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Shin Y, Kim SY, Greene EC. ATP hydrolysis-driven structural transitions within the S. cerevisiae Rad51 and Dmc1 nucleoprotein filaments. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2025.03.19.644215. [PMID: 40166259 PMCID: PMC11957116 DOI: 10.1101/2025.03.19.644215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/02/2025]
Abstract
Homologous recombination (HR) is essential for the maintenance of genome stability and for generating genetic diversity during meiosis. The eukaryotic protein Rad51 is member of the Rad51/RecA family of DNA recombinases and is responsible for guiding the DNA pairing reactions that take place in HR during mitosis. Dmc1 is a meiosis-specific paralog of Rad51 and is responsible for the DNA pairing reactions that take place in HR during meiosis. Rad51 and Dmc1 are both ATP-dependent DNA-binding proteins and both form extended helical filaments on ssDNA which are key intermediates in HR. The stability of these nucleoprotein filaments is highly regulated and is also tightly coupled to nucleotide binding and hydrolysis. ATP binding promotes filament assembly whereas the hydrolysis of ATP to ADP reduces filament stability to promote filament disassembly. Here, we present CryoEM structures of the Saccharomyces cerevisiae recombinases Rad51 and Dmc1 in the ADP-bound states and provide a detailed structural comparison to the ATP-bound filaments. Our findings yield insights into the structural transitions that take place during the hydrolysis of ATP to ADP and suggest a new model for how these structural changes may be linked to nucleoprotein filament disassembly.
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Affiliation(s)
- Yeonoh Shin
- Department of Biochemistry & Molecular Biophysics, Columbia University Irving Medical Center, New York, NY, 10032, USA
| | - Stefan Y Kim
- Department of Biochemistry & Molecular Biophysics, Columbia University Irving Medical Center, New York, NY, 10032, USA
| | - Eric C Greene
- Department of Biochemistry & Molecular Biophysics, Columbia University Irving Medical Center, New York, NY, 10032, USA
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2
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Petassi M, Shin Y, Jessop AM, Morse K, Kim SY, Matei R, Raina VB, Greene EC. Lineage-specific amino acids define functional attributes of the protomer-protomer interfaces for the Rad51 and Dmc1 recombinases. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.12.03.626531. [PMID: 39677717 PMCID: PMC11642858 DOI: 10.1101/2024.12.03.626531] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2024]
Abstract
Most eukaryotes possess two Rad51/RecA family DNA recombinases that are thought to have arisen from an ancient gene duplication event: Rad51, which is expressed in both mitosis and meiosis; and Dmc1, which is only expressed in meiosis. To explore the evolutionary relationship between these recombinases, here, we present high-resolution CryoEM structures of S. cerevisiae Rad51 filaments and S. cerevisiae Dmc1 filaments bound to ssDNA, which reveal a pair of stacked interfacial aromatic amino acid residues that are nearly universally conserved in Rad51 but are absent from Dmc1. We use a combination of bioinformatics, genetic analysis of natural sequence variation, and deep mutational analysis to probe the functionally tolerated sequence space for these stacked aromatic residues. Our findings demonstrate that the functional landscape of the interfacial aromatic residues within the Rad51 filament is highly constrained. In contrast, the amino acids at the equivalent positions within the Dmc1 filament exhibit a broad functional landscape. This work helps highlight the distinct evolutionary trajectories of these two eukaryotic recombinases, which may have contributed to their functional and mechanistic divergence.
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Affiliation(s)
- Mike Petassi
- Department of Biochemistry & Molecular Biophysics, Columbia University Irving Medical Center, New York, NY, 10032, USA
| | - Yeonoh Shin
- Department of Biochemistry & Molecular Biophysics, Columbia University Irving Medical Center, New York, NY, 10032, USA
| | - Aidan M Jessop
- Department of Biochemistry & Molecular Biophysics, Columbia University Irving Medical Center, New York, NY, 10032, USA
| | - Katherine Morse
- Department of Biochemistry & Molecular Biophysics, Columbia University Irving Medical Center, New York, NY, 10032, USA
| | - Stefan Y Kim
- Department of Biochemistry & Molecular Biophysics, Columbia University Irving Medical Center, New York, NY, 10032, USA
| | - Razvan Matei
- Department of Biochemistry & Molecular Biophysics, Columbia University Irving Medical Center, New York, NY, 10032, USA
| | - Vivek B Raina
- Department of Biochemistry & Molecular Biophysics, Columbia University Irving Medical Center, New York, NY, 10032, USA
| | - Eric C Greene
- Department of Biochemistry & Molecular Biophysics, Columbia University Irving Medical Center, New York, NY, 10032, USA
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3
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Shaw DE, Ross WD, Lambert AV, White MA. Single cell RNA-sequencing reveals no evidence for meiotic sex chromosome inactivation in the threespine stickleback fish. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.11.26.625488. [PMID: 39651240 PMCID: PMC11623615 DOI: 10.1101/2024.11.26.625488] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2024]
Abstract
Sex chromosomes often evolve unique patterns of gene expression in spermatogenesis. In many species, sex-linked genes are downregulated during meiosis in response to asynapsis of the heterogametic sex chromosome pair (meiotic sex chromosome inactivation; MSCI). Our understanding of this process has been limited to a handful of species, including mammals, Drosophila , and C. elegans. Based on findings from these taxa, MSCI has been viewed as likely a conserved process. However, in other groups like teleost fish, our understanding of this process is limited. Teleost fish are a noteworthy group to investigate because sex chromosomes can rapidly evolve between closely related species. Transcriptional profiling of spermatogenesis at the single-cell level is a useful approach to investigate whether MSCI occurs in other species with independently derived sex chromosomes. Here, we investigate whether MSCI occurs in the threespine stickleback fish ( Gasterosteus aculeatus ), which have an X and Y chromosome that evolved less than 26 million years ago. Using single-cell RNA-seq, we found that the X and Y chromosomes do not have a signature of MSCI, maintaining gene expression across meiosis. Using immunofluorescence, we also show the threespine stickleback do not form a condensed sex body around the X and Y, a conserved feature of MSCI in many species. We did not see patterns of gene content evolution documented in other species with MSCI. Y-linked ampliconic gene families were expressed across multiple stages of spermatogenesis, rather than being restricted to post-meiotic stages, like in mammals. Our work shows MSCI does not occur in the threespine stickleback fish and has not shaped the evolution of the Y chromosome. In addition, the absence of MSCI in the threespine stickleback suggests this process may not be a conserved feature of teleost fish and argues for additional investigation in other species. Author Summary As male germ cells enter meiosis, the X and Y chromosome of many species undergo a drastic repression of gene expression. In mammals, this process has been shown to be essential for fertility, and the expression of sex-linked genes can lead to meiotic arrest and cell death. This process has only been studied in a handful of organisms, which limits our understanding how conserved MSCI is across the tree of life. Teleost fish are an understudied group with many examples of independently derived sex chromosomes across closely related species. Here, we investigate whether MSCI occurs in the threespine stickleback fish, using single-cell transcriptional profiling. We found gene expression remains active throughout meiosis on the sex chromosomes, indicating MSCI does not occur. This indicates that MSCI is not a conserved feature of all taxa and is not an inevitable outcome of degenerating Y chromosomes.
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Rizos I, Frada MJ, Bittner L, Not F. Life cycle strategies in free-living unicellular eukaryotes: Diversity, evolution, and current molecular tools to unravel the private life of microorganisms. J Eukaryot Microbiol 2024; 71:e13052. [PMID: 39085163 PMCID: PMC11603280 DOI: 10.1111/jeu.13052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Revised: 06/12/2024] [Accepted: 07/08/2024] [Indexed: 08/02/2024]
Abstract
An astonishing range of morphologies and life strategies has arisen across the vast diversity of protists, allowing them to thrive in most environments. In model protists, like Tetrahymena, Dictyostelium, or Trypanosoma, life cycles involving multiple life stages with different morphologies have been well characterized. In contrast, knowledge of the life cycles of free-living protists, which primarily consist of uncultivated environmental lineages, remains largely fragmentary. Various life stages and lineage-specific cellular innovations have been observed in the field for uncultivated protists, but such innovations generally lack functional characterization and have unknown physiological and ecological roles. In the actual state of knowledge, evidence of sexual processes is confirmed for 20% of free-living protist lineages. Nevertheless, at the onset of eukaryotic diversification, common molecular trends emerged to promote genetic recombination, establishing sex as an inherent feature of protists. Here, we review protist life cycles from the viewpoint of life cycle transitions and genetics across major eukaryotic lineages. We focus on the scarcely observed sexual cycle of free-living protists, summarizing evidence for its existence and describing key genes governing its progression, as well as, current methods for studying the genetics of sexual cycles in both cultivable and uncultivated protist groups.
