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Mi-Ichi F, Hamano S, Yoshida H. Links between cholesteryl sulfate-dependent and -independent processes in the morphological and physiological changes of Entamoeba encystation. Parasitol Int 2024; 99:102844. [PMID: 38103862 DOI: 10.1016/j.parint.2023.102844] [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: 10/02/2023] [Revised: 11/20/2023] [Accepted: 12/10/2023] [Indexed: 12/19/2023]
Abstract
The protozoan parasite Entamoeba histolytica causes amoebiasis, a global public health problem. Amoebiasis is solely transmitted by cysts that are produced from proliferative trophozoites by encystation in the large intestine of humans. During encystation, various metabolites, pathways, and cascades sequentially orchestrate the morphological and physiological changes required to produce cysts. Cholesteryl sulfate (CS) has recently been revealed to be among the key molecules that control the morphological and physiological changes of encystation by exerting pleiotropic effects. CS promotes the rounding of encysting Entamoeba cells and maintains this spherical morphology as encysting cells are surrounded by the cyst wall, a prerequisite for resistance against environmental stresses. CS is also involved in the development of membrane impermeability, another prerequisite for resistance. The initiation of cyst wall formation is, however, CS-independent. Here, we overview CS-dependent and -independent processes during encystation and discuss their functional linkage. We also discuss a potential transcriptional cascade that controls the processes necessary to produce dormant Entamoeba cysts.
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Affiliation(s)
- Fumika Mi-Ichi
- Central Laboratory, Institute of Tropical Medicine (NEKKEN), Nagasaki University, 1-12-4 Sakamoto, Nagasaki 852-8523, Japan; Division of Molecular and Cellular Immunoscience, Department of Biomolecular Sciences, Faculty of Medicine, Saga University, 5-1-1 Nabeshima, Saga 849-8501, Japan; The Joint Research Center on Tropical Diseases, Institute of Tropical Medicine (NEKKEN), Nagasaki University, Nagasaki, Japan.
| | - Shinjiro Hamano
- The Joint Research Center on Tropical Diseases, Institute of Tropical Medicine (NEKKEN), Nagasaki University, Nagasaki, Japan; Department of Parasitology, Institute of Tropical Medicine (NEKKEN), Nagasaki University, 1-12-4 Sakamoto, Nagasaki 852-8523, Japan
| | - Hiroki Yoshida
- Division of Molecular and Cellular Immunoscience, Department of Biomolecular Sciences, Faculty of Medicine, Saga University, 5-1-1 Nabeshima, Saga 849-8501, Japan
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2
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Cuellar P, Castañeda-Ortiz EJ, Rosales-Zarza C, Martínez-Rodríguez CE, Canela-Pérez I, Rodríguez MA, Valdés J, Azuara-Liceaga E. Genome-Wide Classification of Myb Domain-Containing Protein Families in Entamoeba invadens. Genes (Basel) 2024; 15:201. [PMID: 38397191 PMCID: PMC10887745 DOI: 10.3390/genes15020201] [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: 12/26/2023] [Revised: 01/22/2024] [Accepted: 01/26/2024] [Indexed: 02/25/2024] Open
Abstract
Entamoeba histolytica, the causative agent of amebiasis, is the third leading cause of death among parasitic diseases globally. Its life cycle includes encystation, which has been mostly studied in Entamoeba invadens, responsible for reptilian amebiasis. However, the molecular mechanisms underlying this process are not fully understood. Therefore, we focused on the identification and characterization of Myb proteins, which regulate the expression of encystation-related genes in various protozoan parasites. Through bioinformatic analysis, we identified 48 genes in E. invadens encoding MYB-domain-containing proteins. These were classified into single-repeat 1R (20), 2R-MYB proteins (27), and one 4R-MYB protein. The in-silico analysis suggests that these proteins are multifunctional, participating in transcriptional regulation, chromatin remodeling, telomere maintenance, and splicing. Transcriptomic data analysis revealed expression signatures of eimyb genes, suggesting a potential orchestration in the regulation of early and late encystation-excystation genes. Furthermore, we identified probable target genes associated with reproduction, the meiotic cell cycle, ubiquitin-dependent protein catabolism, and endosomal transport. In conclusion, our findings suggest that E. invadens Myb proteins regulate stage-specific proteins and a wide array of cellular processes. This study provides a foundation for further exploration of the molecular mechanisms governing encystation and unveils potential targets for therapeutic intervention in amebiasis.
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Affiliation(s)
- Patricia Cuellar
- Posgrado en Ciencias Genómicas, Universidad Autónoma de la Ciudad de México, Mexico City C.P. 03100, Mexico; (P.C.); (E.J.C.-O.)
| | - Elizabeth J. Castañeda-Ortiz
- Posgrado en Ciencias Genómicas, Universidad Autónoma de la Ciudad de México, Mexico City C.P. 03100, Mexico; (P.C.); (E.J.C.-O.)
| | - César Rosales-Zarza
- Licenciatura Ciencias Genómicas, Universidad Autónoma de la Ciudad de México, Mexico City C.P. 03100, Mexico;
| | | | - Israel Canela-Pérez
- Departamento de Bioquímica, CINVESTAV-IPN, Mexico City C.P. 07360, Mexico; (I.C.-P.); (J.V.)
| | - Mario Alberto Rodríguez
- Departamento de Infectómica y Patogénesis Molecular, CINVESTAV-IPN, Mexico City C.P. 07360, Mexico;
| | - Jesús Valdés
- Departamento de Bioquímica, CINVESTAV-IPN, Mexico City C.P. 07360, Mexico; (I.C.-P.); (J.V.)
| | - Elisa Azuara-Liceaga
- Posgrado en Ciencias Genómicas, Universidad Autónoma de la Ciudad de México, Mexico City C.P. 03100, Mexico; (P.C.); (E.J.C.-O.)
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3
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Guillén N. Pathogenicity and virulence of Entamoeba histolytica, the agent of amoebiasis. Virulence 2023; 14:2158656. [PMID: 36519347 DOI: 10.1080/21505594.2022.2158656] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Accepted: 12/11/2022] [Indexed: 12/23/2022] Open
Abstract
The amoeba parasite Entamoeba histolytica is the causative agent of human amebiasis, an enteropathic disease affecting millions of people worldwide. This ancient protozoan is an elementary example of how parasites evolve with humans, e.g. taking advantage of multiple mechanisms to evade immune responses, interacting with microbiota for nutritional and protective needs, utilizing host resources for growth, division, and encystation. These skills of E. histolytica perpetuate the species and incidence of infection. However, in 10% of infected cases, the parasite turns into a pathogen; the host-parasite equilibrium is then disorganized, and the simple lifecycle based on two cell forms, trophozoites and cysts, becomes unbalanced. Trophozoites acquire a virulent phenotype which, when non-controlled, leads to intestinal invasion with the onset of amoebiasis symptoms. Virulent E. histolytica must cross mucus, epithelium, connective tissue and possibly blood. This highly mobile parasite faces various stresses and a powerful host immune response, with oxidative stress being a challenge for its survival. New emerging research avenues and omics technologies target gene regulation to determine human or parasitic factors activated upon infection, their role in virulence activation, and in pathogenesis; this research bears in mind that E. histolytica is a resident of the complex intestinal ecosystem. The goal is to eradicate amoebiasis from the planet, but the parasitic life of E. histolytica is ancient and complex and will likely continue to evolve with humans. Advances in these topics are summarized here.
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Affiliation(s)
- Nancy Guillén
- Cell Biology and Infection Department, Institut Pasteur and Centre National de la Recherche Scientifique CNRS-ERM9195, Paris, France
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4
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Balbhim SS, Sarkar S, Vasudevan M, Ghosh SK. Three-amino acid loop extension homeodomain proteins regulate stress responses and encystation in Entamoeba. Mol Microbiol 2023. [PMID: 37424153 DOI: 10.1111/mmi.15121] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Revised: 06/22/2023] [Accepted: 06/26/2023] [Indexed: 07/11/2023]
Abstract
It is interesting to identify factors involved in the regulation of the encystation of Entamoeba histolytica that differentiate trophozoites into cysts. Evolutionarily conserved three amino acid loop extension (TALE) homeodomain proteins act as transcription factors and execute a variety of functions that are essential for life. A TALE homeodomain (EhHbox) protein-encoding gene has been identified in E. histolytica (Eh) that is highly upregulated during heat shock, glucose, and serum starvation. Its ortholog, EiHbox1, a putative homeobox protein in E. invadens (Ei), is also highly upregulated during the early hours of encystation, glucose starvation, and heat shock. They belong to the PBX family of TALE homeobox proteins and have conserved residues in the homeodomain that are essential for DNA binding. Both are localized in the nucleus during encystation and under different stress conditions. The electrophoretic mobility shift assay confirmed that the recombinant GST-EhHbox binds to the reported TGACAG and TGATTGAT motifs. Down-regulation of EiHbox1 by gene silencing reduced Chitin synthase, Jacob, and increased Jessie gene expression, resulting in defective cysts and decreased encystation efficiency and viability. Overall, our results suggest that the TALE homeobox family has been conserved during evolution and acts as a transcription factor to control the differentiation of Entamoeba by regulating the key encystation-induced genes.
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Affiliation(s)
- Sonar Shubham Balbhim
- Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, India
| | - Shilpa Sarkar
- Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, India
| | | | - Sudip K Ghosh
- Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, India
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5
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Bernard C, Locard-Paulet M, Noël C, Duchateau M, Giai Gianetto Q, Moumen B, Rattei T, Hechard Y, Jensen LJ, Matondo M, Samba-Louaka A. A time-resolved multi-omics atlas of Acanthamoeba castellanii encystment. Nat Commun 2022; 13:4104. [PMID: 35835784 PMCID: PMC9283445 DOI: 10.1038/s41467-022-31832-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Accepted: 06/30/2022] [Indexed: 12/14/2022] Open
Abstract
Encystment is a common stress response of most protists, including free-living amoebae. Cyst formation protects the amoebae from eradication and can increase virulence of the bacteria they harbor. Here, we mapped the global molecular changes that occur in the facultatively pathogenic amoeba Acanthamoeba castellanii during the early steps of the poorly understood process of encystment. By performing transcriptomic, proteomic, and phosphoproteomic experiments during encystment, we identified more than 150,000 previously undescribed transcripts and thousands of protein sequences absent from the reference genome. These results provide molecular details to the regulation of expected biological processes, such as cell proliferation shutdown, and reveal new insights such as a rapid phospho-regulation of sites involved in cytoskeleton remodeling and translation regulation. This work constitutes the first time-resolved molecular atlas of an encysting organism and a useful resource for further investigation of amoebae encystment to allow for a better control of pathogenic amoebae.
