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Williams FN, Scaglione KM. Insights on Microsatellite Characteristics, Evolution, and Function From the Social Amoeba Dictyostelium discoideum. Front Neurosci 2022; 16:886837. [PMID: 35769695 PMCID: PMC9234386 DOI: 10.3389/fnins.2022.886837] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Accepted: 05/16/2022] [Indexed: 11/13/2022] Open
Abstract
Microsatellites are repetitive sequences commonly found in the genomes of higher organisms. These repetitive sequences are prone to expansion or contraction, and when microsatellite expansion occurs in the regulatory or coding regions of genes this can result in a number of diseases including many neurodegenerative diseases. Unlike in humans and other organisms, the social amoeba Dictyostelium discoideum contains an unusually high number of microsatellites. Intriguingly, many of these microsatellites fall within the coding region of genes, resulting in nearly 10,000 homopolymeric repeat proteins within the Dictyostelium proteome. Surprisingly, among the most common of these repeats are polyglutamine repeats, a type of repeat that causes a class of nine neurodegenerative diseases in humans. In this minireview, we summarize what is currently known about homopolymeric repeats and microsatellites in Dictyostelium discoideum and discuss the potential utility of Dictyostelium for identifying novel mechanisms that utilize and regulate regions of repetitive DNA.
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Affiliation(s)
- Felicia N. Williams
- Department of Molecular Genetics and Microbiology, Duke University, Durham, NC, United States
| | - K. Matthew Scaglione
- Department of Molecular Genetics and Microbiology, Duke University, Durham, NC, United States
- Department of Neurology, Duke University, Durham, NC, United States
- Duke Center for Neurodegeneration and Neurotherapeutics, Duke University, Durham, NC, United States
- *Correspondence: K. Matthew Scaglione,
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The genetic architecture underlying prey-dependent performance in a microbial predator. Nat Commun 2022; 13:319. [PMID: 35031602 PMCID: PMC8760311 DOI: 10.1038/s41467-021-27844-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Accepted: 12/10/2021] [Indexed: 11/30/2022] Open
Abstract
Natural selection should favour generalist predators that outperform specialists across all prey types. Two genetic solutions could explain why intraspecific variation in predatory performance is, nonetheless, widespread: mutations beneficial on one prey type are costly on another (antagonistic pleiotropy), or mutational effects are prey-specific, which weakens selection, allowing variation to persist (relaxed selection). To understand the relative importance of these alternatives, we characterised natural variation in predatory performance in the microbial predator Dictyostelium discoideum. We found widespread nontransitive differences among strains in predatory success across different bacterial prey, which can facilitate stain coexistence in multi-prey environments. To understand the genetic basis, we developed methods for high throughput experimental evolution on different prey (REMI-seq). Most mutations (~77%) had prey-specific effects, with very few (~4%) showing antagonistic pleiotropy. This highlights the potential for prey-specific effects to dilute selection, which would inhibit the purging of variation and prevent the emergence of an optimal generalist predator. What prevents a generalist predator from evolving and outperforming specialist predators? By combing analyses of natural variation with experimental evolution, Stewart et al. suggest that predator variation persists because most mutations have prey-specific effects, which results in relaxed selection
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Pears CJ, Brustel J, Lakin ND. Dictyostelium discoideum as a Model to Assess Genome Stability Through DNA Repair. Front Cell Dev Biol 2021; 9:752175. [PMID: 34692705 PMCID: PMC8529158 DOI: 10.3389/fcell.2021.752175] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Accepted: 09/20/2021] [Indexed: 11/25/2022] Open
Abstract
Preserving genome integrity through repair of DNA damage is critical for human health and defects in these pathways lead to a variety of pathologies, most notably cancer. The social amoeba Dictyostelium discoideum is remarkably resistant to DNA damaging agents and genome analysis reveals it contains orthologs of several DNA repair pathway components otherwise limited to vertebrates. These include the Fanconi Anemia DNA inter-strand crosslink and DNA strand break repair pathways. Loss of function of these not only results in malignancy, but also neurodegeneration, immune-deficiencies and congenital abnormalities. Additionally, D. discoideum displays remarkable conservations of DNA repair factors that are targets in cancer and other therapies, including poly(ADP-ribose) polymerases that are targeted to treat breast and ovarian cancers. This, taken together with the genetic tractability of D. discoideum, make it an attractive model to assess the mechanistic basis of DNA repair to provide novel insights into how these pathways can be targeted to treat a variety of pathologies. Here we describe progress in understanding the mechanisms of DNA repair in D. discoideum, and how these impact on genome stability with implications for understanding development of malignancy.
