Recent Advances in Biology: RNA Interference, Drug Entamoeba
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F1000Research 2016, 5(F1000 Faculty Rev):2578 Last updated: 17 JUL 2019 REVIEW Recent advances in Entamoeba biology: RNA interference, drug discovery, and gut microbiome [version 1; peer review: 4 approved] Pedro Morgado1*, Dipak Manna1*, Upinder Singh1,2 1Division of Infectious Diseases, Department of Internal Medicine, Stanford University School of Medicine, Stanford, California, USA 2Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, USA * Equal contributors First published: 26 Oct 2016, 5(F1000 Faculty Rev):2578 ( Open Peer Review v1 https://doi.org/10.12688/f1000research.9241.1) Latest published: 26 Oct 2016, 5(F1000 Faculty Rev):2578 ( https://doi.org/10.12688/f1000research.9241.1) Reviewer Status Abstract Invited Reviewers In recent years, substantial progress has been made in understanding the 1 2 3 4 molecular and cell biology of the human parasite Entamoeba histolytica, an important pathogen with significant global impact. This review outlines version 1 some recent advances in the Entamoeba field in the last five years, published focusing on areas that have not recently been discussed in detail: (i) 26 Oct 2016 molecular mechanisms regulating parasite gene expression, (ii) new efforts at drug discovery using high-throughput drug screens, and (iii) the effect of gut microbiota on amoebiasis. F1000 Faculty Reviews are written by members of the prestigious F1000 Faculty. They are Keywords Entamoeba , amoebiasis , parasite , protozoa commissioned and are peer reviewed before publication to ensure that the final, published version is comprehensive and accessible. The reviewers who approved the final version are listed with their names and affiliations. 1 Lesly Temesvari, Clemson University, South Carolina, USA 2 Sudha Bhattacharya, Jawaharlal Nehru University, New Delhi, India 3 Sharon Reed, School of Medicine, University of California San Diego, CA, USA 4 Tomoyoshi Nozaki, National Institute of Infectious Diseases, Tokyo, Japan University of Tsukuba, Tsukuba, Japan Any comments on the article can be found at the end of the article. Page 1 of 9 F1000Research 2016, 5(F1000 Faculty Rev):2578 Last updated: 17 JUL 2019 Corresponding author: Upinder Singh ([email protected]) Competing interests: The authors declare that they have no competing interests. Grant information: The author(s) declared that no grants were involved in supporting this work. Copyright: © 2016 Morgado P et al. This is an open access article distributed under the terms of the Creative Commons Attribution Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. How to cite this article: Morgado P, Manna D and Singh U. Recent advances in Entamoeba biology: RNA interference, drug discovery, and gut microbiome [version 1; peer review: 4 approved] F1000Research 2016, 5(F1000 Faculty Rev):2578 ( https://doi.org/10.12688/f1000research.9241.1) First published: 26 Oct 2016, 5(F1000 Faculty Rev):2578 (https://doi.org/10.12688/f1000research.9241.1) Page 2 of 9 F1000Research 2016, 5(F1000 Faculty Rev):2578 Last updated: 17 JUL 2019 Introduction the target genes regulated by specific signaling transduction Entamoeba histolytica is a unicellular protozoan parasite transmit- pathways26. Additionally, transcriptome analyses in Entamoeba ted to humans via contaminated food or water and is the causative have helped to identify cis-elements and trans-acting factors agent of amoebiasis1,2. The infectious cycle begins with ingestion involved in regulating gene expression27,28. However, despite of the cyst, which is able to survive in the environment outside ongoing efforts, only a handful of DNA motifs and transcription the human host3,4. After ingestion, parasites excyst as trophozoites factors have thus far been characterized29. in the small intestine and eventually reach the colon, where they adhere to colonic mucins and epithelial cells. The most common In a follow-up to their initial report characterizing the tran- disease attributed to E. histolytica is amoebic colitis, whose symp- scription factor EhPC4 (E. histolytica positive cofactor 4) and toms range from asymptomatic colonization of the colon to severe, its role in regulating the expression of genes involved in cell bloody diarrhea. In a subset of patients, extra-intestinal disease migration30, Hernández de la Cruz et al. recently identified a occurs following dissemination of the parasite to the liver, lung, new role for EhPC4 in regulating DNA replication and genome or brain5. Owing to unknown factors, some trophozoites encyst, stability31. E. histolytica trophozoites exist in cultures as poly- allowing them to be excreted in the stool and to go on to infect new ploid cells (a