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Tekle YI, Tefera H. A Small Genome amidst the Giants: Evidence of Genome Reduction in a Small Tubulinid Free-Living Amoeba. Genome Biol Evol 2024; 16:evae058. [PMID: 38504610 PMCID: PMC10980511 DOI: 10.1093/gbe/evae058] [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: 12/04/2023] [Revised: 01/22/2024] [Accepted: 03/14/2024] [Indexed: 03/21/2024] Open
Abstract
This study investigates the genomic characteristics of Echinamoeba silvestris, a small-sized amoeba within the Tubulinea clade of the Amoebozoa supergroup. Despite Tubulinea's significance in various fields, genomic data for this clade have been scarce. E. silvestris presents the smallest free-living amoeba genome within Tubulinea and Amoebozoa to date. Comparative analysis reveals intriguing parallels with parasitic lineages in terms of genome size and predicted gene numbers, emphasizing the need to understand the consequences of reduced genomes in free-living amoebae. Functional categorization of predicted genes in E. silvestris shows similar percentages of ortholog groups to other amoebae in various categories, but a distinctive feature is the extensive gene contraction in orphan (ORFan) genes and those involved in biological processes. Notably, among the few genes that underwent expansion, none are related to cellular components, suggesting adaptive processes that streamline biological processes and cellular components for efficiency and energy conservation. Additionally, our investigation into noncoding and repetitive elements sheds light on the evolution of genome size in amoebae, with E. silvestris distinguished by low percentage of repetitive elements. Furthermore, the analysis reveals that E. silvestris has the lowest mean number of introns per gene among the species studied, providing further support for its observed compact genome. Overall, this research underscores the diversity within Tubulinea, highlights knowledge gaps in Amoebozoa genomics, and positions E. silvestris as a valuable addition to genomic data sets, prompting further exploration of complexities in Amoebozoa diversity and genome evolution.
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Affiliation(s)
- Yonas I Tekle
- Department of Biology, Spelman College, 350 Spelman Lane Southwest, Atlanta, GA 30314, USA
| | - Hanna Tefera
- Department of Biology, Spelman College, 350 Spelman Lane Southwest, Atlanta, GA 30314, USA
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2
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Tekle YI, Tran H, Wang F, Singla M, Udu I. Omics of an Enigmatic Marine Amoeba Uncovers Unprecedented Gene Trafficking from Giant Viruses and Provides Insights into Its Complex Life Cycle. MICROBIOLOGY RESEARCH 2023; 14:656-672. [PMID: 37752971 PMCID: PMC10521059 DOI: 10.3390/microbiolres14020047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/28/2023] Open
Abstract
Amoebozoa include lineages of diverse ecology, behavior, and morphology. They are assumed to encompass members with the largest genome sizes of all living things, yet genomic studies in the group are limited. Trichosphaerium, a polymorphic, multinucleate, marine amoeba with a complicated life cycle, has puzzled experts for over a century. In an effort to explore the genomic diversity and investigate extraordinary behavior observed among the Amoebozoa, we used integrated omics approaches to study this enigmatic marine amoeba. Omics data, including single-cell transcriptomics and cytological data, demonstrate that Trichosphaerium sp. possesses the complete meiosis toolkit genes. These genes are expressed in life stages of the amoeba including medium and large cells. The life cycle of Trichosphaerium sp. involves asexual processes via binary fission and multiple fragmentation of giant cells, as well as sexual-like processes involving genes implicated in sexual reproduction and polyploidization. These findings are in stark contrast to a life cycle previously reported for this amoeba. Despite the extreme morphological plasticity observed in Trichosphaerium, our genomic data showed that populations maintain a species-level intragenomic variation. A draft genome of Trichosphaerium indicates elevated lateral gene transfer (LGT) from bacteria and giant viruses. Gene trafficking in Trichosphaerium is the highest within Amoebozoa and among the highest in microbial eukaryotes.
