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Dorantes-Palma D, Pérez-Mora S, Azuara-Liceaga E, Pérez-Rueda E, Pérez-Ishiwara DG, Coca-González M, Medel-Flores MO, Gómez-García C. Screening and Structural Characterization of Heat Shock Response Elements (HSEs) in Entamoeba histolytica Promoters. Int J Mol Sci 2024; 25:1319. [PMID: 38279319 PMCID: PMC10815948 DOI: 10.3390/ijms25021319] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Revised: 01/09/2024] [Accepted: 01/11/2024] [Indexed: 01/28/2024] Open
Abstract
Entamoeba histolytica (E. histolytica) exhibits a remarkable capacity to respond to thermal shock stress through a sophisticated genetic regulation mechanism. This process is carried out via Heat Shock Response Elements (HSEs), which are recognized by Heat Shock Transcription Factors (EhHSTFs), enabling fine and precise control of gene expression. Our study focused on screening for HSEs in the promoters of the E. histolytica genome, specifically analyzing six HSEs, including Ehpgp5, EhrabB1, EhrabB4, EhrabB5, Ehmlbp, and Ehhsp100. We discovered 2578 HSEs, with 1412 in promoters of hypothetical genes and 1166 in coding genes. We observed that a single promoter could contain anywhere from one to five HSEs. Gene ontology analysis revealed the presence of HSEs in essential genes for the amoeba, including cysteine proteinases, ribosomal genes, Myb family DNA-binding proteins, and Rab GTPases, among others. Complementarily, our molecular docking analyses indicate that these HSEs are potentially recognized by EhHSTF5, EhHSTF6, and EhHSTF7 factors in their trimeric conformation. These findings suggest that E. histolytica has the capability to regulate a wide range of critical genes via HSE-EhHSTFs, not only for thermal stress response but also for vital functions of the parasite. This is the first comprehensive study of HSEs in the genome of E. histolytica, significantly contributing to the understanding of its genetic regulation and highlighting the complexity and precision of this mechanism in the parasite's survival.
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Affiliation(s)
- David Dorantes-Palma
- Laboratorio de Biomedicina Molecular 1, ENMyH, Instituto Politécnico Nacional, Mexico City 07320, Mexico; (D.D.-P.); (S.P.-M.); (D.G.P.-I.); (M.C.-G.); (M.O.M.-F.)
| | - Salvador Pérez-Mora
- Laboratorio de Biomedicina Molecular 1, ENMyH, Instituto Politécnico Nacional, Mexico City 07320, Mexico; (D.D.-P.); (S.P.-M.); (D.G.P.-I.); (M.C.-G.); (M.O.M.-F.)
| | - Elisa Azuara-Liceaga
- Posgrado en Ciencias Genómicas, Universidad Autónoma de la Ciudad de México, Mexico City 03100, Mexico;
| | - Ernesto Pérez-Rueda
- Unidad Académica del Estado de Yucatán, Instituto de Investigaciones en Matemáticas Aplicadas y en Sistemas, Universidad Nacional Autónoma de México, Mexico City 97302, Mexico;
| | - David Guillermo Pérez-Ishiwara
- Laboratorio de Biomedicina Molecular 1, ENMyH, Instituto Politécnico Nacional, Mexico City 07320, Mexico; (D.D.-P.); (S.P.-M.); (D.G.P.-I.); (M.C.-G.); (M.O.M.-F.)
| | - Misael Coca-González
- Laboratorio de Biomedicina Molecular 1, ENMyH, Instituto Politécnico Nacional, Mexico City 07320, Mexico; (D.D.-P.); (S.P.-M.); (D.G.P.-I.); (M.C.-G.); (M.O.M.-F.)
| | - María Olivia Medel-Flores
- Laboratorio de Biomedicina Molecular 1, ENMyH, Instituto Politécnico Nacional, Mexico City 07320, Mexico; (D.D.-P.); (S.P.-M.); (D.G.P.-I.); (M.C.-G.); (M.O.M.-F.)
| | - Consuelo Gómez-García
- Laboratorio de Biomedicina Molecular 1, ENMyH, Instituto Politécnico Nacional, Mexico City 07320, Mexico; (D.D.-P.); (S.P.-M.); (D.G.P.-I.); (M.C.-G.); (M.O.M.-F.)
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2
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Lozano-Amado D, Ávila-López PA, Hernández-Montes G, Briseño-Díaz P, Vargas M, Lopez-Rubio JJ, Carrero JC, Hernández-Rivas R. A class I histone deacetylase is implicated in the encystation of Entamoeba invadens. Int J Parasitol 2020; 50:1011-1022. [PMID: 32822677 DOI: 10.1016/j.ijpara.2020.05.014] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Revised: 05/26/2020] [Accepted: 05/28/2020] [Indexed: 12/29/2022]
Abstract
Epigenetic mechanisms such as histone acetylation and deacetylation participate in regulation of the genes involved in encystation of Entamoeba invadens. However, the histones and target residues involved, and whether the acetylation and deacetylation of the histones leads to the regulation of gene expression associated with the encystation of this parasite, remain unknown. In this study, we found that E. invadens histone H4 is acetylated in both stages of the parasite and is more highly acetylated during the trophozoite stage than in the cyst. Histone hyperacetylation induced by Trichostatin A negatively affects the encystation of E. invadens, and this inhibition is associated with the downregulation of the expression of genes implicated in the synthesis of chitin, polyamines, gamma-aminobutyric acid pathways and cyst wall proteins, all of which are important in the formation of cysts. Finally, in silico analysis and activity assays suggest that a class I histone deacetylase (EiHDAC3) could be involved in control of the expression of a subset of genes that are important in several pathways during encystation. Therefore, the identification of enzymes that acetylate and/or deacetylate histones that control encystation in E. invadens could be a promising therapeutic target for preventing transmission of other amoebic parasites such as E. histolytica, the causative agent of amoebiasis in humans.