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Affiliation(s)
- Iris Rizos
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum National d'Histoire Naturelle, CNRS, Sorbonne Université, EPHEUniversité Des AntillesParisFrance
- CNRS, AD2M‐UMR7144 Station Biologique de RoscoffSorbonne UniversitéRoscoffFrance
| | - Miguel J. Frada
- Department of Ecology, Evolution and Behavior, Silberman Institute of Life SciencesThe Hebrew University of JerusalemJerusalemIsrael
- The Interuniversity Institute for Marine Sciences in EilatEilatIsrael
| | - Lucie Bittner
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum National d'Histoire Naturelle, CNRS, Sorbonne Université, EPHEUniversité Des AntillesParisFrance
- Institut Universitaire de FranceParisFrance
| | - Fabrice Not
- CNRS, AD2M‐UMR7144 Station Biologique de RoscoffSorbonne UniversitéRoscoffFrance
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5
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Berger F. Meiosis as a mechanism for epigenetic reprogramming and cellular rejuvenation. Development 2024; 151:dev203046. [PMID: 39399899 DOI: 10.1242/dev.203046] [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] [Indexed: 10/15/2024]
Abstract
Meiosis is a hallmark of sexual reproduction because it represents the transition from one life cycle to the next and, in animals, meiosis produces gametes. Why meiosis evolved has been debated and most studies have focused on recombination of the parental alleles as the main function of meiosis. However, 40 years ago, Robin Holliday proposed that an essential function of meiosis is to oppose the consequence of successive mitoses that cause cellular aging. Cellular aging results from accumulated defective organelles and proteins and modifications of chromatin in the form of DNA methylation and histone modifications referred to collectively as epigenetic marks. Here, recent findings supporting the hypothesis that meiosis opposes cellular aging are reviewed and placed in the context of the diversity of the life cycles of eukaryotes, including animals, yeast, flowering plants and the bryophyte Marchantia.
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Affiliation(s)
- Frédéric Berger
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna BioCenter, Dr. Bohr-Gasse 3, 1030 Vienna, Austria
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6
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Sun S, Defosse T, Boyd A, Sop J, Verderose F, Surray D, Aziz M, Howland M, Wu S, Changela N, Jang J, Schindler K, Xing J, McKim KS. Whole transcriptome screening for novel genes involved in meiosis and fertility in Drosophila melanogaster. Sci Rep 2024; 14:3602. [PMID: 38351116 PMCID: PMC10864285 DOI: 10.1038/s41598-024-53346-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Accepted: 01/31/2024] [Indexed: 02/16/2024] Open
Abstract
Reproductive success requires the development of viable oocytes and the accurate segregation of chromosomes during meiosis. Failure to segregate chromosomes properly can lead to infertility, miscarriages, or developmental disorders. A variety of factors contribute to accurate chromosome segregation and oocyte development, such as spindle assembly and sister chromatid cohesion. However, many proteins required for meiosis remain unknown. In this study, we aimed to develop a screening pipeline for identifying novel meiotic and fertility genes using the genome of Drosophila melanogaster. To accomplish this goal, genes upregulated within meiotically active tissues were identified. More than 240 genes with no known function were silenced using RNA interference (RNAi) and the effects on meiosis and fertility were assessed. We identified 94 genes that when silenced caused infertility and/or high levels of chromosomal nondisjunction. The vast majority of these genes have human and mouse homologs that are also poorly studied. Through this screening process, we identified novel genes that are crucial for meiosis and oocyte development but have not been extensively studied in human or model organisms. Understanding the function of these genes will be an important step towards the understanding of their biological significance during reproduction.
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Affiliation(s)
- Siqi Sun
- Department of Genetics, Rutgers, The State University of New Jersey, Piscataway, NJ, USA
| | - Tyler Defosse
- Waksman Institute, Rutgers, The State University of New Jersey, 190 Frelinghuysen Road, Piscataway, NJ, 08854, USA
| | - Ayla Boyd
- Waksman Institute, Rutgers, The State University of New Jersey, 190 Frelinghuysen Road, Piscataway, NJ, 08854, USA
| | - Joel Sop
- Waksman Institute, Rutgers, The State University of New Jersey, 190 Frelinghuysen Road, Piscataway, NJ, 08854, USA
| | - Faith Verderose
- Waksman Institute, Rutgers, The State University of New Jersey, 190 Frelinghuysen Road, Piscataway, NJ, 08854, USA
| | - Diya Surray
- Waksman Institute, Rutgers, The State University of New Jersey, 190 Frelinghuysen Road, Piscataway, NJ, 08854, USA
| | - Mark Aziz
- Waksman Institute, Rutgers, The State University of New Jersey, 190 Frelinghuysen Road, Piscataway, NJ, 08854, USA
| | - Margaret Howland
- Waksman Institute, Rutgers, The State University of New Jersey, 190 Frelinghuysen Road, Piscataway, NJ, 08854, USA
| | - Siwen Wu
- Waksman Institute, Rutgers, The State University of New Jersey, 190 Frelinghuysen Road, Piscataway, NJ, 08854, USA
| | - Neha Changela
- Waksman Institute, Rutgers, The State University of New Jersey, 190 Frelinghuysen Road, Piscataway, NJ, 08854, USA
| | - Janet Jang
- Waksman Institute, Rutgers, The State University of New Jersey, 190 Frelinghuysen Road, Piscataway, NJ, 08854, USA
| | - Karen Schindler
- Department of Genetics, Rutgers, The State University of New Jersey, Piscataway, NJ, USA
- Human Genetics Institute of New Jersey, Rutgers, The State University of New Jersey, 145 Bevier Road, Piscataway, NJ, 08854, USA
| | - Jinchuan Xing
- Department of Genetics, Rutgers, The State University of New Jersey, Piscataway, NJ, USA.
- Human Genetics Institute of New Jersey, Rutgers, The State University of New Jersey, 145 Bevier Road, Piscataway, NJ, 08854, USA.
| | - Kim S McKim
- Department of Genetics, Rutgers, The State University of New Jersey, Piscataway, NJ, USA.
- Waksman Institute, Rutgers, The State University of New Jersey, 190 Frelinghuysen Road, Piscataway, NJ, 08854, USA.
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7
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Popovic A, Cao EY, Han J, Nursimulu N, Alves-Ferreira EVC, Burrows K, Kennard A, Alsmadi N, Grigg ME, Mortha A, Parkinson J. The commensal protist Tritrichomonas musculus exhibits a dynamic life cycle that induces extensive remodeling of the gut microbiota. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.06.528774. [PMID: 37090671 PMCID: PMC10120700 DOI: 10.1101/2023.03.06.528774] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Commensal protists and gut bacterial communities exhibit complex relationships, mediated at least in part through host immunity. To improve our understanding of this tripartite interplay, we investigated community and functional dynamics between the murine protist Tritrichomonas musculus ( T. mu ) and intestinal bacteria in healthy and B cell-deficient mice. We identified dramatic, protist-driven remodeling of resident microbiome growth and activities, in parallel with T. mu functional changes, accelerated in the absence of B cells. Metatranscriptomic data revealed nutrient-based competition between bacteria and the protist. Single cell transcriptomics identified distinct T. mu life stages, providing new evidence for trichomonad sexual replication and the formation of pseudocysts. Unique cell states were validated in situ through microscopy and flow cytometry. Our results reveal complex microbial dynamics during the establishment of a commensal protist in the gut, and provide valuable datasets to drive future mechanistic studies.
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Abstract
Meiosis is a specialized cell division program that is essential for sexual reproduction. The two meiotic divisions reduce chromosome number by half, typically generating haploid genomes that are packaged into gametes. To achieve this ploidy reduction, meiosis relies on highly unusual chromosomal processes including the pairing of homologous chromosomes, assembly of the synaptonemal complex, programmed formation of DNA breaks followed by their processing into crossovers, and the segregation of homologous chromosomes during the first meiotic division. These processes are embedded in a carefully orchestrated cell differentiation program with multiple interdependencies between DNA metabolism, chromosome morphogenesis, and waves of gene expression that together ensure the correct number of chromosomes is delivered to the next generation. Studies in the budding yeast Saccharomyces cerevisiae have established essentially all fundamental paradigms of meiosis-specific chromosome metabolism and have uncovered components and molecular mechanisms that underlie these conserved processes. Here, we provide an overview of all stages of meiosis in this key model system and highlight how basic mechanisms of genome stability, chromosome architecture, and cell cycle control have been adapted to achieve the unique outcome of meiosis.
