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Walters HA, Welter BH, Knight EW, Villano MA, Keramati CA, Morris MT, Temesvari LA. Hypothetical proteins play a role in stage conversion, virulence, and the stress response in the Entamoeba species. Exp Parasitol 2022; 243:108410. [DOI: 10.1016/j.exppara.2022.108410] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 09/26/2022] [Accepted: 10/18/2022] [Indexed: 11/30/2022]
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Eukaryotic Initiation Factor 2α Kinases Regulate Virulence Functions, Stage Conversion, and the Stress Response in Entamoeba invadens. mSphere 2022; 7:e0013122. [PMID: 35638357 PMCID: PMC9241534 DOI: 10.1128/msphere.00131-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Entamoeba histolytica is a protozoan parasite that causes amoebic dysentery and liver abscess. This pathogen possesses a two-stage life cycle consisting of an environmentally stable cyst and a pathogenic amoeboid trophozoite. Since infection is acquired by ingestion of cysts from contaminated food and water, this parasite is prevalent in underdeveloped countries. A reptilian pathogen, Entamoeba invadens, which can encyst in culture, has long served as a surrogate to study stage conversion. In the host, Entamoeba species must manage stress, including nutrient deprivation and host immune pressure. In many systems, the stress response is characterized by downregulation of translation, which is initiated by the phosphorylation of eukaryotic initiation factor-2 alpha (eIF2α). In mammalian cells, this phosphorylation is carried out by a family of eIF2α kinases. A canonical eIF2α translational control system exists in Entamoeba species; however, no eIF2α kinases have been characterized. In this study, we identified two eIF2α kinases in E. invadens, EiIF2K-A and EiIF2K-B. Their identity as eIF2α kinases was validated using a heterologous yeast system. We used an RNA interference (RNAi) trigger-mediated silencing system to reduce expression of EiIF2K-A, which also reduced expression of EiIF2K-B. Parasites with decreased kinase expression exhibited decreased phosphorylation of eIF2α and increased sensitivity to oxidative stress. Diminished kinase expression also correlated with an increased rate of encystation, a decreased rate of excystation, and an increase in several virulence functions, erythrophagocytosis and adhesion to host cells. Taken together, these data suggest that EiIF2K-A and EiIF2K-B are authentic eIF2α kinases that may regulate the Entamoeba stress response. IMPORTANCEEntamoeba histolytica is a human pathogen that causes dysentery and affects millions of people worldwide. This parasite possesses a two-stage life cycle: an environmentally stable cyst and the pathogenic trophozoite. Cysts are ingested from contaminated food and water; thus, this parasite in prevalent in underdeveloped countries. Current therapies commonly cause adverse side effects; therefore, new treatments are needed. In the host, Entamoeba experiences stress brought on, in part, by the host immune system. Understanding stage conversion and the stress response of this pathogen may lead to new drug therapies. Using the model organism E. invadens, we identified two kinases similar to those involved in stress and stage conversion in other systems. We determined that these kinases may regulate the oxidative stress response, stage conversion, and virulence. This work is significant, as it will inform future studies on the life cycle and pathogenicity of Entamoeba species.
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The application of genome-wide CRISPR-Cas9 screens to dissect the molecular mechanisms of toxins. Comput Struct Biotechnol J 2022; 20:5076-5084. [PMID: 36187925 PMCID: PMC9489804 DOI: 10.1016/j.csbj.2022.09.012] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 09/07/2022] [Accepted: 09/08/2022] [Indexed: 11/29/2022] Open
Abstract
Many toxins are life-threatening to both animals and humans. However, specific antidotes are not available for most of those toxins. The molecular mechanisms underlying the toxicology of well-known toxins are not yet fully characterized. Recently, the advance in CRISPR-Cas9 technologies has greatly accelerated the process of revealing the toxic mechanisms of some common toxins on hosts from a genome-wide perspective. The high-throughput CRISPR screen has made it feasible to untangle complicated interactions between a particular toxin and its corresponding targeting tissue(s). In this review, we present an overview of recent advances in molecular dissection of toxins’ cytotoxicity by using genome-wide CRISPR screens, summarize the components essential for toxin-specific CRISPR screens, and propose new strategies for future research.
