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Gerrick ER, Zlitni S, West PT, Carter MM, Mechler CM, Olm MR, Caffrey EB, Li JA, Higginbottom SK, Severyn CJ, Kracke F, Spormann AM, Sonnenburg JL, Bhatt AS, Howitt MR. Metabolic diversity in commensal protists regulates intestinal immunity and trans-kingdom competition. Cell 2024; 187:62-78.e20. [PMID: 38096822 DOI: 10.1016/j.cell.2023.11.018] [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: 08/26/2022] [Revised: 08/01/2023] [Accepted: 11/14/2023] [Indexed: 01/05/2024]
Abstract
The microbiota influences intestinal health and physiology, yet the contributions of commensal protists to the gut environment have been largely overlooked. Here, we discover human- and rodent-associated parabasalid protists, revealing substantial diversity and prevalence in nonindustrialized human populations. Genomic and metabolomic analyses of murine parabasalids from the genus Tritrichomonas revealed species-level differences in excretion of the metabolite succinate, which results in distinct small intestinal immune responses. Metabolic differences between Tritrichomonas species also determine their ecological niche within the microbiota. By manipulating dietary fibers and developing in vitro protist culture, we show that different Tritrichomonas species prefer dietary polysaccharides or mucus glycans. These polysaccharide preferences drive trans-kingdom competition with specific commensal bacteria, which affects intestinal immunity in a diet-dependent manner. Our findings reveal unappreciated diversity in commensal parabasalids, elucidate differences in commensal protist metabolism, and suggest how dietary interventions could regulate their impact on gut health.
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Affiliation(s)
- Elias R Gerrick
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Soumaya Zlitni
- Department of Genetics, Stanford University, Stanford, CA 94305, USA; Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Patrick T West
- Department of Genetics, Stanford University, Stanford, CA 94305, USA; Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Matthew M Carter
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Claire M Mechler
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Matthew R Olm
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Elisa B Caffrey
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Jessica A Li
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Steven K Higginbottom
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Christopher J Severyn
- Department of Genetics, Stanford University, Stanford, CA 94305, USA; Department of Pediatrics, Division of Hematology/Oncology/Stem Cell Transplant and Regenerative Medicine Stanford University, Palo Alto, CA 94305, USA
| | - Frauke Kracke
- Department of Civil and Environmental Engineering, Stanford University, Stanford, CA 94305, USA
| | - Alfred M Spormann
- Department of Civil and Environmental Engineering, Stanford University, Stanford, CA 94305, USA; Department of Chemical Engineering, Stanford University, Stanford, CA 94305, USA
| | - Justin L Sonnenburg
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
| | - Ami S Bhatt
- Department of Genetics, Stanford University, Stanford, CA 94305, USA; Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Michael R Howitt
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA.
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Dewees SI, Vargová R, Hardin KR, Turn RE, Devi S, Linnert J, Wolfrum U, Caspary T, Eliáš M, Kahn RA. Phylogenetic profiling and cellular analyses of ARL16 reveal roles in traffic of IFT140 and INPP5E. Mol Biol Cell 2022; 33:ar33. [PMID: 35196065 PMCID: PMC9250359 DOI: 10.1091/mbc.e21-10-0509-t] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Revised: 01/11/2022] [Accepted: 02/18/2022] [Indexed: 12/14/2022] Open
Abstract
The ARF family of regulatory GTPases is ancient, with 16 members predicted to have been present in the last eukaryotic common ancestor. Our phylogenetic profiling of paralogues in diverse species identified four family members whose presence correlates with that of a cilium/flagellum: ARL3, ARL6, ARL13, and ARL16. No prior evidence links ARL16 to cilia or other cell functions, despite its presence throughout eukaryotes. Deletion of ARL16 in mouse embryonic fibroblasts (MEFs) results in decreased ciliogenesis yet increased ciliary length. We also found Arl16 knockout (KO) in MEFs to alter ciliary protein content, including loss of ARL13B, ARL3, INPP5E, and the IFT-A core component IFT140. Instead, both INPP5E and IFT140 accumulate at the Golgi in Arl16 KO lines, while other intraflagellar transport (IFT) proteins do not, suggesting a specific defect in traffic from Golgi to cilia. We propose that ARL16 regulates a Golgi-cilia traffic pathway and is required specifically in the export of IFT140 and INPP5E from the Golgi.
