences were utilized for generating extrachromosomal circular amplicons. Our results are consistent with break-induced replication as a mechanism for the generation of this regional polyploidy to compensate for the inactivation of an essential gene. This chromosomal repeat expansion through repeated sequences could be implicated in locus duplication in Leishmania.
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Affiliation(s)
- Angana Mukherjee
- Département de Microbiologie, Immunologie and Infectiologie, Université Laval, Québec, Canada
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25
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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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26
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Kushnir S, Cirstea IC, Basiliya L, Lupilova N, Breitling R, Alexandrov K. Artificial linear episome-based protein expression system for protozoon Leishmania tarentolae. Mol Biochem Parasitol 2010; 176:69-79. [PMID: 21167214 DOI: 10.1016/j.molbiopara.2010.12.002] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2010] [Revised: 12/01/2010] [Accepted: 12/03/2010] [Indexed: 11/28/2022]
Abstract
The trypanosomatid protozoon Leishmania tarentolae is a well-established model organism for studying causative agents of several tropical diseases that was more recently developed as a host for recombinant protein production. Although several expression architectures based on foreign RNA polymerases have been established for this organism, all of them rely on integration of the expression cassette into the genome. Here, we exploit a new type of expression architecture based on linear elements. These expression vectors were propagated in Escherichia coli as circular plasmids and converted into linear episomes with telomere-like structures prior to transfection of L. tarentolae. Overexpression of recombinant proteins in transgenic organisms exceeding 10% of total cellular protein, one of the highest overexpression levels obtained in a eukaryotic organism for a cytosolic protein. We show that the linear elements are stably propagated in L. tarentolae cells over long periods of time (> 90 generations) without major changes in structure or expression yields. Overexpressing cultures can be obtained without clonal selection of the transfected cells. To establish the utility of the developed system for protein production in a parallelized format, we expressed 37 cytosolic, peripheral, and membrane proteins as fusions with EGFP in L. tarentolae using linear vectors. We detected the expression of 30 of these targets and describe the preparative purification of two arbitrarily selected proteins.
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Affiliation(s)
- Susanna Kushnir
- Department of Chemical Biology Max-Planck-Institute for Molecular Physiology, Otto-Hahn-Strasse 11, 44227 Dortmund, Germany
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27
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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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28
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Abstract
Iron is almost ubiquitous in living organisms due to the utility of its redox chemistry. It is also dangerous as it can catalyse the formation of reactive free radicals - a classical double-edged sword. In this review, we examine the uptake and usage of iron by trypanosomatids and discuss how modulation of host iron metabolism plays an important role in the protective response. Trypanosomatids require iron for crucial processes including DNA replication, antioxidant defence, mitochondrial respiration, synthesis of the modified base J and, in African trypanosomes, the alternative oxidase. The source of iron varies between species. Bloodstream-form African trypanosomes acquire iron from their host by uptake of transferrin, and Leishmania amazonensis expresses a ZIP family cation transporter in the plasma membrane. In other trypanosomatids, iron uptake has been poorly characterized. Iron-withholding responses by the host can be a major determinant of disease outcome. Their role in trypanosomatid infections is becoming apparent. For example, the cytosolic sequestration properties of NRAMP1, confer resistance against leishmaniasis. Conversely, cytoplasmic sequestration of iron may be favourable rather than detrimental to Trypanosoma cruzi. The central role of iron in both parasite metabolism and the host response is attracting interest as a possible point of therapeutic intervention.
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29
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Abstract
Epigenetic regulation is important in many facets of eukaryotic biology. Recent work has suggested that the basic mechanisms underlying epigenetic regulation extend to eukaryotic parasites. The identification of post-translational histone modifications and chromatin-modifying enzymes is beginning to reveal both common and novel functions for chromatin in these parasites. In this Review, we compare the role of epigenetics in African trypanosomes and humans in several biological processes. We discuss how the study of trypanosome chromatin might help us to better understand the evolution of epigenetic processes.