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Affiliation(s)
- Yonas I. Tekle
- Department of Biology, Spelman College, 350 Spelman Lane Southwest, Atlanta, GA 30314, USA
| | - Hanh Tran
- Department of Biology, Spelman College, 350 Spelman Lane Southwest, Atlanta, GA 30314, USA
| | - Fang Wang
- Department of Biology, Spelman College, 350 Spelman Lane Southwest, Atlanta, GA 30314, USA
| | - Mandakini Singla
- Department of Biology, Spelman College, 350 Spelman Lane Southwest, Atlanta, GA 30314, USA
| | - Isimeme Udu
- Department of Biology, Spelman College, 350 Spelman Lane Southwest, Atlanta, GA 30314, USA
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3
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Tekle YI, Wang F, Tran H, Hayes TD, Ryan JF. The draft genome of Cochliopodium minus reveals a complete meiosis toolkit and provides insight into the evolution of sexual mechanisms in Amoebozoa. Sci Rep 2022; 12:9841. [PMID: 35701521 PMCID: PMC9198077 DOI: 10.1038/s41598-022-14131-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Accepted: 05/06/2022] [Indexed: 11/23/2022] Open
Abstract
To date, genomic analyses in amoebozoans have been mostly limited to model organisms or medically important lineages. Consequently, the vast diversity of Amoebozoa genomes remain unexplored. A draft genome of Cochliopodium minus, an amoeba characterized by extensive cellular and nuclear fusions, is presented. C. minus has been a subject of recent investigation for its unusual sexual behavior. Cochliopodium's sexual activity occurs during vegetative stage making it an ideal model for studying sexual development, which is sorely lacking in the group. Here we generate a C. minus draft genome assembly. From this genome, we detect a substantial number of lateral gene transfer (LGT) instances from bacteria (15%), archaea (0.9%) and viruses (0.7%) the majority of which are detected in our transcriptome data. We identify the complete meiosis toolkit genes in the C. minus genome, as well as the absence of several key genes involved in plasmogamy and karyogamy. Comparative genomics of amoebozoans reveals variation in sexual mechanism exist in the group. Similar to complex eukaryotes, C. minus (some amoebae) possesses Tyrosine kinases and duplicate copies of SPO11. We report a first example of alternative splicing in a key meiosis gene and draw important insights on molecular mechanism of sex in C. minus using genomic and transcriptomic data.
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Affiliation(s)
- Yonas I Tekle
- Department of Biology, Spelman College, 350 Spelman Lane Southwest, Atlanta, GA, 30314, USA.
| | - Fang Wang
- Department of Biology, Spelman College, 350 Spelman Lane Southwest, Atlanta, GA, 30314, USA
| | - Hanh Tran
- Department of Biology, Spelman College, 350 Spelman Lane Southwest, Atlanta, GA, 30314, USA
| | - T Danielle Hayes
- Whitney Laboratory for Marine Bioscience, University of Florida, St. Augustine, FL, USA
- Iowa State University, Ames, IA, USA
| | - Joseph F Ryan
- Whitney Laboratory for Marine Bioscience, University of Florida, St. Augustine, FL, USA
- Department of Biology, University of Florida, Gainesville, FL, USA
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4
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Gibson W. The sexual side of parasitic protists. Mol Biochem Parasitol 2021; 243:111371. [PMID: 33872659 DOI: 10.1016/j.molbiopara.2021.111371] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 03/26/2021] [Accepted: 04/13/2021] [Indexed: 01/09/2023]
Abstract
Much of the vast evolutionary landscape occupied by Eukaryotes is dominated by protists. Though parasitism has arisen in many lineages, there are three main groups of parasitic protists of relevance to human and livestock health: the Apicomplexa, including the malaria parasite Plasmodium and coccidian pathogens of livestock such as Eimeria; the excavate flagellates, encompassing a diverse range of protist pathogens including trypanosomes, Leishmania, Giardia and Trichomonas; and the Amoebozoa, including pathogenic amoebae such as Entamoeba. These three groups represent separate, deep branches of the eukaryote tree, underlining their divergent evolutionary histories. Here, I explore what is known about sex in these three main groups of parasitic protists.
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Affiliation(s)
- Wendy Gibson
- School of Biological Sciences, Life Sciences Building, University of Bristol, Bristol, BS8 1TQ, United Kingdom.
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5
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Cell-cell fusions and cell-in-cell phenomena in healthy cells and cancer: Lessons from protists and invertebrates. Semin Cancer Biol 2021; 81:96-105. [PMID: 33713795 DOI: 10.1016/j.semcancer.2021.03.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Revised: 02/28/2021] [Accepted: 03/04/2021] [Indexed: 02/08/2023]
Abstract
Herein we analyze two special routes of the multinucleated cells' formation - the fusion of mononuclear cells and the formation of cell-in-cell structures - in the healthy tissues and in tumorigenesis. There are many theories of tumorigenesis based on the phenomenon of emergence of the hybrid cancer cells. We consider the phenomena, which are rarely mentioned in those theories: namely, cellularization of syncytium or coenocytes, and the reversible or irreversible somatogamy. The latter includes the short-term and the long-term vegetative (somatic) cells' fusions in the life cycles of unicellular organisms. The somatogamy and multinuclearity have repeatedly and independently emerged in various groups of unicellular eukaryotes. These phenomena are among dominant survival and biodiversity sustaining strategies in protists and we admit that they can likely play an analogous role in cancer cells.