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Affiliation(s)
- Skylar I. Dewees
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322
- Biochemistry, Cell & Developmental Biology Graduate Program, Laney Graduate School, Emory University, Atlanta, GA 30307
| | - Romana Vargová
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, CZ-710 00, Ostrava, Czech Republic
| | - Katherine R. Hardin
- Department of Cell Biology, Emory University School of Medicine, Atlanta, GA 30322
- Biochemistry, Cell & Developmental Biology Graduate Program, Laney Graduate School, Emory University, Atlanta, GA 30307
| | - Rachel E. Turn
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322
- Biochemistry, Cell & Developmental Biology Graduate Program, Laney Graduate School, Emory University, Atlanta, GA 30307
- Department of Microbiology and Immunology, Stanford University, Palo Alto, CA 94305-5124
| | - Saroja Devi
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322
| | - Joshua Linnert
- Institute of Molecular Physiology, Johannes Gutenberg University, Mainz 55128, Germany
| | - Uwe Wolfrum
- Institute of Molecular Physiology, Johannes Gutenberg University, Mainz 55128, Germany
| | - Tamara Caspary
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322
| | - Marek Eliáš
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, CZ-710 00, Ostrava, Czech Republic
| | - Richard A. Kahn
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322
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Small RNAs Are Implicated in Regulation of Gene and Transposable Element Expression in the Protist Trichomonas vaginalis. mSphere 2021; 6:6/1/e01061-20. [PMID: 33408230 PMCID: PMC7845603 DOI: 10.1128/msphere.01061-20] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Trichomoniasis, caused by the protozoan Trichomonas vaginalis, is the most common nonviral sexually transmitted infection in humans. The millions of cases each year have sequelae that may include complications during pregnancy and increased risk of HIV infection. Trichomonas vaginalis is the causative agent of trichomoniasis, the most prevalent nonviral sexually transmitted infection worldwide. Repetitive elements, including transposable elements (TEs) and virally derived repeats, comprise more than half of the ∼160-Mb T. vaginalis genome. An intriguing question is how the parasite controls its potentially lethal complement of mobile elements, which can disrupt transcription of protein-coding genes and genome functions. In this study, we generated high-throughput RNA sequencing (RNA-Seq) and small RNA-Seq data sets in triplicate for the T. vaginalis G3 reference strain and characterized the mRNA and small RNA populations and their mapping patterns along all six chromosomes. Mapping the RNA-Seq transcripts to the genome revealed that the majority of genes predicted within repetitive elements are not expressed. Interestingly, we identified a novel species of small RNA that maps bidirectionally along the chromosomes and is correlated with reduced protein-coding gene expression and reduced RNA-Seq coverage in repetitive elements. This novel small RNA family may play a regulatory role in gene and repetitive element expression. Our results identify a possible small RNA pathway mechanism by which the parasite regulates expression of genes and TEs and raise intriguing questions as to the role repeats may play in shaping T. vaginalis genome evolution and the diversity of small RNA pathways in general. IMPORTANCE Trichomoniasis, caused by the protozoan Trichomonas vaginalis, is the most common nonviral sexually transmitted infection in humans. The millions of cases each year have sequelae that may include complications during pregnancy and increased risk of HIV infection. Given its evident success in this niche, it is paradoxical that T. vaginalis harbors in its genome thousands of transposable elements that have the potential to be extremely detrimental to normal genomic function. In many organisms, transposon expression is regulated by the activity of endogenously expressed short (∼21 to 35 nucleotides [nt]) small RNA molecules that effect gene silencing by targeting mRNAs for degradation or by recruiting epigenetic silencing machinery to locations in the genome. Our research has identified small RNA molecules correlated with reduced expression of T. vaginalis genes and transposons. This suggests that a small RNA pathway is a major contributor to gene expression patterns in the parasite and opens up new avenues for investigation into small RNA biogenesis, function, and diversity.