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Affiliation(s)
- Clément Bernard
- Laboratoire Ecologie et Biologie des Interactions, Université de Poitiers, UMR CNRS, 7267, Poitiers, France
| | - Marie Locard-Paulet
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | - Cyril Noël
- IFREMER-IRSI-Service de Bioinformatique (SeBiMER), Centre Bretagne, Plouzane, France
| | - Magalie Duchateau
- Institut Pasteur, Université de Paris, Proteomics Platform, Mass Spectrometry for Biology Unit, UAR2024, CNRS 2000, Paris, France
| | - Quentin Giai Gianetto
- Institut Pasteur, Université de Paris, Proteomics Platform, Mass Spectrometry for Biology Unit, UAR2024, CNRS 2000, Paris, France
- Institut Pasteur, Université de Paris, Department of Computation Biology, Bioinformatics and Biostatistics Hub, Paris, France
| | - Bouziane Moumen
- Laboratoire Ecologie et Biologie des Interactions, Université de Poitiers, UMR CNRS, 7267, Poitiers, France
| | - Thomas Rattei
- Centre for Microbiology and Environmental Systems Science; Doctoral School Microbiology and Environmental Science, University of Vienna, Vienna, Austria
| | - Yann Hechard
- Laboratoire Ecologie et Biologie des Interactions, Université de Poitiers, UMR CNRS, 7267, Poitiers, France
| | - Lars Juhl Jensen
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | - Mariette Matondo
- Institut Pasteur, Université de Paris, Proteomics Platform, Mass Spectrometry for Biology Unit, UAR2024, CNRS 2000, Paris, France
| | - Ascel Samba-Louaka
- Laboratoire Ecologie et Biologie des Interactions, Université de Poitiers, UMR CNRS, 7267, Poitiers, France.
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6
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In-depth comparative analysis of Tritrichomonas foetus transcriptomics reveals novel genes linked with adaptation to feline host. Sci Rep 2022; 12:10057. [PMID: 35710931 PMCID: PMC9203502 DOI: 10.1038/s41598-022-14310-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2022] [Accepted: 06/06/2022] [Indexed: 11/09/2022] Open
Abstract
Tritrichomonas foetus is a flagellated parasite able to infect cattle, cats, and pigs. Despite its prevalence, feline tritrichomonosis has received markedly less attention than venereal infection, and little information about the molecular mechanisms that participate in feline host infection is available. Through a bioinformatics approach, we integrated public transcriptomic data for three T. foetus isolates and explored the differences at transcript level with a focus on pathogenesis and adaptation processes, particularly for the feline isolate. Our analysis revealed higher abundance levels of predicted virulence factors, such as proteases and surface antigens. Additionally, by a comparative and expression analysis of T. foetus genes, we proposed putative virulence factors that could be involved in feline infection. Finally, we identified a great proportion of predicted transcription factors of the MYB protein family and, by a promoter analysis, we revealed that MYB-related proteins could participate in the regulation of gene transcription in T. foetus. In conclusion, this integrated approach is a valuable resource for future studies of host–pathogen interactions and identifying new gene targets for improved feline tritrichomonosis diagnosis and treatment.
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Shih HW, Alas GCM, Paredez AR. A cell-cycle-dependent GARP-like transcriptional repressor regulates the initiation of differentiation in Giardia lamblia. Proc Natl Acad Sci U S A 2022; 119:e2204402119. [PMID: 35613049 PMCID: PMC9295799 DOI: 10.1073/pnas.2204402119] [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: 03/14/2022] [Accepted: 04/21/2022] [Indexed: 11/18/2022] Open
Abstract
Transcriptional regulation of differentiation is critical for parasitic pathogens to adapt to environmental changes and regulate transmission. In response to encystation stimuli, Giardia lamblia shifts the distribution of the cell cycle toward G2 and induces the expression of cyst wall proteins (CWPs) within 2 to 4 h, indicating that key regulatory steps occur within the first 4 h of encystation. However, the role of transcription factors (TFs) in encystation has primarily been investigated at later time points. How TFs initiate encystation and link it to the cell cycle remains enigmatic. Here, we systematically screened six putative early up-regulated TFs for nuclear localization, established their dynamic expression profiles, and determined their functional role in regulating encystation. We found a critical repressor, Golden2, ARR-B, Psr-1–like protein 1 (GARP)–like protein 4 (GLP4), that increases rapidly after 30 min of encystation stimuli and down-regulates encystation-specific markers, including CWPs and enzymes in the cyst N-acetylgalactosamine pathway. Depletion of GLP4 increases cyst production. Importantly, we observe that G2+M cells exhibit higher levels of CWP1, resulting from the activation of myeloblastosis domain protein 2 (MYB2), a TF previously linked to encystation in Giardia. GLP4 up-regulation occurs in G1+S cells, suggesting a role in repressing MYB2 and encystation-specific genes in the G1+S phase of the cell cycle. Furthermore, we demonstrate that depletion of GLP4 up-regulates MYB2 and promotes encystation while overexpression of GLP4 down-regulates MYB2 and represses encystation. Together, these results suggest that Giardia employs a dose-dependent transcriptional response that involves the cell-cycle–regulated repressor GLP4 to orchestrate MYB2 and entry into the encystation pathway.
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Affiliation(s)
- Han-Wei Shih
- Department of Biology, University of Washington, Seattle, WA 98195
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8
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Walters HA, Temesvari LA. Target acquired: transcriptional regulators as drug targets for protozoan parasites. Int J Parasitol 2021; 51:599-611. [PMID: 33722681 PMCID: PMC8169582 DOI: 10.1016/j.ijpara.2020.12.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Revised: 12/09/2020] [Accepted: 12/17/2020] [Indexed: 11/22/2022]
Abstract
Protozoan parasites are single-celled eukaryotic organisms that cause significant human disease and pose a substantial health and socioeconomic burden worldwide. They are responsible for at least 1 million deaths annually. The treatment of such diseases is hindered by the ability of parasites to form latent cysts, develop drug resistance, or be transmitted by insect vectors. Additionally, these pathogens have developed complex mechanisms to alter host gene expression. The prevalence of these diseases is predicted to increase as climate change leads to the augmentation of ambient temperatures, insect ranges, and warm water reservoirs. Therefore, the discovery of novel treatments is necessary. Transcription factors lie at the junction of multiple signalling pathways in eukaryotes and aberrant transcription factor function contributes to the progression of numerous human diseases including cancer, diabetes, inflammatory disorders and cardiovascular disease. Transcription factors were previously thought to be undruggable. However, due to recent advances, transcription factors now represent appealing drug targets. It is conceivable that transcription factors, and the pathways they regulate, may also serve as targets for anti-parasitic drug design. Here, we review transcription factors and transcriptional modulators of protozoan parasites, and discuss how they may be useful in drug discovery. We also provide information on transcription factors that play a role in stage conversion of parasites, TATA box-binding proteins, and transcription factors and cofactors that participate with RNA polymerases I, II and III. We also highlight a significant gap in knowledge in that the transcription factors of some of parasites have been under-investigated. Understanding parasite transcriptional pathways and how parasites alter host gene expression will be essential in discovering innovative drug targets.
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Affiliation(s)
- H A Walters
- Department of Biological Sciences, Clemson University, Clemson, SC 29634, United States; Eukaryotic Pathogens Innovation Center, Clemson University, Clemson, SC 29634, United States
| | - L A Temesvari
- Department of Biological Sciences, Clemson University, Clemson, SC 29634, United States; Eukaryotic Pathogens Innovation Center, Clemson University, Clemson, SC 29634, United States.
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9
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Cárdenas-Hernández H, Titaux-Delgado GA, Castañeda-Ortiz EJ, Torres-Larios A, Brieba LG, Del Río-Portilla F, Azuara-Liceaga E. Genome-wide and structural analysis of the Myb-SHAQKYF family in Entamoeba histolytica. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2021; 1869:140601. [PMID: 33422669 DOI: 10.1016/j.bbapap.2021.140601] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Revised: 12/19/2020] [Accepted: 01/04/2021] [Indexed: 10/22/2022]
Abstract
Amoebiasis is the third leading cause of death among protozoon parasitic diseases in the lower-middle income countries. Understanding the molecular events that control gene expression such as transcription factors, their DNA binding mode and target sequences can help to develop new antiamoebic drugs against Entamoeba histolytica. In this paper we performed a genome and structural analysis of a specific transcription factor. The genome of E. histolytica codifies for 9 EhMybSHAQKYF proteins, which are a family within a large group of 34 Myb-DNA-binding domain (Myb-DBD) containing proteins. Here we compared Entamoeba Myb-SHAQKYF proteins with Myb-like proteins from the Reveille (RVE) family, important regulators of plant circadian networks. This comparison could lead to stablish their role in E. histolytica life cycle. We show that the ehmybshaqkyf genes are differentially expressed in trophozoites under basal cell culture conditions. An in-silico analysis predicts that members of this group harbor a highly conserved and structured Myb-DBD and a large portion of intrinsically disordered residues. As the Myb-DBD of these proteins harbors a distinctive Q[VI]R[ST]HAQK[YF]F sequence in its putative third α-helix, we consider relevant to determine the three-dimensional (3D) structure of one of them. An NMR structure of the Myb-DBD of EhMybS3 shows that this protein is composed of three α-helices stabilized by a hydrophobic core, similar to Myb proteins of different kingdoms. It is remarkable that despite not sharing similarities in their amino acid sequences, the structure of the Myb-DBD of the EhMybS3 is well conserved in this early branching eukaryote.