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30
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Cliffe LJ, Kieft R, Southern T, Birkeland SR, Marshall M, Sweeney K, Sabatini R. JBP1 and JBP2 are two distinct thymidine hydroxylases involved in J biosynthesis in genomic DNA of African trypanosomes. Nucleic Acids Res 2009; 37:1452-62. [PMID: 19136460 PMCID: PMC2655668 DOI: 10.1093/nar/gkn1067] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Genomic DNA of African trypanosomes contains a hypermodified thymidine residue termed base J (beta-d-glucosyl-HOMedU). This modified base is localized primarily to repetitive DNA, namely the telomeres, and is implicated in the regulation of antigenic variation. The base is synthesized in a two-step pathway. Initially, a thymidine residue in DNA is hydroxylated by a thymidine hydroxylase (TH). This intermediate (HOMedU) is then glucosylated to form base J. Two proteins involved in J synthesis, JBP1 (J binding protein 1) and JBP2, contain a putative TH domain related to the family of Fe(2+)/2-oxoglutarate-dependent hydroxylases. We have previously shown that mutations in the TH domain of JBP1 kill its ability to stimulate J synthesis. Here we show that mutation of key residues in the TH domain of JBP2 ablate its ability to induce de novo J synthesis. While the individual JBP1 null and JBP2 null trypanosomes have reduced J levels, the deletion of both JBP1 and JBP2 generates a cell line that completely lacks base J but still contains glucosyl-transferase activity. Reintroduction of JBP2 in the J-null trypanosome stimulates HOMedU formation and site-specific synthesis of base J. We conclude that JBP2 and JBP1 are the TH enzymes involved in J biosynthesis.
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Affiliation(s)
- Laura J Cliffe
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia 30602, USA
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31
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Romao S, Castro H, Sousa C, Carvalho S, Tomás AM. The cytosolic tryparedoxin of Leishmania infantum is essential for parasite survival. Int J Parasitol 2008; 39:703-11. [PMID: 19135056 DOI: 10.1016/j.ijpara.2008.11.009] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2008] [Revised: 11/05/2008] [Accepted: 11/13/2008] [Indexed: 11/28/2022]
Abstract
Leishmania infantum cytosolic tryparedoxin (LiTXN1) can be regarded as a potential candidate for drug targeting. This redox active molecule, which belongs to the thioredoxin superfamily, is one constituent of the hydroperoxide elimination cascade in L. infantum and may also be involved in other cellular processes such as DNA synthesis or host-parasite interaction. In order to validate LiTXN1 as a drug target we have employed a gene replacement strategy. We observed that substitution of both chromosomal LiTXN1 alleles was only possible upon parasite complementation with an episomal copy of the gene. Furthermore, contrary to control parasites carrying the empty vector, both the insect and the mammalian stages of L. infantum retained the episomal copy of LiTXN1 in the absence of drug pressure. These results confirm the essentiality of LiTXN1 throughout the life cycle of the parasite, namely in the disease-causing amastigote stage. In addition, the data obtained showed that disruption of one allele of this gene leads only to a 25% reduction in the expression of LiTXN1. Even though this does not affect promastigote growth and susceptibility to hydrogen peroxide, ex vivo infection assays suggest that wild-type levels of LiTXN1 are required for optimal L. infantum virulence.
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Affiliation(s)
- Susana Romao
- Instituto de Biologia Molecular e Celular, Universidade do Porto, Rua do Campo Alegre 823, 4150-180 Porto, Portugal
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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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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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34
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Ommen G, Lorenz S, Clos J. One-step generation of double-allele gene replacement mutants in Leishmania donovani. Int J Parasitol 2008; 39:541-6. [PMID: 19028498 DOI: 10.1016/j.ijpara.2008.10.009] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2008] [Revised: 10/27/2008] [Accepted: 10/28/2008] [Indexed: 10/21/2022]
Abstract
Due to the apparent lack of sexual recombination in Leishmania spp., gene replacement strategies in this diploid organism necessitate the subsequent targeting of two gene alleles by using two constructs, bearing different antibiotic resistance markers. This approach is time consuming and often gives rise to spontaneous amplification of the targeted gene, nullifying efforts to create functional null mutants. Here, we show that by using two homologous recombination constructs in a co-transfection of Leishmania donovani promastigotes, we can obtain double-allele gene replacement mutants. This approach reduces the time required for the generation of functional null mutants and the number of in vitro passage cycles, potentially limiting culture-associated artefacts.