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Affiliation(s)
- Daniela Lozano-Amado
- Departamento de Biomedicina Molecular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Ciudad de México, Mexico
| | - Pedro Antonio Ávila-López
- Departamento de Biomedicina Molecular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Ciudad de México, Mexico
| | - Georgina Hernández-Montes
- Coordinación de la Investigación Científica, Red de Apoyo a la Investigación, Universidad Nacional Autónoma de México, Ciudad Universitaria, Ciudad de México, Mexico
| | - Paola Briseño-Díaz
- Departamento de Biomedicina Molecular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Ciudad de México, Mexico
| | - Miguel Vargas
- Departamento de Biomedicina Molecular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Ciudad de México, Mexico
| | - Jose-Juan Lopez-Rubio
- LPHI - Laboratory of Pathogen Host Interactions - UMR5235, CNRS, INSERM, Université de Montpellier, Montpellier, France
| | - Julio César Carrero
- Departamento de Inmunología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad Universitaria, Ciudad de México, Mexico
| | - Rosaura Hernández-Rivas
- Departamento de Biomedicina Molecular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Ciudad de México, Mexico.
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Hernández‐Cuevas NA, Jhingan GD, Petropolis D, Vargas M, Guillen N. Acetylation is the most abundant actin modification in
Entamoeba histolytica
and modifications of actin's amino‐terminal domain change cytoskeleton activities. Cell Microbiol 2018; 21:e12983. [DOI: 10.1111/cmi.12983] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Revised: 09/27/2018] [Accepted: 10/30/2018] [Indexed: 12/16/2022]
Affiliation(s)
| | | | - Debora Petropolis
- Institut Pasteur Unité Biologie Cellulaire du Parasitisme Paris France
- INSERM Unit 786 Paris France
| | - Miguel Vargas
- Departamento de Biomedicina Molecular Instituto Politécnico Nacional, Centro de Investigación y de Estudios Avanzados CINVESTAV Mexico City Mexico
| | - Nancy Guillen
- Institut Pasteur Unité Biologie Cellulaire du Parasitisme Paris France
- INSERM Unit 786 Paris France
- Centre National de la Recherche Scientifique, ERL9195 Paris France
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Foda BM, Singh U. Dimethylated H3K27 Is a Repressive Epigenetic Histone Mark in the Protist Entamoeba histolytica and Is Significantly Enriched in Genes Silenced via the RNAi Pathway. J Biol Chem 2015; 290:21114-21130. [PMID: 26149683 DOI: 10.1074/jbc.m115.647263] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2015] [Indexed: 01/02/2023] Open
Abstract
RNA interference (RNAi) is a fundamental biological process that plays a crucial role in regulation of gene expression in many organisms. Transcriptional gene silencing (TGS) is one of the important nuclear roles of RNAi. Our previous data show that Entamoeba histolytica has a robust RNAi pathway that links to TGS via Argonaute 2-2 (Ago2-2) associated 27-nucleotide small RNAs with 5'-polyphosphate termini. Here, we report the first repressive histone mark to be identified in E. histolytica, dimethylation of H3K27 (H3K27Me2), and demonstrate that it is enriched at genes that are silenced by RNAi-mediated TGS. An RNAi-silencing trigger can induce H3K27Me2 deposits at both episomal and chromosomal loci, mediating gene silencing. Our data support two phases of RNAi-mediated TGS: an active silencing phase where the RNAi trigger is present and both H3K27Me2 and Ago2-2 concurrently enrich at chromosomal loci; and an established silencing phase in which the RNAi trigger is removed, but gene silencing with H3K27Me2 enrichment persist independently of Ago2-2 deposition. Importantly, some genes display resistance to chromosomal silencing despite induction of functional small RNAs. In those situations, the RNAi-triggering plasmid that is maintained episomally gets partially silenced and has H3K27Me2 enrichment, but the chromosomal copy displays no repressive histone enrichment. Our data are consistent with a model in which H3K27Me2 is a repressive histone modification, which is strongly associated with transcriptional repression. This is the first example of an epigenetic histone modification that functions to mediate RNAi-mediated TGS in the deep-branching eukaryote E. histolytica.
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Affiliation(s)
- Bardees M Foda
- Departments of Internal Medicine, Division of Infectious Diseases, School of Medicine, Stanford University, Stanford, California 94305; Department of Molecular Genetics and Enzymology, National Research Centre, Dokki, Egypt
| | - Upinder Singh
- Departments of Internal Medicine, Division of Infectious Diseases, School of Medicine, Stanford University, Stanford, California 94305; Departments of Microbiology and Immunology, School of Medicine, Stanford University, Stanford, California 94305.
