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Dereeper A, Allouch N, Guerlais V, Garnier M, Ma L, De Jonckheere JF, Joseph SJ, Ali IKM, Talarmin A, Marcelino I. Naegleria genus pangenome reveals new structural and functional insights into the versatility of these free-living amoebae. Front Microbiol 2023; 13:1056418. [PMID: 36817109 PMCID: PMC9928731 DOI: 10.3389/fmicb.2022.1056418] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Accepted: 12/21/2022] [Indexed: 02/04/2023] Open
Abstract
Introduction Free-living amoebae of the Naegleria genus belong to the major protist clade Heterolobosea and are ubiquitously distributed in soil and freshwater habitats. Of the 47 Naegleria species described, N. fowleri is the only one being pathogenic to humans, causing a rare but fulminant primary amoebic meningoencephalitis. Some Naegleria genome sequences are publicly available, but the genetic basis for Naegleria diversity and ability to thrive in diverse environments (including human brain) remains unclear. Methods Herein, we constructed a high-quality Naegleria genus pangenome to obtain a comprehensive catalog of genes encoded by these amoebae. For this, we first sequenced, assembled, and annotated six new Naegleria genomes. Results and Discussion Genome architecture analyses revealed that Naegleria may use genome plasticity features such as ploidy/aneuploidy to modulate their behavior in different environments. When comparing 14 near-to-complete genome sequences, our results estimated the theoretical Naegleria pangenome as a closed genome, with 13,943 genes, including 3,563 core and 10,380 accessory genes. The functional annotations revealed that a large fraction of Naegleria genes show significant sequence similarity with those already described in other kingdoms, namely Animalia and Plantae. Comparative analyses highlighted a remarkable genomic heterogeneity, even for closely related strains and demonstrate that Naegleria harbors extensive genome variability, reflected in different metabolic repertoires. If Naegleria core genome was enriched in conserved genes essential for metabolic, regulatory and survival processes, the accessory genome revealed the presence of genes involved in stress response, macromolecule modifications, cell signaling and immune response. Commonly reported N. fowleri virulence-associated genes were present in both core and accessory genomes, suggesting that N. fowleri's ability to infect human brain could be related to its unique species-specific genes (mostly of unknown function) and/or to differential gene expression. The construction of Naegleria first pangenome allowed us to move away from a single reference genome (that does not necessarily represent each species as a whole) and to identify essential and dispensable genes in Naegleria evolution, diversity and biology, paving the way for further genomic and post-genomic studies.
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Affiliation(s)
- Alexis Dereeper
- Institut Pasteur de la Guadeloupe, Unité TReD-Path, Les Abymes, Guadeloupe, France
| | - Nina Allouch
- Institut Pasteur de la Guadeloupe, Unité TReD-Path, Les Abymes, Guadeloupe, France
| | - Vincent Guerlais
- Institut Pasteur de la Guadeloupe, Unité TReD-Path, Les Abymes, Guadeloupe, France
| | - Maëlle Garnier
- Institut Pasteur de la Guadeloupe, Unité TReD-Path, Les Abymes, Guadeloupe, France
| | - Laurence Ma
- Institut Pasteur de Paris, Biomics, Paris, France
| | | | - Sandeep J. Joseph
- Centers for Disease Control and Prevention (CDC), Atlanta, GA, United States
| | - Ibne Karim M. Ali
- Centers for Disease Control and Prevention (CDC), Atlanta, GA, United States
| | - Antoine Talarmin
- Institut Pasteur de la Guadeloupe, Unité TReD-Path, Les Abymes, Guadeloupe, France
| | - Isabel Marcelino
- Institut Pasteur de la Guadeloupe, Unité TReD-Path, Les Abymes, Guadeloupe, France,*Correspondence: Isabel Marcelino,
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Bernard C, Locard-Paulet M, Noël C, Duchateau M, Giai Gianetto Q, Moumen B, Rattei T, Hechard Y, Jensen LJ, Matondo M, Samba-Louaka A. A time-resolved multi-omics atlas of Acanthamoeba castellanii encystment. Nat Commun 2022; 13:4104. [PMID: 35835784 PMCID: PMC9283445 DOI: 10.1038/s41467-022-31832-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Accepted: 06/30/2022] [Indexed: 12/14/2022] Open
Abstract
Encystment is a common stress response of most protists, including free-living amoebae. Cyst formation protects the amoebae from eradication and can increase virulence of the bacteria they harbor. Here, we mapped the global molecular changes that occur in the facultatively pathogenic amoeba Acanthamoeba castellanii during the early steps of the poorly understood process of encystment. By performing transcriptomic, proteomic, and phosphoproteomic experiments during encystment, we identified more than 150,000 previously undescribed transcripts and thousands of protein sequences absent from the reference genome. These results provide molecular details to the regulation of expected biological processes, such as cell proliferation shutdown, and reveal new insights such as a rapid phospho-regulation of sites involved in cytoskeleton remodeling and translation regulation. This work constitutes the first time-resolved molecular atlas of an encysting organism and a useful resource for further investigation of amoebae encystment to allow for a better control of pathogenic amoebae.