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Bettadapur A, Hunter SS, Suleiman RL, Ruyechan MC, Huang W, Barbieri CG, Miller HW, Tam TSY, Settles ML, Ralston KS. Establishment of quantitative RNAi-based forward genetics in Entamoeba histolytica and identification of genes required for growth. PLoS Pathog 2021; 17:e1010088. [PMID: 34843592 PMCID: PMC8716031 DOI: 10.1371/journal.ppat.1010088] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Revised: 12/29/2021] [Accepted: 11/03/2021] [Indexed: 01/05/2023] Open
Abstract
While Entamoeba histolytica remains a globally important pathogen, it is dramatically understudied. The tractability of E. histolytica has historically been limited, which is largely due to challenging features of its genome. To enable forward genetics, we constructed and validated the first genome-wide E. histolytica RNAi knockdown mutant library. This library allows for Illumina deep sequencing analysis for quantitative identification of mutants that are enriched or depleted after selection. We developed a novel analysis pipeline to precisely define and quantify gene fragments. We used the library to perform the first RNAi screen in E. histolytica and identified slow growth (SG) mutants. Among genes targeted in SG mutants, many had annotated functions consistent with roles in cellular growth or metabolic pathways. Some targeted genes were annotated as hypothetical or lacked annotated domains, supporting the power of forward genetics in uncovering functional information that cannot be gleaned from databases. While the localization of neither of the proteins targeted in SG1 nor SG2 mutants could be predicted by sequence analysis, we showed experimentally that SG1 localized to the cytoplasm and cell surface, while SG2 localized to the cytoplasm. Overexpression of SG1 led to increased growth, while expression of a truncation mutant did not lead to increased growth, and thus aided in defining functional domains in this protein. Finally, in addition to establishing forward genetics, we uncovered new details of the unusual E. histolytica RNAi pathway. These studies dramatically improve the tractability of E. histolytica and open up the possibility of applying genetics to improve understanding of this important pathogen.
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Affiliation(s)
- Akhila Bettadapur
- Department of Microbiology and Molecular Genetics, University of California, Davis, California, United States of America
| | - Samuel S. Hunter
- Genome Center, University of California, Davis, California, United States of America
| | - Rene L. Suleiman
- Department of Microbiology and Molecular Genetics, University of California, Davis, California, United States of America
| | - Maura C. Ruyechan
- Department of Microbiology and Molecular Genetics, University of California, Davis, California, United States of America
| | - Wesley Huang
- Department of Microbiology and Molecular Genetics, University of California, Davis, California, United States of America
| | | | - Hannah W. Miller
- Department of Microbiology and Molecular Genetics, University of California, Davis, California, United States of America
| | - Tammie S. Y. Tam
- Department of Microbiology and Molecular Genetics, University of California, Davis, California, United States of America
| | - Matthew L. Settles
- Genome Center, University of California, Davis, California, United States of America
| | - Katherine S. Ralston
- Department of Microbiology and Molecular Genetics, University of California, Davis, California, United States of America
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Swann J, Jamshidi N, Lewis NE, Winzeler EA. Systems analysis of host-parasite interactions. WILEY INTERDISCIPLINARY REVIEWS-SYSTEMS BIOLOGY AND MEDICINE 2015; 7:381-400. [PMID: 26306749 PMCID: PMC4679367 DOI: 10.1002/wsbm.1311] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/17/2015] [Revised: 06/25/2015] [Accepted: 06/29/2015] [Indexed: 12/16/2022]
Abstract
Parasitic diseases caused by protozoan pathogens lead to hundreds of thousands of deaths per year in addition to substantial suffering and socioeconomic decline for millions of people worldwide. The lack of effective vaccines coupled with the widespread emergence of drug‐resistant parasites necessitates that the research community take an active role in understanding host–parasite infection biology in order to develop improved therapeutics. Recent advances in next‐generation sequencing and the rapid development of publicly accessible genomic databases for many human pathogens have facilitated the application of systems biology to the study of host–parasite interactions. Over the past decade, these technologies have led to the discovery of many important biological processes governing parasitic disease. The integration and interpretation of high‐throughput ‐omic data will undoubtedly generate extraordinary insight into host–parasite interaction networks essential to navigate the intricacies of these complex systems. As systems analysis continues to build the foundation for our understanding of host–parasite biology, this will provide the framework necessary to drive drug discovery research forward and accelerate the development of new antiparasitic therapies. WIREs Syst Biol Med 2015, 7:381–400. doi: 10.1002/wsbm.1311 For further resources related to this article, please visit the WIREs website.