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Diversity profiling of xenic cultures of Dientamoeba fragilis following systematic antibiotic treatment and prospects for genome sequencing. Parasitology 2019; 147:29-38. [PMID: 31452478 DOI: 10.1017/s0031182019001173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
The presence of bacterial DNA in Dientamoeba fragilis DNA extracts from culture poses a substantial challenge to sequencing the D. fragilis genome. However, elimination of bacteria from D. fragilis cultures has proven difficult in the past, presumably due to its dependence on some unknown prokaryote/s. This study explored options for removal of bacteria from D. fragilis cultures and for the generation of genome sequence data from D. fragilis. DNA was extracted from human faecal samples and xenic D. fragilis cultures. Extracts were subjected to 16S ribosomal DNA bacterial diversity profiling. Xenic D. fragilis cultures were then subject to antibiotic treatment regimens that systematically removed bacterial species depending on their membrane structure (Gram-positive or Gram-negative) and aerobic requirements. The impact of these treatments on cultures was assessed by 16S amplicon sequencing. Prior to antibiotic treatment, the cultures were dominated by Gram-negative bacteria. Addition of meropenem to cultures eliminated anaerobic Gram-negative bacteria, but it also led to protozoan death after 5 days incubation. The seeding of meropenem resistant Klebsiella pneumoniae strain KPC-2 into cultures before treatment by meropenem prevented death of D. fragilis cells beyond this 5 day period, suggesting that one or more species of Gram-negative bacteria may be an essential nutritional requirement for D. fragilis. Gram-positive cells were completely eliminated using vancomycin without affecting trophozoite growth. Finally, this study shows that genome sequencing of D. fragilis is feasible following bacterial elimination from cultures as the result of the major advances occurring in bioinformatics. We provide evidence on this fact by successfully sequencing the D. fragilis 28S large ribosomal DNA subunit gene using culture-derived DNA.
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Handrich MR, Garg SG, Sommerville EW, Hirt RP, Gould SB. Characterization of the BspA and Pmp protein family of trichomonads. Parasit Vectors 2019; 12:406. [PMID: 31426868 PMCID: PMC6701047 DOI: 10.1186/s13071-019-3660-z] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Accepted: 08/08/2019] [Indexed: 11/16/2022] Open
Abstract
Background Trichomonas vaginalis is a human-infecting trichomonad and as such the best studied and the only for which the full genome sequence is available considering its parasitic lifestyle, T. vaginalis encodes an unusually high number of proteins. Many gene families are massively expanded and some genes are speculated to have been acquired from prokaryotic sources. Among the latter are two gene families that harbour domains which share similarity with proteins of Bacteroidales/Spirochaetales and Chlamydiales: the BspA and the Pmp proteins, respectively. Results We sequenced the transcriptomes of five trichomonad species and screened for the presence of BspA and Pmp domain-containing proteins and characterized individual candidate proteins from both families in T. vaginalis. Here, we demonstrate that (i) BspA and Pmp domain-containing proteins are universal to trichomonads, but specifically expanded in T. vaginalis; (ii) in line with a concurrent expansion of the endocytic machinery, there is a high number of BspA and Pmp proteins which carry C-terminal endocytic motifs; and (iii) both families traffic through the ER and have the ability to increase adhesion performance in a non-virulent T. vaginalis strain and Tetratrichomonas gallinarum by a so far unknown mechanism. Conclusions Our results initiate the functional characterization of these two broadly distributed protein families and help to better understand the origin and evolution of BspA and Pmp domains in trichomonads. Electronic supplementary material The online version of this article (10.1186/s13071-019-3660-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Maria R Handrich
- Institute for Molecular Evolution, Heinrich-Heine-University, Universitätsstraße 1, 40225, Düsseldorf, Germany
| | - Sriram G Garg
- Institute for Molecular Evolution, Heinrich-Heine-University, Universitätsstraße 1, 40225, Düsseldorf, Germany
| | - Ewen W Sommerville
- Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
| | - Robert P Hirt
- Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
| | - Sven B Gould
- Institute for Molecular Evolution, Heinrich-Heine-University, Universitätsstraße 1, 40225, Düsseldorf, Germany.