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Affiliation(s)
- Clément Bernard
- Laboratoire Ecologie et Biologie des Interactions, Université de Poitiers, UMR CNRS, 7267, Poitiers, France
| | - Marie Locard-Paulet
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | - Cyril Noël
- IFREMER-IRSI-Service de Bioinformatique (SeBiMER), Centre Bretagne, Plouzane, France
| | - Magalie Duchateau
- Institut Pasteur, Université de Paris, Proteomics Platform, Mass Spectrometry for Biology Unit, UAR2024, CNRS 2000, Paris, France
| | - Quentin Giai Gianetto
- Institut Pasteur, Université de Paris, Proteomics Platform, Mass Spectrometry for Biology Unit, UAR2024, CNRS 2000, Paris, France
- Institut Pasteur, Université de Paris, Department of Computation Biology, Bioinformatics and Biostatistics Hub, Paris, France
| | - Bouziane Moumen
- Laboratoire Ecologie et Biologie des Interactions, Université de Poitiers, UMR CNRS, 7267, Poitiers, France
| | - Thomas Rattei
- Centre for Microbiology and Environmental Systems Science; Doctoral School Microbiology and Environmental Science, University of Vienna, Vienna, Austria
| | - Yann Hechard
- Laboratoire Ecologie et Biologie des Interactions, Université de Poitiers, UMR CNRS, 7267, Poitiers, France
| | - Lars Juhl Jensen
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | - Mariette Matondo
- Institut Pasteur, Université de Paris, Proteomics Platform, Mass Spectrometry for Biology Unit, UAR2024, CNRS 2000, Paris, France
| | - Ascel Samba-Louaka
- Laboratoire Ecologie et Biologie des Interactions, Université de Poitiers, UMR CNRS, 7267, Poitiers, France.
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Schaap P. From environmental sensing to developmental control: cognitive evolution in dictyostelid social amoebas. Philos Trans R Soc Lond B Biol Sci 2021; 376:20190756. [PMID: 33487113 PMCID: PMC7934950 DOI: 10.1098/rstb.2019.0756] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Dictyostelid social amoebas respond to starvation by self-organizing into multicellular slugs that migrate towards light to construct spore-bearing structures. These behaviours depend on excitable networks that enable amoebas to produce propagating waves of the chemoattractant cAMP, and to respond by directional movement. cAMP additionally regulates cell differentiation throughout development, with differentiation and cell movement being coordinated by interaction of the stalk inducer c-di-GMP with the adenylate cyclase that generates cAMP oscillations. Evolutionary studies indicate how the manifold roles of cAMP in multicellular development evolved from a role as intermediate for starvation-induced encystation in the unicellular ancestor. A merger of this stress response with the chemotaxis excitable networks yielded the developmental complexity and cognitive capabilities of extant Dictyostelia. This article is part of the theme issue ‘Basal cognition: conceptual tools and the view from the single cell’.
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Affiliation(s)
- Pauline Schaap
- School of Life Sciences, University of Dundee, Dundee DD15EH, UK
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Anwar A, Siddiqui R, Khan NA. Whole Organism Model to Study Molecular Mechanisms of Differentiation and Dedifferentiation. BIOLOGY 2020; 9:E79. [PMID: 32316619 PMCID: PMC7235994 DOI: 10.3390/biology9040079] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Revised: 04/14/2020] [Accepted: 04/15/2020] [Indexed: 12/25/2022]
Abstract
Cancer recurrence has remained a significant challenge, despite advances in therapeutic approaches. In part, this is due to our incomplete understanding of the biology of cancer stem cells and the underlying molecular mechanisms. The phenomenon of differentiation and dedifferentiation (phenotypic switching) is not only unique to stem cells but it is also observed in several other organisms, as well as evolutionary-related microbes. Here, we propose the use of a primitive eukaryotic unicellular organism, Acanthamoeba castellanii, as a model to study the molecular mechanisms of cellular differentiation and dedifferentiation.
