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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Bettadapur A, Ralston KS. Direct and high-throughput assays for human cell killing through trogocytosis by Entamoeba histolytica. Mol Biochem Parasitol 2020; 239:111301. [PMID: 32687867 DOI: 10.1016/j.molbiopara.2020.111301] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Revised: 07/14/2020] [Accepted: 07/15/2020] [Indexed: 02/08/2023]
Abstract
Entamoeba histolytica is the causative agent of amoebiasis. Pathogenesis is associated with profound damage to human tissues. We previously showed that amoebae kill human cells through trogocytosis. Trogocytosis is likely to underlie tissue damage during infection, although the mechanism is still unknown. Trogocytosis is difficult to assay quantitatively, which makes it difficult to study. Here, we developed two new, complementary assays to measure trogocytosis by quantifying human cell death. One assay uses CellTiterGlo, a luminescent readout for ATP, as a proxy for cell death. We found that the CellTiterGlo could be used to detect death of human cells after co-incubation with amoebae, and that it was sensitive to inhibition of actin or the amoeba surface Gal/GalNAc lectin, two conditions that are known to inhibit amoebic trogocytosis. The other assay uses two fluorescent nuclear stains to directly differentiate live and dead human cells by microscopy, and is also sensitive to inhibition of amoebic trogocytosis through interference with actin. Both assays are simple and inexpensive, can be used with suspension and adherent human cell types, and are amenable to high-throughput approaches. These new assays are tools to improve understanding of trogocytosis and amoebiasis pathogenesis.
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Affiliation(s)
- Akhila Bettadapur
- Department of Microbiology and Molecular Genetics, University of California, Davis, USA
| | - Katherine S Ralston
- Department of Microbiology and Molecular Genetics, University of California, Davis, USA.
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Raissig MT, Matos JL, Anleu Gil MX, Kornfeld A, Bettadapur A, Abrash E, Allison HR, Badgley G, Vogel JP, Berry JA, Bergmann DC. Mobile MUTE specifies subsidiary cells to build physiologically improved grass stomata. Science 2017; 355:1215-1218. [PMID: 28302860 DOI: 10.1126/science.aal3254] [Citation(s) in RCA: 123] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2016] [Accepted: 02/16/2017] [Indexed: 01/19/2023]
Abstract
Plants optimize carbon assimilation while limiting water loss by adjusting stomatal aperture. In grasses, a developmental innovation-the addition of subsidiary cells (SCs) flanking two dumbbell-shaped guard cells (GCs)-is linked to improved stomatal physiology. Here, we identify a transcription factor necessary and sufficient for SC formation in the wheat relative Brachypodium distachyon. Unexpectedly, the transcription factor is an ortholog of the stomatal regulator AtMUTE, which defines GC precursor fate in Arabidopsis The novel role of BdMUTE in specifying lateral SCs appears linked to its acquisition of cell-to-cell mobility in Brachypodium Physiological analyses on SC-less plants experimentally support classic hypotheses that SCs permit greater stomatal responsiveness and larger range of pore apertures. Manipulation of SC formation and function in crops, therefore, may be an effective approach to enhance plant performance.
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Affiliation(s)
- Michael T Raissig
- Department of Biology, Stanford University, 371 Serra Mall, Stanford, CA 94305, USA.
| | - Juliana L Matos
- Department of Biology, Stanford University, 371 Serra Mall, Stanford, CA 94305, USA
| | - M Ximena Anleu Gil
- Howard Hughes Medical Institute (HHMI), Stanford University, 371 Serra Mall, Stanford, CA 94305, USA
| | - Ari Kornfeld
- Department of Global Ecology, Carnegie Institution for Science, 260 Panama Street, Stanford, CA 94305, USA
| | - Akhila Bettadapur
- Howard Hughes Medical Institute (HHMI), Stanford University, 371 Serra Mall, Stanford, CA 94305, USA
| | - Emily Abrash
- Department of Biology, Stanford University, 371 Serra Mall, Stanford, CA 94305, USA
| | - Hannah R Allison
- Department of Biology, Stanford University, 371 Serra Mall, Stanford, CA 94305, USA
| | - Grayson Badgley
- Department of Global Ecology, Carnegie Institution for Science, 260 Panama Street, Stanford, CA 94305, USA
| | - John P Vogel
- U.S. Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA
| | - Joseph A Berry
- Department of Global Ecology, Carnegie Institution for Science, 260 Panama Street, Stanford, CA 94305, USA
| | - Dominique C Bergmann
- Department of Biology, Stanford University, 371 Serra Mall, Stanford, CA 94305, USA. .,Howard Hughes Medical Institute (HHMI), Stanford University, 371 Serra Mall, Stanford, CA 94305, USA
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