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Was the Mitochondrion Necessary to Start Eukaryogenesis? Trends Microbiol 2018; 27:96-104. [PMID: 30466901 DOI: 10.1016/j.tim.2018.10.005] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Revised: 09/21/2018] [Accepted: 10/11/2018] [Indexed: 12/11/2022]
Abstract
Arguments based on cell energetics favour the view that a mitochondrion capable of oxidative phosphorylation was a prerequisite for the evolution of other features of the eukaryotic cell, including increased volume, genome size and, eventually, phagotrophy. Contrary to this we argue that: (i) extant amitochondriate eukaryotes possess voluminous phagotrophic cells with large genomes; (ii) picoeukaryotes demonstrate that phagotrophy is feasible at prokaryotic cell sizes; and (iii) the assumption that evolution of complex features requires extra ATP, often mentioned in this context, is unfounded and should not be used in such considerations. We claim that the diversity of cell organisations and functions observed today in eukaryotes gives no reason to postulate that a mitochondrion must have preceded phagocytosis in eukaryogenesis.
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Schneider C, O'Leary CE, von Moltke J, Liang HE, Ang QY, Turnbaugh PJ, Radhakrishnan S, Pellizzon M, Ma A, Locksley RM. A Metabolite-Triggered Tuft Cell-ILC2 Circuit Drives Small Intestinal Remodeling. Cell 2018; 174:271-284.e14. [PMID: 29887373 PMCID: PMC6046262 DOI: 10.1016/j.cell.2018.05.014] [Citation(s) in RCA: 282] [Impact Index Per Article: 47.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Revised: 03/26/2018] [Accepted: 05/07/2018] [Indexed: 12/13/2022]
Abstract
The small intestinal tuft cell-ILC2 circuit mediates epithelial responses to intestinal helminths and protists by tuft cell chemosensory-like sensing and IL-25-mediated activation of lamina propria ILC2s. Small intestine ILC2s constitutively express the IL-25 receptor, which is negatively regulated by A20 (Tnfaip3). A20 deficiency in ILC2s spontaneously triggers the circuit and, unexpectedly, promotes adaptive small-intestinal lengthening and remodeling. Circuit activation occurs upon weaning and is enabled by dietary polysaccharides that render mice permissive for Tritrichomonas colonization, resulting in luminal accumulation of acetate and succinate, metabolites of the protist hydrogenosome. Tuft cells express GPR91, the succinate receptor, and dietary succinate, but not acetate, activates ILC2s via a tuft-, TRPM5-, and IL-25-dependent pathway. Also induced by parasitic helminths, circuit activation and small intestinal remodeling impairs infestation by new helminths, consistent with the phenomenon of concomitant immunity. We describe a metabolic sensing circuit that may have evolved to facilitate mutualistic responses to luminal pathosymbionts.
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Affiliation(s)
- Christoph Schneider
- Department of Medicine, University of California San Francisco (UCSF), San Francisco, CA 94143, USA
| | - Claire E O'Leary
- Department of Medicine, University of California San Francisco (UCSF), San Francisco, CA 94143, USA
| | - Jakob von Moltke
- Department of Medicine, University of California San Francisco (UCSF), San Francisco, CA 94143, USA
| | - Hong-Erh Liang
- Department of Medicine, University of California San Francisco (UCSF), San Francisco, CA 94143, USA
| | - Qi Yan Ang
- Department of Microbiology & Immunology, University of California San Francisco (UCSF), San Francisco, CA 94143, USA
| | - Peter J Turnbaugh
- Department of Microbiology & Immunology, University of California San Francisco (UCSF), San Francisco, CA 94143, USA
| | | | | | - Averil Ma
- Department of Medicine, University of California San Francisco (UCSF), San Francisco, CA 94143, USA
| | - Richard M Locksley
- Department of Medicine, University of California San Francisco (UCSF), San Francisco, CA 94143, USA; Department of Microbiology & Immunology, University of California San Francisco (UCSF), San Francisco, CA 94143, USA; Howard Hughes Medical Institute, UCSF.