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Borbolla-Vázquez J, Orozco E, Betanzos A, Rodríguez MA. Entamoeba histolytica: protein arginine transferase 1a methylates arginine residues and potentially modify the H4 histone. Parasit Vectors 2015; 8:219. [PMID: 25889855 PMCID: PMC4393863 DOI: 10.1186/s13071-015-0820-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2014] [Accepted: 03/21/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND In eukaryotes, histone arginine methylation associates with both active and repressed chromatin states depending on the residues involved and the status of methylation. Even when the amino-terminus of Entamoeba histolytica histones diverge from metazoan sequences, these regions contain arginine residues that are potential targets for methylation. However, histone arginine methylation as well as the activity of arginine methyltransferases (PRMTs) has not been studied in this parasite. The aim of this work was to examine the dimethylation of arginine 3 of H4 histone (H4R3me2) and to identify the parasite PRMT that could be responsible for this modification (EhPRMT1). METHODS To examine the presence of H4R3me2 in E histolytica, we performed Western blot and immunofluorescence assays on trophozoites using an antibody against this epigenetic mark. To recognize the PRMT1 enzyme of this parasite that possibly perform that modification, we first performed a phylogenetic analysis of E. histolytica and human PRMTs. RT-PCR assays were carried out to analyze the expression of the putative PRMT1 genes. One of these genes was cloned and expressed in Escherichia coli. The recombinant protein was tested by its recognition by an antibody against human PRMT1 and in its ability to form homodimers and to methylate commercial histones. RESULTS The arginine 3 of human H4, which is subjected to post translational methylation, was aligned with the arginine 8 of E. histolytica H4, suggesting that this residue could be methylated. The recognition of an 18 kDa nuclear protein of E. histolytica by an antibody against H4R3me2 confirmed this assumption. We found that this parasite expresses three phylogenetic and structural proteins related to PRMT1. Antibodies against the human PRMT1 detected E. histolytica proteins in cytoplasm and nuclei and recognized a recombinant PRMT1 of this parasite. The recombinant protein was able to form homodimers and homotetramers and displayed methyltransferase activity on arginine 3 of chicken H4. CONCLUSION All these results suggest that E. histolytica contains as a minimum one structural and functional protein ortholog to PRMT1, enzyme that potentially dimethylates H4R8. This modification may play an important role in the gene expression regulation of this microorganism.
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Affiliation(s)
- Jessica Borbolla-Vázquez
- Departamento de Infectómica y Patogénesis Molecular, Centro de Investigación y de Estudios Avanzados del IPN, A.P. 14-740, México, D.F., 07000, Mexico.
| | - Esther Orozco
- Departamento de Infectómica y Patogénesis Molecular, Centro de Investigación y de Estudios Avanzados del IPN, A.P. 14-740, México, D.F., 07000, Mexico.
| | - Abigail Betanzos
- Departamento de Infectómica y Patogénesis Molecular, Centro de Investigación y de Estudios Avanzados del IPN, A.P. 14-740, México, D.F., 07000, Mexico.
| | - Mario A Rodríguez
- Departamento de Infectómica y Patogénesis Molecular, Centro de Investigación y de Estudios Avanzados del IPN, A.P. 14-740, México, D.F., 07000, Mexico.
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6
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Pearson RJ, Singh U. Approaches to characterizing Entamoeba histolytica transcriptional regulation. Cell Microbiol 2010; 12:1681-90. [DOI: 10.1111/j.1462-5822.2010.01524.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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7
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Regulation of gene expression in protozoa parasites. J Biomed Biotechnol 2010; 2010:726045. [PMID: 20204171 PMCID: PMC2830571 DOI: 10.1155/2010/726045] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2009] [Revised: 11/10/2009] [Accepted: 01/08/2010] [Indexed: 12/25/2022] Open
Abstract
Infections with protozoa parasites are associated with high burdens of morbidity and mortality across the developing world. Despite extensive efforts to control the transmission of these parasites, the spread of populations resistant to drugs and the lack of effective vaccines against them contribute to their persistence as major public health problems. Parasites should perform a strict control on the expression of genes involved in their pathogenicity, differentiation, immune evasion, or drug resistance, and the comprehension of the mechanisms implicated in that control could help to develop novel therapeutic strategies. However, until now these mechanisms are poorly understood in protozoa. Recent investigations into gene expression in protozoa parasites suggest that they possess many of the canonical machineries employed by higher eukaryotes for the control of gene expression at transcriptional, posttranscriptional, and epigenetic levels, but they also contain exclusive mechanisms. Here, we review the current understanding about the regulation of gene expression in Plasmodium sp., Trypanosomatids, Entamoeba histolytica and Trichomonas vaginalis.
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8
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Epigenetic transcriptional gene silencing in Entamoeba histolytica: insight into histone and chromatin modifications. Parasitology 2009; 137:619-27. [PMID: 19849886 DOI: 10.1017/s0031182009991363] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
We have previously discovered a unique mechanism of epigenetic transcriptional gene silencing in the Entamoeba histolytica trophozoites of strain HM-1:IMSS that resulted in the persistent downregulation of the amoebapore A (ap-a) gene, and that could be successfully applied to silence other virulence genes (cpA5, lgl1). In order to understand how the silencing is maintained throughout generations, we analysed whether modifications occurred at the chromatin level. Chromatin immunoprecipitation assays were done with antibodies specific to the methylated lysine 4 of E. histolytica histone H3. When the genes were in a transcriptionally silent state, the methylation levels of H3K4 in their coding region were significantly reduced. In contrast, the levels of core histone H3 were consistently higher in the silenced genes. Controlled chromatin digestion with micrococcal nuclease was used to assess changes in nucleosome compaction. We found a significant resistance to digestion in the promoter region of the silenced ap-a and cpA5 genes as compared to the parental strain that expresses those genes. Our data lend further support to the idea that histone modifications and heterochromatin formations are at the basis of the transcriptional silencing of genes in E. histolytica.