subpopulation of cells having either a single hosts. Although E. histolytica encysts naturally inside the human polyploid nucleus or multiple nuclei), whereas cysts contain host, no culturing method has been able to induce encystation in four haploid nuclei. In trophozoites, heterogeneous DNA con- laboratory conditions. However, Entamoeba invadens, a reptilian tent is due to genome re-duplication and uncoupling of nuclear amoeba, can successfully be induced to undergo encystation in division and cytokinesis32,33. Therefore, the recent data presented the laboratory and is the accepted model to study amoebic stage by Hernández de la Cruz et al. are important because they are conversion in vitro. among the first to identify a protein involved in polyploidy and genetic heterogeneity in Entamoeba. The complexity of DNA Amoebiasis is widespread among infants in developing countries organization and structure in Entamoeba has posed a challenge because of poor hygiene and sanitation, contamination of food toward unraveling aspects of parasite biology that regulate the and water with feces, and malnourishment6–8. For instance, in an flow of information, which arguably influences all other aspects of urban slum of Dhaka, Bangladesh, one-third of infants are infected parasite biology (that is, metabolism and development). Impor- with E. histolytica within the first year of life8–10. Consequently, tantly, polyploidy has posed some limitations on parasite genetic amoebiasis prevalence is higher in developing countries, such as engineering, and further molecular dissection of this pathway the Indian subcontinent, tropical and central regions of Africa, and could aid in the development of improved genetic tools, which can South America11,12. However, recent reports also identified amoe- be applied to the study of parasite biology. bic infections in east Asian developed countries and Australia13–16. In developed countries, E. histolytica infection is typically seen Advances in amoebic RNA interference and gene regulation in new immigrants and travelers returning from regions where The RNA interference (RNAi) pathway is an important basic amoebiasis is endemic, and in Japan there is a relatively high biological process for regulating gene expression and genome incidence of disease in homosexual men13,15–17. These findings stability as well as a robust tool for genetic manipulation34–36. Mul- suggest that amoebiasis can also be a re-emerging disease in devel- tiple pathways exist for biogenesis and function of small RNAs; oped countries. however, all mature small RNAs ultimately associate with an Argo- naute (Ago) protein to form an RNA-induced silencing complex, In this review, we will highlight a few topics that have emerged which mediates gene silencing37–39. Silencing occurs via target RNA in the study of Entamoeba in the last five years. A number of cleavage, translational repression, or transcriptional gene silenc- excellent reviews have recently been published on the immune ing (TGS)40. In the case of TGS, RNAi components mediate gene response to Entamoeba18, immune evasion mechanisms by the silencing by recruiting histone modification enzymes to targeted parasite19, trogocytosis (nibbling of host cells by the amoeba)20–22, loci. Post-translational modifications of the amino terminal tails of and virulence determinants23. Thus, we will focus on topics for histones alter the condensation state of chromatin, regulating the which recent reviews are not available. accessibility of DNA-binding sites for components of the transcrip- tional machinery41. Molecular methods regulating parasite gene expression Studies in model systems have provided much of what is known Elucidating the molecular mechanisms regulating gene about RNAi42,43, although data from non-model organisms have expression uncovered important variations44–46. E. histolytica has a robust and Regulation of gene expression is a complex process requiring non-canonical endogenous RNAi pathway, which regulates gene the simultaneous coordination of large-scale cellular processes expression44,47. Entamoeba has an abundant population of 27nt (for example, DNA replication and chromosomal segregation) as small RNAs that have 5′-polyphosphate (polyP) termini, indicat- well as more local processes (for example, euchromatin stabiliza- ing that they are not Dicer products—an observation made only tion and RNA polymerase recruitment). The processes governing in amoeba, Caenorhabditis elegans, and parasitic nematodes43,44,48. transcription and gene expression in Entamoeba remain poorly The repertoire of non-canonical RNAi proteins was recently understood. Recent efforts have elucidated mechanisms for expanded with the characterization of EhRNaseIII, a minimal and stabilizing