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Affiliation(s)
- Catherine J. Pears
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
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Gruenheit N, Baldwin A, Stewart B, Jaques S, Keller T, Parkinson K, Salvidge W, Baines R, Brimson C, Wolf JB, Chisholm R, Harwood AJ, Thompson CRL. Mutant resources for functional genomics in Dictyostelium discoideum using REMI-seq technology. BMC Biol 2021; 19:172. [PMID: 34429112 PMCID: PMC8386026 DOI: 10.1186/s12915-021-01108-y] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2021] [Accepted: 07/22/2021] [Indexed: 01/26/2023] Open
Abstract
Background Genomes can be sequenced with relative ease, but ascribing gene function remains a major challenge. Genetically tractable model systems are crucial to meet this challenge. One powerful model is the social amoeba Dictyostelium discoideum, a eukaryotic microbe widely used to study diverse questions in the cell, developmental and evolutionary biology. Results We describe REMI-seq, an adaptation of Tn-seq, which allows high throughput, en masse, and quantitative identification of the genomic site of insertion of a drug resistance marker after restriction enzyme-mediated integration. We use REMI-seq to develop tools which greatly enhance the efficiency with which the sequence, transcriptome or proteome variation can be linked to phenotype in D. discoideum. These comprise (1) a near genome-wide resource of individual mutants and (2) a defined pool of ‘barcoded’ mutants to allow large-scale parallel phenotypic analyses. These resources are freely available and easily accessible through the REMI-seq website that also provides comprehensive guidance and pipelines for data analysis. We demonstrate that integrating these resources allows novel regulators of cell migration, phagocytosis and macropinocytosis to be rapidly identified. Conclusions We present methods and resources, generated using REMI-seq, for high throughput gene function analysis in a key model system. Supplementary Information The online version contains supplementary material available at 10.1186/s12915-021-01108-y.
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Affiliation(s)
- Nicole Gruenheit
- Centre for Life's Origins and Evolution, Department of Genetics, Evolution and Environment, University College London, Darwin Building, Gower Street, London, WC1E 6BT, UK
| | - Amy Baldwin
- Cardiff School of Biosciences, Cardiff University, Hadyn Ellis Building, Maindy Road, Cardiff, CF24 4HQ, UK
| | - Balint Stewart
- Centre for Life's Origins and Evolution, Department of Genetics, Evolution and Environment, University College London, Darwin Building, Gower Street, London, WC1E 6BT, UK
| | - Sarah Jaques
- Cardiff School of Biosciences, Cardiff University, Hadyn Ellis Building, Maindy Road, Cardiff, CF24 4HQ, UK
| | - Thomas Keller
- Division of Developmental Biology and Medicine, Faculty of Biology, Medicine and Health, The University of Manchester, Michael Smith Building, Oxford Road, Manchester, M13 9PT, UK
| | - Katie Parkinson
- Division of Developmental Biology and Medicine, Faculty of Biology, Medicine and Health, The University of Manchester, Michael Smith Building, Oxford Road, Manchester, M13 9PT, UK
| | - William Salvidge
- Centre for Life's Origins and Evolution, Department of Genetics, Evolution and Environment, University College London, Darwin Building, Gower Street, London, WC1E 6BT, UK
| | - Robert Baines
- Centre for Life's Origins and Evolution, Department of Genetics, Evolution and Environment, University College London, Darwin Building, Gower Street, London, WC1E 6BT, UK
| | - Chris Brimson
- Centre for Life's Origins and Evolution, Department of Genetics, Evolution and Environment, University College London, Darwin Building, Gower Street, London, WC1E 6BT, UK
| | - Jason B Wolf
- Milner Centre for Evolution and Department of Biology and Biochemistry, University of Bath, Claverton Down, Bath, BA2 7AY, UK
| | - Rex Chisholm
- Feinberg School of Medicine, Northwestern University, Chicago, Illinois, 60611, USA
| | - Adrian J Harwood
- Cardiff School of Biosciences, Cardiff University, Hadyn Ellis Building, Maindy Road, Cardiff, CF24 4HQ, UK.
| | - Christopher R L Thompson
- Centre for Life's Origins and Evolution, Department of Genetics, Evolution and Environment, University College London, Darwin Building, Gower Street, London, WC1E 6BT, UK.