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Mirelman D, Anbar M, Bracha R. Epigenetic transcriptional gene silencing in Entamoeba histolytica. IUBMB Life 2008; 60:598-604. [PMID: 18493998 DOI: 10.1002/iub.96] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The human intestinal pathogen Entamoeba histolytica has a number of virulence factors which can cause damage to the host. Transcriptional silencing of the gene coding for one of its major toxic molecules, the amoebapore (Ehap-a), occurred following the transfection of amoebic trophozoites with a plasmid containing the 5' promoter region of Ehap-a as well as a truncated segment of a neighboring, upstream SINE1 element that is transcribed from the opposite strand. Silencing was dependent on the presence of the truncated SINE1 sequences. Small amounts of short (approximately 140 n), ssRNA molecules with homology to SINE1 were detected in the silenced amoeba but no siRNA. The silenced Ehap-a gene domain had a chromatin modification indicating transcriptional inactivation without any DNA methylation. Removal of the plasmid did not restore transcription of Ehap-a. Transcription analysis by microarrays revealed that a number of additional genes were silenced and some were also up-regulated. Transfections of amoeba which already had a silenced Ehap-a, with a plasmid containing a second gene ligated to the 5' upstream region of Ehap-a, enabled the silencing, in-trans, of other genes of choice. The nonvirulent phenotype of the gene-silenced amoeba was demonstrated in various assays and the results suggest that they may have a potential use for vaccination.
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Affiliation(s)
- David Mirelman
- Department of Biological Chemistry, Weizmann Institute of Science, Rehovot 76100, Israel.
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Bracha R, Nuchamowitz Y, Anbar M, Mirelman D. Transcriptional silencing of multiple genes in trophozoites of Entamoeba histolytica. PLoS Pathog 2006; 2:e48. [PMID: 16733544 PMCID: PMC1464398 DOI: 10.1371/journal.ppat.0020048] [Citation(s) in RCA: 96] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2005] [Accepted: 04/10/2006] [Indexed: 01/19/2023] Open
Abstract
In a previous work we described the transcriptional silencing of the amoebapore A (AP-A) gene (Ehap-a) of Entamoeba histolytica strain HM-1:IMSS. The silencing occurred following transfection with a plasmid containing a 5′ upstream region (473 bp) of Ehap-a that included a truncated segment (140 bp) of a short interspersed nuclear element (SINE1). Silencing remained in effect even after removal of the plasmid (clone G3). Neither short interfering RNA nor methylated DNA were detected, but the chromatin domain of Ehap-a in the gene-silenced trophozoites was modified. Two other similar genes (Ehap-b and one encoding a Saposin-like protein, SAPLIP 1) also became silenced. In the present work we demonstrate the silencing of a second gene of choice, one that encodes the light subunit of the Gal/GalNAc inhibitable lectin (Ehlgl1) and the other, the cysteine proteinase 5 (EhCP-5). This silencing occurred in G3 trophozoites transfected with a plasmid in which the 473 bp 5′ upstream Ehap-a fragment was directly ligated to the second gene. Transcriptional silencing occurred in both the transgene and the chromosomal gene. SINE1 sequences were essential, as was a direct connection between the Ehap-a upstream region and the beginning of the open reading frame of the second gene. Gene silencing did not occur in strain HM-1:IMSS with any of these plasmid constructs. The trophozoites with two silenced genes were virulence-attenuated as were those of clone G3. In addition, trophozoites not expressing Lgl1 and AP-A proteins had a significantly reduced ability to cap the Gal/GalNAc-lectin to the uroid region when incubated with antibodies against the heavy (170 kDa) subunit of the lectin. Lysates of trophozoites lacking cysteine proteinase 5 and AP-A proteins had 30% less cysteine proteinase activity than those of HM-1:IMSS strain or the G3 clone. Silencing of other genes in G3 amoebae could provide a model to study their various functions. In addition, double gene-silenced, virulence-attenuated trophozoites may be an important tool in vaccine development. The human intestinal parasite Entamoeba histolytica has numerous genes that code for virulence. Silencing the expression of individual genes is useful to determine their roles. In previous work the authors demonstrated the silencing of the gene coding for amoebapore, which is responsible for killing of human cells. They transfected amoebic trophozoites with a plasmid that contained DNA sequences homologous to the promoter region of the amoebapore gene, as well as a portion of a repetitive DNA element (called a short interspersed nuclear element). This construct induced a modification of the chromatin and prevented the expression of the gene. Removal of the plasmid resulted in stable, amoebapore-deficient parasites possessing low virulence. In the present work, Bracha and colleagues show silencing of additional genes following transfection of E. histolytica trophozoites already silenced in amoebapore with a plasmid containing the second gene directly ligated to the upstream region of the amoebapore gene. The DNA sequences that are essential for transferring the silencing from the plasmid to the chromosomal gene copy were identified. Additional virulence genes that the authors irreversibly silenced are those encoding a subunit of a surface lectin that mediates the adherence of the parasite to host cells, and a cysteine proteinase that plays a role in inflammation and invasion of the intestine.
