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Babonis LS. On the evolutionary developmental biology of the cell. Trends Genet 2024:S0168-9525(24)00150-1. [PMID: 38971670 DOI: 10.1016/j.tig.2024.06.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2024] [Revised: 06/11/2024] [Accepted: 06/12/2024] [Indexed: 07/08/2024]
Abstract
Organisms are complex assemblages of cells, cells that produce light, shoot harpoons, and secrete glue. Therefore, identifying the mechanisms that generate novelty at the level of the individual cell is essential for understanding how multicellular life evolves. For decades, the field of evolutionary developmental biology (Evo-Devo) has been developing a framework for connecting genetic variation that arises during embryonic development to the emergence of diverse adult forms. With increasing access to new single cell 'omics technologies and an array of techniques for manipulating gene expression, we can now extend these inquiries inward to the level of the individual cell. In this opinion, I argue that applying an Evo-Devo framework to single cells makes it possible to explore the natural history of cells, where this was once only possible at the organismal level.
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Affiliation(s)
- Leslie S Babonis
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY 14853, USA.
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2
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Fukaya S, Masuda L, Takemura M. Analysis of Morphological Changes in the Nucleus and Vacuoles of Acanthamoeba castellanii following Giant Virus Infection. Microbiol Spectr 2023; 11:e0418222. [PMID: 36943052 PMCID: PMC10100661 DOI: 10.1128/spectrum.04182-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Accepted: 02/28/2023] [Indexed: 03/23/2023] Open
Abstract
Acanthamoeba castellanii medusavirus is a member of the phylum Nucleocytoviricota, also known as giant viruses, and has a unique strategy of infecting Acanthamoeba castellanii and replicating viral genes in the host nucleus. Here, we show time series changes in the intracellular morphology, including the nucleus, of host cells infected with four types of giant viruses, including medusavirus, using time-lapse phase-contrast microscopy and image analysis. We updated our phase-contrast-based kinetic analysis algorithm for amoebae (PKA3) to use multiple microscopic images with different focus positions to allow a more detailed analysis of their intracellular structures. Image analysis using PKA3 revealed that as medusavirus infection progressed, the host nucleus increased in size and the number of vacuoles decreased. In addition, infected host cells are known to become smaller and rounder at later stages of infection, but here they were found to be larger than uninfected cells at earlier stages. These results suggested that the propagation mechanism of medusavirus includes the formation of empty virus particles in the host cytoplasm, packaging of the viral genome replicated in the host nucleus, and then the release of viral particles. IMPORTANCE In this study, we quantitatively revealed how long the increase in host cell size or the increase in host nucleus size occurs after infection with giant viruses, especially medusavirus. To understand the underlying mechanism, we performed image analysis and determined that the host cell size increased at approximately 6 h postinfection (hpi) and the host nucleus enlarged at approximately 22 hpi, pointing to the importance of biochemical experiments. In addition, we showed that the intracellular structures could be quantitatively analyzed using multiple phase-contrast microscopy images with different focus positions at the same time point. Hence, morphological analyses of intracellular structures using phase-contrast microscopy, which have wide applications in live-cell observations, may be useful in studying various organisms that infect or are symbiotic with A. castellanii.