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Tekle YI, Wang F, Heidari A, Stewart AJ. Differential gene expression analysis and cytological evidence reveal a sexual stage of an amoeba with multiparental cellular and nuclear fusion. PLoS One 2020; 15:e0235725. [PMID: 33147262 PMCID: PMC7641356 DOI: 10.1371/journal.pone.0235725] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Accepted: 10/06/2020] [Indexed: 12/20/2022] Open
Abstract
Sex is a hallmark of eukaryotes but its evolution in microbial eukaryotes is poorly elucidated. Recent genomic studies revealed microbial eukaryotes possess a genetic toolkit necessary for sexual reproduction. However, the mechanism of sexual development in a majority of microbial eukaryotes including amoebozoans is poorly characterized. The major hurdle in studying sex in microbial eukaryotes is a lack of observational evidence, primarily due to its cryptic nature. In this study, we used a tractable fusing amoeba, Cochliopodium, to investigate sexual development using stage-specific Differential Gene Expression (DGE) and cytological analyses. Both DGE and cytological results showed that most of the meiosis and sex-related genes are upregulated in Cochliopodium undergoing fusion in laboratory culture. Relative gene ontology (GO) category representations in unfused and fused cells revealed a functional skew of the fused transcriptome toward DNA metabolism, nucleus and ligases that are suggestive of a commitment to sexual development. However, the GO categories of unfused cells were dominated by metabolic pathways and other processes indicative of a vegetative phase. Our study provides strong evidence that the fused cells represent a sexual stage in Cochliopodium. Our findings have further implications in understanding the evolution and mechanism of inheritance involving multiparents in other eukaryotes with a similar reproductive strategy.
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Affiliation(s)
- Yonas I. Tekle
- Department of Biology, Spelman College, Atlanta, Georgia, United States of America
- * E-mail:
| | - Fang Wang
- Department of Biology, Spelman College, Atlanta, Georgia, United States of America
| | - Alireza Heidari
- Department of Biology, Spelman College, Atlanta, Georgia, United States of America
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Liu L, Qin L, Zhou Z, Hendriks WGHM, Liu S, Wei Y. Refining the Life Cycle of Plasmodiophora brassicae. PHYTOPATHOLOGY 2020; 110:1704-1712. [PMID: 32407251 DOI: 10.1094/phyto-02-20-0029-r] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
As a soilborne protist pathogen, Plasmodiophora brassicae causes the devastating clubroot disease on Brassicaeae crops worldwide. Due to its intracellular obligate biotrophic nature, the life cycle of P. brassicae is still not fully understood. Here, we used fluorescent probe-based confocal microscopy and transmission electron microscopy (TEM) to investigate the infection process of P. brassicae on the susceptible host Arabidopsis under controlled conditions. We found that P. brassicae can initiate the primary infection in both root hairs and epidermal cells, producing the uninucleate primary plasmodium at 1 day postinoculation (dpi). After that, the developed multinucleate primary plasmodium underwent condensing and cytoplasm cleavage into uninucleate zoosporangia from 1 to 4 dpi. This was subsequently followed by the formation of multinucleate zoosporangia and the production of secondary zoospores within zoosporangium. Importantly, the secondary zoospores performed a conjugation in the root epidermal cells after their release. TEM revealed extensive uninucleate secondary plasmodium in cortical cells at 8 dpi, indicating the establishment of the secondary infection. The P. brassicae subsequently developed into binucleate, quadrinucleate, and multinucleate secondary plasmodia from 10 to 15 dpi, during which the clubroot symptoms appeared. The uninucleate resting spores were first observed in the cortical cells at 24 dpi, marking the completion of a life cycle. We also provided evidence that the secondary infection of P. brassicae may represent the diploid sexual life stage. From these findings, we propose a refined life cycle of P. brassicae which will contribute to understanding of the complicated infection biology of P. brassicae.