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Affiliation(s)
- G Valentin Börner
- Center for Gene Regulation in Health and Disease (GRHD), Department of Biological, Geological and Environmental Sciences, Cleveland State University, Cleveland, OH 44115, USA
| | | | - Amy J MacQueen
- Department of Molecular Biology and Biochemistry, Wesleyan University, Middletown, CT 06459, USA
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Bhattacharya S. Episomal and chromosomal DNA replication and recombination in Entamoeba histolytica. Front Mol Biosci 2023; 10:1212082. [PMID: 37363402 PMCID: PMC10285105 DOI: 10.3389/fmolb.2023.1212082] [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: 04/25/2023] [Accepted: 05/26/2023] [Indexed: 06/28/2023] Open
Abstract
Entamoeba histolytica is the causative agent of amoebiasis. DNA replication studies in E. histolytica first started with the ribosomal RNA genes located on episomal circles. Unlike most plasmids, Entamoeba histolytica rDNA circles lacked a fixed origin. Replication initiated from multiple sites on the episome, and these were preferentially used under different growth conditions. In synchronized cells the early origins mapped within the rDNA transcription unit, while at later times an origin in the promoter-proximal upstream intergenic spacer was activated. This is reminiscent of eukaryotic chromosomal replication where multiple potential origins are used. Biochemical studies on replication and recombination proteins in Entamoeba histolytica picked up momentum once the genome sequence was available. Sequence search revealed homologs of DNA replication and recombination proteins, including meiotic genes. The replicative DNA polymerases identified included the α, δ, ε of polymerase family B; lesion repair polymerases Rev1 and Rev3; a translesion repair polymerase of family A, and five families of polymerases related to family B2. Biochemical analysis of EhDNApolA confirmed its polymerase activity with expected kinetic constants. It could perform strand displacement, and translesion synthesis. The purified EhDNApolB2 had polymerase and exonuclease activities, and could efficiently bypass some types of DNA lesions. The single DNA ligase (EhDNAligI) was similar to eukaryotic DNA ligase I. It was a high-fidelity DNA ligase, likely involved in both replication and repair. Its interaction with EhPCNA was also demonstrated. The recombination-related proteins biochemically characterized were EhRad51 and EhDmc1. Both shared the canonical properties of a recombinase and could catalyse strand exchange over long DNA stretches. Presence of Dmc1 indicates the likelihood of meiosis in this parasite. Direct evidence of recombination in Entamoeba histolytica was provided by use of inverted repeat sequences located on plasmids or chromosomes. In response to a variety of stress conditions, and during encystation in Entamoeba invadens, recombination-related genes were upregulated and homologous recombination was enhanced. These data suggest that homologous recombination could have critical roles in trophozoite growth and stage conversion. Availability of biochemically characterized replication and recombination proteins is an important resource for exploration of novel anti-amoebic drug targets.
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10
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Emmenecker C, Mézard C, Kumar R. Repair of DNA double-strand breaks in plant meiosis: role of eukaryotic RecA recombinases and their modulators. PLANT REPRODUCTION 2023; 36:17-41. [PMID: 35641832 DOI: 10.1007/s00497-022-00443-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Accepted: 05/09/2022] [Indexed: 06/15/2023]
Abstract
Homologous recombination during meiosis is crucial for the DNA double-strand breaks (DSBs) repair that promotes the balanced segregation of homologous chromosomes and enhances genetic variation. In most eukaryotes, two recombinases RAD51 and DMC1 form nucleoprotein filaments on single-stranded DNA generated at DSB sites and play a central role in the meiotic DSB repair and genome stability. These nucleoprotein filaments perform homology search and DNA strand exchange to initiate repair using homologous template-directed sequences located elsewhere in the genome. Multiple factors can regulate the assembly, stability, and disassembly of RAD51 and DMC1 nucleoprotein filaments. In this review, we summarize the current understanding of the meiotic functions of RAD51 and DMC1 and the role of their positive and negative modulators. We discuss the current models and regulators of homology searches and strand exchange conserved during plant meiosis. Manipulation of these repair factors during plant meiosis also holds a great potential to accelerate plant breeding for crop improvements and productivity.
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Affiliation(s)
- Côme Emmenecker
- Institut Jean-Pierre Bourgin (IJPB), Université Paris-Saclay, INRAE, AgroParisTech, 78000, Versailles, France
- University of Paris-Sud, Université Paris-Saclay, 91405, Orsay, France
| | - Christine Mézard
- Institut Jean-Pierre Bourgin (IJPB), CNRS, Université Paris-Saclay, INRAE, AgroParisTech, 78000, Versailles, France.
| | - Rajeev Kumar
- Institut Jean-Pierre Bourgin (IJPB), Université Paris-Saclay, INRAE, AgroParisTech, 78000, Versailles, France.
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11
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Cofre J, Saalfeld K. The first embryo, the origin of cancer and animal phylogeny. I. A presentation of the neoplastic process and its connection with cell fusion and germline formation. Front Cell Dev Biol 2023; 10:1067248. [PMID: 36684435 PMCID: PMC9846517 DOI: 10.3389/fcell.2022.1067248] [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: 10/12/2022] [Accepted: 11/16/2022] [Indexed: 01/05/2023] Open
Abstract
The decisive role of Embryology in understanding the evolution of animal forms is founded and deeply rooted in the history of science. It is recognized that the emergence of multicellularity would not have been possible without the formation of the first embryo. We speculate that biophysical phenomena and the surrounding environment of the Ediacaran ocean were instrumental in co-opting a neoplastic functional module (NFM) within the nucleus of the first zygote. Thus, the neoplastic process, understood here as a biological phenomenon with profound embryologic implications, served as the evolutionary engine that favored the formation of the first embryo and cancerous diseases and allowed to coherently create and recreate body shapes in different animal groups during evolution. In this article, we provide a deep reflection on the Physics of the first embryogenesis and its contribution to the exaptation of additional NFM components, such as the extracellular matrix. Knowledge of NFM components, structure, dynamics, and origin advances our understanding of the numerous possibilities and different innovations that embryos have undergone to create animal forms via Neoplasia during evolutionary radiation. The developmental pathways of Neoplasia have their origins in ctenophores and were consolidated in mammals and other apical groups.
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Affiliation(s)
- Jaime Cofre
- Laboratório de Embriologia Molecular e Câncer, Federal University of Santa Catarina, Florianópolis, Santa Catarina, Brazil,*Correspondence: Jaime Cofre,
| | - Kay Saalfeld
- Laboratório de Filogenia Animal, Federal University of Santa Catarina, Florianópolis, Santa Catarina, Brazil
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12
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Ferreira TR, Sacks DL. Experimental Hybridization in Leishmania: Tools for the Study of Genetic Exchange. Pathogens 2022; 11:pathogens11050580. [PMID: 35631101 PMCID: PMC9144296 DOI: 10.3390/pathogens11050580] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Revised: 05/11/2022] [Accepted: 05/13/2022] [Indexed: 02/06/2023] Open
Abstract
Despite major advances over the last decade in our understanding of Leishmania reproductive strategies, the sexual cycle in Leishmania has defied direct observation and remains poorly investigated due to experimental constraints. Here, we summarize the findings and conclusions drawn from genetic analysis of experimental hybrids generated in sand flies and highlight the recent advances in generating hybrids in vitro. The ability to hybridize between culture forms of different species and strains of Leishmania should invite more intensive investigation of the mechanisms underlying genetic exchange and provide a rich source of recombinant parasites for future genetic analyses.
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13
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Zajaczkowski P, Lee R, Fletcher-Lartey SM, Alexander K, Mahimbo A, Stark D, Ellis JT. The controversies surrounding Giardia intestinalis assemblages A and B. CURRENT RESEARCH IN PARASITOLOGY & VECTOR-BORNE DISEASES 2022; 1:100055. [PMID: 35284870 PMCID: PMC8906113 DOI: 10.1016/j.crpvbd.2021.100055] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Accepted: 10/09/2021] [Indexed: 11/27/2022]
Abstract
Giardia intestinalis continues to be one of the most encountered parasitic diseases around the world. Although more frequently detected in developing countries, Giardia infections nonetheless pose significant public health problems in developed countries as well. Molecular characterisation of Giardia isolates from humans and animals reveals that there are two genetically different assemblages (known as assemblage A and B) that cause human infections. However, the current molecular assays used to genotype G. intestinalis isolates are quite controversial. This is in part due to a complex phenomenon where assemblages are incorrectly typed and underreported depending on which targeted locus is sequenced. In this review, we outline current knowledge based on molecular epidemiological studies and raise questions as to the reliability of current genotyping assays and a lack of a globally accepted method. Additionally, we discuss the clinical symptoms caused by G. intestinalis infection and how these symptoms vary depending on the assemblage infecting an individual. We also introduce the host-parasite factors that play a role in the subsequent clinical presentation of an infected person, and explore which assemblages are most seen globally.
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Affiliation(s)
- Patricia Zajaczkowski
- Faculty of Science, School of Life Sciences, University of Technology Sydney, Australia
| | - Rogan Lee
- Centre for Infectious Diseases and Microbiology Laboratory Services, ICPMR, Westmead Hospital, Westmead, New South Wales, Australia.,Westmead Clinical School, Faculty of Medicine and Health, The University of Sydney, Westmead Hospital, Westmead, NSW, Australia
| | | | - Kate Alexander
- Public Health Unit, South Western Sydney Local Health District, Liverpool, Australia
| | - Abela Mahimbo
- Faculty of Health, School of Public Health, University of Technology Sydney, Australia
| | - Damien Stark
- Department of Microbiology, St Vincent's Hospital Sydney, Darlinghurst, New South Wales, Australia
| | - John T Ellis
- Faculty of Science, School of Life Sciences, University of Technology Sydney, Australia
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14
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Gerber T, Loureiro C, Schramma N, Chen S, Jain A, Weber A, Weigert A, Santel M, Alim K, Treutlein B, Camp JG. Spatial transcriptomic and single-nucleus analysis reveals heterogeneity in a gigantic single-celled syncytium. eLife 2022; 11:e69745. [PMID: 35195068 PMCID: PMC8865844 DOI: 10.7554/elife.69745] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2021] [Accepted: 02/07/2022] [Indexed: 11/25/2022] Open
Abstract
In multicellular organisms, the specification, coordination, and compartmentalization of cell types enable the formation of complex body plans. However, some eukaryotic protists such as slime molds generate diverse and complex structures while remaining in a multinucleate syncytial state. It is unknown if different regions of these giant syncytial cells have distinct transcriptional responses to environmental encounters and if nuclei within the cell diversify into heterogeneous states. Here, we performed spatial transcriptome analysis of the slime mold Physarum polycephalum in the plasmodium state under different environmental conditions and used single-nucleus RNA-sequencing to dissect gene expression heterogeneity among nuclei. Our data identifies transcriptome regionality in the organism that associates with proliferation, syncytial substructures, and localized environmental conditions. Further, we find that nuclei are heterogenous in their transcriptional profile and may process local signals within the plasmodium to coordinate cell growth, metabolism, and reproduction. To understand how nuclei variation within the syncytium compares to heterogeneity in single-nucleus cells, we analyzed states in single Physarum amoebal cells. We observed amoebal cell states at different stages of mitosis and meiosis, and identified cytokinetic features that are specific to nuclei divisions within the syncytium. Notably, we do not find evidence for predefined transcriptomic states in the amoebae that are observed in the syncytium. Our data shows that a single-celled slime mold can control its gene expression in a region-specific manner while lacking cellular compartmentalization and suggests that nuclei are mobile processors facilitating local specialized functions. More broadly, slime molds offer the extraordinary opportunity to explore how organisms can evolve regulatory mechanisms to divide labor, specialize, balance competition with cooperation, and perform other foundational principles that govern the logic of life.