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Affiliation(s)
- Helios Cárdenas-Hernández
- Posgrado en Ciencias Genómicas, Universidad Autónoma de la Ciudad de México, Ciudad de México, México
| | | | | | - Alfredo Torres-Larios
- Departamento de Bioquímica y Biología Estructural, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Luis G Brieba
- Grupo de Bioquímica Estructural, Laboratorio Nacional de Genómica para la Biodiversidad, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, México
| | | | - Elisa Azuara-Liceaga
- Posgrado en Ciencias Genómicas, Universidad Autónoma de la Ciudad de México, Ciudad de México, México.
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Guillen N. Signals and signal transduction pathways in Entamoeba histolytica during the life cycle and when interacting with bacteria or human cells. Mol Microbiol 2020; 115:901-915. [PMID: 33249684 DOI: 10.1111/mmi.14657] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Revised: 11/22/2020] [Accepted: 11/23/2020] [Indexed: 01/17/2023]
Abstract
Entamoeba histolytica is the etiological agent of amebiasis in humans. This ameba parasite resides as a commensal in the intestine where it shares intestinal resources with the bacterial microbiome. In the intestinal ecosystem, the ameba encysts and eventually develops disease by invading the tissues. E. histolytica possesses cell surface receptors for the proper sensing of signals involved in encystation or sustaining parasite interaction with bacteria and human cells. Among those receptors are the Gal/GalNAc lectin, G protein-coupled receptors, and transmembrane kinases. In addition there are recently discovered, promising proteins, including orthologs of Toll-type receptors and β trefoil lectins. These proteins trigger a wide variety of signal transduction pathways; however, most of the players involved in the signaling pathways evoked in this parasite are unknown. This review provides an overview of amoebic receptors and their role in encystation, adherence to bacteria or human cells, as well as the reported intracellular signal transduction processes that they can trigger. This knowledge is essential for understanding the lifestyle of E. histolytica and its cytopathic effect on bacteria and human cells that are responsible for infection.
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Affiliation(s)
- Nancy Guillen
- Institut Pasteur, Centre National de la Recherche Scientifique, CNRS-ERL9195, Paris, France
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11
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Mornico D, Hon CC, Koutero M, Weber C, Coppee JY, Dillies MA, Guillen N. Genomic determinants for initiation and length of natural antisense transcripts in Entamoeba histolytica. Sci Rep 2020; 10:20190. [PMID: 33214622 PMCID: PMC7677554 DOI: 10.1038/s41598-020-77010-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Accepted: 11/02/2020] [Indexed: 01/27/2023] Open
Abstract
Natural antisense transcripts (NAT) have been reported in prokaryotes and eukaryotes. While the functions of most reported NATs remain unknown, their potentials in regulating the transcription of their counterparts have been speculated. Entamoeba histolytica, which is a unicellular eukaryotic parasite, has a compact protein-coding genome with very short intronic and intergenic regions. The regulatory mechanisms of gene expression in this compact genome are under-described. In this study, by genome-wide mapping of RNA-Seq data in the genome of E. histolytica, we show that a substantial fraction of its protein-coding genes (28%) has significant transcription on their opposite strand (i.e. NAT). Intriguingly, we found the location of transcription start sites or polyadenylation sites of NAT are determined by the specific motifs encoded on the opposite strand of the gene coding sequences, thereby providing a compact regulatory system for gene transcription. Moreover, we demonstrated that NATs are globally up-regulated under various environmental conditions including temperature stress and pathogenicity. While NATs do not appear to be consequences of spurious transcription, they may play a role in regulating gene expression in E. histolytica, a hypothesis which needs to be tested.
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Affiliation(s)
- Damien Mornico
- Hub de Bioinformatique et Biostatistique - Département Biologie Computationnelle, CNRS USR 3756, Institut Pasteur, Paris, France.
| | - Chung-Chau Hon
- Unité Biologie Cellulaire du Parasitisme, Institut Pasteur, Paris, France.,Institut National de La Santé Et de La Recherche Médicale, INSERM U786, Paris, France.,Laboratory for Genome Information Analysis, RIKEN Center for Integrative Medical Sciences, 1-7-22 Suehiro-cho. Tsurumi-ku, Yokohama, 230-0045, Japan
| | - Mikael Koutero
- Plate-forme Transcriptome et Epigénome, Institut Pasteur, Paris, France
| | - Christian Weber
- Unité Biologie Cellulaire du Parasitisme, Institut Pasteur, Paris, France.,Institut National de La Santé Et de La Recherche Médicale, INSERM U786, Paris, France
| | - Jean-Yves Coppee
- Plate-forme Transcriptome et Epigénome, Institut Pasteur, Paris, France
| | - Marie-Agnes Dillies
- Hub de Bioinformatique et Biostatistique - Département Biologie Computationnelle, CNRS USR 3756, Institut Pasteur, Paris, France
| | - Nancy Guillen
- Unité Biologie Cellulaire du Parasitisme, Institut Pasteur, Paris, France. .,Institut National de La Santé Et de La Recherche Médicale, INSERM U786, Paris, France. .,Centre National de La Recherche Scientifique, CNRS ERL9195, Paris, France.
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12
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Manna D, Ehrenkaufer GM, Lozano-Amado D, Singh U. Entamoeba stage conversion: progress and new insights. Curr Opin Microbiol 2020; 58:62-68. [PMID: 33032142 DOI: 10.1016/j.mib.2020.09.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Accepted: 09/10/2020] [Indexed: 12/17/2022]
Abstract
Entamoeba histolytica, an anaerobic protozoan, is an important global health problem. This parasite has a biphasic life cycle consisting of a dormant cyst stage which is environmentally resistant and transmits the infection, and the proliferative trophozoite stage which is motile and causes invasive disease. The stage conversion process remains poorly understood despite being central to amoebic biology. In this review, we will highlight recent progress in our understanding of Entamoeba stage conversion including dissecting transcriptome analysis in development, characterization of transcriptional networks, demonstration of epigenetic regulation, and role of small molecules that regulate Entamoeba development.
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Affiliation(s)
- Dipak Manna
- Division of Infectious Diseases, Stanford University School of Medicine, United States
| | | | - Daniela Lozano-Amado
- Division of Infectious Diseases, Stanford University School of Medicine, United States
| | - Upinder Singh
- Division of Infectious Diseases, Stanford University School of Medicine, United States; Department of Microbiology and Immunology, Stanford University School of Medicine, United States.
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Huerta M, Reyes L, García-Rivera G, Bañuelos C, Betanzos A, Díaz-Hernández M, Galindo A, Bolaños J, Cárdenas H, Azuara-Liceaga E, Chávez-Munguía B, Orozco E. A noncanonical GATA transcription factor of Entamoeba histolytica modulates genes involved in phagocytosis. Mol Microbiol 2020; 114:1019-1037. [PMID: 32808689 DOI: 10.1111/mmi.14592] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Revised: 08/12/2020] [Accepted: 08/14/2020] [Indexed: 12/21/2022]
Abstract
In this paper, we explored the presence of GATA in Entamoeba histolytica and their function as regulators of phagocytosis-related genes. Bioinformatics analyses evidenced a single 579 bp sequence encoding for a protein (EhGATA), smaller than GATA factors of other organisms. EhGATA appeared phylogenetically close to Dictyostelium discoideum and Schistosoma mansoni GATA proteins. Its sequence predicts the presence of a zinc-finger DNA binding domain and an AT-Hook motif; it also has two nuclear localization signals. By transmission electron and confocal microscopy, anti-EhGATA antibodies revealed the protein in the cytoplasm and nucleus, and 65% of nuclear signal was in the heterochromatin. EhGATA recombinant protein and trophozoites nuclear extracts bound to GATA-DNA consensus sequence. By in silico scrutiny, 1,610 gene promoters containing GATA-binding sequences appeared, including Ehadh and Ehvps32 promoters, whose genes participate in phagocytosis. Chromatin immunoprecipitation assays showed that EhGATA interact with Ehadh and Ehvps32 promoters. In EhGATA-overexpressing trophozoites (NeoGATA), the Ehadh and Ehvps32 mRNAs amount was modified, strongly supporting that EhGATA could regulate their transcription. NeoGATA trophozoites exhibited rounded shapes, high proliferation rates, and diminished erythrophagocytosis. Our results provide new insights into the role of EhGATA as a noncanonical transcription factor, regulating genes associated with phagocytosis.
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Affiliation(s)
- Miriam Huerta
- Departamento de Infectómica y Patogénesis Molecular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Ciudad de México, México
| | - Luz Reyes
- Departamento de Infectómica y Patogénesis Molecular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Ciudad de México, México
| | - Guillermina García-Rivera
- Departamento de Infectómica y Patogénesis Molecular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Ciudad de México, México
| | - Cecilia Bañuelos
- Programa de Doctorado Transdisciplinario en Desarrollo Científico y Tecnológico para la Sociedad, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Ciudad de México, México
| | - Abigail Betanzos
- Departamento de Infectómica y Patogénesis Molecular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Ciudad de México, México.,Consejo Nacional de Ciencia y Tecnología, Ciudad de México, México
| | - Mitzi Díaz-Hernández
- Departamento de Infectómica y Patogénesis Molecular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Ciudad de México, México
| | - Ausencio Galindo
- Departamento de Infectómica y Patogénesis Molecular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Ciudad de México, México
| | - Jeni Bolaños
- Departamento de Infectómica y Patogénesis Molecular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Ciudad de México, México
| | - Helios Cárdenas
- Posgrado en Ciencias Genómicas, Universidad Autónoma de la Ciudad de México, Ciudad de México, México
| | - Elisa Azuara-Liceaga
- Posgrado en Ciencias Genómicas, Universidad Autónoma de la Ciudad de México, Ciudad de México, México
| | - Bibiana Chávez-Munguía
- Departamento de Infectómica y Patogénesis Molecular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Ciudad de México, México
| | - Esther Orozco
- Departamento de Infectómica y Patogénesis Molecular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Ciudad de México, México
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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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15
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Manna D, Lozano-Amado D, Ehrenkaufer G, Singh U. The NAD + Responsive Transcription Factor ERM-BP Functions Downstream of Cellular Aggregation and Is an Early Regulator of Development and Heat Shock Response in Entamoeba. Front Cell Infect Microbiol 2020; 10:363. [PMID: 32766170 PMCID: PMC7379229 DOI: 10.3389/fcimb.2020.00363] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Accepted: 06/11/2020] [Indexed: 12/20/2022] Open
Abstract
Entamoeba histolytica is a protozoan parasite and a major cause of dysentery and diarrheal disease in developing countries. Disease transmission from one host to another occurs via cysts which can survive in environmental extremes and are transmitted through contaminated food and water. Recent studies in our lab identified a novel transcription factor, Encystation Regulatory Motif- Binding Protein (ERM-BP), which is responsive to NAD+ and has an important role in encystation. The key residues important for ERM-BP function were demonstrated in vitro using recombinant protein. In this study we demonstrate the in vivo functional consequences of mutations in key domains and their impact on Entamoeba encystation. Our results show that mutations in the DNA binding domain (ERM-BP-DBM) and in the nicotinamidase domain (ERM-BP-C198A) lead to protein mis-localization in both trophozoites and cysts and significantly reduce encystation efficiency. Additionally, we showed that silencing of ERM-BP significantly decreased the size and number of multi-nucleated giant cells (MGC) that form during encystation, indicating that ERM-BP functions upstream of the cellular aggregation that precedes stage conversion. Dissection of epistatic interactions between ERM-BP and a second encystation-related transcription factor, NF-Y revealed that ERM-BP is upstream of NF-Y in controlling the developmental cascade and appears to be one of the earliest regulators of development identified to date in Entamoeba. We also demonstrated that ERM-BP is upregulated during heat stress in Entamoeba, another condition which increases intracellular NAD+ levels and that overexpression of ERM-BP makes E. histolytica and E. invadens parasites more resistant to heat stress. Overexpression of ERM-BP in E. histolytica also induced the formation of cyst-like quadrinucleated cells and formation of MGCs. Overall, our work has identified an important role of ERM-BP in Entamoeba stress response and links an NAD+-responsive transcription factor to both development and heat shock response. Characterization of stress and developmental cascades are important avenues to investigate for Entamoeba, an important human parasitic pathogen.