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Affiliation(s)
- Sho Fukaya
- Department of Applied Information Engineering, Faculty of Engineering, Suwa University of Science, Chino, Nagano, Japan
- Laboratory of Biology, Institute of Arts and Sciences, Tokyo University of Science, Shinjuku, Tokyo, Japan
| | - Lisa Masuda
- Laboratory of Biology, Graduate School of Mathematics and Science Education, Tokyo University of Science, Shinjuku, Tokyo, Japan
| | - Masaharu Takemura
- Laboratory of Biology, Institute of Arts and Sciences, Tokyo University of Science, Shinjuku, Tokyo, Japan
- Laboratory of Biology, Graduate School of Mathematics and Science Education, Tokyo University of Science, Shinjuku, Tokyo, Japan
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Iriarte LS, Martinez CI, de Miguel N, Coceres VM. Tritrichomonas foetus Cell Division Involves DNA Endoreplication and Multiple Fissions. Microbiol Spectr 2023; 11:e0325122. [PMID: 36728437 PMCID: PMC10100903 DOI: 10.1128/spectrum.03251-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Accepted: 01/16/2023] [Indexed: 02/03/2023] Open
Abstract
Tritrichomonas foetus and Trichomonas vaginalis are extracellular flagellated parasites that inhabit animals and humans, respectively. Cell division is a crucial process in most living organisms that leads to the formation of 2 daughter cells from a single mother cell. It has been assumed that T. vaginalis and T. foetus modes of reproduction are exclusively by binary fission. However, here, we showed that multinuclearity is a phenomenon regularly observed in different T. foetus and T. vaginalis strains in standard culture conditions. Additionally, we revealed that nutritional depletion or nutritional deprivation led to different dormant phenotypes. Although multinucleated T. foetus are mostly observed during nutritional depletion, numerous cells with 1 larger nucleus have been observed under nutritional deprivation conditions. In both cases, when the standard culture media conditions are restored, the cytoplasm of these multinucleated cells separates, and numerous parasites are generated in a short period of time by the fission multiple. We also revealed that DNA endoreplication occurs both in large and multiple nuclei of parasites under nutritional deprivation and depletion conditions, suggesting an important function in stress nutritional situations. These results provide valuable data about the cell division process of these extracellular parasites. IMPORTANCE Nowadays, it's known that T. foetus and T. vaginalis generate daughter cells by binary fission. Here, we report that both parasites are also capable of dividing by multiple fission under stress conditions. We also demonstrated, for the first time, that T. foetus can increase its DNA content per parasite without concluding the cytokinesis process (endoreplication) under stress conditions, which represents an efficient strategy for subsequent fast multiplication when the context becomes favorable. Additionally, we revealed the existence of novel dormant forms of resistance (multinucleated or mononucleated polyploid parasites), different than the previously described pseudocysts, that are formed under stress conditions. Thus, it is necessary to evaluate the role of these structures in the parasites' transmission in the future.
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Affiliation(s)
- Lucrecia S. Iriarte
- Laboratorio de Parásitos Anaerobios, Instituto Tecnológico Chascomús (INTECH), CONICET-UNSAM, Chascomús, Argentina
- Escuela de Bio y Nanotecnologías, Universidad Nacional de San Martin (UNSAM), Buenos Aires, Argentina
| | - Cristian I. Martinez
- Laboratorio de Parásitos Anaerobios, Instituto Tecnológico Chascomús (INTECH), CONICET-UNSAM, Chascomús, Argentina
- Escuela de Bio y Nanotecnologías, Universidad Nacional de San Martin (UNSAM), Buenos Aires, Argentina
| | - Natalia de Miguel
- Laboratorio de Parásitos Anaerobios, Instituto Tecnológico Chascomús (INTECH), CONICET-UNSAM, Chascomús, Argentina
- Escuela de Bio y Nanotecnologías, Universidad Nacional de San Martin (UNSAM), Buenos Aires, Argentina
| | - Veronica M. Coceres
- Laboratorio de Parásitos Anaerobios, Instituto Tecnológico Chascomús (INTECH), CONICET-UNSAM, Chascomús, Argentina
- Escuela de Bio y Nanotecnologías, Universidad Nacional de San Martin (UNSAM), Buenos Aires, Argentina
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4
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Wang Y, Jiang L, Zhao Y, Ju X, Wang L, Jin L, Fine RD, Li M. Biological characteristics and pathogenicity of Acanthamoeba. Front Microbiol 2023; 14:1147077. [PMID: 37089530 PMCID: PMC10113681 DOI: 10.3389/fmicb.2023.1147077] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Accepted: 03/21/2023] [Indexed: 04/25/2023] Open
Abstract
Acanthamoeba is an opportunistic protozoa, which exists widely in nature and is mainly distributed in soil and water. Acanthamoeba usually exists in two forms, trophozoites and cysts. The trophozoite stage is one of growth and reproduction while the cyst stage is characterized by cellular quiescence, commonly resulting in human infection, and the lack of effective monotherapy after initial infection leads to chronic disease. Acanthamoeba can infect several human body tissues such as the skin, cornea, conjunctiva, respiratory tract, and reproductive tract, especially when the tissue barriers are damaged. Furthermore, serious infections can cause Acanthamoeba keratitis, granulomatous amoebic encephalitis, skin, and lung infections. With an increasing number of Acanthamoeba infections in recent years, the pathogenicity of Acanthamoeba is becoming more relevant to mainstream clinical care. This review article will describe the etiological characteristics of Acanthamoeba infection in detail from the aspects of biological characteristic, classification, disease, and pathogenic mechanism in order to provide scientific basis for the diagnosis, treatment, and prevention of Acanthamoeba infection.