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Affiliation(s)
- Tobias Gerber
- Max Planck Institute for Evolutionary AnthropologyLeipzigGermany
| | - Cristina Loureiro
- Department of Biosystems Science and Engineering, ETH ZürichBaselSwitzerland
| | - Nico Schramma
- Max Planck Institute for Dynamics and Self-OrganizationGöttingenGermany
| | - Siyu Chen
- Max Planck Institute for Dynamics and Self-OrganizationGöttingenGermany
- Physics Department, Technical University of MunichMünchenGermany
| | - Akanksha Jain
- Department of Biosystems Science and Engineering, ETH ZürichBaselSwitzerland
| | - Anne Weber
- Max Planck Institute for Dynamics and Self-OrganizationGöttingenGermany
| | - Anne Weigert
- Max Planck Institute for Evolutionary AnthropologyLeipzigGermany
| | - Malgorzata Santel
- Department of Biosystems Science and Engineering, ETH ZürichBaselSwitzerland
| | - Karen Alim
- Max Planck Institute for Dynamics and Self-OrganizationGöttingenGermany
- Physics Department, Technical University of MunichMünchenGermany
| | - Barbara Treutlein
- Max Planck Institute for Evolutionary AnthropologyLeipzigGermany
- Department of Biosystems Science and Engineering, ETH ZürichBaselSwitzerland
| | - J Gray Camp
- Max Planck Institute for Evolutionary AnthropologyLeipzigGermany
- Roche Institute for Translational Bioengineering (ITB), Roche Pharma Research and Early Development, Roche Innovation CenterBaselSwitzerland
- University of BaselBaselSwitzerland
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15
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Brukman NG, Li X, Podbilewicz B. Fusexins, HAP2/GCS1 and Evolution of Gamete Fusion. Front Cell Dev Biol 2022; 9:824024. [PMID: 35083224 PMCID: PMC8784728 DOI: 10.3389/fcell.2021.824024] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2021] [Accepted: 12/21/2021] [Indexed: 12/14/2022] Open
Abstract
Gamete fusion is the climax of fertilization in all sexually reproductive organisms, from unicellular fungi to humans. Similarly to other cell-cell fusion events, gamete fusion is mediated by specialized proteins, named fusogens, that overcome the energetic barriers during this process. In recent years, HAPLESS 2/GENERATIVE CELL-SPECIFIC 1 (HAP2/GCS1) was identified as the fusogen mediating sperm-egg fusion in flowering plants and protists, being both essential and sufficient for the membrane merger in some species. The identification of HAP2/GCS1 in invertebrates, opens the possibility that a similar fusogen may be used in vertebrate fertilization. HAP2/GCS1 proteins share a similar structure with two distinct families of exoplasmic fusogens: the somatic Fusion Family (FF) proteins discovered in nematodes, and class II viral glycoproteins (e.g., rubella and dengue viruses). Altogether, these fusogens form the Fusexin superfamily. While some attributes are shared among fusexins, for example the overall structure and the possibility of assembly into trimers, some other characteristics seem to be specific, such as the presence or not of hydrophobic loops or helices at the distal tip of the protein. Intriguingly, HAP2/GCS1 or other fusexins have neither been identified in vertebrates nor in fungi, raising the question of whether these genes were lost during evolution and were replaced by other fusion machinery or a significant divergence makes their identification difficult. Here, we discuss the biology of HAP2/GCS1, its involvement in gamete fusion and the structural, mechanistic and evolutionary relationships with other fusexins.
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Affiliation(s)
- Nicolas G Brukman
- Department of Biology, Technion- Israel Institute of Technology, Haifa, Israel
| | - Xiaohui Li
- Department of Biology, Technion- Israel Institute of Technology, Haifa, Israel
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16
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Louradour I, Ferreira TR, Duge E, Karunaweera N, Paun A, Sacks D. Stress conditions promote Leishmania hybridization in vitro marked by expression of the ancestral gamete fusogen HAP2 as revealed by single-cell RNA-seq. eLife 2022; 11:73488. [PMID: 34994687 PMCID: PMC8794473 DOI: 10.7554/elife.73488] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Accepted: 01/06/2022] [Indexed: 12/18/2022] Open
Abstract
Leishmania are protozoan parasites transmitted by the bite of sand fly vectors producing a wide spectrum of diseases in their mammalian hosts. These diverse clinical outcomes are directly associated with parasite strain and species diversity. Although Leishmania reproduction is mainly clonal, a cryptic sexual cycle capable of producing hybrid genotypes has been inferred from population genetic studies and directly demonstrated by laboratory crosses. Experimentally, mating competence has been largely confined to promastigotes developing in the sand fly midgut. The ability to hybridize culture promastigotes in vitro has been limited so far to low-efficiency crosses between two Leishmania tropica strains, L747 and MA37, that mate with high efficiency in flies. Here, we show that exposure of promastigote cultures to DNA damage stress produces a remarkably enhanced efficiency of in vitro hybridization of the L. tropica strains and extends to other species, including Leishmania donovani, Leishmania infantum, and Leishmania braziliensis, a capacity to generate intra- and interspecific hybrids. Whole-genome sequencing and total DNA content analyses indicate that the hybrids are in each case full genome, mostly tetraploid hybrids. Single-cell RNA sequencing of the L747 and MA37 parental lines highlights the transcriptome heterogeneity of culture promastigotes and reveals discrete clusters that emerge post-irradiation in which genes potentially involved in genetic exchange are expressed, including the ancestral gamete fusogen HAP2. By generating reporter constructs for HAP2, we could select for promastigotes that could either hybridize or not in vitro. Overall, this work reveals that there are specific populations involved in Leishmania hybridization associated with a discernible transcriptomic signature, and that stress facilitated in vitro hybridization can be a transformative approach to generate large numbers of hybrid genotypes between diverse species and strains.
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Affiliation(s)
- Isabelle Louradour
- Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, Bethesda, United States
| | - Tiago Rodrigues Ferreira
- Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, Bethesda, United States
| | - Emma Duge
- Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, Bethesda, United States
| | - Nadira Karunaweera
- Department of Parasitology, Faculty of Medicine, University of Colombo, Colombo, Sri Lanka
| | - Andrea Paun
- Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, Bethesda, United States
| | - David Sacks
- Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, Bethesda, United States
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17
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A Detailed Gene Expression Map of Giardia Encystation. Genes (Basel) 2021; 12:genes12121932. [PMID: 34946882 PMCID: PMC8700996 DOI: 10.3390/genes12121932] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Revised: 11/23/2021] [Accepted: 11/26/2021] [Indexed: 12/13/2022] Open
Abstract
Giardia intestinalis is an intestinal protozoan parasite that causes diarrheal infections worldwide. A key process to sustain its chain of transmission is the formation of infectious cysts in the encystation process. We combined deep RNAseq of a broad range of encystation timepoints to produce a high-resolution gene expression map of Giardia encystation. This detailed transcriptomic map of encystation confirmed a gradual change of gene expression along the time course of encystation, showing the most significant gene expression changes during late encystation. Few genes are differentially expressed early in encystation, but the major cyst wall proteins CWP-1 and -2 are highly up-regulated already after 3.5 h encystation. Several transcription factors are sequentially up-regulated throughout the process, but many up-regulated genes at 7, 10, and 14 h post-induction of encystation have binding sites in the upstream regions for the Myb2 transcription factor, suggesting that Myb2 is a master regulator of encystation. We observed major changes in gene expression of several meiotic-related genes from 10.5 h of encystation to the cyst stage, and at 17.5 h encystation, there are changes in many different metabolic pathways and protein synthesis. Late encystation, 21 h to cysts, show extensive gene expression changes, most of all in VSP and HCMP genes, which are involved in antigenic variation, and genes involved in chromatin modifications. This high-resolution gene expression map of Giardia encystation will be an important tool in further studies of this important differentiation process.