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Affiliation(s)
- Dipak Manna
- Division of Infectious Diseases, Stanford University School of Medicine, Stanford, CA, United States
| | - Daniela Lozano-Amado
- Division of Infectious Diseases, Stanford University School of Medicine, Stanford, CA, United States
| | - Gretchen Ehrenkaufer
- Division of Infectious Diseases, Stanford University School of Medicine, Stanford, CA, United States
| | - Upinder Singh
- Division of Infectious Diseases, Stanford University School of Medicine, Stanford, CA, United States
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, United States
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16
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Waldman BS, Schwarz D, Wadsworth MH, Saeij JP, Shalek AK, Lourido S. Identification of a Master Regulator of Differentiation in Toxoplasma. Cell 2020; 180:359-372.e16. [PMID: 31955846 PMCID: PMC6978799 DOI: 10.1016/j.cell.2019.12.013] [Citation(s) in RCA: 137] [Impact Index Per Article: 34.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Revised: 10/28/2019] [Accepted: 12/10/2019] [Indexed: 01/06/2023]
Abstract
Toxoplasma gondii chronically infects a quarter of the world's population, and its recrudescence can cause life-threatening disease in immunocompromised individuals and recurrent ocular lesions in the immunocompetent. Acute-stage tachyzoites differentiate into chronic-stage bradyzoites, which form intracellular cysts resistant to immune clearance and existing therapies. The molecular basis of this differentiation is unknown, despite being efficiently triggered by stresses in culture. Through Cas9-mediated screening and single-cell profiling, we identify a Myb-like transcription factor (BFD1) necessary for differentiation in cell culture and in mice. BFD1 accumulates during stress and its synthetic expression is sufficient to drive differentiation. Consistent with its function as a transcription factor, BFD1 binds the promoters of many stage-specific genes and represents a counterpoint to the ApiAP2 factors that dominate our current view of parasite gene regulation. BFD1 provides a genetic switch to study and control Toxoplasma differentiation and will inform prevention and treatment of chronic infections.
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Affiliation(s)
- Benjamin S Waldman
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Dominic Schwarz
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Institute of Pharmacy and Molecular Biotechnology, University of Heidelberg, Im Neuenheimer Feld 364, 69120 Heidelberg, Germany
| | - Marc H Wadsworth
- Institute for Medical Engineering & Science, Department of Chemistry, and Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02319, USA
| | - Jeroen P Saeij
- Department of Pathology, Microbiology and Immunology, School of Veterinary Medicine, University of California, Davis, Davis, CA 95616, USA
| | - Alex K Shalek
- Institute for Medical Engineering & Science, Department of Chemistry, and Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02319, USA
| | - Sebastian Lourido
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA.
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Nuclear Factor Y (NF-Y) Modulates Encystation in Entamoeba via Stage-Specific Expression of the NF-YB and NF-YC Subunits. mBio 2019; 10:mBio.00737-19. [PMID: 31213550 PMCID: PMC6581852 DOI: 10.1128/mbio.00737-19] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The human parasite Entamoeba histolytica is an important pathogen with significant global impact and is a leading cause of parasitic death in humans. Since only the cyst form can be transmitted, blocking encystation would prevent new infections, making the encystation pathway an attractive target for the development of new drugs. Identification of the genetic signals and transcriptional regulatory networks that control encystation would be an important advance in understanding the developmental cascade. We show that the Entamoeba NF-Y complex plays a crucial role in regulating the encystation process in Entamoeba. Nuclear factor Y (NF-Y) is a heterotrimeric transcription factor composed of three subunits, namely, NF-YA, NF-YB, and NF-YC, which are conserved throughout evolution. In higher eukaryotes, NF-Y plays important roles in several cellular processes (development, cell cycle regulation, apoptosis, and response to growth, stress, and DNA damage) by controlling gene expression through binding to a CCAAT promoter motif. We demonstrated that NF-Y subunits in the protist Entamoeba, while significantly divergent from those of higher eukaryotes, have well-conserved domains important for subunit interactions and DNA binding and that NF-YB and NF-YC are developmentally expressed during encystation. Electrophoretic mobility shift assays confirmed that the NF-Y protein(s) from Entamoeba cysts binds to a CCAAT motif. Consistent with a role as a transcription factor, the NF-Y proteins show nuclear localization during development. Additionally, we demonstrated that NF-YC localizes to the chromatoid body (an RNA processing center) during development, indicating that it may have a role in RNA processing. Finally, silencing of the NF-YC subunit resulted in reduced stability of the NF-Y complex and decreased encystation efficiency. We demonstrated that the NF-Y complex functions at a time point subsequent to the NAD+ flux and expression of the transcription factor encystation regulatory motif-binding protein, both of which are early regulators of Entamoeba development. Taken together, our results demonstrate that the NF-Y complex plays an important role in regulating encystation in Entamoeba and add to our understanding of the transcriptional networks and signals that control this essential developmental pathway in an important human pathogen.
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18
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Manna D, Lentz CS, Ehrenkaufer GM, Suresh S, Bhat A, Singh U. An NAD +-dependent novel transcription factor controls stage conversion in Entamoeba. eLife 2018; 7:e37912. [PMID: 30375973 PMCID: PMC6207428 DOI: 10.7554/elife.37912] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Accepted: 10/17/2018] [Indexed: 12/22/2022] Open
Abstract
Developmental switching between life-cycle stages is a common feature among parasitic pathogens to facilitate disease transmission and pathogenesis. The protozoan parasite Entamoeba switches between invasive trophozoites and dormant cysts, but the encystation process remains poorly understood despite being central to amoebic biology. We identify a transcription factor, Encystation Regulatory Motif-Binding Protein (ERM-BP), that regulates encystation. Down-regulation of ERM-BP decreases encystation efficiency resulting in abnormal cysts with defective cyst walls. We demonstrate that direct binding of NAD+ to ERM-BP affects ERM-BP conformation and facilitates its binding to promoter DNA. Additionally, cellular NAD+ levels increase during encystation and exogenous NAD+ enhances encystation consistent with the role of carbon source depletion in triggering Entamoeba encystation. Furthermore, ERM-BP catalyzes conversion of nicotinamide to nicotinic acid, which might have second messenger effects on stage conversion. Our findings link the metabolic cofactors nicotinamide and NAD+ to transcriptional regulation via ERM-BP and provide the first mechanistic insights into Entamoeba encystation.
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Affiliation(s)
- Dipak Manna
- Division of Infectious Diseases, Department of Internal MedicineStanford University School of MedicineStanfordUnited States
| | | | - Gretchen Marie Ehrenkaufer
- Division of Infectious Diseases, Department of Internal MedicineStanford University School of MedicineStanfordUnited States
| | - Susmitha Suresh
- Division of Infectious Diseases, Department of Internal MedicineStanford University School of MedicineStanfordUnited States
| | - Amrita Bhat
- Division of Infectious Diseases, Department of Internal MedicineStanford University School of MedicineStanfordUnited States
| | - Upinder Singh
- Division of Infectious Diseases, Department of Internal MedicineStanford University School of MedicineStanfordUnited States
- Department of Microbiology and ImmunologyStanford University School of MedicineStanfordUnited States
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19
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Narayanasamy RK, Castañón-Sanchez CA, Luna-Arias JP, García-Rivera G, Avendaño-Borromeo B, Labra-Barrios ML, Valdés J, Herrera-Aguirre ME, Orozco E. The Entamoeba histolytica TBP and TRF1 transcription factors are GAAC-box binding proteins, which display differential gene expression under different stress stimuli and during the interaction with mammalian cells. Parasit Vectors 2018. [PMID: 29514716 PMCID: PMC5842622 DOI: 10.1186/s13071-018-2698-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Entamoeba histolytica is the protozoan parasite responsible for human amebiasis. It causes up to 100,000 deaths worldwide each year. This parasite has two closely related basal transcription factors, the TATA-box binding protein (EhTBP) and the TBP-related factor 1 (EhTRF1). TBP binds to the canonical TATTTAAA-box, as well as to different TATA variants. TRF1 also binds to the TATTTAAA-box. However, their binding capacity to diverse core promoter elements, including the GAAC-element, and their role in gene regulation in this parasite remains unknown. METHODS EMSA experiments were performed to determine the binding capacity of recombinant TBP and TRF1 to TATA variants, GAAC and GAAC-like boxes. For the functional analysis under different stress stimuli (e.g. growth curve, serum depletion, heat-shock, and UV-irradiation) and during the interaction with mammalian cells (erythrocytes, MDCK cell monolayers, and hepatocytes of hamsters), RT-qPCR, and gene knockdown were performed. RESULTS Both transcription factors bound to the different TATA variants tested, as well as to the GAAC-boxes, suggesting that they are GAAC-box-binding proteins. The K D values determined for TBP and TRF1 for the different TATA variants and GAAC-box were in the range of 10-12 M to 10-11 M. During the death phase of growth or in serum depletion, Ehtbp mRNA levels significantly increased, whereas the mRNA level of Ehtrf1 did not change under these conditions. Ehtrf1 gene expression was negatively regulated by UV-irradiation and heat-shock stress, with no changes in Ehtbp gene expression. Moreover, Ehtrf1 gene also showed a negative regulation during erythrophagocytosis, liver abscess formation, and a transient expression level increase at the initial phase of MDCK cell destruction. Finally, the Ehtbp gene knockdown displayed a drastic decrease in the efficiency of erythrophagocytosis in G3 trophozoites. CONCLUSIONS To our knowledge, this study reveals that these basal transcription factors are able to bind multiple core promoter elements. However, their immediate change in gene expression level in response to different stimuli, as well as during the interaction with mammalian cells, and the diminishing of erythrophagocytosis by silencing the Ehtbp gene indicate the different physiological roles of these transcription factors in E. histolytica.