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Affiliation(s)
- Yuehua Wang
- College of Laboratory Medicine, Jilin Medical University, Jilin City, China
| | - Linzhe Jiang
- General Surgery, Jilin People’s Hospital, Jilin City, China
| | - Yitong Zhao
- College of Laboratory Medicine, Jilin Medical University, Jilin City, China
| | - Xiaohong Ju
- College of Laboratory Medicine, Jilin Medical University, Jilin City, China
| | - Le Wang
- Department of Laboratory Medicine, Jilin Hospital of Integrated Chinese and Western Medicine, Jilin City, China
| | - Liang Jin
- Department of Laboratory Medicine, Jilin Hospital of Integrated Chinese and Western Medicine, Jilin City, China
| | - Ryan D. Fine
- Center for Human Genetics and Genomics, New York University Grossman School of Medicine, New York City, NY, United States
| | - Mingguang Li
- College of Laboratory Medicine, Jilin Medical University, Jilin City, China
- *Correspondence: Mingguang Li,
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Matthey-Doret C, Colp MJ, Escoll P, Thierry A, Moreau P, Curtis B, Sahr T, Sarrasin M, Gray MW, Lang BF, Archibald JM, Buchrieser C, Koszul R. Chromosome-scale assemblies of Acanthamoeba castellanii genomes provide insights into Legionella pneumophila infection-related chromatin reorganization. Genome Res 2022; 32:1698-1710. [PMID: 36109147 PMCID: PMC9528979 DOI: 10.1101/gr.276375.121] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Accepted: 07/25/2022] [Indexed: 11/24/2022]
Abstract
The unicellular amoeba Acanthamoeba castellanii is ubiquitous in aquatic environments, where it preys on bacteria. The organism also hosts bacterial endosymbionts, some of which are parasitic, including human pathogens such as Chlamydia and Legionella spp. Here we report complete, high-quality genome sequences for two extensively studied A. castellanii strains, Neff and C3. Combining long- and short-read data with Hi-C, we generated near chromosome-level assemblies for both strains with 90% of the genome contained in 29 scaffolds for the Neff strain and 31 for the C3 strain. Comparative genomics revealed strain-specific functional enrichment, most notably genes related to signal transduction in the C3 strain and to viral replication in Neff. Furthermore, we characterized the spatial organization of the A. castellanii genome and showed that it is reorganized during infection by Legionella pneumophila Infection-dependent chromatin loops were found to be enriched in genes for signal transduction and phosphorylation processes. In genomic regions where chromatin organization changed during Legionella infection, we found functional enrichment for genes associated with metabolism, organelle assembly, and cytoskeleton organization. Given Legionella infection is known to alter its host's cell cycle, to exploit the host's organelles, and to modulate the host's metabolism in its favor, these changes in chromatin organization may partly be related to mechanisms of host control during Legionella infection.