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18
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A Novel Spo11 Homologue Functions as a Positive Regulator in Cyst Differentiation in Giardia lamblia. Int J Mol Sci 2021; 22:ijms222111902. [PMID: 34769330 PMCID: PMC8584520 DOI: 10.3390/ijms222111902] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 10/27/2021] [Accepted: 10/28/2021] [Indexed: 01/14/2023] Open
Abstract
Giardia lamblia persists in a dormant state with a protective cyst wall for transmission. It is incompletely known how three cyst wall proteins (CWPs) are coordinately synthesized during encystation. Meiotic recombination is required for sexual reproduction in animals, fungi, and plants. It is initiated by formation of double-stranded breaks by a topoisomerase-like Spo11. It has been shown that exchange of genetic material in the fused nuclei occurs during Giardia encystation, suggesting parasexual recombination processes of this protozoan. Giardia possesses an evolutionarily conserved Spo11 with typical domains for cleavage reaction and an upregulated expression pattern during encystation. In this study, we asked whether Spo11 can activate encystation process, like other topoisomerases we previously characterized. We found that Spo11 was capable of binding to both single-stranded and double-stranded DNA in vitro and that it could also bind to the cwp promoters in vivo as accessed in chromatin immunoprecipitation assays. Spo11 interacted with WRKY and MYB2 (named from myeloblastosis), transcription factors that can activate cwp gene expression during encystation. Interestingly, overexpression of Spo11 resulted in increased expression of cwp1-3 and myb2 genes and cyst formation. Mutation of the Tyr residue for the active site or two conserved residues corresponding to key DNA-binding residues for Arabidopsis Spo11 reduced the levels of cwp1-3 and myb2 gene expression and cyst formation. Targeted disruption of spo11 gene with CRISPR/Cas9 system led to a significant decrease in cwp1-3 and myb2 gene expression and cyst number. Our results suggest that Spo11 acts as a positive regulator for Giardia differentiation into cyst.
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19
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Salas-Leiva DE, Tromer EC, Curtis BA, Jerlström-Hultqvist J, Kolisko M, Yi Z, Salas-Leiva JS, Gallot-Lavallée L, Williams SK, Kops GJPL, Archibald JM, Simpson AGB, Roger AJ. Genomic analysis finds no evidence of canonical eukaryotic DNA processing complexes in a free-living protist. Nat Commun 2021; 12:6003. [PMID: 34650064 PMCID: PMC8516963 DOI: 10.1038/s41467-021-26077-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Accepted: 09/14/2021] [Indexed: 12/14/2022] Open
Abstract
Cells replicate and segregate their DNA with precision. Previous studies showed that these regulated cell-cycle processes were present in the last eukaryotic common ancestor and that their core molecular parts are conserved across eukaryotes. However, some metamonad parasites have secondarily lost components of the DNA processing and segregation apparatuses. To clarify the evolutionary history of these systems in these unusual eukaryotes, we generated a genome assembly for the free-living metamonad Carpediemonas membranifera and carried out a comparative genomics analysis. Here, we show that parasitic and free-living metamonads harbor an incomplete set of proteins for processing and segregating DNA. Unexpectedly, Carpediemonas species are further streamlined, lacking the origin recognition complex, Cdc6 and most structural kinetochore subunits. Carpediemonas species are thus the first known eukaryotes that appear to lack this suite of conserved complexes, suggesting that they likely rely on yet-to-be-discovered or alternative mechanisms to carry out these fundamental processes.
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Affiliation(s)
- Dayana E. Salas-Leiva
- grid.55602.340000 0004 1936 8200Institute for Comparative Genomics (ICG), Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS B3H 4R2 Canada ,grid.5335.00000000121885934Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
| | - Eelco C. Tromer
- grid.5335.00000000121885934Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom ,grid.4830.f0000 0004 0407 1981Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, Netherlands
| | - Bruce A. Curtis
- grid.55602.340000 0004 1936 8200Institute for Comparative Genomics (ICG), Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS B3H 4R2 Canada
| | - Jon Jerlström-Hultqvist
- grid.55602.340000 0004 1936 8200Institute for Comparative Genomics (ICG), Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS B3H 4R2 Canada
| | - Martin Kolisko
- grid.418095.10000 0001 1015 3316Institute of Parasitology, Biology Centre, Czech Acad. Sci, České Budějovice, Czech Republic
| | - Zhenzhen Yi
- grid.263785.d0000 0004 0368 7397Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, School of Life Science, South China Normal University, Guangzhou, 510631 China
| | - Joan S. Salas-Leiva
- grid.466575.30000 0001 1835 194XCONACyT-Centro de Investigación en Materiales Avanzados, Departamento de medio ambiente y energía, Miguel de Cervantes 120, Complejo Industrial Chihuahua, 31136 Chihuahua, Chih. México
| | - Lucie Gallot-Lavallée
- grid.55602.340000 0004 1936 8200Institute for Comparative Genomics (ICG), Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS B3H 4R2 Canada
| | - Shelby K. Williams
- grid.55602.340000 0004 1936 8200Institute for Comparative Genomics (ICG), Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS B3H 4R2 Canada
| | - Geert J. P. L. Kops
- grid.7692.a0000000090126352Oncode Institute, Hubrecht Institute – KNAW (Royal Netherlands Academy of Arts and Sciences) and University Medical Centre Utrecht, Utrecht, The Netherlands
| | - John M. Archibald
- grid.55602.340000 0004 1936 8200Institute for Comparative Genomics (ICG), Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS B3H 4R2 Canada
| | - Alastair G. B. Simpson
- grid.55602.340000 0004 1936 8200Institute for Comparative Genomics (ICG), Department of Biology, Dalhousie University, Halifax, NS B3H 4R2 Canada
| | - Andrew J. Roger
- grid.55602.340000 0004 1936 8200Institute for Comparative Genomics (ICG), Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS B3H 4R2 Canada
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20
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Grishaeva TM, Bogdanov YF. Synaptonemal Complex Proteins: Unicity or Universality? RUSS J GENET+ 2021. [DOI: 10.1134/s1022795421080068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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21
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Picard MAL, Vicoso B, Bertrand S, Escriva H. Diversity of Modes of Reproduction and Sex Determination Systems in Invertebrates, and the Putative Contribution of Genetic Conflict. Genes (Basel) 2021; 12:1136. [PMID: 34440310 PMCID: PMC8391622 DOI: 10.3390/genes12081136] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Revised: 07/08/2021] [Accepted: 07/11/2021] [Indexed: 12/30/2022] Open
Abstract
About eight million animal species are estimated to live on Earth, and all except those belonging to one subphylum are invertebrates. Invertebrates are incredibly diverse in their morphologies, life histories, and in the range of the ecological niches that they occupy. A great variety of modes of reproduction and sex determination systems is also observed among them, and their mosaic-distribution across the phylogeny shows that transitions between them occur frequently and rapidly. Genetic conflict in its various forms is a long-standing theory to explain what drives those evolutionary transitions. Here, we review (1) the different modes of reproduction among invertebrate species, highlighting sexual reproduction as the probable ancestral state; (2) the paradoxical diversity of sex determination systems; (3) the different types of genetic conflicts that could drive the evolution of such different systems.
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Affiliation(s)
- Marion Anne Lise Picard
- Sorbonne Université, CNRS, Biologie Intégrative des Organismes Marins (BIOM), Observatoire Océanologique, 66650 Banyuls-sur-Mer, France; (S.B.); (H.E.)
| | - Beatriz Vicoso
- Institute of Science and Technology Austria, Am Campus 1, 3400 Klosterneuburg, Austria;
| | - Stéphanie Bertrand
- Sorbonne Université, CNRS, Biologie Intégrative des Organismes Marins (BIOM), Observatoire Océanologique, 66650 Banyuls-sur-Mer, France; (S.B.); (H.E.)
| | - Hector Escriva
- Sorbonne Université, CNRS, Biologie Intégrative des Organismes Marins (BIOM), Observatoire Océanologique, 66650 Banyuls-sur-Mer, France; (S.B.); (H.E.)
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22
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Skejo J, Garg SG, Gould SB, Hendriksen M, Tria FDK, Bremer N, Franjević D, Blackstone NW, Martin WF. Evidence for a Syncytial Origin of Eukaryotes from Ancestral State Reconstruction. Genome Biol Evol 2021; 13:evab096. [PMID: 33963405 PMCID: PMC8290118 DOI: 10.1093/gbe/evab096] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/28/2021] [Indexed: 12/11/2022] Open
Abstract
Modern accounts of eukaryogenesis entail an endosymbiotic encounter between an archaeal host and a proteobacterial endosymbiont, with subsequent evolution giving rise to a unicell possessing a single nucleus and mitochondria. The mononucleate state of the last eukaryotic common ancestor (LECA) is seldom, if ever, questioned, even though cells harboring multiple (syncytia, coenocytes, and polykaryons) are surprisingly common across eukaryotic supergroups. Here, we present a survey of multinucleated forms. Ancestral character state reconstruction for representatives of 106 eukaryotic taxa using 16 different possible roots and supergroup sister relationships, indicate that LECA, in addition to being mitochondriate, sexual, and meiotic, was multinucleate. LECA exhibited closed mitosis, which is the rule for modern syncytial forms, shedding light on the mechanics of its chromosome segregation. A simple mathematical model shows that within LECA's multinucleate cytosol, relationships among mitochondria and nuclei were neither one-to-one, nor one-to-many, but many-to-many, placing mitonuclear interactions and cytonuclear compatibility at the evolutionary base of eukaryotic cell origin. Within a syncytium, individual nuclei and individual mitochondria function as the initial lower-level evolutionary units of selection, as opposed to individual cells, during eukaryogenesis. Nuclei within a syncytium rescue each other's lethal mutations, thereby postponing selection for viable nuclei and cytonuclear compatibility to the generation of spores, buffering transitional bottlenecks at eukaryogenesis. The prokaryote-to-eukaryote transition is traditionally thought to have left no intermediates, yet if eukaryogenesis proceeded via a syncytial common ancestor, intermediate forms have persisted to the present throughout the eukaryotic tree as syncytia but have so far gone unrecognized.