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Affiliation(s)
- Ravi Kumar Narayanasamy
- Departamento de Infectómica y Patogénesis Molecular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (Cinvestav-IPN), Av. Instituto Politécnico Nacional 2508, Col. San Pedro Zacatenco, C.P, 07360, Ciudad de México, Mexico
| | - Carlos Alberto Castañón-Sanchez
- Programa de Biomedicina Molecular, Escuela Nacional de Medicina y Homeopatía del Instituto Politécnico Nacional (ENMH-IPN), Guillermo Massieu Helguera 239, Col. La Escalera, C.P, 07320, Ciudad de México, Mexico.,Laboratorio de Investigación Biomédica, Subdirección de Enseñanza e Investigación, Hospital Regional de Alta Especialidad de Oaxaca, Aldama S/N, San Bartolo Coyotepec, C.P, 71256, Oaxaca, Mexico
| | - Juan Pedro Luna-Arias
- Departamento de Biología Celular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (Cinvestav-IPN), Av. Instituto Politécnico Nacional 2508, Col. San Pedro Zacatenco, C.P, 07360, Ciudad de México, Mexico.
| | - Guillermina García-Rivera
- Departamento de Infectómica y Patogénesis Molecular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (Cinvestav-IPN), Av. Instituto Politécnico Nacional 2508, Col. San Pedro Zacatenco, C.P, 07360, Ciudad de México, Mexico
| | - Bartolo Avendaño-Borromeo
- Departamento de Biología Celular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (Cinvestav-IPN), Av. Instituto Politécnico Nacional 2508, Col. San Pedro Zacatenco, C.P, 07360, Ciudad de México, Mexico
| | - María Luisa Labra-Barrios
- Departamento de Biología Celular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (Cinvestav-IPN), Av. Instituto Politécnico Nacional 2508, Col. San Pedro Zacatenco, C.P, 07360, Ciudad de México, Mexico
| | - Jesús Valdés
- Departamento de Bioquímica, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (Cinvestav-IPN), Av. Instituto Politécnico Nacional 2508, Col. San Pedro Zacatenco, C.P, 07360, Ciudad de México, Mexico
| | - María Esther Herrera-Aguirre
- Departamento de Biología Celular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (Cinvestav-IPN), Av. Instituto Politécnico Nacional 2508, Col. San Pedro Zacatenco, C.P, 07360, Ciudad de México, Mexico
| | - Esther Orozco
- Departamento de Infectómica y Patogénesis Molecular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (Cinvestav-IPN), Av. Instituto Politécnico Nacional 2508, Col. San Pedro Zacatenco, C.P, 07360, Ciudad de México, Mexico
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20
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Thiriet-Rupert S, Carrier G, Chénais B, Trottier C, Bougaran G, Cadoret JP, Schoefs B, Saint-Jean B. Transcription factors in microalgae: genome-wide prediction and comparative analysis. BMC Genomics 2016; 17:282. [PMID: 27067009 PMCID: PMC4827209 DOI: 10.1186/s12864-016-2610-9] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2015] [Accepted: 04/05/2016] [Indexed: 11/28/2022] Open
Abstract
Background Studying transcription factors, which are some of the key players in gene expression, is of outstanding interest for the investigation of the evolutionary history of organisms through lineage-specific features. In this study we performed the first genome-wide TF identification and comparison between haptophytes and other algal lineages. Results For TF identification and classification, we created a comprehensive pipeline using a combination of BLAST, HMMER and InterProScan software. The accuracy evaluation of the pipeline shows its applicability for every alga, plant and cyanobacterium, with very good PPV and sensitivity. This pipeline allowed us to identify and classified the transcription factor complement of the three haptophytes Tisochrysis lutea, Emiliania huxleyi and Pavlova sp.; the two stramenopiles Phaeodactylum tricornutum and Nannochloropsis gaditana; the chlorophyte Chlamydomonas reinhardtii and the rhodophyte Porphyridium purpureum. By using T. lutea and Porphyridium purpureum, this work extends the variety of species included in such comparative studies, allowing the detection and detailed study of lineage-specific features, such as the presence of TF families specific to the green lineage in Porphyridium purpureum, haptophytes and stramenopiles. Our comprehensive pipeline also allowed us to identify fungal and cyanobacterial TF families in the algal nuclear genomes. Conclusions This study provides examples illustrating the complex evolutionary history of algae, some of which support the involvement of a green alga in haptophyte and stramenopile evolution. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-2610-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Stanislas Thiriet-Rupert
- IFREMER, Physiology and Biotechnology of Algae Laboratory, rue de l'Ile d'Yeu, 44311, Nantes, France.
| | - Grégory Carrier
- IFREMER, Physiology and Biotechnology of Algae Laboratory, rue de l'Ile d'Yeu, 44311, Nantes, France
| | - Benoît Chénais
- MicroMar, Mer Molécules Santé, IUML - FR 3473 CNRS, University of Le Mans, Le Mans, France
| | - Camille Trottier
- IFREMER, Physiology and Biotechnology of Algae Laboratory, rue de l'Ile d'Yeu, 44311, Nantes, France
| | - Gaël Bougaran
- IFREMER, Physiology and Biotechnology of Algae Laboratory, rue de l'Ile d'Yeu, 44311, Nantes, France
| | - Jean-Paul Cadoret
- IFREMER, Physiology and Biotechnology of Algae Laboratory, rue de l'Ile d'Yeu, 44311, Nantes, France
| | - Benoît Schoefs
- MicroMar, Mer Molécules Santé, IUML - FR 3473 CNRS, University of Le Mans, Le Mans, France
| | - Bruno Saint-Jean
- IFREMER, Physiology and Biotechnology of Algae Laboratory, rue de l'Ile d'Yeu, 44311, Nantes, France
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21
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Development of RNA Interference Trigger-Mediated Gene Silencing in Entamoeba invadens. Infect Immun 2016; 84:964-975. [PMID: 26787723 DOI: 10.1128/iai.01161-15] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2015] [Accepted: 01/14/2016] [Indexed: 01/08/2023] Open
Abstract
Entamoeba histolytica, a protozoan parasite, is an important human pathogen and a leading parasitic cause of death. The organism has two life cycle stages, trophozoites, which are responsible for tissue invasion, and cysts, which are involved in pathogen transmission. Entamoeba invadens is the model system to study Entamoeba developmental biology, as high-grade regulated encystation and excystation are readily achievable. However, the lack of gene-silencing tools in E. invadens has limited the molecular studies that can be performed. Using the endogenous RNA interference (RNAi) pathway in Entamoeba, we developed an RNAi-based trigger gene-silencing approach inE. invadens We demonstrate that a gene's coding region that has abundant antisense small RNAs (sRNAs) can trigger silencing of a gene that is fused to it. The trigger fusion leads to the generation of abundant antisense sRNAs that map to the target gene, with silencing occurring independently of trigger location at the 5' or 3' end of a gene. Gene silencing is stably maintained during development, including encystation and excystation. We have used this approach to successfully silence two E. invadens genes: a putative rhomboid protease gene and a SHAQKY family Myb gene. The Myb gene is upregulated during oxidative stress and development, and its downregulation led, as predicted, to decreased viability under oxidative stress and decreased cyst formation. Thus, the RNAi trigger silencing method can be used to successfully investigate the molecular functions of genes inE. invadens Dissection of the molecular basis of Entamoeba stage conversion is now possible, representing an important technical advance for the system.
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Watanabe K, Petri WA. Molecular biology research to benefit patients with Entamoeba histolytica infection. Mol Microbiol 2015; 98:208-17. [PMID: 26173474 DOI: 10.1111/mmi.13131] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/13/2015] [Indexed: 12/28/2022]
Abstract
The development of molecular microbiology has made it possible for us to deepen our understanding of the pathogenesis of amebiasis. Research using the trophozoite form of Entamoeba histolytica has clearly shown us the importance of the interface between the parasite and host cells in vitro. Immuno-pathogenesis after excystation was similarly well advanced by the use of a novel murine model of amebic colitis. However, it is still challenging to apply these findings to clinical and epidemiological settings. This is mainly because of the lack of a complete infection animal model of amebiasis by oral-fecal infection. Moreover, in vitro experiments have predominantly been performed using the same axenic cultured strain HM-1: IMSS isolated about 50 years ago, whereas highly diverse strains are prevalent all over the world. Translational research informed by clinical observations has the greatest potential for the development of effective interventions. Here, we highlight discoveries of the experiments designed from cohort observation and discuss remaining problems to be solved.