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Affiliation(s)
- Cyril Matthey-Doret
- Institut Pasteur, CNRS UMR 3525, Université de Paris, Unité Régulation Spatiale des Génomes, F-75015 Paris, France
- Collège Doctoral, Sorbonne Université, F-75005 Paris, France
| | - Morgan J Colp
- Department of Biochemistry and Molecular Biology and Institute for Comparative Genomics, Dalhousie University, Halifax, Nova Scotia B3H 4R2, Canada
| | - Pedro Escoll
- Institut Pasteur, Université de Paris, Biologie des Bactéries Intracellulaires and CNRS UMR 6047, F-75015 Paris, France
| | - Agnès Thierry
- Institut Pasteur, CNRS UMR 3525, Université de Paris, Unité Régulation Spatiale des Génomes, F-75015 Paris, France
| | - Pierrick Moreau
- Institut Pasteur, CNRS UMR 3525, Université de Paris, Unité Régulation Spatiale des Génomes, F-75015 Paris, France
| | - Bruce Curtis
- Department of Biochemistry and Molecular Biology and Institute for Comparative Genomics, Dalhousie University, Halifax, Nova Scotia B3H 4R2, Canada
| | - Tobias Sahr
- Institut Pasteur, Université de Paris, Biologie des Bactéries Intracellulaires and CNRS UMR 6047, F-75015 Paris, France
| | - Matt Sarrasin
- Robert Cedergren Centre for Bioinformatics and Genomics, Département de Biochimie, Université de Montréal, Montréal, Quebec H3C 3J7, Canada
| | - Michael W Gray
- Department of Biochemistry and Molecular Biology and Institute for Comparative Genomics, Dalhousie University, Halifax, Nova Scotia B3H 4R2, Canada
| | - B Franz Lang
- Robert Cedergren Centre for Bioinformatics and Genomics, Département de Biochimie, Université de Montréal, Montréal, Quebec H3C 3J7, Canada
| | - John M Archibald
- Department of Biochemistry and Molecular Biology and Institute for Comparative Genomics, Dalhousie University, Halifax, Nova Scotia B3H 4R2, Canada
| | - Carmen Buchrieser
- Institut Pasteur, Université de Paris, Biologie des Bactéries Intracellulaires and CNRS UMR 6047, F-75015 Paris, France
| | - Romain Koszul
- Institut Pasteur, CNRS UMR 3525, Université de Paris, Unité Régulation Spatiale des Génomes, F-75015 Paris, France
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6
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Kambouris ME, Goudoudaki S, Kritikou S, Milioni A, Karamperis K, Giavasis I, Patrinos GP, Velegraki A, Manoussopoulos Y. Beyond the Microbiome: Germ-ganism? An Integrative Idea for Microbial Existence, Organization, Growth, Pathogenicity, and Therapeutics. OMICS : A JOURNAL OF INTEGRATIVE BIOLOGY 2022; 26:204-217. [PMID: 35255221 DOI: 10.1089/omi.2022.0015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
The advances made by microbiome research call for new vocabulary and expansion of our thinking in microbiology. For example, the life-forms presenting in both unicellular and multicellular formats invite us to rethink microbial existence, organization, growth, pathogenicity, and therapeutics in the 21st century. A view of such populations as parts of single organisms with a loose, distributed multicellular organization, introduced here as a germ-ganism, rather than communities, might open up interesting prospects for diagnostics and therapeutics innovation. This study tested and further contextualized the concept of germ-ganism using solid cultures of bacteria and fungi. Based on our findings and the literature reviewed herein, we propose that germ-ganism has synergy with a systems medicine approach by broadening host-environment interactions from cells and microorganisms to a scale of biological ecosystems. Germ-ganism also brings about the possibility of studying the multilevel impacts of novel therapeutic agents within and across networks of microbial ecosystems. The germ-ganism would lend itself, in the long term, to a veritable biocybernetics system, while in the mid-term, we anticipate it will contribute to new diagnostics and therapeutics. Biosecurity applications would be immensely affected by germ-ganism. Industrial applications of germ-ganism are of interest as a more sustainable alternative to costly solutions such as tampered strains/microorganisms. In conclusion, germ-ganism is informed by lessons from microbiome research and invites rethinking microbial existence, organization, and growth as an organism. Germ-ganism has vast ramifications for understanding pathogenicity, and clinical, biosecurity, and biotechnology applications in the current historical moment of the COVID-19 pandemic and beyond.