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Bradic M, Warring SD, Tooley GE, Scheid P, Secor WE, Land KM, Huang PJ, Chen TW, Lee CC, Tang P, Sullivan SA, Carlton JM. Genetic Indicators of Drug Resistance in the Highly Repetitive Genome of Trichomonas vaginalis. Genome Biol Evol 2018. [PMID: 28633446 PMCID: PMC5522705 DOI: 10.1093/gbe/evx110] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Trichomonas vaginalis, the most common nonviral sexually transmitted parasite, causes ∼283 million trichomoniasis infections annually and is associated with pregnancy complications and increased risk of HIV-1 acquisition. The antimicrobial drug metronidazole is used for treatment, but in a fraction of clinical cases, the parasites can become resistant to this drug. We undertook sequencing of multiple clinical isolates and lab derived lines to identify genetic markers and mechanisms of metronidazole resistance. Reduced representation genome sequencing of ∼100 T. vaginalis clinical isolates identified 3,923 SNP markers and presence of a bipartite population structure. Linkage disequilibrium was found to decay rapidly, suggesting genome-wide recombination and the feasibility of genetic association studies in the parasite. We identified 72 SNPs associated with metronidazole resistance, and a comparison of SNPs within several lab-derived resistant lines revealed an overlap with the clinically resistant isolates. We identified SNPs in genes for which no function has yet been assigned, as well as in functionally-characterized genes relevant to drug resistance (e.g., pyruvate:ferredoxin oxidoreductase). Transcription profiles of resistant strains showed common changes in genes involved in drug activation (e.g., flavin reductase), accumulation (e.g., multidrug resistance pump), and detoxification (e.g., nitroreductase). Finally, we identified convergent genetic changes in lab-derived resistant lines of Tritrichomonas foetus, a distantly related species that causes venereal disease in cattle. Shared genetic changes within and between T. vaginalis and Tr. foetus parasites suggest conservation of the pathways through which adaptation has occurred. These findings extend our knowledge of drug resistance in the parasite, providing a panel of markers that can be used as a diagnostic tool.
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Affiliation(s)
- Martina Bradic
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York
| | - Sally D Warring
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York
| | - Grace E Tooley
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York
| | - Paul Scheid
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York
| | - William E Secor
- Division of Parasitic Diseases and Malaria, Center for Global Health, Centers for Disease Control and Prevention, Atlanta, GE
| | - Kirkwood M Land
- Department of Biological Sciences, University of the Pacific, Stockton, CA
| | - Po-Jung Huang
- Bioinformatics Center/Molecular Medicine Research Center, Chang Gung University, Taoyuan, Taiwan
| | - Ting-Wen Chen
- Bioinformatics Center/Molecular Medicine Research Center, Chang Gung University, Taoyuan, Taiwan
| | - Chi-Ching Lee
- Bioinformatics Center/Molecular Medicine Research Center, Chang Gung University, Taoyuan, Taiwan
| | - Petrus Tang
- Bioinformatics Center/Molecular Medicine Research Center, Chang Gung University, Taoyuan, Taiwan
| | - Steven A Sullivan
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York
| | - Jane M Carlton
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York
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Mazumdar R, Endler L, Monoyios A, Hess M, Bilic I. Establishment of a de novo Reference Transcriptome of Histomonas meleagridis Reveals Basic Insights About Biological Functions and Potential Pathogenic Mechanisms of the Parasite. Protist 2017; 168:663-685. [DOI: 10.1016/j.protis.2017.09.004] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2017] [Revised: 08/21/2017] [Accepted: 09/23/2017] [Indexed: 12/28/2022]
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