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Affiliation(s)
- Gabi Ommen
- Leishmaniasis Research Group, Bernhard Nocht Institute for Tropical Medicine, Bernhard Nocht St 74, D-20359 Hamburg, Germany
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35
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Ubeda JM, Légaré D, Raymond F, Ouameur AA, Boisvert S, Rigault P, Corbeil J, Tremblay MJ, Olivier M, Papadopoulou B, Ouellette M. Modulation of gene expression in drug resistant Leishmania is associated with gene amplification, gene deletion and chromosome aneuploidy. Genome Biol 2008; 9:R115. [PMID: 18638379 PMCID: PMC2530873 DOI: 10.1186/gb-2008-9-7-r115] [Citation(s) in RCA: 130] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2008] [Revised: 06/06/2008] [Accepted: 07/18/2008] [Indexed: 12/02/2022] Open
Abstract
Gene expression and DNA copy number analyses using full genome oligonucleotide microarrays of Leishmania reveal molecular mechanisms of methotrexate resistance. Background Drug resistance can be complex, and several mutations responsible for it can co-exist in a resistant cell. Transcriptional profiling is ideally suited for studying complex resistance genotypes and has the potential to lead to novel discoveries. We generated full genome 70-mer oligonucleotide microarrays for all protein coding genes of the human protozoan parasites Leishmania major and Leishmania infantum. These arrays were used to monitor gene expression in methotrexate resistant parasites. Results Leishmania is a eukaryotic organism with minimal control at the level of transcription initiation and few genes were differentially expressed without concomitant changes in DNA copy number. One exception was found in Leishmania major, where the expression of whole chromosomes was down-regulated. The microarrays highlighted several mechanisms by which the copy number of genes involved in resistance was altered; these include gene deletion, formation of extrachromosomal circular or linear amplicons, and the presence of supernumerary chromosomes. In the case of gene deletion or gene amplification, the rearrangements have occurred at the sites of repeated (direct or inverted) sequences. These repeats appear highly conserved in both species to facilitate the amplification of key genes during environmental changes. When direct or inverted repeats are absent in the vicinity of a gene conferring a selective advantage, Leishmania will resort to supernumerary chromosomes to increase the levels of a gene product. Conclusion Aneuploidy has been suggested as an important cause of drug resistance in several organisms and additional studies should reveal the potential importance of this phenomenon in drug resistance in Leishmania.
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Affiliation(s)
- Jean-Michel Ubeda
- Université Laval, Division de Microbiologie, Centre de Recherche en Infectiologie, boulevard Laurier, Québec, G1V 4G2, Canada.
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Requena JM, Folgueira C, López MC, Thomas MC. The SIDER2 elements, interspersed repeated sequences that populate the Leishmania genomes, constitute subfamilies showing chromosomal proximity relationship. BMC Genomics 2008; 9:263. [PMID: 18518959 PMCID: PMC2424063 DOI: 10.1186/1471-2164-9-263] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2008] [Accepted: 06/02/2008] [Indexed: 12/03/2022] Open
Abstract
Background Protozoan parasites of the genus Leishmania are causative agents of a diverse spectrum of human diseases collectively known as leishmaniasis. These eukaryotic pathogens that diverged early from the main eukaryotic lineage possess a number of unusual genomic, molecular and biochemical features. The completion of the genome projects for three Leishmania species has generated invaluable information enabling a direct analysis of genome structure and organization. Results By using DNA macroarrays, made with Leishmania infantum genomic clones and hybridized with total DNA from the parasite, we identified a clone containing a repeated sequence. An analysis of the recently completed genome sequence of L. infantum, using this repeated sequence as bait, led to the identification of a new class of repeated elements that are interspersed along the different L. infantum chromosomes. These elements turned out to be homologues of SIDER2 sequences, which were recently identified in the Leishmania major genome; thus, we adopted this nomenclature for the Leishmania elements described herein. Since SIDER2 elements are very heterogeneous in sequence, their precise identification is rather laborious. We have characterized 54 LiSIDER2 elements in chromosome 32 and 27 ones in chromosome 20. The mean size for these elements is 550 bp and their sequence is G+C rich (mean value of 66.5%). On the basis of sequence similarity, these elements can be grouped in subfamilies that show a remarkable relationship of proximity, i.e. SIDER2s of a given subfamily locate close in a chromosomal region without intercalating elements. For comparative purposes, we have identified the SIDER2 elements existing in L. major and Leishmania braziliensis chromosomes 32. While SIDER2 elements are highly conserved both in number and location between L. infantum and L. major, no such conservation exists when comparing with SIDER2s in L. braziliensis chromosome 32. Conclusion SIDER2 elements constitute a relevant piece in the Leishmania genome organization. Sequence characteristics, genomic distribution and evolutionarily conservation of SIDER2s are suggestive of relevant functions for these elements in Leishmania. Apart from a proved involvement in post-trancriptional mechanisms of gene regulation, SIDER2 elements could be involved in DNA amplification processes and, perhaps, in chromosome segregation as centromeric sequences.