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Affiliation(s)
- Manousos E Kambouris
- Laboratory of Pharmacogenomics and Individualized Therapy, Department of Pharmacy, School of Health Sciences, University of Patras, Patras, Greece
| | - Stavroula Goudoudaki
- Plant Protection Division of Patras, Institute of Industrial and Forage Plants, Patras, Greece
| | - Stavroula Kritikou
- NCPF/UoA, Laboratory of Microbiology, Medical School, National & Kapodistrian University of Athens, Athens, Greece
| | - Aphroditi Milioni
- NCPF/UoA, Laboratory of Microbiology, Medical School, National & Kapodistrian University of Athens, Athens, Greece
| | - Kariofyllis Karamperis
- Laboratory of Pharmacogenomics and Individualized Therapy, Department of Pharmacy, School of Health Sciences, University of Patras, Patras, Greece
| | - Ioannis Giavasis
- Laboratory of Food Microbiology and Biotechnology, Department of Food Science and Nutrition, University of Thessaly, Karditsa, Greece
| | - George P Patrinos
- Laboratory of Pharmacogenomics and Individualized Therapy, Department of Pharmacy, School of Health Sciences, University of Patras, Patras, Greece
| | - Aristea Velegraki
- NCPF/UoA, Laboratory of Microbiology, Medical School, National & Kapodistrian University of Athens, Athens, Greece
| | - Yiannis Manoussopoulos
- Plant Protection Division of Patras, Institute of Industrial and Forage Plants, Patras, Greece
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Fukaya S, Takemura M. Kinetic Analysis of Acanthamoeba castellanii Infected with Giant Viruses Quantitatively Revealed Process of Morphological and Behavioral Changes in Host Cells. Microbiol Spectr 2021; 9:e0036821. [PMID: 34431709 PMCID: PMC8552732 DOI: 10.1128/spectrum.00368-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Accepted: 07/27/2021] [Indexed: 01/22/2023] Open
Abstract
Most virus-infected cells show morphological and behavioral changes, which are called cytopathic effects. Acanthamoeba castellanii, an abundant, free-living protozoan, serves as a laboratory host for some viruses of the phylum Nucleocytoviricota-the giant viruses. Many of these viruses cause cell rounding in the later stages of infection in the host cells. Here, we show the changes that lead to cell rounding in the host cells through time-lapse microscopy and image analysis. Time-lapse movies of A. castellanii cells infected with Mimivirus shirakomae, kyotovirus, medusavirus, or Pandoravirus japonicus were generated using a phase-contrast microscope. We updated our phase-contrast-based kinetic analysis algorithm for amoebae (PKA3) and used it to analyze these time-lapse movies. Image analysis revealed that the process leading to cell rounding varies among the giant viruses; for example, M. shirakomae infection did not cause changes for some time after the infection, kyotovirus infection caused an early decrease in the number of cells with typical morphologies, and medusavirus and P. japonicus infection frequently led to the formation of intercellular bridges and rotational behavior of host cells. These results suggest that in the case of giant viruses, the putative reactions of host cells against infection and the putative strategies of virus spread are diverse. IMPORTANCE Quantitative analysis of the infection process is important for a better understanding of viral infection strategies and virus-host interactions. Here, an image analysis of the phase-contrast time-lapse movies displayed quantitative differences in the process of cytopathic effects due to the four giant viruses in Acanthamoeba castellanii, which were previously unclear. It was revealed that medusavirus and Pandoravirus japonicus infection led to the formation of a significant number of elongated particles related to intercellular bridges, emphasizing the importance of research on the interaction of viruses with host cell nuclear function. Mimivirus shirakomae infection did not cause any changes in the host cells initially, so it is thought that the infected cells can actively move and spread over a wider area, emphasizing the importance of observation in a wider area and analysis of infection efficiency. These results suggest that a kinetic analysis using the phase-contrast-based kinetic analysis algorithm for amoebae (PKA3) reveals the infection strategies of each giant virus.
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Affiliation(s)
- Sho Fukaya
- Department of Applied Information Engineering, Faculty of Engineering, Suwa University of Science, Chino, Nagano, Japan
- Laboratory of Biology, Institute of Arts and Sciences, Tokyo University of Science, Shinjuku, Tokyo, Japan
| | - Masaharu Takemura
- Laboratory of Biology, Institute of Arts and Sciences, Tokyo University of Science, Shinjuku, Tokyo, Japan
- Laboratory of Biology, Graduate School of Mathematics and Science Education, Tokyo University of Science, Shinjuku, Tokyo, Japan
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