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Affiliation(s)
- Lijiang Liu
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, Hubei, 430062, China
- Department of Biology, University of Saskatchewan, Saskatoon, SK, S7N 5E2, Canada
| | - Li Qin
- Department of Biology, University of Saskatchewan, Saskatoon, SK, S7N 5E2, Canada
| | - Zhuqing Zhou
- Department of Biology, University of Saskatchewan, Saskatoon, SK, S7N 5E2, Canada
| | | | - Shengyi Liu
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, Hubei, 430062, China
| | - Yangdou Wei
- Department of Biology, University of Saskatchewan, Saskatoon, SK, S7N 5E2, Canada
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8
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Quinet T, Samba-Louaka A, Héchard Y, Van Doninck K, Van der Henst C. Delayed cytokinesis generates multinuclearity and potential advantages in the amoeba Acanthamoeba castellanii Neff strain. Sci Rep 2020; 10:12109. [PMID: 32694508 PMCID: PMC7374626 DOI: 10.1038/s41598-020-68694-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Accepted: 06/26/2020] [Indexed: 12/29/2022] Open
Abstract
Multinuclearity is a widespread phenomenon across the living world, yet how it is achieved, and the potential related advantages, are not systematically understood. In this study, we investigate multinuclearity in amoebae. We observe that non-adherent amoebae are giant multinucleate cells compared to adherent ones. The cells solve their multinuclearity by a stretchy cytokinesis process with cytosolic bridge formation when adherence resumes. After initial adhesion to a new substrate, the progeny of the multinucleate cells is more numerous than the sibling cells generated from uninucleate amoebae. Hence, multinucleate amoebae show an advantage for population growth when the number of cells is quantified over time. Multiple nuclei per cell are observed in different amoeba species, and the lack of adhesion induces multinuclearity in diverse protists such as Acanthamoeba castellanii, Vermamoeba vermiformis, Naegleria gruberi and Hartmannella rhysodes. In this study, we observe that agitation induces a cytokinesis delay, which promotes multinuclearity. Hence, we propose the hypothesis that multinuclearity represents a physiological adaptation under non-adherent conditions that can lead to biologically relevant advantages.
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Affiliation(s)
- Théo Quinet
- Laboratory of Evolutionary Genetics and Ecology, URBE, University of Namur, Namur, Belgium
| | - Ascel Samba-Louaka
- Laboratoire Ecologie et Biologie des Interactions, Equipe Microbiologie de L'Eau, Université de Poitiers, UMR CNRS 7267, 86073, Poitiers, France
| | - Yann Héchard
- Laboratoire Ecologie et Biologie des Interactions, Equipe Microbiologie de L'Eau, Université de Poitiers, UMR CNRS 7267, 86073, Poitiers, France
| | - Karine Van Doninck
- Laboratory of Evolutionary Genetics and Ecology, URBE, University of Namur, Namur, Belgium
| | - Charles Van der Henst
- Laboratory of Evolutionary Genetics and Ecology, URBE, University of Namur, Namur, Belgium. .,Research Unit in the Biology of Microorganisms (URBM), NARILIS, University of Namur (UNamur), Namur, Belgium. .,Microbial Resistance and Drug Discovery, Center for Structural Biology (CSB), Flanders Institute for Biotechnology (VIB), Vrije Universiteit Brussel (VUB), Pleinlaan 2, Building E-3, 1050, Brussels, Belgium. .,Structural Biology Brussels, Vrije Universiteit Brussel (VUB), Brussels, Belgium.
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9
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Maciver SK, Koutsogiannis Z, de Obeso Fernández Del Valle A. 'Meiotic genes' are constitutively expressed in an asexual amoeba and are not necessarily involved in sexual reproduction. Biol Lett 2019; 15:20180871. [PMID: 30836881 DOI: 10.1098/rsbl.2018.0871] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
The amoebae (and many other protists) have traditionally been considered as asexual organisms, but suspicion has been growing that these organisms are cryptically sexual or are at least related to sexual lineages. This contention is mainly based on genome studies in which the presence of 'meiotic genes' has been discovered. Using RNA-seq (next-generation shotgun sequencing, identifying and quantifying the RNA species in a sample), we have found that the entire repertoire of meiotic genes is expressed in exponentially growing Acanthamoeba and we argue that these so-called meiotic genes are involved in the related process of homologous recombination in this amoeba. We contend that they are only involved in meiosis in other organisms that indulge in sexual reproduction and that homologous recombination is important in asexual protists as a guard against the accumulation of mutations. We also suggest that asexual reproduction is the ancestral state.