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Affiliation(s)
- Jose M Requena
- Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Universidad Autónoma de Madrid, 28049 Madrid, Spain.
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Grover RK, Pond SJK, Cui Q, Subramaniam P, Case DA, Millar DP, Wentworth P. O-glycoside orientation is an essential aspect of base J recognition by the kinetoplastid DNA-binding protein JBP1. Angew Chem Int Ed Engl 2007; 46:2839-43. [PMID: 17295375 DOI: 10.1002/anie.200604635] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Rajesh K Grover
- Department of Chemistry and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
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O-Glycoside Orientation Is an Essential Aspect of Base J Recognition by the Kinetoplastid DNA-Binding Protein JBP1. Angew Chem Int Ed Engl 2007. [DOI: 10.1002/ange.200604635] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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Dias FC, Ruiz JC, Lopes WCZ, Squina FM, Renzi A, Cruz AK, Tosi LRO. Organization of H locus conserved repeats in Leishmania (Viannia) braziliensis correlates with lack of gene amplification and drug resistance. Parasitol Res 2007; 101:667-76. [PMID: 17393181 DOI: 10.1007/s00436-007-0528-5] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2007] [Accepted: 03/14/2007] [Indexed: 11/27/2022]
Abstract
Resistance to antimonials is a major problem when treating visceral leishmaniasis in India and has already been described for New World parasites. Clinical response to meglumine antimoniate in patients infected with parasites of the Viannia sub-genus can be widely variable, suggesting the presence of mechanisms of drug resistance. In this work, we have compared L. major and L. braziliensis mutants selected in different drugs. The cross-resistance profiles of some cell lines resembled those of mutants bearing H locus amplicons. However, amplified episomal molecules were exclusively detected in L. major mutants. The analysis of the L. braziliensis H region revealed a strong conservation of gene synteny. The typical intergenic repeats that are believed to mediate the amplification of the H locus in species of the Leishmania sub-genus are partially conserved in the Viannia species. The conservation of these non-coding elements in equivalent positions in both species is indicative of their relevance within this locus. The absence of amplicons in L. braziliensis suggests that this species may not favour extra-chromosomal gene amplification as a source of phenotypic heterogeneity and fitness maintenance in changing environments.