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Affiliation(s)
- Josip Skejo
- Institute for Molecular Evolution, Heinrich-Heine University Düsseldorf, Düsseldorf, Germany
- Faculty of Science, Division of Zoology, Department of Biology, University of Zagreb, Evolution Lab, Zagreb, Croatia
| | - Sriram G Garg
- Institute for Molecular Evolution, Heinrich-Heine University Düsseldorf, Düsseldorf, Germany
| | - Sven B Gould
- Institute for Molecular Evolution, Heinrich-Heine University Düsseldorf, Düsseldorf, Germany
| | - Michael Hendriksen
- Institute for Molecular Evolution, Heinrich-Heine University Düsseldorf, Düsseldorf, Germany
| | - Fernando D K Tria
- Institute for Molecular Evolution, Heinrich-Heine University Düsseldorf, Düsseldorf, Germany
| | - Nico Bremer
- Institute for Molecular Evolution, Heinrich-Heine University Düsseldorf, Düsseldorf, Germany
| | - Damjan Franjević
- Faculty of Science, Division of Zoology, Department of Biology, University of Zagreb, Evolution Lab, Zagreb, Croatia
| | - Neil W Blackstone
- Department of Biological Sciences, Northern Illinois University, DeKalb, IL, USA
| | - William F Martin
- Institute for Molecular Evolution, Heinrich-Heine University Düsseldorf, Düsseldorf, Germany
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23
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Radzvilavicius A, Layh S, Hall MD, Dowling DK, Johnston IG. Sexually antagonistic evolution of mitochondrial and nuclear linkage. J Evol Biol 2021; 34:757-766. [PMID: 33644926 DOI: 10.1111/jeb.13776] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Revised: 02/13/2021] [Accepted: 02/24/2021] [Indexed: 12/21/2022]
Abstract
Across eukaryotes, genes encoding bioenergetic machinery are located in both mitochondrial and nuclear DNA, and incompatibilities between the two genomes can be devastating. Mitochondria are often inherited maternally, and theory predicts sex-specific fitness effects of mitochondrial mutational diversity. Yet how evolution acts on linkage patterns between mitochondrial and nuclear genomes is poorly understood. Using novel mito-nuclear population-genetic models, we show that the interplay between nuclear and mitochondrial genes maintains mitochondrial haplotype diversity within populations, and selects both for sex-independent segregation of mitochondrion-interacting genes and for paternal leakage. These effects of genetic linkage evolution can eliminate male-harming fitness effects of mtDNA mutational diversity. With maternal mitochondrial inheritance, females maintain a tight mitochondrial-nuclear match, but males accumulate mismatch mutations because of the weak statistical associations between the two genomic components. Sex-independent segregation of mitochondria-interacting loci improves the mito-nuclear match. In a sexually antagonistic evolutionary process, male nuclear alleles evolve to increase the rate of recombination, whereas females evolve to suppress it. Paternal leakage of mitochondria can evolve as an alternative mechanism to improve the mito-nuclear linkage. Our modelling framework provides an evolutionary explanation for the observed paucity of mitochondrion-interacting genes on mammalian sex chromosomes and for paternal leakage in protists, plants, fungi and some animals.
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Affiliation(s)
- Arunas Radzvilavicius
- Department of Mathematics, University of Bergen, Bergen, Norway.,Charles Perkins Centre, University of Sydney, Sydney, NSW, Australia
| | - Sean Layh
- School of Biological Sciences, Monash University, Melbourne, Vic., Australia
| | - Matthew D Hall
- School of Biological Sciences, Monash University, Melbourne, Vic., Australia
| | - Damian K Dowling
- School of Biological Sciences, Monash University, Melbourne, Vic., Australia
| | - Iain G Johnston
- Department of Mathematics, University of Bergen, Bergen, Norway.,Computational Biology Unit, University of Bergen, Bergen, Norway
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24
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Peacock L, Kay C, Farren C, Bailey M, Carrington M, Gibson W. Sequential production of gametes during meiosis in trypanosomes. Commun Biol 2021; 4:555. [PMID: 33976359 PMCID: PMC8113336 DOI: 10.1038/s42003-021-02058-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Accepted: 03/24/2021] [Indexed: 02/03/2023] Open
Abstract
Meiosis is a core feature of eukaryotes that occurs in all major groups, including the early diverging excavates. In this group, meiosis and production of haploid gametes have been described in the pathogenic protist, Trypanosoma brucei, and mating occurs in the salivary glands of the insect vector, the tsetse fly. Here, we searched for intermediate meiotic stages among trypanosomes from tsetse salivary glands. Many different cell types were recovered, including trypanosomes in Meiosis I and gametes. Significantly, we found trypanosomes containing three nuclei with a 1:2:1 ratio of DNA contents. Some of these cells were undergoing cytokinesis, yielding a mononucleate gamete and a binucleate cell with a nuclear DNA content ratio of 1:2. This cell subsequently produced three more gametes in two further rounds of division. Expression of the cell fusion protein HAP2 (GCS1) was not confined to gametes, but also extended to meiotic intermediates. We propose a model whereby the two nuclei resulting from Meiosis I undergo asynchronous Meiosis II divisions with sequential production of haploid gametes.
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Affiliation(s)
- Lori Peacock
- School of Biological Sciences University of Bristol, Bristol, UK
- Bristol Veterinary School, University of Bristol, Bristol, UK
| | - Chris Kay
- School of Biological Sciences University of Bristol, Bristol, UK
| | - Chloe Farren
- School of Biological Sciences University of Bristol, Bristol, UK
| | - Mick Bailey
- Bristol Veterinary School, University of Bristol, Bristol, UK
| | - Mark Carrington
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Wendy Gibson
- School of Biological Sciences University of Bristol, Bristol, UK.
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25
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Tromer EC, Wemyss TA, Ludzia P, Waller RF, Akiyoshi B. Repurposing of synaptonemal complex proteins for kinetochores in Kinetoplastida. Open Biol 2021; 11:210049. [PMID: 34006126 PMCID: PMC8131943 DOI: 10.1098/rsob.210049] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Accepted: 04/16/2021] [Indexed: 12/25/2022] Open
Abstract
Chromosome segregation in eukaryotes is driven by the kinetochore, a macromolecular complex that connects centromeric DNA to microtubules of the spindle apparatus. Kinetochores in well-studied model eukaryotes consist of a core set of proteins that are broadly conserved among distant eukaryotic phyla. By contrast, unicellular flagellates of the class Kinetoplastida have a unique set of 36 kinetochore components. The evolutionary origin and history of these kinetochores remain unknown. Here, we report evidence of homology between axial element components of the synaptonemal complex and three kinetoplastid kinetochore proteins KKT16-18. The synaptonemal complex is a zipper-like structure that assembles between homologous chromosomes during meiosis to promote recombination. By using sensitive homology detection protocols, we identify divergent orthologues of KKT16-18 in most eukaryotic supergroups, including experimentally established chromosomal axis components, such as Red1 and Rec10 in budding and fission yeast, ASY3-4 in plants and SYCP2-3 in vertebrates. Furthermore, we found 12 recurrent duplications within this ancient eukaryotic SYCP2-3 gene family, providing opportunities for new functional complexes to arise, including KKT16-18 in the kinetoplastid parasite Trypanosoma brucei. We propose the kinetoplastid kinetochore system evolved by repurposing meiotic components of the chromosome synapsis and homologous recombination machinery that were already present in early eukaryotes.