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Affiliation(s)
- Rivka Bracha
- Department of Biological Chemistry, Weizmann Institute of Science, Rehovot, Israel
| | - Yael Nuchamowitz
- Department of Biological Chemistry, Weizmann Institute of Science, Rehovot, Israel
| | - Michael Anbar
- Department of Biological Chemistry, Weizmann Institute of Science, Rehovot, Israel
| | - David Mirelman
- Department of Biological Chemistry, Weizmann Institute of Science, Rehovot, Israel
- * To whom correspondence should be addressed. E-mail:
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11
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Mirelman D, Anbar M, Nuchamowitz Y, Bracha R. Epigenetic silencing of gene expression in Entamoeba histolytica. Arch Med Res 2006; 37:226-33. [PMID: 16380323 DOI: 10.1016/j.arcmed.2005.09.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2005] [Accepted: 09/30/2005] [Indexed: 01/21/2023]
Abstract
Transcriptional silencing of an amebapore (ap-a) gene occurred in Entamoeba histolytica following the transfection of plasmids containing a DNA segment (473 bp) homologous to the 5' upstream region of the gene. This segment contains the promoter region of the ap-a gene, a T-rich stretch, followed by a truncated SINE1 (short interspersed element) that is transcribed from the opposite strand. The downstream silencing of the ap-a gene did not occur with plasmids containing the entire SINE1 sequence or lacking the entire SINE1 sequences including the T-rich stretch. Such plasmids promoted the overexpression of the ap-a gene. The transcription of the SINE element required both the T-rich stretch as well as sequences from the 5' end of SINE. RNA extracts from gene-silenced cultures showed small amounts of short (approximately 140 nt), single-stranded molecules with homology to SINE1 transcripts but no siRNA. Chromatin immunoprecipitation (ChIP) analysis of silenced G3 trophozoites with an antibody against methylated K4 of histone H3 revealed a demethylation of K4 at the domain of the ap-a gene indicating transcriptional inactivation. These results suggest the involvement of the SINE1 element in triggering the gene silencing and the role of histone modification in its epigenetic maintenance. The avirulent phenotype of the silenced trophozoites was demonstrated in various assays and the results suggest they may have a potential use for vaccination.
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Affiliation(s)
- David Mirelman
- Department of Biological Chemistry, Weizmann Institute of Science, Rehovot, Israel.
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12
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Anbar M, Bracha R, Nuchamowitz Y, Li Y, Florentin A, Mirelman D. Involvement of a short interspersed element in epigenetic transcriptional silencing of the amoebapore gene in Entamoeba histolytica. EUKARYOTIC CELL 2006; 4:1775-84. [PMID: 16278444 PMCID: PMC1287852 DOI: 10.1128/ec.4.11.1775-1784.2005] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Transcriptional silencing of an amoebapore (ap-a) gene occurred in Entamoeba histolytica following the transfection of plasmids containing a DNA segment (473 bp) homologous to the 5' upstream region of the gene (R. Bracha, Y. Nuchamowitz, and D. Mirelman, Eukaryot. Cell 2:295-305, 2003). This segment contains the promoter region of the ap-a gene, a T-rich stretch, followed by a truncated SINE1 (short interspersed element 1) that is transcribed from the antisense strand. Transfection of plasmids containing truncated SINE1 sequences which lack their 3' regulatory elements upstream of the ap-a gene was essential for the downstream silencing of the ap-a gene while transfection with plasmids containing the entire SINE1 sequence or without the T-rich stretch promoted the overexpression of the ap-a gene. Both the T-rich stretch and sequences of the 5' SINE1 were essential for the transcription of SINE1. RNA extracts from gene-silenced cultures showed small amounts of short (approximately 140-nucleotide), single-stranded molecules with homology to SINE1 but no short interfering RNA. Chromatin immunoprecipitation analysis with an antibody against methylated K4 of histone H3 showed a demethylation of K4 at the domain of the ap-a gene, indicating transcriptional inactivation. These results suggest the involvement of SINE1 in triggering the gene silencing and the role of histone modification in its epigenetic maintenance.
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Affiliation(s)
- Michael Anbar
- Department of Biological Chemistry, Weizmann Institute of Science, P.O. Box 26, Rehovot 76100, Israel
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13
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Ramakrishnan G, Gilchrist CA, Musa H, Torok MS, Grant PA, Mann BJ, Petri WA. Histone acetyltransferases and deacetylase in Entamoeba histolytica. Mol Biochem Parasitol 2005; 138:205-16. [PMID: 15555732 DOI: 10.1016/j.molbiopara.2004.09.002] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2004] [Accepted: 09/02/2004] [Indexed: 11/20/2022]
Abstract
In our efforts to understand how transcription may be regulated in Entamoeba histolytica, we have examined if this parasite has conserved enzymatic mechanisms for targeted acetylation and deacetylation of histones. Western blotting indicated that basic nuclear proteins in the size range of 16-23 kDa were acetylated in amebic trophozoites, suggesting histone acetylation. Single representatives of the GNAT and MYST family of histone acetyltransferases (HATs) were identified in the E. histolytica genome and their expression in amebic trophozoites was detected by reverse transcription of RNA followed by the polymerase chain reaction (RT-PCR). Full-length recombinant EhMYST protein demonstrated HAT activity with calf thymus histones and showed a preference for histone H4, similar to the yeast MYST protein, Esa1. However, ehMYST did not complement a yeast esa1 mutation. Histone deacetylase (HDAC) activity was detected in nuclear extracts from E. histolytica, and characteristically, was inhibited by trichostatin A (TSA). Consistent with the observation of HDAC activity, RT-PCR analysis demonstrated that an amebic hdac1 homolog (ehHDAC) is expressed and appropriately spliced in E. histolytica trophozoites. Our results suggest that mechanisms for histone acetylation and deacetylation are operational in E. histolytica.