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Affiliation(s)
- Sutherland K Maciver
- Centre for Discovery Brain Sciences, Edinburgh Medical School, Biomedical Sciences, University of Edinburgh , Hugh Robson Building, George Square, Edinburgh EH8 9XD , UK
| | - Zisis Koutsogiannis
- Centre for Discovery Brain Sciences, Edinburgh Medical School, Biomedical Sciences, University of Edinburgh , Hugh Robson Building, George Square, Edinburgh EH8 9XD , UK
| | - Alvaro de Obeso Fernández Del Valle
- Centre for Discovery Brain Sciences, Edinburgh Medical School, Biomedical Sciences, University of Edinburgh , Hugh Robson Building, George Square, Edinburgh EH8 9XD , UK
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10
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Maciver SK. Ancestral Eukaryotes Reproduced Asexually, Facilitated by Polyploidy: A Hypothesis. Bioessays 2019; 41:e1900152. [DOI: 10.1002/bies.201900152] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Revised: 10/10/2019] [Indexed: 12/29/2022]
Affiliation(s)
- Sutherland K. Maciver
- Centre for Discovery Brain Sciences, Edinburgh Medical SchoolBiomedical SciencesUniversity of Edinburgh Hugh Robson Building, George Square Edinburgh EH8 9XD Scotland UK
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11
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Melton JT, Singla M, Wood FC, Collins SJ, Tekle YI. Three New Freshwater Cochliopodium Species (Himatismenida, Amoebozoa) from the Southeastern United States. J Eukaryot Microbiol 2019; 67:154-166. [PMID: 31560817 DOI: 10.1111/jeu.12764] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Revised: 09/04/2019] [Accepted: 09/22/2019] [Indexed: 11/30/2022]
Abstract
Cochliopodium is a lens-shaped genus of Amoebozoa characterized by a flexible layer of microscopic dorsal scales. Recent taxonomic and molecular studies reported cryptic diversity in this group and suggested that the often-used scale morphology is not a reliable character for species delineation in the genus. Here, we described three freshwater Cochliopodium spp. from the southeastern United States based on morphological, immunocytochemistry (ICC), and molecular data. A maximum-likelihood phylogenetic analysis and pairwise comparison of COI sequences of Cochliopodium species showed that each of these monoclonal cultures were genetically distinct from each other and any described species with molecular data. Two of the new isolates, "crystal UK-YT2" (Cochliopodium crystalli n. sp.) and "crystal-like UK-YT3" (C. jaguari n. sp.), formed a clade with C. larifeili, which all share a prominent microtubule organizing center (MTOC) and have cubical-shaped crystals. The "Marrs Spring UK-YT4" isolate, C. marrii n. sp., was 100% identical to "Cochliopodium sp. SG-2014 KJ569724." These sequences formed a clade with C. actinophorum and C. arabianum. While the new isolates can be separated morphologically, most of the taxonomic features used in the group show plasticity; therefore, Cochliopodium species can only be reliably identified with the help of molecular data.
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Affiliation(s)
- James T Melton
- Department of Biology, Spelman College, 350 Spelman Lane Southwest, Atlanta, Georgia, 30314
| | - Mandakini Singla
- Department of Biology, Spelman College, 350 Spelman Lane Southwest, Atlanta, Georgia, 30314
| | - Fiona C Wood
- Department of Biology, Spelman College, 350 Spelman Lane Southwest, Atlanta, Georgia, 30314
| | - Shawndasia J Collins
- Department of Biology, Spelman College, 350 Spelman Lane Southwest, Atlanta, Georgia, 30314
| | - Yonas I Tekle
- Department of Biology, Spelman College, 350 Spelman Lane Southwest, Atlanta, Georgia, 30314
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12
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Krishnan D, Ghosh SK. Cellular Events of Multinucleated Giant Cells Formation During the Encystation of Entamoeba invadens. Front Cell Infect Microbiol 2018; 8:262. [PMID: 30109218 PMCID: PMC6079502 DOI: 10.3389/fcimb.2018.00262] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Accepted: 07/13/2018] [Indexed: 12/21/2022] Open
Abstract
Entamoeba histolytica, the causative agent of amoebiasis, does not form cysts in vitro, so reptilian pathogen Entamoeba invadens is used as an Entamoeba encystation model. During the in vitro encystation of E. invadens, a few multinucleated giant cells (MGC) were also appeared in the culture along with cysts. Like the cyst, these MGC's were also formed in the multicellular aggregates found in the encystation culture. Time-lapse live cell imaging revealed that MGC's were the result of repeated cellular fusion with fusion-competent trophozoites as a starting point. The early MGC were non-adherent, and they moved slowly and randomly in the media, but under confinement, MGC became highly motile and directionally persistent. The increased motility resulted in rapid cytoplasmic fissions, which indicated the possibility of continuous cell fusion and division taking place inside the compact multicellular aggregates. Following cell fusion, each nucleus obtained from the fusion-competent trophozoites gave rise to four nuclei with half genomic content. All the haploid nuclei in MGC later aggregated and fused to form a polyploid nucleus. These observations have important implications on Entamoeba biology as they point toward the possibility of E. invadens undergoing sexual or parasexual reproduction.