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Affiliation(s)
- Fabricio C Dias
- Departamento de Biologia Celular e Molecular e Bioagentes Patogênicos, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, 14049-900, Ribeirão Preto, Sao Paulo, Brazil
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40
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Yu Z, Genest PA, ter Riet B, Sweeney K, DiPaolo C, Kieft R, Christodoulou E, Perrakis A, Simmons JM, Hausinger RP, van Luenen HG, Rigden DJ, Sabatini R, Borst P. The protein that binds to DNA base J in trypanosomatids has features of a thymidine hydroxylase. Nucleic Acids Res 2007; 35:2107-15. [PMID: 17389644 PMCID: PMC1874643 DOI: 10.1093/nar/gkm049] [Citation(s) in RCA: 67] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Trypanosomatids contain an unusual DNA base J (beta-d-glucosylhydroxymethyluracil), which replaces a fraction of thymine in telomeric and other DNA repeats. To determine the function of base J, we have searched for enzymes that catalyze J biosynthesis. We present evidence that a protein that binds to J in DNA, the J-binding protein 1 (JBP1), may also catalyze the first step in J biosynthesis, the conversion of thymine in DNA into hydroxymethyluracil. We show that JBP1 belongs to the family of Fe(2+) and 2-oxoglutarate-dependent dioxygenases and that replacement of conserved residues putatively involved in Fe(2+) and 2-oxoglutarate-binding inactivates the ability of JBP1 to contribute to J synthesis without affecting its ability to bind to J-DNA. We propose that JBP1 is a thymidine hydroxylase responsible for the local amplification of J inserted by JBP2, another putative thymidine hydroxylase.
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Affiliation(s)
- Zhong Yu
- Division of Molecular Biology and Centre of Biomedical Genetics, The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands, Global Infectious Diseases Program Marine Biological Laboratory, Woods Hole, MA 02543, USA, Division of Molecular Carcinogenesis, The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands, Department of Biochemistry & Molecular Biology and Department of Microbiology & Molecular Genetics, Michigan State University, East Lansing, MI 48824-4320, USA and School of Biological Sciences, University of Liverpool, Liverpool L69 7ZB, UK
| | - Paul-André Genest
- Division of Molecular Biology and Centre of Biomedical Genetics, The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands, Global Infectious Diseases Program Marine Biological Laboratory, Woods Hole, MA 02543, USA, Division of Molecular Carcinogenesis, The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands, Department of Biochemistry & Molecular Biology and Department of Microbiology & Molecular Genetics, Michigan State University, East Lansing, MI 48824-4320, USA and School of Biological Sciences, University of Liverpool, Liverpool L69 7ZB, UK
| | - Bas ter Riet
- Division of Molecular Biology and Centre of Biomedical Genetics, The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands, Global Infectious Diseases Program Marine Biological Laboratory, Woods Hole, MA 02543, USA, Division of Molecular Carcinogenesis, The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands, Department of Biochemistry & Molecular Biology and Department of Microbiology & Molecular Genetics, Michigan State University, East Lansing, MI 48824-4320, USA and School of Biological Sciences, University of Liverpool, Liverpool L69 7ZB, UK
| | - Kate Sweeney
- Division of Molecular Biology and Centre of Biomedical Genetics, The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands, Global Infectious Diseases Program Marine Biological Laboratory, Woods Hole, MA 02543, USA, Division of Molecular Carcinogenesis, The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands, Department of Biochemistry & Molecular Biology and Department of Microbiology & Molecular Genetics, Michigan State University, East Lansing, MI 48824-4320, USA and School of Biological Sciences, University of Liverpool, Liverpool L69 7ZB, UK
| | - Courtney DiPaolo
- Division of Molecular Biology and Centre of Biomedical Genetics, The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands, Global Infectious Diseases Program Marine Biological Laboratory, Woods Hole, MA 02543, USA, Division of Molecular Carcinogenesis, The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands, Department of Biochemistry & Molecular Biology and Department of Microbiology & Molecular Genetics, Michigan State University, East Lansing, MI 48824-4320, USA and School of Biological Sciences, University of Liverpool, Liverpool L69 7ZB, UK
| | - Rudo Kieft