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Affiliation(s)
- Koji Watanabe
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, VA, USA.,AIDS Clinical Center, National Center for Global Health and Medicine, Tokyo, Japan
| | - William A Petri
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, VA, USA
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Kim Y, Kim H, Son H, Choi GJ, Kim JC, Lee YW. MYT3, a Myb-like transcription factor, affects fungal development and pathogenicity of Fusarium graminearum. PLoS One 2014; 9:e94359. [PMID: 24722578 PMCID: PMC3983115 DOI: 10.1371/journal.pone.0094359] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2014] [Accepted: 03/12/2014] [Indexed: 11/19/2022] Open
Abstract
We previously characterized members of the Myb protein family, MYT1 and MYT2, in Fusarium graminearum. MYT1 and MYT2 are involved in female fertility and perithecium size, respectively. To expand knowledge of Myb proteins in F. graminearum, in this study, we characterized the functions of the MYT3 gene, which encodes a putative Myb-like transcription factor containing two Myb DNA-binding domains and is conserved in the subphylum Pezizomycotina of Ascomycota. MYT3 proteins were localized in nuclei during most developmental stages, suggesting the role of MYT3 as a transcriptional regulator. Deletion of MYT3 resulted in impairment of conidiation, germination, and vegetative growth compared to the wild type, whereas complementation of MYT3 restored the wild-type phenotype. Additionally, the Δmyt3 strain grew poorly on nitrogen-limited media; however, the mutant grew robustly on minimal media supplemented with ammonium. Moreover, expression level of nitrate reductase gene in the Δmyt3 strain was decreased in comparison to the wild type and complemented strain. On flowering wheat heads, the Δmyt3 strain exhibited reduced pathogenicity, which corresponded with significant reductions in trichothecene production and transcript levels of trichothecene biosynthetic genes. When the mutant was selfed, mated as a female, or mated as a male for sexual development, perithecia were not observed on the cultures, indicating that the Δmyt3 strain lost both male and female fertility. Taken together, these results demonstrate that MYT3 is required for pathogenesis and sexual development in F. graminearum, and will provide a robust foundation to establish the regulatory networks for all Myb-like proteins in F. graminearum.
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Affiliation(s)
- Yongsoo Kim
- Department of Agricultural Biotechnology and Center for Fungal Pathogenesis, Seoul National University, Seoul, Republic of Korea
| | - Hun Kim
- Department of Agricultural Biotechnology and Center for Fungal Pathogenesis, Seoul National University, Seoul, Republic of Korea
| | - Hokyoung Son
- Department of Agricultural Biotechnology and Center for Fungal Pathogenesis, Seoul National University, Seoul, Republic of Korea
| | - Gyung Ja Choi
- Eco-friendly New Materials Research Group, Research Center for Biobased Chemistry, Division of Convergence Chemistry, Korea Research Institute of Chemical Technology, Daejeon, Republic of Korea
| | - Jin-Cheol Kim
- Eco-friendly New Materials Research Group, Research Center for Biobased Chemistry, Division of Convergence Chemistry, Korea Research Institute of Chemical Technology, Daejeon, Republic of Korea
| | - Yin-Won Lee
- Department of Agricultural Biotechnology and Center for Fungal Pathogenesis, Seoul National University, Seoul, Republic of Korea
- * E-mail:
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Proteomic profiling reveals that EhPC4 transcription factor induces cell migration through up-regulation of the 16-kDa actin-binding protein EhABP16 in Entamoeba histolytica. J Proteomics 2014; 111:46-58. [PMID: 24721673 DOI: 10.1016/j.jprot.2014.03.041] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2014] [Revised: 03/24/2014] [Accepted: 03/28/2014] [Indexed: 11/20/2022]
Abstract
UNLABELLED Actin cytoskeleton is an essential structure involved in cell migration and invasion in parasites. In Entamoeba histolytica, the protozoan parasite causing human amoebiasis, the mechanisms underlying the expression of migration-related genes are poorly understood. Here, we investigated the biological effects of ectopic overexpression of EhPC4 (positive coactivator 4) in cell migration of E. histolytica trophozoites. Using differential in gel two-dimensional electrophoresis, 33 modulated proteins were detected in EhPC4-overexpressing cells. By electrospray ionization tandem mass spectrometry (ESI-MS/MS) analysis, 16 of these proteins were identified. Interestingly, four up-regulated proteins involved in cytoskeleton organization and cell migration were identified. Particularly, we found the up-regulation of a 16-kDa actin-binding protein (EhABP16) which is a putative member of the cofilin/tropomyosin family involved in actin polymerization. EhPC4 overexpression induced a significant increase in migration of trophozoites and in the destruction of human SW480 colon cells. Consistently, silencing of gene expression by RNA interference of EhABP16 significantly impairs cell migration. These changes were associated to alterations in the organization of actin cytoskeleton, and suppression of uropod-like structure formation in EhABP16-deficient cells. In summary, we have uncovered novel proteins modulated by EhPC4, including EhABP16, with a potential role in cell migration, cytopathogenicity and virulence in E. histolytica. BIOLOGICAL SIGNIFICANCE The human pathogen Entamoeba histolytica infects around 50million people worldwide resulting in 40,000-100,000 deaths annually. Cell motility is a complex trait that is critical for parasites adaptation, spread and invasion processes into host tissues; it has been associated with virulence. In this study, we used a differential proteomic approach to demonstrate that E. histolytica EhPC4 induces changes in the expression of actin cytoskeleton proteins, including EhABP16, promoting a significant increase in cell motility and destruction of intestinal human cells. Particularly, we demonstrated for the first time that abrogation of EhABP16 impairs cell migration by altering the actin cytoskeleton dynamics and uropod-like structure formation in trophozoites. These data contribute to the understanding of molecular mechanisms that regulate virulence properties in this neglected protozoan parasite.
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López-Camarillo C, López-Rosas I, Ospina-Villa JD, Marchat LA. Deciphering molecular mechanisms of mRNA metabolism in the deep-branching eukaryoteEntamoeba histolytica. WILEY INTERDISCIPLINARY REVIEWS-RNA 2013; 5:247-62. [DOI: 10.1002/wrna.1205] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2013] [Revised: 10/04/2013] [Accepted: 10/09/2013] [Indexed: 11/05/2022]
Affiliation(s)
| | - Itzel López-Rosas
- Genomics Sciences Program; Autonomous University of Mexico City; Mexico City Mexico
| | - Juan David Ospina-Villa
- Institutional Program of Molecular Biomedicine; National School of Medicine and Homeopathy of the National Polytechnic Institute; Mexico City Mexico
| | - Laurence A. Marchat
- Institutional Program of Molecular Biomedicine; National School of Medicine and Homeopathy of the National Polytechnic Institute; Mexico City Mexico
- Biotechnology Program; National School of Medicine and Homeopathy of the National Polytechnic Institute; Mexico City Mexico
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De Cádiz AE, Jeelani G, Nakada-Tsukui K, Caler E, Nozaki T. Transcriptome analysis of encystation in Entamoeba invadens. PLoS One 2013; 8:e74840. [PMID: 24040350 PMCID: PMC3770568 DOI: 10.1371/journal.pone.0074840] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2012] [Accepted: 08/08/2013] [Indexed: 11/23/2022] Open
Abstract
Encystation is an essential differentiation process for the completion of the life cycle of a group of intestinal protozoa including Entamoeba histolytica, the causative agent of intestinal and extraintestinal amebiasis. However, regulation of gene expression during encystation is poorly understood. To comprehensively understand the process at the molecular level, the transcriptomic profiles of E. invadens, which is a related reptilian species that causes an invasive disease similar to that of E. histolytica, was investigated during encystation. Using a custom-generated Affymetrix platform microarray, we performed time course (0.5, 2, 8, 24, 48, and 120 h) gene expression analysis of encysting E. invadens. ANOVA analysis revealed that a total of 1,528 genes showed ≥3 fold up-regulation at one or more time points, relative to the trophozoite stage. Of these modulated genes, 8% (116 genes) were up-regulated at the early time points (0.5, 2 and 8h), while 63% (962 genes) were up-regulated at the later time points (24, 48, and 120 h). Twenty nine percent (450 genes) are either up-regulated at 2 to 5 time points or constitutively up-regulated in both early and late stages. Among the up-regulated genes are the genes encoding transporters, cytoskeletal proteins, proteins involved in vesicular trafficking (small GTPases), Myb transcription factors, cysteine proteases, components of the proteasome, and enzymes for chitin biosynthesis. This study represents the first kinetic analysis of gene expression during differentiation from the invasive trophozoite to the dormant, infective cyst stage in Entamoeba. Functional analysis on individual genes and their encoded products that are modulated during encystation may lead to the discovery of targets for the development of new chemotherapeutics that interfere with stage conversion of the parasite.
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Affiliation(s)
- Aleyla Escueta De Cádiz
- Department of Parasitology, National Institute of Infectious Diseases, Tokyo, Japan
- Department of Biological Science and Environmental Studies, College of Science and Mathematics, University of the Philippines Mindanao, Davao, Philippines
| | - Ghulam Jeelani
- Department of Parasitology, National Institute of Infectious Diseases, Tokyo, Japan
| | - Kumiko Nakada-Tsukui
- Department of Parasitology, National Institute of Infectious Diseases, Tokyo, Japan
| | - Elisabet Caler
- J. Craig Venter Institute, Rockville, Maryland, United States of America
| | - Tomoyoshi Nozaki
- Department of Parasitology, National Institute of Infectious Diseases, Tokyo, Japan
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan
- * E-mail:
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Morf L, Pearson RJ, Wang AS, Singh U. Robust gene silencing mediated by antisense small RNAs in the pathogenic protist Entamoeba histolytica. Nucleic Acids Res 2013; 41:9424-37. [PMID: 23935116 PMCID: PMC3814356 DOI: 10.1093/nar/gkt717] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
RNA interference uses small RNAs (sRNA), which target genes for sequence-specific silencing. The parasite Entamoeba histolytica contains an abundant repertoire of 27 nt antisense (AS) sRNA with 5′-polyphosphate termini, but their roles in regulating gene expression have not been well established. We demonstrate that a gene-coding region to which large numbers of AS sRNAs map can serve as a ‘trigger’ and silence the gene fused to it. Silencing is mediated by generation of AS sRNAs with 5′-polyphosphate termini that have sequence specificity to the fused gene. The mechanism of silencing is independent of the placement of the trigger relative to the silenced gene but is dependent on the sRNA concentration to the trigger. Silencing requires transcription of the trigger-gene fusion and is maintained despite loss of the trigger plasmid. We used this approach to silence multiple amebic genes, including an E. histolytica Myb gene, which is upregulated during oxidative stress response. Silencing of the EhMyb gene decreased parasite viability under oxidative stress conditions. Thus, we have developed a new tool for genetic manipulation in E. histolytica with many advantages over currently available technologies. Additionally, these data shed mechanistic insights into a eukaryotic RNA interference pathway with many novel aspects.