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Affiliation(s)
- Deepak Krishnan
- Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, India
| | - Sudip K Ghosh
- Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, India
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13
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Abstract
Sex in social amoebae (or dictyostelids) has a number of striking features. Dictyostelid zygotes do not proliferate but grow to a large size by feeding on other cells of the same species, each zygote ultimately forming a walled structure called a macrocyst. The diploid macrocyst nucleus undergoes meiosis, after which a single meiotic product survives to restart haploid vegetative growth. Meiotic recombination is generally initiated by the Spo11 enzyme, which introduces DNA double-strand breaks. Uniquely, as far as is known among sexual eukaryotes, dictyostelids lack a SPO11 gene. Despite this, recombination occurs at high frequencies during meiosis in dictyostelids, through unknown mechanisms. The molecular processes underlying these events, and the evolutionary drivers that brought them into being, may shed light on the genetic conflicts that occur within and between genomes, and how they can be resolved.
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14
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Wood FC, Heidari A, Tekle YI. Genetic Evidence for Sexuality in Cochliopodium (Amoebozoa). J Hered 2018; 108:769-779. [PMID: 29036297 PMCID: PMC5892394 DOI: 10.1093/jhered/esx078] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2017] [Accepted: 09/18/2017] [Indexed: 12/18/2022] Open
Abstract
Microbial eukaryotes, including amoeboids, display diverse and complex life cycles that may or may not involve sexual reproduction. A recent comprehensive gene inventory study concluded that the Amoebozoa are ancestrally sexual. However, the detection of sex genes in some lineages known for their potentially sexual life cycle was very low. Particularly, the genus Cochliopodium, known to undergo a process of cell fusion, karyogamy, and subsequent fission previously described as parasexual, had no meiosis genes detected. This is likely due to low data representation, given the extensive nuclear fusion observed in the genus. In this study, we generate large amounts of transcriptome data for 2 species of Cochliopodium, known for their high frequency of cellular and nuclear fusion, in order to study the genetic basis of the complex life cycle observed in the genus. We inventory 60 sex-related genes, including 11 meiosis-specific genes, and 31 genes involved in fusion and karyogamy. We find a much higher detection of sex-related genes, including 5 meiosis-specific genes not previously detected in Cochliopodium, in this large transcriptome data. The expressed genes form a near-complete recombination machinery, indicating that Cochliopodium is an actively recombining sexual lineage. We also find 9 fusion-related genes in Cochliopodium, although no conserved fusion-specific genes were detected in the transcriptomes. Cochliopodium thus likely uses lineage specific genes for the fusion and depolyploidization processes. Our results demonstrate that Cochliopodium possess the genetic toolkit for recombination, while the mechanism involving fusion and genome reduction remains to be elucidated.
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Affiliation(s)
- Fiona C Wood
- Department of Biology, Spelman College, 350 Spelman Lane Southwest, Atlanta, GA 30314
| | - Alireza Heidari
- Department of Biology, Spelman College, 350 Spelman Lane Southwest, Atlanta, GA 30314
| | - Yonas I Tekle
- Department of Biology, Spelman College, 350 Spelman Lane Southwest, Atlanta, GA 30314
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15
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Schulz G, Maraun M, Völcker E, Scheu S, Krashevska V. Evaluation of Morphological Characteristics to Delineate Taxa of the Genus Trigonopyxis (Amoebozoa, Arcellinida). Protist 2018; 169:190-205. [PMID: 29614434 DOI: 10.1016/j.protis.2018.02.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Revised: 02/19/2018] [Accepted: 02/20/2018] [Indexed: 10/17/2022]
Abstract
Morphological features are often the only characteristics suitable for identification of taxa in testate amoebae, especially in ecological and palaeoecological studies. However, whereas the morphology of some species is rather stable it may vary considerably in others. Within the order Arcellinida the genus Trigonopyxis with the type species Trigonopyxis arcula is morphologically highly variable. To identify reliable characteristics for morphology-based taxon delineation we investigated variations in shell size, pseudostome diameter and pseudostome form in T. arcula from three different sites of the Ecuadorian Andes, where these characteristics vary even more than previously described. Further, we investigated if morphological characteristics in Trigonopyxis varied with changes in environmental factors. We studied 951 shells of Trigonopyxis collected along an altitudinal gradient with varying abiotic factors. We established a method for characterization of the pseudostome form, which lead to five different morphotypes. Our results suggest that shell size alone is not an appropriate character for taxon delineation but can be used as an indicator for changes in environmental conditions. In contrast, the pseudostome form might be used for taxon delineation, but likely also varies considerably within taxa. Overall, the study provides an overview of the morphological variability of the genus Trigonopyxis.