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Affiliation(s)
- Areeba Anwar
- Department of Biological Sciences, School of Science and Technology, Sunway University, Bandar Sunway 47500, Malaysia;
| | - Ruqaiyyah Siddiqui
- Department of Biology, Chemistry and Environmental Sciences, College of Arts and Sciences, American University of Sharjah, University City 26666, UAE;
| | - Naveed Ahmed Khan
- Department of Biology, Chemistry and Environmental Sciences, College of Arts and Sciences, American University of Sharjah, University City 26666, UAE;
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Schaap P, Schilde C. Encystation: the most prevalent and underinvestigated differentiation pathway of eukaryotes. MICROBIOLOGY-SGM 2018; 164:727-739. [PMID: 29620506 DOI: 10.1099/mic.0.000653] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Not long ago, protists were considered one of four eukaryote kingdoms, but recent gene-based phylogenies show that they contribute to all nine eukaryote subdomains. The former kingdoms of animals, plants and fungi are now relegated to lower ranks within subdomains. Most unicellular protists respond to adverse conditions by differentiating into dormant walled cysts. As cysts, they survive long periods of starvation, drought and other environmental threats, only to re-emerge when conditions improve. For protists pathogens, the resilience of their cysts can prevent successful treatment or eradication of the disease. In this context, effort has been directed towards understanding the molecular mechanisms that control encystation. We here firstly summarize the prevalence of encystation across protists and next focus on Amoebozoa, where most of the health-related issues occur. We review current data on processes and genes involved in encystation of the obligate parasite Entamoeba histolytica and the opportunistic pathogen Acanthamoeba. We show how the cAMP-mediated signalling pathway that controls spore and stalk cell encapsulation in Dictyostelium fruiting bodies could be retraced to a stress-induced pathway controlling encystation in solitary Amoebozoa. We highlight the conservation and prevalence of cAMP signalling genes in Amoebozoan genomes and the suprisingly large and varied repertoire of proteins for sensing and processing environmental signals in individual species.
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Affiliation(s)
- Pauline Schaap
- School of Life Sciences, University of Dundee, Dundee DD15EH, UK
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Aqeel Y, Siddiqui R, Khan NA. Silencing of xylose isomerase and cellulose synthase by siRNA inhibits encystation in Acanthamoeba castellanii. Parasitol Res 2012; 112:1221-7. [DOI: 10.1007/s00436-012-3254-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2012] [Accepted: 12/12/2012] [Indexed: 10/27/2022]
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Abstract
SUMMARYThe ability of cyst-forming protists such asAcanthamoebato escape death by transforming into a cyst form, that is resistant to harsh physiological, environmental and pharmacological conditions, has continued to pose a serious challenge to human and animal health. A complete understanding of the fundamental principles of genome evolution and biochemical pathways of cellular differentiation offers unprecedented opportunities to counter detrimental outcomes.Acanthamoebacan elude inhospitable conditions by forming cysts. Here we unravel the processes involved in the phenotypic switching ofAcanthamoeba, which are critical in our efforts to find potential targets for chemotherapy.
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Janssens PM, Van Haastert PJ. Molecular basis of transmembrane signal transduction in Dictyostelium discoideum. Microbiol Rev 1987; 51:396-418. [PMID: 2893972 PMCID: PMC373123 DOI: 10.1128/mr.51.4.396-418.1987] [Citation(s) in RCA: 100] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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Abstract
Preincubation of Acanthamoeba palestinensis homogenates in 0.25M sucrose-TM (2mM MgSO4 and 5mM Tris-HCl, pH 7.4) at 0 degree C for increasing periods of time up to 3 h, leads to a progressive increase in the activity of adenylated cyclase. In contrast, preincubation of isolated membrane fractions enriched in enzyme activity in the same medium results in no activation. However, preincubation of membrane fractions in medium containing a high density of sugars (sucrose, glucose or fructose) mimics the activation obtained with homogenates. The high density sugar activation is time and temperature dependent, and reversible upon return to a low density medium. The high osmotic pressure of the sugars utilized may be a factor, since high concentrations of the sucrose polymer, Ficoll, which has low osmotic activity, causes not activation. Soluble activators, protein synthesis and changes in cyclic nucleotide phosphodiesterase activity were all eliminated as possible effectors of the apparent activation of adenylate cyclase. In contrast to mammalian adenylate cyclase, the endoplasmic reticulum localized enzyme of Acanthamoeba is inhibited by NaF and is unaffected by GTP, adenosine, epinephrine, prostaglandin E1, propranolol, and meclofenamic acid. These data indicate that the adenylate cyclase of Acanthamoeba is structurally different from that of most mammalian cells.
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Krishna Murti CR, Shukla OP. Differentiation of pathogenic amoebae: encystation and excystation ofAcanthamoeba culbertsoni — A model. J Biosci 1984. [DOI: 10.1007/bf02703900] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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