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Affiliation(s)
- Laura Morf
- Division of Infectious Diseases, Department of Internal Medicine, Stanford University School of Medicine, Stanford, California 94305-5107, USA and Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California 94305-5107, USA
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Ehrenkaufer GM, Weedall GD, Williams D, Lorenzi HA, Caler E, Hall N, Singh U. The genome and transcriptome of the enteric parasite Entamoeba invadens, a model for encystation. Genome Biol 2013; 14:R77. [PMID: 23889909 PMCID: PMC4053983 DOI: 10.1186/gb-2013-14-7-r77] [Citation(s) in RCA: 75] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2013] [Accepted: 07/26/2013] [Indexed: 12/27/2022] Open
Abstract
Background Several eukaryotic parasites form cysts that transmit infection. The process is found in diverse organisms such as Toxoplasma, Giardia, and nematodes. In Entamoeba histolytica this process cannot be induced in vitro, making it difficult to study. In Entamoeba invadens, stage conversion can be induced, but its utility as a model system to study developmental biology has been limited by a lack of genomic resources. We carried out genome and transcriptome sequencing of E. invadens to identify molecular processes involved in stage conversion. Results We report the sequencing and assembly of the E. invadens genome and use whole transcriptome sequencing to characterize changes in gene expression during encystation and excystation. The E. invadens genome is larger than that of E. histolytica, apparently largely due to expansion of intergenic regions; overall gene number and the machinery for gene regulation are conserved between the species. Over half the genes are regulated during the switch between morphological forms and a key signaling molecule, phospholipase D, appears to regulate encystation. We provide evidence for the occurrence of meiosis during encystation, suggesting that stage conversion may play a key role in recombination between strains. Conclusions Our analysis demonstrates that a number of core processes are common to encystation between distantly related parasites, including meiosis, lipid signaling and RNA modification. These data provide a foundation for understanding the developmental cascade in the important human pathogen E. histolytica and highlight conserved processes more widely relevant in enteric pathogens.
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Pearson RJ, Morf L, Singh U. Regulation of H2O2 stress-responsive genes through a novel transcription factor in the protozoan pathogen Entamoeba histolytica. J Biol Chem 2012; 288:4462-74. [PMID: 23250742 DOI: 10.1074/jbc.m112.423467] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Outcome of infection depends upon complex interactions between the invading pathogen and the host. As part of the host's innate immune response, the release of reactive oxygen and nitrogen species by phagocytes represents a major obstacle to the establishment of infection. The ability of the human parasite Entamoeba histolytica to survive reactive oxygen and nitrogen species is central to its pathogenic potential and contributes to disease outcome. In order to define the transcriptional network associated with oxidative stress, we utilized the MEME and MAST programs to analyze the promoter regions of 57 amoebic genes that had increased expression specifically in response to H(2)O(2) exposure. We functionally characterized an H(2)O(2)-regulatory motif (HRM) ((1)AAACCTCAATGAAGA(15)), which was enriched in these promoters and specifically bound amoebic nuclear protein(s). Assays with promoter-luciferase fusions established the importance of key residues and that the HRM motif directly impacted the ability of H(2)O(2)-responsive promoters to drive gene expression. DNA affinity chromatography and mass spectrometry identified EHI_108720 as an HRM DNA-binding protein. Overexpression and down-regulation of EHI_108720 demonstrated the specificity of EHI_108720 protein binding to the HRM, and overexpression increased basal expression from an H(2)O(2)-responsive wild-type promoter but not from its mutant counterpart. Thus, EHI_108720, or HRM-binding protein, represents a new stress-responsive transcription factor in E. histolytica that controls a transcriptional regulatory network associated with oxidative stress. Overexpression of EHI_108720 increased parasite virulence. Insight into how E. histolytica responds to oxidative stress increases our understanding of how this important human pathogen establishes invasive disease.
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Affiliation(s)
- Richard J Pearson
- Division of Infectious Diseases, Department of Internal Medicine, Stanford University School of Medicine, Stanford, California 94305, USA
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Ali IKM, Haque R, Siddique A, Kabir M, Sherman NE, Gray SA, Cangelosi GA, Petri WA. Proteomic analysis of the cyst stage of Entamoeba histolytica. PLoS Negl Trop Dis 2012; 6:e1643. [PMID: 22590659 PMCID: PMC3348168 DOI: 10.1371/journal.pntd.0001643] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2011] [Accepted: 03/30/2012] [Indexed: 11/23/2022] Open
Abstract
Background The category B agent of bioterrorism, Entamoeba histolytica has a two-stage life cycle: an infective cyst stage, and an invasive trophozoite stage. Due to our inability to effectively induce encystation in vitro, our knowledge about the cyst form remains limited. This also hampers our ability to develop cyst-specific diagnostic tools. Aims Three main aims were (i) to identify E. histolytica proteins in cyst samples, (ii) to enrich our knowledge about the cyst stage, and (iii) to identify candidate proteins to develop cyst-specific diagnostic tools. Methods Cysts were purified from the stool of infected individuals using Percoll (gradient) purification. A highly sensitive LC-MS/MS mass spectrometer (Orbitrap) was used to identify cyst proteins. Results A total of 417 non-redundant E. histolytica proteins were identified including 195 proteins that were never detected in trophozoite-derived proteomes or expressed sequence tag (EST) datasets, consistent with cyst specificity. Cyst-wall specific glycoproteins Jacob, Jessie and chitinase were positively identified. Antibodies produced against Jacob identified cysts in fecal specimens and have potential utility as a diagnostic reagent. Several protein kinases, small GTPase signaling molecules, DNA repair proteins, epigenetic regulators, and surface associated proteins were also identified. Proteins we identified are likely to be among the most abundant in excreted cysts, and therefore show promise as diagnostic targets. Major Conclusions The proteome data generated here are a first for naturally-occurring E. histolytica cysts, and they provide important insights into the infectious cyst form. Additionally, numerous unique candidate proteins were identified which will aid the development of new diagnostic tools for identification of E. histolytica cysts. We used tandem mass spectrometry to identify E. histolytica cyst proteins in 5 cyst positive stool samples. We report the identification of 417 non-redundant E. histolytica proteins including 195 proteins that were not identified in existing trophozoite derived proteome or EST datasets, consistent with cyst specificity. Because the cysts were derived directly from patient samples with incomplete purification, a limited number of proteins were identified (N = 417) that probably represent only a partial proteome. Nevertheless, the study succeeded in identifying proteins that are likely to be abundant in the cyst stage of the parasite. Several of these proteins may play roles in E. histolytica stage conversion or cyst function. Proteins identified in this study may be useful markers for diagnostic detection of E. histolytica cysts. Overall, the data generated in this study promises to aid the understanding of the cyst stage of the parasite which is vital for disease transmission and pathogenesis in E. histolytica.
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Affiliation(s)
- Ibne Karim M. Ali
- Division of Infectious Disease and International Health, University of Virginia Health System, Charlottesville, Virginia, United States of America
- * E-mail: (IKMA); (WAP)
| | - Rashidul Haque
- International Center for Diarrhoeal Disease Research Bangladesh, Mohakhali, Dhaka, Bangladesh
| | - Abdullah Siddique
- International Center for Diarrhoeal Disease Research Bangladesh, Mohakhali, Dhaka, Bangladesh
| | - Mamun Kabir
- International Center for Diarrhoeal Disease Research Bangladesh, Mohakhali, Dhaka, Bangladesh
| | - Nicholas E. Sherman
- W. M. Keck Biomedical Mass Spectrometry Core, University of Virginia Health Sciences Center, Charlottesville, Virginia, United States of America
| | - Sean A. Gray
- Seattle Biomedical Research Institute, Seattle, Washington, United States of America
| | - Gerard A. Cangelosi
- Seattle Biomedical Research Institute, Seattle, Washington, United States of America
| | - William A. Petri
- Division of Infectious Disease and International Health, University of Virginia Health System, Charlottesville, Virginia, United States of America
- * E-mail: (IKMA); (WAP)
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Transient and stable transfection in the protozoan parasite Entamoeba invadens. Mol Biochem Parasitol 2012; 184:59-62. [PMID: 22561071 DOI: 10.1016/j.molbiopara.2012.04.007] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2012] [Revised: 04/16/2012] [Accepted: 04/17/2012] [Indexed: 11/22/2022]
Abstract
Entamoeba histolytica is an important human pathogen and a major health problem worldwide. Many aspects of parasite biology can be studied with the exception of stage conversion, which cannot be reproduced adequately in E. histolytica. The reptile parasite Entamoeba invadens is a vital model system for studying stage conversion since it can be induced to undergo both encystation and excystation with high efficiency in vitro. However, functional studies using E. invadens have been limited by the lack of genetic tools in this species. Here, we report a new method for both transient and stable transfection of E. invadens. These new tools will greatly enhance research into Entamoeba development.