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Affiliation(s)
- Garvin Schulz
- University of Göttingen, J.F. Blumenbach Institute of Zoology and Anthropology, Untere Karspüle 2, D-37073 Göttingen, Germany.
| | - Mark Maraun
- University of Göttingen, J.F. Blumenbach Institute of Zoology and Anthropology, Untere Karspüle 2, D-37073 Göttingen, Germany
| | - Eckhard Völcker
- Penard Laboratory, 18 Stellenberg Avenue, Cape Town 7708, South Africa
| | - Stefan Scheu
- University of Göttingen, J.F. Blumenbach Institute of Zoology and Anthropology, Untere Karspüle 2, D-37073 Göttingen, Germany
| | - Valentyna Krashevska
- University of Göttingen, J.F. Blumenbach Institute of Zoology and Anthropology, Untere Karspüle 2, D-37073 Göttingen, Germany
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Tekle YI, Wood FC, Katz LA, Cerón-Romero MA, Gorfu LA. Amoebozoans Are Secretly but Ancestrally Sexual: Evidence for Sex Genes and Potential Novel Crossover Pathways in Diverse Groups of Amoebae. Genome Biol Evol 2017; 9:375-387. [PMID: 28087686 PMCID: PMC5381635 DOI: 10.1093/gbe/evx002] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/10/2017] [Indexed: 12/12/2022] Open
Abstract
Sex is beneficial in eukaryotes as it can increase genetic diversity, reshuffle their genomes, and purge deleterious mutations. Yet, its evolution remains a mystery. The eukaryotic clade supergroup Amoebozoa encompasses diverse lineages of polymorphic amoeboid forms, including both free-living and parasitic lineages. The group is generally believed to be asexual, though recent studies show that some of its members are implicated in cryptic forms of sexual cycles. In this study, we conduct a comprehensive inventory and analysis of genes involved in meiosis and related processes, in order to investigate the evolutionary history of sex in the clade. We analyzed genomic and transcriptomic data of 39 amoebozoans representing all major subclades of Amoebozoa. Our results show that Amoebozoa possess most of the genes exclusive to meiosis but lack genes encoding synaptonemal complex (SC). The absence of SC genes is discussed in the context of earlier studies that reported ultrastructural evidence of SC in some amoebae. We also find interclade and intrageneric variation in sex gene distribution, indicating diversity in sexual pathways in the group. Particularly, members of Mycetozoa engage in a novel sexual pathway independent of the universally conserved meiosis initiator gene, SPO11. Our findings strongly suggest that not only do amoebozoans possess sex genes in their genomes, but also, based on the transcriptome evidence, the present sex genes are functional. We conclude that Amoebozoa is ancestrally sexual, contrary to the long held belief that most of its members are asexual. Thus, asexuality in Amoebozoa, if confirmed to be present, is a derived-trait that appeared later in their evolution.
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Affiliation(s)
- Yonas I Tekle
- Department of Biology, Spelman College, Atlanta, Georgia
| | - Fiona C Wood
- Department of Biology, Spelman College, Atlanta, Georgia
| | - Laura A Katz
- Department of Biological Sciences, Smith College, Northampton, Massachusetts.,Graduate Program in Organismic and Evolutionary Biology, University of Massachusetts, Amherst
| | - Mario A Cerón-Romero
- Department of Biological Sciences, Smith College, Northampton, Massachusetts.,Graduate Program in Organismic and Evolutionary Biology, University of Massachusetts, Amherst
| | - Lydia A Gorfu
- Department of Biology, Spelman College, Atlanta, Georgia
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17
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Wrzosek M, Ruszkiewicz-Michalska M, Sikora K, Damszel M, Sierota Z. The plasticity of fungal interactions. Mycol Prog 2016. [DOI: 10.1007/s11557-016-1257-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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18
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Asexual Amoebae Escape Muller's Ratchet through Polyploidy. Trends Parasitol 2016; 32:855-862. [PMID: 27599632 DOI: 10.1016/j.pt.2016.08.006] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2016] [Revised: 08/05/2016] [Accepted: 08/08/2016] [Indexed: 11/23/2022]
Abstract
While some amoebae reproduce sexually, many amoebae (e.g., Acanthamoeba, Naegleria) reproduce asexually and therefore, according to popular doctrine, are likely to have been genetically disadvantaged as a consequence. In the absence of sex, mutations are proposed to accumulate by a mechanism known as Muller's ratchet. I hypothesise that amoebae can escape the ravages of accumulated mutation by virtue of their being polyploid. The polyploid state reduces spontaneous mutation accumulation by gene conversion, the freshly mutated copy being corrected by the presence of the many other wild-type copies. In this manner these amoebae reap the benefits of an asexual reproductive existence: principally, that it is rapid and convenient. Evidence for this mechanism comes from polyploid plants, bacteria, and archaea.