- Division of Molecular Biology and Centre of Biomedical Genetics, The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands, Global Infectious Diseases Program Marine Biological Laboratory, Woods Hole, MA 02543, USA, Division of Molecular Carcinogenesis, The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands, Department of Biochemistry & Molecular Biology and Department of Microbiology & Molecular Genetics, Michigan State University, East Lansing, MI 48824-4320, USA and School of Biological Sciences, University of Liverpool, Liverpool L69 7ZB, UK
| | - Evangelos Christodoulou
- Division of Molecular Biology and Centre of Biomedical Genetics, The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands, Global Infectious Diseases Program Marine Biological Laboratory, Woods Hole, MA 02543, USA, Division of Molecular Carcinogenesis, The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands, Department of Biochemistry & Molecular Biology and Department of Microbiology & Molecular Genetics, Michigan State University, East Lansing, MI 48824-4320, USA and School of Biological Sciences, University of Liverpool, Liverpool L69 7ZB, UK
| | - Anastassis Perrakis
- Division of Molecular Biology and Centre of Biomedical Genetics, The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands, Global Infectious Diseases Program Marine Biological Laboratory, Woods Hole, MA 02543, USA, Division of Molecular Carcinogenesis, The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands, Department of Biochemistry & Molecular Biology and Department of Microbiology & Molecular Genetics, Michigan State University, East Lansing, MI 48824-4320, USA and School of Biological Sciences, University of Liverpool, Liverpool L69 7ZB, UK
| | - Jana M. Simmons
- Division of Molecular Biology and Centre of Biomedical Genetics, The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands, Global Infectious Diseases Program Marine Biological Laboratory, Woods Hole, MA 02543, USA, Division of Molecular Carcinogenesis, The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands, Department of Biochemistry & Molecular Biology and Department of Microbiology & Molecular Genetics, Michigan State University, East Lansing, MI 48824-4320, USA and School of Biological Sciences, University of Liverpool, Liverpool L69 7ZB, UK
| | - Robert P. Hausinger
- Division of Molecular Biology and Centre of Biomedical Genetics, The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands, Global Infectious Diseases Program Marine Biological Laboratory, Woods Hole, MA 02543, USA, Division of Molecular Carcinogenesis, The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands, Department of Biochemistry & Molecular Biology and Department of Microbiology & Molecular Genetics, Michigan State University, East Lansing, MI 48824-4320, USA and School of Biological Sciences, University of Liverpool, Liverpool L69 7ZB, UK
| | - Henri G.A.M. van Luenen
- Division of Molecular Biology and Centre of Biomedical Genetics, The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands, Global Infectious Diseases Program Marine Biological Laboratory, Woods Hole, MA 02543, USA, Division of Molecular Carcinogenesis, The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands, Department of Biochemistry & Molecular Biology and Department of Microbiology & Molecular Genetics, Michigan State University, East Lansing, MI 48824-4320, USA and School of Biological Sciences, University of Liverpool, Liverpool L69 7ZB, UK
| | - Daniel J. Rigden
- Division of Molecular Biology and Centre of Biomedical Genetics, The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands, Global Infectious Diseases Program Marine Biological Laboratory, Woods Hole, MA 02543, USA, Division of Molecular Carcinogenesis, The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands, Department of Biochemistry & Molecular Biology and Department of Microbiology & Molecular Genetics, Michigan State University, East Lansing, MI 48824-4320, USA and School of Biological Sciences, University of Liverpool, Liverpool L69 7ZB, UK
| | - Robert Sabatini
- Division of Molecular Biology and Centre of Biomedical Genetics, The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands, Global Infectious Diseases Program Marine Biological Laboratory, Woods Hole, MA 02543, USA, Division of Molecular Carcinogenesis, The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands, Department of Biochemistry & Molecular Biology and Department of Microbiology & Molecular Genetics, Michigan State University, East Lansing, MI 48824-4320, USA and School of Biological Sciences, University of Liverpool, Liverpool L69 7ZB, UK
| | - Piet Borst
- Division of Molecular Biology and Centre of Biomedical Genetics, The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands, Global Infectious Diseases Program Marine Biological Laboratory, Woods Hole, MA 02543, USA, Division of Molecular Carcinogenesis, The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands, Department of Biochemistry & Molecular Biology and Department of Microbiology & Molecular Genetics, Michigan State University, East Lansing, MI 48824-4320, USA and School of Biological Sciences, University of Liverpool, Liverpool L69 7ZB, UK