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Kolb AL, Hsu DW, Wallis ABA, Ura S, Rakhimova A, Pears CJ, Lakin ND. Dictyostelium as a Model to Assess Site-Specific ADP-Ribosylation Events. Methods Mol Biol 2019; 1813:125-148. [PMID: 30097865 DOI: 10.1007/978-1-4939-8588-3_9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
The amoeba Dictyostelium discoideum is a single-cell organism that can undergo a simple developmental program, making it an excellent model to study the molecular mechanisms of cell motility, signal transduction, and cell-type differentiation. A variety of human genes that are absent or show limited conservation in other invertebrate models have been identified in this organism. This includes ADP-ribosyltransferases, also known as poly-ADP-ribose polymerases (PARPs), a family of proteins that catalyze the addition of single or poly-ADP-ribose moieties onto target proteins. The genetic tractability of Dictyostelium and its relatively simple genome structure makes it possible to disrupt PARP gene combinations, in addition to specific ADP-ribosylation sites at endogenous loci. Together, this makes Dictyostelium an attractive model to assess how ADP-ribosylation regulates a variety of cellular processes including DNA repair, transcription, and cell-type specification. Here we describe a range of techniques to study ADP-ribosylation in Dictyostelium, including analysis of ADP-ribosylation events in vitro and in vivo, in addition to approaches to assess the functional roles of this modification in vivo.
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Affiliation(s)
- Anna-Lena Kolb
- Department of Biochemistry, University of Oxford, Oxford, UK
| | - Duen-Wei Hsu
- Department of Biochemistry, University of Oxford, Oxford, UK
| | - Ana B A Wallis
- Department of Biochemistry, University of Oxford, Oxford, UK
| | - Seiji Ura
- Department of Biochemistry, University of Oxford, Oxford, UK
| | - Alina Rakhimova
- Department of Biochemistry, University of Oxford, Oxford, UK
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Dunn JD, Bosmani C, Barisch C, Raykov L, Lefrançois LH, Cardenal-Muñoz E, López-Jiménez AT, Soldati T. Eat Prey, Live: Dictyostelium discoideum As a Model for Cell-Autonomous Defenses. Front Immunol 2018; 8:1906. [PMID: 29354124 PMCID: PMC5758549 DOI: 10.3389/fimmu.2017.01906] [Citation(s) in RCA: 112] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Accepted: 12/13/2017] [Indexed: 12/11/2022] Open
Abstract
The soil-dwelling social amoeba Dictyostelium discoideum feeds on bacteria. Each meal is a potential infection because some bacteria have evolved mechanisms to resist predation. To survive such a hostile environment, D. discoideum has in turn evolved efficient antimicrobial responses that are intertwined with phagocytosis and autophagy, its nutrient acquisition pathways. The core machinery and antimicrobial functions of these pathways are conserved in the mononuclear phagocytes of mammals, which mediate the initial, innate-immune response to infection. In this review, we discuss the advantages and relevance of D. discoideum as a model phagocyte to study cell-autonomous defenses. We cover the antimicrobial functions of phagocytosis and autophagy and describe the processes that create a microbicidal phagosome: acidification and delivery of lytic enzymes, generation of reactive oxygen species, and the regulation of Zn2+, Cu2+, and Fe2+ availability. High concentrations of metals poison microbes while metal sequestration inhibits their metabolic activity. We also describe microbial interference with these defenses and highlight observations made first in D. discoideum. Finally, we discuss galectins, TNF receptor-associated factors, tripartite motif-containing proteins, and signal transducers and activators of transcription, microbial restriction factors initially characterized in mammalian phagocytes that have either homologs or functional analogs in D. discoideum.
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Affiliation(s)
- Joe Dan Dunn
- Faculty of Sciences, Department of Biochemistry, University of Geneva, Geneva, Switzerland
| | - Cristina Bosmani
- Faculty of Sciences, Department of Biochemistry, University of Geneva, Geneva, Switzerland
| | - Caroline Barisch
- Faculty of Sciences, Department of Biochemistry, University of Geneva, Geneva, Switzerland
| | - Lyudmil Raykov
- Faculty of Sciences, Department of Biochemistry, University of Geneva, Geneva, Switzerland
| | - Louise H Lefrançois
- Faculty of Sciences, Department of Biochemistry, University of Geneva, Geneva, Switzerland
| | - Elena Cardenal-Muñoz
- Faculty of Sciences, Department of Biochemistry, University of Geneva, Geneva, Switzerland
| | | | - Thierry Soldati
- Faculty of Sciences, Department of Biochemistry, University of Geneva, Geneva, Switzerland
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