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Prouse MB, Campbell MM. The interaction between MYB proteins and their target DNA binding sites. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2012; 1819:67-77. [DOI: 10.1016/j.bbagrm.2011.10.010] [Citation(s) in RCA: 106] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2011] [Revised: 10/17/2011] [Accepted: 10/18/2011] [Indexed: 02/02/2023]
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Zhang H, Alramini H, Tran V, Singh U. Nucleus-localized antisense small RNAs with 5'-polyphosphate termini regulate long term transcriptional gene silencing in Entamoeba histolytica G3 strain. J Biol Chem 2011; 286:44467-79. [PMID: 22049083 PMCID: PMC3247957 DOI: 10.1074/jbc.m111.278184] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2011] [Revised: 11/01/2011] [Indexed: 11/06/2022] Open
Abstract
In the deep-branching eukaryotic parasite Entamoeba histolytica, transcriptional gene silencing (TGS) of the Amoebapore A gene (ap-a) in the G3 strain has been reported with subsequent development of this parasite strain for gene silencing. However, the mechanisms underlying this gene silencing approach are poorly understood. Here we report that antisense small RNAs (sRNAs) specific to the silenced ap-a gene can be identified in G3 parasites. Furthermore, when additional genes are silenced in the G3 strain, antisense sRNAs to the newly silenced genes can also be detected. Characterization of these sRNAs demonstrates that they are ~27 nucleotides in size, have 5'-polyphosphate termini, and persist even after removal of the silencing plasmid. Immunofluorescence analysis (IFA) and fluorescence in situ hybridization (FISH) show that both the Argonaute protein EhAGO2-2 and antisense sRNAs to the silenced genes are localized to the parasite nucleus. Furthermore, α-EhAGO2-2 immunoprecipitation confirmed the direct association of the antisense sRNAs with EhAGO2-2. Finally, chromatin immunoprecipitation (ChIP) assays demonstrate that the loci of the silenced genes are enriched for histone H3 and EhAGO2-2, indicating that both chromatin modification and the RNA-induced transcriptional silencing complex are involved in permanent gene silencing in G3 parasites. In conclusion, our data demonstrate that G3-based gene silencing in E. histolytica is mediated by an siRNA pathway, which utilizes antisense 5'-polyphosphate sRNAs. To our knowledge, this is the first study to show that 5'- polyphosphate antisense sRNAs can mediate TGS, and it is the first example of RNAi-mediated TGS in protozoan parasites.
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Affiliation(s)
- Hanbang Zhang
- From the Division of Infectious Diseases, Department of Internal Medicine, and
| | - Hussein Alramini
- From the Division of Infectious Diseases, Department of Internal Medicine, and
| | - Vy Tran
- From the Division of Infectious Diseases, Department of Internal Medicine, and
| | - Upinder Singh
- From the Division of Infectious Diseases, Department of Internal Medicine, and
- the Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California 94305-5107
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Cyst and encystment in protozoan parasites: optimal targets for new life-cycle interrupting strategies? Trends Parasitol 2011; 27:450-8. [PMID: 21775209 DOI: 10.1016/j.pt.2011.06.003] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2011] [Revised: 06/15/2011] [Accepted: 06/16/2011] [Indexed: 11/24/2022]
Abstract
Certain protozoan parasites use survival strategies to reside outside the host such as the formation of cysts. This dormant and resistant stage results from the complex process of encystment that involves diverse molecular and cellular modifications. The stimuli and changes associated with cyst biogenesis are a matter of ongoing studies in human and animal protozoan parasites such as amoeba and Giardia species because blocking every step in the encystment pathway should, in theory, interrupt their life cycles. The present review thoroughly examines this essential process in those protozoan parasites and discusses the possibility of using that information to develop new kinds of anti-parasite specific and life cycle-interrupting drugs, aimed at holding back the dissemination of these infections.
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Identification of a polypeptide containing Tudor and staphyloccocal nuclease-like domains as the sequence-specific binding protein to the upstream regulatory element 1 of Entamoeba histolytica. Int J Parasitol 2011; 41:775-82. [DOI: 10.1016/j.ijpara.2011.02.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2010] [Revised: 02/02/2011] [Accepted: 02/04/2011] [Indexed: 11/21/2022]
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Novel core promoter elements and a cognate transcription factor in the divergent unicellular eukaryote Trichomonas vaginalis. Mol Cell Biol 2011; 31:1444-58. [PMID: 21245378 DOI: 10.1128/mcb.00745-10] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A highly conserved DNA initiator (Inr) element has been the only core promoter element described in the divergent unicellular eukaryote Trichomonas vaginalis, although genome analyses reveal that only ∼75% of protein-coding genes appear to contain an Inr. In search of another core promoter element(s), a nonredundant database containing 5' untranslated regions of expressed T. vaginalis genes was searched for overrepresented DNA motifs and known eukaryotic core promoter elements. In addition to identifying the Inr, two elements that lack sequence similarity to the known protein-coding gene core promoter, motif 3 (M3) and motif 5 (M5), were identified. Mutational and functional analyses demonstrate that both are novel core promoter elements. M3 [(A/G/T)(A/G)C(G/C)G(T/C)T(T/A/G)] resembles a Myb recognition element (MRE) and is bound specifically by a unique protein with a Myb-like DNA binding domain. The M5 element (CCTTT) overlaps the transcription start site and replaces the Inr as an alternative, gene-specific initiator element. Transcription specifically initiates at the second cytosine within M5, in contrast to characteristic initiation by RNA polymerase II at an adenosine. In promoters that combine M3 with either M5 or Inr, transcription initiation is regulated by the M3 motif.
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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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Singh N, Bhattacharya S, Paul J. Entamoeba invadens: dynamics of DNA synthesis during differentiation from trophozoite to cyst. Exp Parasitol 2010; 127:329-33. [PMID: 20727884 DOI: 10.1016/j.exppara.2010.08.013] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2010] [Revised: 05/26/2010] [Accepted: 08/13/2010] [Indexed: 11/24/2022]
Abstract
The DNA dynamics which mediate conversion of uni-nucleate trophozoite into quadrinucleate cyst in Entamoeba histolytica is not well understood. Here, we have addressed this question in Entamoeba invadens (a model system for encystation) through a detailed time course study of the differentiation process. We combined flow cytometric analysis with the change in rate of thymidine incorporation and the number of nuclei per cell. Our data shows that during encystment the cell population passes through three phases: (1) Early phase (0-8h); of rapid DNA synthesis which may correspond to completion of ongoing DNA replication. Bi-nucleated cells increase with concomitant drop in uni-nucleated cells. (2) Commitment phase (8-24h); in which DNA synthesis rate slows down. Possibly new rounds of replication are initiated which proceed slowly, followed by mitosis at 20 h. After this the number of bi- and uni-nucleated cells gradually decline and the tri- and tetra-nucleated cells begin to increase. (3) Consolidation phase (24-72 h); in which the rate of DNA synthesis shows a small increase till 32 h and then begins to decline. The G2/M peak reappears at 48 h, showing that more rounds of DNA replication may be getting completed, followed by nuclear division. By 72 h the encystment is virtually complete. The bi-nucleated stage could be an intermediate both in the conversion of trophozoite to cyst and back. Our study provides a comprehensive view of DNA dynamics during encystation and excystation of E. invadens.
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Affiliation(s)
- Nishant Singh
- School of Environmental Sciences, Jawaharlal Nehru University, New Delhi, India
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Meneses E, Cárdenas H, Zárate S, Brieba LG, Orozco E, López-Camarillo C, Azuara-Liceaga E. The R2R3 Myb protein family in Entamoeba histolytica. Gene 2010; 455:32-42. [DOI: 10.1016/j.gene.2010.02.004] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2009] [Revised: 02/04/2010] [Accepted: 02/05/2010] [Indexed: 11/16/2022]
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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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Dam S, Lohia A. Entamoeba histolytica sirtuin EhSir2a deacetylates tubulin and regulates the number of microtubular assemblies during the cell cycle. Cell Microbiol 2010; 12:1002-14. [PMID: 20148900 DOI: 10.1111/j.1462-5822.2010.01449.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We have discovered four sirtuin genes in Entamoeba histolytica, two of which are similar to eukaryotic sirtuins and two to bacterial and archaeal sirtuins. The eukaryotic sirtuin homologue, EhSir2a, showed NAD(+)-dependent deacetylase activity and was sensitive to class III HDAC inhibitors. Localization of EhSir2a at different cellular sites suggested that this deacetylase could have multiple targets. Using an E. histolytica cDNA library in the yeast two-hybrid genetic screen, we identified several proteins that bound to EhSir2a. These proteins included Eh alpha-tubulin, whose interaction with EhSir2a was validated in E. histolytica. We have shown that EhSir2a deacetylated tubulin and localized with microtubules in E. histolytica. Increased expression levels of EhSir2a in stable transformants led to reduced number of microtubular assemblies in serum synchronized cells. This effect was abrogated by mutations in the deacetylase domain of EhSir2a, showing that EhSir2a deacetylase activity affected the stability and number of microtubular assemblies during the cell cycle of E. histolytica. Our results suggest that epigenetic modification of tubulin by EhSir2a is one of the mechanisms that regulates microtubular assembly in E. histolytica.
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Affiliation(s)
- Somasri Dam
- Department of Biochemistry, Bose Institute, Kolkata, India
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Xiang Q, Judelson HS. Myb transcription factors in the oomycete Phytophthora with novel diversified DNA-binding domains and developmental stage-specific expression. Gene 2010; 453:1-8. [PMID: 20060444 DOI: 10.1016/j.gene.2009.12.006] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2009] [Revised: 12/14/2009] [Accepted: 12/15/2009] [Indexed: 10/20/2022]
Abstract
Transcription factors containing two or three imperfect tandem repeats of the Myb DNA-binding domain (named R2R3 and R1R2R3, respectively) regulate important processes in growth and development. This study characterizes the structure, evolution, and expression of these proteins in the potato pathogen Phytophthora infestans and other oomycetes. P. infestans was found to encode five R2R3 and nine R1R2R3 transcription factor-like proteins, plus several with additional configurations of Myb domains. Sets of R2R3 and R1R2R3 orthologs are well-conserved in three Phytophthora species. Analyses of sites that bind DNA in canonical Myb transcription factors, such as mammalian c-Myb, revealed unusual diversification in the DNA recognition helices of the oomycete proteins. While oomycete R2R3 proteins contain c-Myb-like helices, R1R2R3 proteins exhibit either c-Myb-like or novel sequences. This suggests divergence in their DNA-binding specificities, which was confirmed by electrophoretic mobility shift assays. Eight of the P. infestans R2R3 and R1R2R3 genes are up-regulated during sporulation and three during zoospore release, which suggests their involvement in spore development. This is supported by the observation that an oomycete that does not form zoospores, Hyaloperonospora arabidopsidis, contains one-third fewer of these genes than Phytophthora.
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Affiliation(s)
- Qijun Xiang
- Department of Plant Pathology and Microbiology, University of California, Riverside, 92521, USA
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