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Affiliation(s)
- Girija Ramakrishnan
- Department of Medicine, University of Virginia, Charlottesville, VA 22908, USA
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14
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Galindo M, Varela N, Espinoza I, Toro GC, Hellman U, Wernstedt C, Galanti N. Chromatin from two classes of platyhelminthes display both protist H1 and higher eukaryote core histones. FEBS Lett 2004; 567:225-9. [PMID: 15178327 DOI: 10.1016/j.febslet.2004.04.065] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2003] [Revised: 04/20/2004] [Accepted: 04/23/2004] [Indexed: 11/25/2022]
Abstract
Histones from the parasitic platyhelminthes, Echinococcus granulosus and Fasciola hepatica, were systematically characterized. Core histones H2A, H2B, H3 and H4, which were identified on the basis of amino acid sequencing and mass spectrometry data, showed conserved electrophoretic patterns. Histones H1, identified on the basis of physicochemical properties, amino acid composition and amino acid sequencing, showed divergence, both in their number and electrophoretic mobilities, between the two species and among other organisms. According to these data, core histones but not H1 histones, would be stabilized during evolution at the level of platyhelminthes.
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Affiliation(s)
- Mario Galindo
- Program of Cellular and Molecular Biology, Institute of Biomedical Sciences, Faculty of Medicine, University of Chile, Casilla 70061, Correo 7, Santiago, Chile
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15
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Triana O, Galanti N, Olea N, Hellman U, Wernstedt C, Lujan H, Medina C, Toro GC. Chromatin and histones from Giardia lamblia: a new puzzle in primitive eukaryotes. J Cell Biochem 2001; 82:573-82. [PMID: 11500935 DOI: 10.1002/jcb.1159] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The three deepest eukaryote lineages in small subunit ribosomal RNA phylogenies are the amitochondriate Microsporidia, Metamonada, and Parabasalia. They are followed by either the Euglenozoa (e.g., Euglena and Trypanosoma) or the Percolozoa as the first mitochondria-containing eukaryotes. Considering the great divergence of histone proteins in protozoa we have extended our studies of histones from Trypanosomes (Trypanosoma cruzi, Crithidia fasciculata and Leishmania mexicana) to the Metamonada Giardia lamblia, since Giardia is thought to be one of the most primitive eukaryotes. In the present work, the structure of G. lamblia chromatin and the histone content of the soluble chromatin were investigated and compared with that of higher eukaryotes, represented by calf thymus. The chromatin is present as nucleosome filaments which resemble the calf thymus array in that they show a more regular arrangement than those described for Trypanosoma. SDS-polyacrylamide gel electrophoresis and protein characterization revealed that the four core histones described in Giardia are in the same range of divergence with the histones from other lower eukaryotes. In addition, G. lamblia presented an H1 histone with electrophoretic mobility resembling the H1 of higher eukaryotes, in spite of the fact that H1 has a different molecular mass in calf thymus. Giardia also presents a basic protein which was identified as an HU-like DNA-binding protein usually present in eubacteria, indicating a chimaeric composition for the DNA-binding protein set in this species. Finally, the phylogenetic analysis of selected core histone protein sequences place Giardia divergence before Trypanosoma, despite the fact that Trypanosoma branch shows an acceleration in the evolutionary rate pointing to an unusual evolutionary behavior in this lineage.
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Affiliation(s)
- O Triana
- Programa de Biología Celular y Molecular, Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, Santiago 7, Chile
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16
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Wu G, McArthur AG, Fiser A, Sali A, Sogin ML, Mllerm M. Core histones of the amitochondriate protist, Giardia lamblia. Mol Biol Evol 2000; 17:1156-63. [PMID: 10908635 DOI: 10.1093/oxfordjournals.molbev.a026398] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Genes coding for the core histones H2a, H2b, H3, and H4 of Giardia lamblia were sequenced. A conserved organism- and gene-specific element, GRGCGCAGATTTVGG, was found upstream of the coding region in all core histone genes. The derived amino acid sequences of all four histones were similar to their homologs in other eukaryotes, although they were among the most divergent members of this protein family. Comparative protein structure modeling combined with energy evaluation of the resulting models indicated that the G. lamblia core histones individually and together can assume the same three-dimensional structures that were established by X-ray crystallography for Xenopus laevis histones and the nucleosome core particle. Since G. lamblia represents one of the earliest-diverging eukaryotes in many different molecular trees, the structure of its histones is potentially of relevance to understanding histone evolution. The G. lamblia proteins do not represent an intermediate stage between archaeal and eukaryotic histones.