- *To whom correspondence should be addressed. +31 20 512 2880+31 20 669 1383
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Genest PA, ter Riet B, Cijsouw T, van Luenen HG, Borst P. Telomeric localization of the modified DNA base J in the genome of the protozoan parasite Leishmania. Nucleic Acids Res 2007; 35:2116-24. [PMID: 17329373 PMCID: PMC1874636 DOI: 10.1093/nar/gkm050] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
Base J or β-d-glucosylhydroxymethyluracil is a DNA modification replacing a fraction of thymine in the nuclear DNA of kinetoplastid parasites and of Euglena. J is located in the telomeric sequences of Trypanosoma brucei and in other simple repeat DNA sequences. In addition, J was found in the inactive variant surface glycoprotein (VSG) expression sites, but not in the active expression site of T. brucei, suggesting that J could play a role in transcription silencing in T. brucei. We have now looked at the distribution of J in the genomes of other kinetoplastid parasites. First, we analyzed the DNA sequences immunoprecipitated with a J-antiserum in Leishmania major Friedlin. Second, we investigated the co-migration of J- and telomeric repeat-containing DNA sequences of various kinetoplastids using J-immunoblots and Southern blots of fragmented DNA. We find only ∼1% of J outside the telomeric repeat sequences of Leishmania sp. and Crithidia fasciculata, in contrast to the substantial fraction of non-telomeric J found in T. brucei, Trypanosoma equiperdum and Trypanoplasma borreli. Our results suggest that J is a telomeric base modification, recruited for other (unknown) functions in some kinetoplastids and Euglena.
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Affiliation(s)
| | | | | | | | - Piet Borst
- *To whom Correspondence should be addressed. +31 20 512 2880+31 20 669 1383
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42
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Squina FM, Pedrosa AL, Nunes VS, Cruz AK, Tosi LRO. Shuttle mutagenesis and targeted disruption of a telomere-located essential gene of Leishmania. Parasitology 2006; 134:511-22. [PMID: 17169165 DOI: 10.1017/s0031182006001892] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2006] [Revised: 10/06/2006] [Accepted: 10/10/2006] [Indexed: 11/06/2022]
Abstract
Leishmania mutants have contributed greatly to extend our knowledge of this parasite's biology. Here we report the use of the mariner in vitro transposition system as a source of reagents for shuttle mutagenesis and targeted disruption of Leishmania genes. The locus-specific integration was achieved by the disruption of the subtelomeric gene encoding a DNA-directed RNA polymerase III subunit (RPC2). Further inactivation of RPC2 alleles required the complementation of the intact gene, which was transfected in an episomal context. However, attempts to generate a RPC2 chromosomal null mutant resulted in genomic rearrangements that maintained copies of the intact locus in the genome. The maintenance of the RPC2 chromosomal locus in complemented mutants was not mediated by an increase in the number of copies and did not involve chromosomal translocations, which are the typical characteristics of the genomic plasticity of this parasite. Unlike the endogenous locus, the selectable marker used to disrupt RPC2 did not display a tendency to remain in its chromosomal location but was targeted into supernumerary episomal molecules.
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Affiliation(s)
- F M Squina
- Departamento de Biologia Celular e Molecular e Bioagentes Patogênicos, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Brasil
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Ginger ML. Trypanosomatid Biology and Euglenozoan Evolution: New Insights and Shifting Paradigms Revealed through Genome Sequencing. Protist 2005; 156:377-92. [PMID: 16310743 DOI: 10.1016/j.protis.2005.10.001] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Michael L Ginger
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK.
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44
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Toaldo CB, Kieft R, Dirks-Mulder A, Sabatini R, van Luenen HGAM, Borst P. A minor fraction of base J in kinetoplastid nuclear DNA is bound by the J-binding protein 1. Mol Biochem Parasitol 2005; 143:111-5. [PMID: 15935489 DOI: 10.1016/j.molbiopara.2005.05.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2005] [Revised: 05/02/2005] [Accepted: 05/02/2005] [Indexed: 11/29/2022]
Affiliation(s)
- Cristiane Bentin Toaldo
- The Netherlands Cancer Institute, Division of Molecular Biology and Centre of Biomedical Genetics, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
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