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Affiliation(s)
- Justine Swann
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Neema Jamshidi
- Department of Radiological Sciences, University of California, Los Angeles, Los Angeles, CA, USA.,Institute of Engineering in Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Nathan E Lewis
- Department of Pediatrics and Novo Nordisk Foundation Center for Biosustainability, University of California, San Diego, La Jolla, CA, USA
| | - Elizabeth A Winzeler
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
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Lever MA, Rogers KL, Lloyd KG, Overmann J, Schink B, Thauer RK, Hoehler TM, Jørgensen BB. Life under extreme energy limitation: a synthesis of laboratory- and field-based investigations. FEMS Microbiol Rev 2015; 39:688-728. [PMID: 25994609 DOI: 10.1093/femsre/fuv020] [Citation(s) in RCA: 179] [Impact Index Per Article: 19.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/25/2015] [Indexed: 11/13/2022] Open
Abstract
The ability of microorganisms to withstand long periods with extremely low energy input has gained increasing scientific attention in recent years. Starvation experiments in the laboratory have shown that a phylogenetically wide range of microorganisms evolve fitness-enhancing genetic traits within weeks of incubation under low-energy stress. Studies on natural environments that are cut off from new energy supplies over geologic time scales, such as deeply buried sediments, suggest that similar adaptations might mediate survival under energy limitation in the environment. Yet, the extent to which laboratory-based evidence of starvation survival in pure or mixed cultures can be extrapolated to sustained microbial ecosystems in nature remains unclear. In this review, we discuss past investigations on microbial energy requirements and adaptations to energy limitation, identify gaps in our current knowledge, and outline possible future foci of research on life under extreme energy limitation.
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Affiliation(s)
- Mark A Lever
- Center for Geomicrobiology, Institute of Bioscience, Aarhus University, Ny Munkegade 114, 8000 Aarhus C, Denmark
| | - Karyn L Rogers
- Rensselaer Polytechnic Institute, Earth and Environmental Sciences, Jonsson-Rowland Science Center, 1W19, 110 8th Street, Troy, NY 12180, USA
| | - Karen G Lloyd
- Department of Microbiology, University of Tennessee at Knoxville, M409 Walters Life Sciences, Knoxville, TN 37996-0845, USA
| | - Jörg Overmann
- Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH, Inhoffenstraße 7B, D-38124 Braunschweig, Germany
| | - Bernhard Schink
- Microbial Ecology, Department of Biology, University of Konstanz, P.O. Box 55 60, D-78457 Konstanz, Germany
| | - Rudolf K Thauer
- Max Planck Institut für terrestrische Mikrobiologie, Karl-von-Frisch-Straße, D-35043 Marburg, Germany
| | - Tori M Hoehler
- NASA Ames Research Center, Mail Stop 239-4, Moffett Field, CA 94035-1000, USA
| | - Bo Barker Jørgensen
- Center for Geomicrobiology, Institute of Bioscience, Aarhus University, Ny Munkegade 114, 8000 Aarhus C, Denmark
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Koushik AB, Welter BH, Rock ML, Temesvari LA. A genomewide overexpression screen identifies genes involved in the phosphatidylinositol 3-kinase pathway in the human protozoan parasite Entamoeba histolytica. EUKARYOTIC CELL 2014; 13:401-11. [PMID: 24442890 PMCID: PMC3957588 DOI: 10.1128/ec.00329-13] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2013] [Accepted: 01/12/2014] [Indexed: 11/20/2022]
Abstract
Entamoeba histolytica is a protozoan parasite that causes amoebic dysentery and liver abscess. E. histolytica relies on motility, phagocytosis, host cell adhesion, and proteolysis of extracellular matrix for virulence. In eukaryotic cells, these processes are mediated in part by phosphatidylinositol 3-kinase (PI3K) signaling. Thus, PI3K may be critical for virulence. We utilized a functional genomics approach to identify genes whose products may operate in the PI3K pathway in E. histolytica. We treated a population of trophozoites that were overexpressing genes from a cDNA library with a near-lethal dose of the PI3K inhibitor wortmannin. This screen was based on the rationale that survivors would be overexpressing gene products that directly or indirectly function in the PI3K pathway. We sequenced the overexpressed genes in survivors and identified a cDNA encoding a Rap GTPase, a protein previously shown to participate in the PI3K pathway. This supports the validity of our approach. Genes encoding a coactosin-like protein, EhCoactosin, and a serine-rich E. histolytica protein (SREHP) were also identified. Cells overexpressing EhCoactosin or SREHP were also less sensitive to a second PI3K inhibitor, LY294002. This corroborates the link between these proteins and PI3K. Finally, a mutant cell line with an increased level of phosphatidylinositol (3,4,5)-triphosphate, the product of PI3K activity, exhibited increased expression of SREHP and EhCoactosin. This further supports the functional connection between these proteins and PI3K in E. histolytica. To our knowledge, this is the first forward-genetics screen adapted to reveal genes participating in a signal transduction pathway in this pathogen.