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19
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Garg SG, Martin WF. Mitochondria, the Cell Cycle, and the Origin of Sex via a Syncytial Eukaryote Common Ancestor. Genome Biol Evol 2016; 8:1950-70. [PMID: 27345956 PMCID: PMC5390555 DOI: 10.1093/gbe/evw136] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/29/2016] [Indexed: 02/07/2023] Open
Abstract
Theories for the origin of sex traditionally start with an asexual mitosing cell and add recombination, thereby deriving meiosis from mitosis. Though sex was clearly present in the eukaryote common ancestor, the order of events linking the origin of sex and the origin of mitosis is unknown. Here, we present an evolutionary inference for the origin of sex starting with a bacterial ancestor of mitochondria in the cytosol of its archaeal host. We posit that symbiotic association led to the origin of mitochondria and gene transfer to host's genome, generating a nucleus and a dedicated translational compartment, the eukaryotic cytosol, in which-by virtue of mitochondria-metabolic energy was not limiting. Spontaneous protein aggregation (monomer polymerization) and Adenosine Tri-phosphate (ATP)-dependent macromolecular movement in the cytosol thereby became selectable, giving rise to continuous microtubule-dependent chromosome separation (reduction division). We propose that eukaryotic chromosome division arose in a filamentous, syncytial, multinucleated ancestor, in which nuclei with insufficient chromosome numbers could complement each other through mRNA in the cytosol and generate new chromosome combinations through karyogamy. A syncytial (or coenocytic, a synonym) eukaryote ancestor, or Coeca, would account for the observation that the process of eukaryotic chromosome separation is more conserved than the process of eukaryotic cell division. The first progeny of such a syncytial ancestor were likely equivalent to meiospores, released into the environment by the host's vesicle secretion machinery. The natural ability of archaea (the host) to fuse and recombine brought forth reciprocal recombination among fusing (syngamy and karyogamy) progeny-sex-in an ancestrally meiotic cell cycle, from which the simpler haploid and diploid mitotic cell cycles arose. The origin of eukaryotes was the origin of vertical lineage inheritance, and sex was required to keep vertically evolving lineages viable by rescuing the incipient eukaryotic lineage from Muller's ratchet. The origin of mitochondria was, in this view, the decisive incident that precipitated symbiosis-specific cell biological problems, the solutions to which were the salient features that distinguish eukaryotes from prokaryotes: A nuclear membrane, energetically affordable ATP-dependent protein-protein interactions in the cytosol, and a cell cycle involving reduction division and reciprocal recombination (sex).
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Affiliation(s)
- Sriram G Garg
- Institute of Molecular Evolution, Heinrich-Heine Universität Düsseldorf, Düsseldorf 40225, Germany
| | - William F Martin
- Institute of Molecular Evolution, Heinrich-Heine Universität Düsseldorf, Düsseldorf 40225, Germany
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Clonal reproduction with androgenesis and somatic recombination: the case of the ant Cardiocondyla kagutsuchi. Naturwissenschaften 2016; 103:22. [PMID: 26922778 DOI: 10.1007/s00114-016-1349-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2015] [Revised: 01/29/2016] [Accepted: 02/14/2016] [Indexed: 10/22/2022]
Abstract
In haplodiploid insects such as ants, male sexuals develop from unfertilised haploid eggs, while female sexuals and workers develop from fertilized diploid eggs. However, some ant species do not exchange their gene pool between sexes; both male and female sexuals are clonally produced, while workers are sexually produced. To date, three ant species, Wasmannia auropunctata, Vollenhovia emeryi, and Paratrechina longicornis, have been reported to reproduce using such reproductive systems. In this study, we reveal that in one lineage of the ant Cardiocondyla kagutsuchi, male and female sexuals are also clonally produced. In contrast to the abovementioned three species, the workers were not only sexually produced but had recombinant sequences in their nuclear internal transcribed spacer regions, although the recombinant sequences were not detected in male or female sexuals. These results suggest that the lineage likely possesses a mechanism to compensate for the reduction in genetic variation due to clonal reproduction with somatic recombination that occurs within the workers.
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21
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Tekle YI, Gorfu LA, Anderson OR. Cochliopodium arabianum
n. sp. (Amorphea, Amoebozoa). J Eukaryot Microbiol 2015; 62:623-8. [DOI: 10.1111/jeu.12218] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2014] [Revised: 12/17/2014] [Accepted: 01/27/2015] [Indexed: 11/28/2022]
Affiliation(s)
- Yonas I. Tekle
- Department of Biology; Spelman College; 350 Spelman Lane Southwest Atlanta Georgia 30314 USA
| | - Lydia A. Gorfu
- Department of Biology; Spelman College; 350 Spelman Lane Southwest Atlanta Georgia 30314 USA
| | - O. Roger Anderson
- Department of Biology; Lamont-Doherty Earth Observatory of Columbia University; Palisades NY 10964 USA
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