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Affiliation(s)
- G Wu
- Laboratory of Biochemical Parasitology, The Rockefeller University, New York, NY 10021, USA
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17
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Abstract
Estimation of genome size of Entamoeba histolytica by different methods has failed to give comparable values due to the inherent complexities of the organism, such as the uncertain level of ploidy, presence of multinucleated cells and a poorly demarcated cell division cycle. The genome of E. histolytica has a low G+C content (22.4%), and is composed of both linear chromosomes and a number of circular plasmid-like molecules. The rRNA genes are located exclusively on some of the circular DNAs. Karyotype analysis by pulsed field gel electrophoresis suggests the presence of 14 conserved linkage groups and an extensive size variation between homologous chromosomes from different isolates. Several repeat families have been identified, some of which have been shown to be present in all the electrophoretically separated chromosomes. The typical nucleosomal structure has not been demonstrated, though most of the histone genes have been identified. Most Entamoeba genes lack introns, have short 3' and 5' untranslated regions, and are tightly packed. Promoter analysis revealed the presence of three conserved motifs and several upstream regulatory elements. Unlike typical eukaryotes, the transcription of protein coding genes is alpha-amanitin resistant. Expressed Sequence Tag analysis has identified a group of highly abundant polyadenylated RNAs which are unlikely to be translated. The Expressed Sequence Tag approach has also helped identify several important genes which encode proteins that may be involved in different biochemical pathways, signal transduction mechanisms and organellar functions.
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Affiliation(s)
- A Bhattacharya
- School of Life Sciences, Jawaharlal Nehru University, New Mehrauli Road, New Delhi, India.
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18
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Tanaka T, Tanaka M, Mitsui Y. Analysis of expressed sequence tags (ESTs) of the parasitic protozoa Entamoeba histolytica. Biochem Biophys Res Commun 1997; 236:611-5. [PMID: 9245698 DOI: 10.1006/bbrc.1997.7019] [Citation(s) in RCA: 24] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
A directional cDNA library constructed from mRNA of the trophozoite of Entamoeba histolytica HM-1:IMSS strain was used for the generation of expressed sequence tags (ESTs). From 5' ends of the distinct cDNA clones, 105 ESTs were obtained. Of these, 30 clones (29%) were previously known E. histolytica genes. Forty-five clones (42%) had matches with entries for other organisms in the databases. These new E. histolytica genes constituted a broad range of transcripts distributed among cytoplasmic structural and regulatory proteins, enzymes, nuclear and other proteins, and proteins of unknown function. Thirty clones (29%) had no significant database matches and thus potentially represent E. histolytica-specific genes. These data of E. histolytica genes identified by nucleotide sequencing indicate the value of the adoption of genome sequencing strategies for the rapid increase in knowledge of organisms causing dysentery and liver abscess.
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Affiliation(s)
- T Tanaka
- Division of Host Defense Mechanism, Tokai University School of Medicine, Isehara, Kanagawa, Japan.
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19
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Jahn CL, Ling Z, Tebeau CM, Klobutcher LA. An unusual histone H3 specific for early macronuclear development in Euplotes crassus. Proc Natl Acad Sci U S A 1997; 94:1332-7. [PMID: 9037053 PMCID: PMC19791 DOI: 10.1073/pnas.94.4.1332] [Citation(s) in RCA: 25] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/1996] [Accepted: 12/06/1996] [Indexed: 02/03/2023] Open
Abstract
Characterization of the histone H3 genes of the ciliated protozoan Euplotes crassus indicates that one gene functions only during the sexual phase of the life cycle. Maximum expression of this gene, as judged by transcript accumulation, correlates with DNA replications leading to polytenization of the micronuclear chromosomes before massive DNA elimination, which produces a transcriptionally active macronucleus. Transcripts of the other gene accumulate primarily during vegetative growth and in the sexual phase of the life cycle during replication phases not related to polytenization. Although both histone H3 genes encode proteins that are fairly divergent in sequence at the amino terminus, the meiotic/polytene-specific histone H3 contains two insertions in the amino terminus that increase the size of the protein by 15 amino acids. Analysis of micrococcal nuclease digests of chromatin using hybridization probes specific for micronuclear vs. macronuclear sequences indicates that a change in nucleosomal spacing correlates with the maximal expression of the meiotic/polytene-specific histone H3 gene. Thus, we surmise that this unusual histone H3 may play a key role in targeting DNA sequences for either transcriptional activation and retention in the macronucleus or heterochromatization and elimination.
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Affiliation(s)
- C L Jahn
- Department of Cell and Molecular Biology, Northwestern University Medical School, Chicago, IL 60611, USA.
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20
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Marinets A, Müller M, Johnson PJ, Kulda J, Scheiner O, Wiedermann G, Duchêne M. The sequence and organization of the core histone H3 and H4 genes in the early branching amitochondriate protist Trichomonas vaginalis. J Mol Evol 1996; 43:563-71. [PMID: 8995053 DOI: 10.1007/bf02202104] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Among the unicellular protists, several of which are parasitic, some of the most divergent eukaryotic species are found. The evolutionary distances between protists are so large that even slowly evolving proteins like histones are strongly divergent. In this study we isolated cDNA and genomic histone H3 and H4 clones from Trichomonas vaginalis. Two histone H3 and three histone H4 genes were detected on three genomic clones with one complete H3 and two complete H4 sequences. H3 and H4 genes were divergently transcribed with very short intergenic regions of only 194 bp, which contained T. vaginalis-specific as well as histone-specific putative promoter elements. Southern blot analysis showed that there may be several more histone gene pairs. The two complete histone H4 genes were different on the nucleotide level but encoded the same amino acid sequence. Comparison of the amino acid sequences of the T. vaginalis H3 and H4 histones with sequences from animals, fungi, and plants as well as other protists revealed a significant divergence not only from the sequences in multicellular organisms but especially from the sequences in other protists like Entamoeba histolytica, Trypanosoma cruzi, and Leishmania infantum.