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Affiliation(s)
- Amrita B. Koushik
- Department of Genetics and Biochemistry, Clemson University, Clemson, South Carolina, USA
- Eukaryotic Pathogens Innovation Center (EPIC), Clemson University, Clemson, South Carolina, USA
| | - Brenda H. Welter
- Department of Biological Sciences, Clemson University, Clemson, South Carolina, USA
- Eukaryotic Pathogens Innovation Center (EPIC), Clemson University, Clemson, South Carolina, USA
| | - Michelle L. Rock
- Department of Biological Sciences, Clemson University, Clemson, South Carolina, USA
- Eukaryotic Pathogens Innovation Center (EPIC), Clemson University, Clemson, South Carolina, USA
| | - Lesly A. Temesvari
- Department of Biological Sciences, Clemson University, Clemson, South Carolina, USA
- Eukaryotic Pathogens Innovation Center (EPIC), Clemson University, Clemson, South Carolina, USA
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Linford AS, Jiang NM, Edwards TE, Sherman NE, Van Voorhis WC, Stewart LJ, Myler PJ, Staker BL, Petri WA. Crystal structure and putative substrate identification for the Entamoeba histolytica low molecular weight tyrosine phosphatase. Mol Biochem Parasitol 2014; 193:33-44. [PMID: 24548880 DOI: 10.1016/j.molbiopara.2014.01.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2013] [Revised: 01/12/2014] [Accepted: 01/22/2014] [Indexed: 11/28/2022]
Abstract
Entamoeba histolytica is a eukaryotic intestinal parasite of humans, and is endemic in developing countries. We have characterized the E. histolytica putative low molecular weight protein tyrosine phosphatase (LMW-PTP). The structure for this amebic tyrosine phosphatase was solved, showing the ligand-induced conformational changes necessary for binding of substrate. In amebae, it was expressed at low but detectable levels as detected by immunoprecipitation followed by immunoblotting. A mutant LMW-PTP protein in which the catalytic cysteine in the active site was replaced with a serine lacked phosphatase activity, and was used to identify a number of trapped putative substrate proteins via mass spectrometry analysis. Seven of these putative substrate protein genes were cloned with an epitope tag and overexpressed in amebae. Five of these seven putative substrate proteins were demonstrated to interact specifically with the mutant LMW-PTP. This is the first biochemical study of a small tyrosine phosphatase in Entamoeba, and sets the stage for understanding its role in amebic biology and pathogenesis.
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Affiliation(s)
- Alicia S Linford
- Department of Biochemistry and Molecular Genetics, University of Virginia Health System, Charlottesville, VA 22908, USA.
| | - Nona M Jiang
- Division of Infectious Diseases and International Health, University of Virginia Health System, Charlottesville, VA 22908, USA
| | - Thomas E Edwards
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), USA; Emerald Bio, Bainbridge Island, WA 98110, USA
| | - Nicholas E Sherman
- Department of Microbiology, Immunology, and Cancer Biology, University of Virginia, Charlottesville, VA 22908, USA
| | - Wesley C Van Voorhis
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), USA; Department of Medicine, University of Washington, Seattle, WA 98195, USA
| | - Lance J Stewart
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), USA; Emerald Bio, Bainbridge Island, WA 98110, USA
| | - Peter J Myler
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), USA; Seattle Biomedical Research Institute, Seattle, WA 98109, USA; Departments of Global Health and Medical Education & Biomedical Informatics, University of Washington, Seattle, WA 98195, USA
| | - Bart L Staker
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), USA; Emerald Bio, Bainbridge Island, WA 98110, USA
| | - William A Petri
- Division of Infectious Diseases and International Health, University of Virginia Health System, Charlottesville, VA 22908, USA; Department of Medicine, University of Virginia, Charlottesville, VA 22908, USA; Department of Pathology, University of Virginia, Charlottesville, VA 22908, USA.
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Baumel-Alterzon S, Weber C, Guillén N, Ankri S. Identification of dihydropyrimidine dehydrogenase as a virulence factor essential for the survival of Entamoeba histolytica in glucose-poor environments. Cell Microbiol 2012; 15:130-44. [PMID: 23016994 DOI: 10.1111/cmi.12036] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2012] [Revised: 09/11/2012] [Accepted: 09/19/2012] [Indexed: 11/28/2022]
Abstract
Adaptation to nutritional changes is a key feature for successful survival of a pathogen within its host. The protozoan parasite Entamoeba histolytica normally colonizes the human colon and in rare occasions, this parasite spread to distant organs, such as the liver. E. histolytica obtains most of its energy from the fermentation of glucose into ethanol. In this study, we were intrigued to know how this parasite reacts to changes in glucose availability and we addressed this issue by performing a DNA microarray analysis of gene expression. Results show that parasites that were adapted to growth in absence of glucose increased their virulence and altered the transcription of several genes. One of these genes is the dihydropyrimidine dehydrogenase (DPD), which is involved in degradation of pyrimidines. We showed that this gene is crucial for the parasite's growth when the availability of glucose is limited. These data contribute to our understanding of the parasite's ability to survive in glucose-poor environments and reveal a new role for the DPD enzyme.
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Affiliation(s)
- Sharon Baumel-Alterzon
- Department of Molecular Microbiology, Bruce Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel
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