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Affiliation(s)
- Eelco C. Tromer
- Department of Biochemistry, University of Cambridge, Cambridge, UK
- Cell Biochemistry, Groningen Institute of Biomolecular Sciences & Biotechnology, University of Groningen, Groningen, The Netherlands
| | - Thomas A. Wemyss
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Patryk Ludzia
- Department of Biochemistry, University of Oxford, Oxford, UK
| | - Ross F. Waller
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Bungo Akiyoshi
- Department of Biochemistry, University of Oxford, Oxford, UK
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26
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Wu C, Twort VG, Newcomb RD, Buckley TR. Divergent Gene Expression Following Duplication of Meiotic Genes in the Stick Insect Clitarchus hookeri. Genome Biol Evol 2021; 13:6245840. [PMID: 33885769 DOI: 10.1093/gbe/evab060] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/17/2021] [Indexed: 01/02/2023] Open
Abstract
Some animal groups, such as stick insects (Phasmatodea), have repeatedly evolved alternative reproductive strategies, including parthenogenesis. Genomic studies have found modification of the genes underlying meiosis exists in some of these animals. Here we examine the evolution of copy number, evolutionary rate, and gene expression in candidate meiotic genes of the New Zealand geographic parthenogenetic stick insect Clitarchus hookeri. We characterized 101 genes from a de novo transcriptome assembly from female and male gonads that have homology with meiotic genes from other arthropods. For each gene we determined copy number, the pattern of gene duplication relative to other arthropod orthologs, and the potential for meiosis-specific expression. There are five genes duplicated in C. hookeri, including one also duplicated in the stick insect Timema cristinae, that are not or are uncommonly duplicated in other arthropods. These included two sister chromatid cohesion associated genes (SA2 and SCC2), a recombination gene (HOP1), an RNA-silencing gene (AGO2) and a cell-cycle regulation gene (WEE1). Interestingly, WEE1 and SA2 are also duplicated in the cyclical parthenogenetic aphid Acyrthosiphon pisum and Daphnia duplex, respectively, indicating possible roles in the evolution of reproductive mode. Three of these genes (SA2, SCC2, and WEE1) have one copy displaying gonad-specific expression. All genes, with the exception of WEE1, have significantly different nonsynonymous/synonymous ratios between the gene duplicates, indicative of a shift in evolutionary constraints following duplication. These results suggest that stick insects may have evolved genes with novel functions in gamete production by gene duplication.
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Affiliation(s)
- Chen Wu
- School of Biological Sciences, The University of Auckland, New Zealand.,Manaaki Whenua-Landcare Research, Auckland, New Zealand.,New Zealand Institute for Plant & Food Research Ltd, Auckland, New Zealand
| | - Victoria G Twort
- School of Biological Sciences, The University of Auckland, New Zealand.,Manaaki Whenua-Landcare Research, Auckland, New Zealand.,Zoology Unit, Finnish Museum of Natural History, LUOMUS, University of Helsinki, Finland
| | - Richard D Newcomb
- School of Biological Sciences, The University of Auckland, New Zealand.,New Zealand Institute for Plant & Food Research Ltd, Auckland, New Zealand
| | - Thomas R Buckley
- School of Biological Sciences, The University of Auckland, New Zealand.,Manaaki Whenua-Landcare Research, Auckland, New Zealand
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27
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Eckelbarger KJ, Hodgson AN. Invertebrate oogenesis – a review and synthesis: comparative ovarian morphology, accessory cell function and the origins of yolk precursors. INVERTEBR REPROD DEV 2021. [DOI: 10.1080/07924259.2021.1927861] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Kevin J. Eckelbarger
- Darling Marine Center, School of Marine Sciences, The University of Maine, Walpole, Maine, U.S.A
| | - Alan N. Hodgson
- Department of Zoology and Entomology, Rhodes University, Grahamstown, South Africa
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28
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Radzvilavicius A. Beyond the "selfish mitochondrion" theory of uniparental inheritance: A unified theory based on mutational variance redistribution. Bioessays 2021; 43:e2100009. [PMID: 33729620 DOI: 10.1002/bies.202100009] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 02/15/2021] [Accepted: 02/16/2021] [Indexed: 11/08/2022]
Abstract
"Selfish" gene theories have offered invaluable insight into eukaryotic genome evolution, but they can also be misleading. The "selfish mitochondrion" hypothesis, developed in the 90s explained uniparental organelle inheritance as a mechanism of conflict resolution, improving cooperation between genetically distinct compartments of the cell. But modern population genetic models provided a more general explanation for uniparental inheritance based on mutational variance redistribution, modulating the efficiency of both purifying and adaptive selection. Nevertheless, as reviewed here, "selfish" conflict theories still dominate the literature. While these hypotheses are rich in metaphor and highly intuitive, selective focus on only one type of mitochondrial mutation limits the generality of our understanding and hinders progress in mito-nuclear evolution theory. Recognizing that uniparental inheritance may have evolved-and is maintained across the eukaryotic tree of life-because of its influence on mutational variance and improved selection will only increase the generality of our evolutionary reasoning, retaining "selfish" conflict explanations as a special case of a much broader theory.
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Affiliation(s)
- Arunas Radzvilavicius
- Department of Philosophy and Charles Perkins Centre, University of Sydney, New South Wales, Australia
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29
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Talavera-López C, Messenger LA, Lewis MD, Yeo M, Reis-Cunha JL, Matos GM, Bartholomeu DC, Calzada JE, Saldaña A, Ramírez JD, Guhl F, Ocaña-Mayorga S, Costales JA, Gorchakov R, Jones K, Nolan MS, Teixeira SMR, Carrasco HJ, Bottazzi ME, Hotez PJ, Murray KO, Grijalva MJ, Burleigh B, Grisard EC, Miles MA, Andersson B. Repeat-Driven Generation of Antigenic Diversity in a Major Human Pathogen, Trypanosoma cruzi. Front Cell Infect Microbiol 2021; 11:614665. [PMID: 33747978 PMCID: PMC7966520 DOI: 10.3389/fcimb.2021.614665] [Citation(s) in RCA: 24] [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: 10/06/2020] [Accepted: 01/22/2021] [Indexed: 12/18/2022] Open
Abstract
Trypanosoma cruzi, a zoonotic kinetoplastid protozoan parasite, is the causative agent of American trypanosomiasis (Chagas disease). Having a very plastic, repetitive and complex genome, the parasite displays a highly diverse repertoire of surface molecules, with pivotal roles in cell invasion, immune evasion and pathogenesis. Before 2016, the complexity of the genomic regions containing these genes impaired the assembly of a genome at chromosomal level, making it impossible to study the structure and function of the several thousand repetitive genes encoding the surface molecules of the parasite. We here describe the genome assembly of the Sylvio X10/1 genome sequence, which since 2016 has been used as a reference genome sequence for T. cruzi clade I (TcI), produced using high coverage PacBio single-molecule sequencing. It was used to analyze deep Illumina sequence data from 34 T. cruzi TcI isolates and clones from different geographic locations, sample sources and clinical outcomes. Resolution of the surface molecule gene distribution showed the unusual duality in the organization of the parasite genome, a synteny of the core genomic region with related protozoa flanked by unique and highly plastic multigene family clusters encoding surface antigens. The presence of abundant interspersed retrotransposons in these multigene family clusters suggests that these elements are involved in a recombination mechanism for the generation of antigenic variation and evasion of the host immune response on these TcI strains. The comparative genomic analysis of the cohort of TcI strains revealed multiple cases of such recombination events involving surface molecule genes and has provided new insights into T. cruzi population structure.