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Affiliation(s)
- A Marinets
- Institute for Specific Prophylaxis and Tropical Medicine, University of Vienna, Austria
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21
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Waterborg JH, Robertson AJ. Common features of analogous replacement histone H3 genes in animals and plants. J Mol Evol 1996; 43:194-206. [PMID: 8703085 DOI: 10.1007/bf02338827] [Citation(s) in RCA: 45] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Phylogenetic analysis of histone H3 protein sequences demonstrates the independent origin of the replacement histone H3 genes in animals and in plants. Multiple introns in the replacement histone H3 genes of animals in a pattern distinct from that in plant replacement H3 genes supports this conclusion. It is suggested that replacement H3 genes arose at the same time that, independently, multicellular forms of animals and of plants evolved. Judged by the degree of invariant and functionally constrained amino acid positions, histones H3 and H4, which form together the tetramer kernel of the nucleosome, have co-evolved with equal rates of sequence divergence. Residues 31 and 87 in histone H3 are the only residues that consistently changed across each gene duplication event that created functional replacement histone H3 variant forms. Once changed, these residues have remained invariant across divergent speciation. This suggests that they are required to allow replacement histone H3 to participate in the assembly of nucleosomes in non-S-phase cells. The abundant occurrence of polypyrimidine sequences in the introns of all replacement H3 genes, and the replacement of an intron by a polypyrimidine motif upstream of the alfalfa replacement H3 gene, suggests a function. It is speculated that they may contribute to the characteristic cell-cycle-independent pattern of replacement histone H3 genes by binding nucleosome-excluding proteins.
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Affiliation(s)
- J H Waterborg
- Division of Cell Biology and Biophysics, School of Biological Sciences, University of Missouri-Kansas City, 5100 Rockhill Road, Kansas City, MO 64110-2499, USA
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22
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Binder M, Ortner S, Plaimauer B, Födinger M, Wiedermann G, Scheiner O, Duchêne M. Sequence and organization of an unusual histone H4 gene in the human parasite Entamoeba histolytica. Mol Biochem Parasitol 1995; 71:243-7. [PMID: 7477106 DOI: 10.1016/0166-6851(94)00044-n] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Affiliation(s)
- M Binder
- Institute for Specific Prophylaxis and Tropical Medicine, Vienna, Austria
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23
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Affiliation(s)
- H J Longhurst
- Division of Parasitology, National Institute for Medical Research, Mill Hill, London, UK
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24
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Soto M, Requena JM, Morales G, Alonso C. The Leishmania infantum histone H3 possesses an extremely divergent N-terminal domain. BIOCHIMICA ET BIOPHYSICA ACTA 1994; 1219:533-5. [PMID: 7918653 DOI: 10.1016/0167-4781(94)90082-5] [Citation(s) in RCA: 26] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
The isolation of a Leishmania cDNA clone coding for an antigen identified as the histone H3 is described. The nucleotide sequence of the cDNA predicts that the Leishmania histone H3 contains 129 residues and that it has a molecular mass of 14,620 Da. Comparison of the amino acid sequence with the consensus sequence of the eukaryotic histone H3 shows that the Leishmania protein has a highly conserved globular region and an extremely divergent amino-terminal portion.
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Affiliation(s)
- M Soto
- Centro de Biologia Molecular Severo Ochoa (CSIC-UAM), Facultad de Ciencias, Universidad Autonoma de Madrid, Spain
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25
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Sanchez LB, Enea V, Eichinger D. Increased levels of polyadenylated histone H2B mRNA accumulate during Entamoeba invadens cyst formation. Mol Biochem Parasitol 1994; 67:137-46. [PMID: 7838174 DOI: 10.1016/0166-6851(94)90103-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
We have isolated cDNA clones of a member of the histone H2B protein family by differential screening of an Entamoeba invadens cDNA library with cDNA probes from vegetatively growing or encysting parasites. The cDNA clones reveal two polyadenylation sites, 26 nucleotides and 31 nucleotides downstream from the stop codon. RNA species recognized by E. invadens histone H2B clones are found at increased levels during cyst formation. Histone H2B RNA could be detected in both the poly(A)+ and poly(A)- RNA fractions, with stage-specific differences in the steady state levels of the two RNAs: trophozoites contain predominantly the poly(A)- RNA, while encysting parasites express predominantly the poly(A)+ RNA. Southern blot analysis suggests that both forms are transcribed from a single copy gene.
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Affiliation(s)
- L B Sanchez
- Department of Medical and Molecular Parasitology, New York University, School of Medicine, NY 10016
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26
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Bontempi EJ, Porcel BM, Henriksson J, Carlsson L, Rydåker M, Segura EL, Ruiz AM, Pettersson U. Genes for histone H3 in Trypanosoma cruzi. Mol Biochem Parasitol 1994; 66:147-51. [PMID: 7984178 DOI: 10.1016/0166-6851(94)90046-9] [Citation(s) in RCA: 24] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- E J Bontempi
- Instituto Nacional de Diagnóstico e Investigación de la Enfermedad de Chagas, Buenos Aires, Argentina
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