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Affiliation(s)
- Carlos Talavera-López
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
- European Bioinformatics Institute, Wellcome Sanger Institute, Hinxton, United Kingdom
| | - Louisa A. Messenger
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Michael D. Lewis
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Matthew Yeo
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - João Luís Reis-Cunha
- Departamento de Parasitologia, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Gabriel Machado Matos
- Departamento de Biologia Celular, Embriologia e Genética, Universidade Federal Santa Catarina, Florianópolis, Brazil
| | | | - José E. Calzada
- Departamento de Parasitología, Instituto Conmemorativo Gorgas de Estudios de la Salud, Ciudad de Panamá, Panama
| | - Azael Saldaña
- Departamento de Parasitología, Instituto Conmemorativo Gorgas de Estudios de la Salud, Ciudad de Panamá, Panama
| | - Juan David Ramírez
- Grupo de Investigaciones Microbiológicas-UR (GIMUR), Departamento de Biología, Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia
| | - Felipe Guhl
- Grupo de Investigaciones en Microbiología y Parasitología Tropical (CIMPAT), Tropical Parasitology Research Center, Universidad de Los Andes, Bogotá, Colombia
| | - Sofía Ocaña-Mayorga
- Centro de Investigación para la Salud en América Latina (CISeAL), Escuela de Ciencias Biológicas, Pontificia Universidad Católica del Ecuador, Quito, Ecuador
| | - Jaime A. Costales
- Centro de Investigación para la Salud en América Latina (CISeAL), Escuela de Ciencias Biológicas, Pontificia Universidad Católica del Ecuador, Quito, Ecuador
| | - Rodion Gorchakov
- Sabin Vaccine Institute and Texas Children’s Hospital Center for Vaccine Development, National School of Tropical Medicine, Department of Pediatrics - Tropical Medicine, Baylor College of Medicine, Houston, TX, United States
| | - Kathryn Jones
- Sabin Vaccine Institute and Texas Children’s Hospital Center for Vaccine Development, National School of Tropical Medicine, Department of Pediatrics - Tropical Medicine, Baylor College of Medicine, Houston, TX, United States
| | - Melissa S. Nolan
- Sabin Vaccine Institute and Texas Children’s Hospital Center for Vaccine Development, National School of Tropical Medicine, Department of Pediatrics - Tropical Medicine, Baylor College of Medicine, Houston, TX, United States
| | - Santuza M. R. Teixeira
- Departamento de Bioquímica e Imunologia, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Hernán José Carrasco
- Laboratorio de Biología Molecular de Protozoarios, Instituto de Medicina Tropical, Facultad de Medicina, Universidad Central de Venezuela, Caracas, Venezuela
| | - Maria Elena Bottazzi
- Sabin Vaccine Institute and Texas Children’s Hospital Center for Vaccine Development, National School of Tropical Medicine, Department of Pediatrics - Tropical Medicine, Baylor College of Medicine, Houston, TX, United States
| | - Peter J. Hotez
- Sabin Vaccine Institute and Texas Children’s Hospital Center for Vaccine Development, National School of Tropical Medicine, Department of Pediatrics - Tropical Medicine, Baylor College of Medicine, Houston, TX, United States
| | - Kristy O. Murray
- Sabin Vaccine Institute and Texas Children’s Hospital Center for Vaccine Development, National School of Tropical Medicine, Department of Pediatrics - Tropical Medicine, Baylor College of Medicine, Houston, TX, United States
| | - Mario J. Grijalva
- Centro de Investigación para la Salud en América Latina (CISeAL), Escuela de Ciencias Biológicas, Pontificia Universidad Católica del Ecuador, Quito, Ecuador
- Department of Biomedical Sciences, Heritage College of Osteopathic Medicine, Infectious and Tropical Disease Institute, Ohio University, Athens, OH, United States
| | - Barbara Burleigh
- Department of Immunology and Infectious Diseases, T.H. Chan School of Public Health, Harvard University, Boston, MA, United States
| | - Edmundo C. Grisard
- Departamento de Microbiologia, Imunologia e Parasitologia, Universidade Federal Santa Catarina, Florianópolis, Brazil
| | - Michael A. Miles
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Björn Andersson
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
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30
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Koutsouveli V, Cárdenas P, Santodomingo N, Marina A, Morato E, Rapp HT, Riesgo A. The Molecular Machinery of Gametogenesis in Geodia Demosponges (Porifera): Evolutionary Origins of a Conserved Toolkit across Animals. Mol Biol Evol 2020; 37:3485-3506. [PMID: 32929503 PMCID: PMC7743902 DOI: 10.1093/molbev/msaa183] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
All animals are capable of undergoing gametogenesis. The ability of forming haploid cells from diploid cells through meiosis and recombination appeared early in eukaryotes, whereas further gamete differentiation is mostly a metazoan signature. Morphologically, the gametogenic process presents many similarities across animal taxa, but little is known about its conservation at the molecular level. Porifera are the earliest divergent animals and therefore are an ideal phylum to understand evolution of the gametogenic toolkits. Although sponge gametogenesis is well known at the histological level, the molecular toolkits for gamete production are largely unknown. Our goal was to identify the genes and their expression levels which regulate oogenesis and spermatogenesis in five gonochoristic and oviparous species of the genus Geodia, using both RNAseq and proteomic analyses. In the early stages of both female and male gametogenesis, genes involved in germ cell fate and cell-renewal were upregulated. Then, molecular signals involved in retinoic acid pathway could trigger the meiotic processes. During later stages of oogenesis, female sponges expressed genes involved in cell growth, vitellogenesis, and extracellular matrix reassembly, which are conserved elements of oocyte maturation in Metazoa. Likewise, in spermatogenesis, genes regulating the whole meiotic cycle, chromatin compaction, and flagellum axoneme formation, that are common across Metazoa were overexpressed in the sponges. Finally, molecular signals possibly related to sperm capacitation were identified during late stages of spermatogenesis for the first time in Porifera. In conclusion, the activated molecular toolkit during gametogenesis in sponges was remarkably similar to that deployed during gametogenesis in vertebrates.
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Affiliation(s)
- Vasiliki Koutsouveli
- Department of Life Sciences, The Natural History Museum of London, London, United Kingdom
- Pharmacognosy, Department of Medicinal Chemistry, Uppsala University, BMC, Uppsala, Sweden
| | - Paco Cárdenas
- Pharmacognosy, Department of Medicinal Chemistry, Uppsala University, BMC, Uppsala, Sweden
| | - Nadiezhda Santodomingo
- Department of Life Sciences, The Natural History Museum of London, London, United Kingdom
| | - Anabel Marina
- Servicio de Proteómica, Centro de Biología Molecular Severo Ochoa (CBMSO), Universidad Autónoma de Madrid (UAM) and Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
| | - Esperanza Morato
- Servicio de Proteómica, Centro de Biología Molecular Severo Ochoa (CBMSO), Universidad Autónoma de Madrid (UAM) and Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
| | - Hans Tore Rapp
- Department of Biological Sciences, University of Bergen, Bergen, Norway
| | - Ana Riesgo
- Department of Life Sciences, The Natural History Museum of London, London, United Kingdom
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31
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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: 0.2] [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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32
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Colnaghi M, Lane N, Pomiankowski A. Genome expansion in early eukaryotes drove the transition from lateral gene transfer to meiotic sex. eLife 2020; 9:58873. [PMID: 32990598 PMCID: PMC7524546 DOI: 10.7554/elife.58873] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Accepted: 09/03/2020] [Indexed: 12/17/2022] Open
Abstract
Prokaryotes acquire genes from the environment via lateral gene transfer (LGT). Recombination of environmental DNA can prevent the accumulation of deleterious mutations, but LGT was abandoned by the first eukaryotes in favour of sexual reproduction. Here we develop a theoretical model of a haploid population undergoing LGT which includes two new parameters, genome size and recombination length, neglected by previous theoretical models. The greater complexity of eukaryotes is linked with larger genomes and we demonstrate that the benefit of LGT declines rapidly with genome size. The degeneration of larger genomes can only be resisted by increases in recombination length, to the same order as genome size - as occurs in meiosis. Our results can explain the strong selective pressure towards the evolution of sexual cell fusion and reciprocal recombination during early eukaryotic evolution - the origin of meiotic sex.
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Affiliation(s)
- Marco Colnaghi
- CoMPLEX, University College London, London, United Kingdom.,Department of Genetics, Evolution and Environment University College London, London, United Kingdom
| | - Nick Lane
- CoMPLEX, University College London, London, United Kingdom.,Department of Genetics, Evolution and Environment University College London, London, United Kingdom
| | - Andrew Pomiankowski
- CoMPLEX, University College London, London, United Kingdom.,Department of Genetics, Evolution and Environment University College London, London, United Kingdom
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33
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Li L, Wang S, Wang H, Sahu SK, Marin B, Li H, Xu Y, Liang H, Li Z, Cheng S, Reder T, Çebi Z, Wittek S, Petersen M, Melkonian B, Du H, Yang H, Wang J, Wong GKS, Xu X, Liu X, Van de Peer Y, Melkonian M, Liu H. The genome of Prasinoderma coloniale unveils the existence of a third phylum within green plants. Nat Ecol Evol 2020; 4:1220-1231. [PMID: 32572216 PMCID: PMC7455551 DOI: 10.1038/s41559-020-1221-7] [Citation(s) in RCA: 83] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Accepted: 05/12/2020] [Indexed: 12/31/2022]
Abstract
Genome analysis of the pico-eukaryotic marine green alga Prasinoderma coloniale CCMP 1413 unveils the existence of a novel phylum within green plants (Viridiplantae), the Prasinodermophyta, which diverged before the split of Chlorophyta and Streptophyta. Structural features of the genome and gene family comparisons revealed an intermediate position of the P. coloniale genome (25.3 Mb) between the extremely compact, small genomes of picoplanktonic Mamiellophyceae (Chlorophyta) and the larger, more complex genomes of early-diverging streptophyte algae. Reconstruction of the minimal core genome of Viridiplantae allowed identification of an ancestral toolkit of transcription factors and flagellar proteins. Adaptations of P. coloniale to its deep-water, oligotrophic environment involved expansion of light-harvesting proteins, reduction of early light-induced proteins, evolution of a distinct type of C4 photosynthesis and carbon-concentrating mechanism, synthesis of the metal-complexing metabolite picolinic acid, and vitamin B1, B7 and B12 auxotrophy. The P. coloniale genome provides first insights into the dawn of green plant evolution.
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Affiliation(s)
- Linzhou Li
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, China
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
| | - Sibo Wang
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, China
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Hongli Wang
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, China
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, China
| | - Sunil Kumar Sahu
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, China
| | - Birger Marin
- Institute for Plant Sciences, Department of Biological Sciences, University of Cologne, Cologne, Germany
| | - Haoyuan Li
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, China
| | - Yan Xu
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, China
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, China
| | - Hongping Liang
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, China
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, China
| | - Zhen Li
- Department of Plant Biotechnology and Bioinformatics (Ghent University) and Center for Plant Systems Biology, Ghent, Belgium
| | - Shifeng Cheng
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, China
| | - Tanja Reder
- Institute for Plant Sciences, Department of Biological Sciences, University of Cologne, Cologne, Germany
| | - Zehra Çebi
- Institute for Plant Sciences, Department of Biological Sciences, University of Cologne, Cologne, Germany
| | - Sebastian Wittek
- Institute for Plant Sciences, Department of Biological Sciences, University of Cologne, Cologne, Germany
| | - Morten Petersen
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Barbara Melkonian
- Institute for Plant Sciences, Department of Biological Sciences, University of Cologne, Cologne, Germany
- Central Collection of Algal Cultures, Faculty of Biology, University of Duisburg-Essen, Essen, Germany
| | - Hongli Du
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| | - Huanming Yang
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, China
| | - Jian Wang
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, China
| | - Gane Ka-Shu Wong
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, China
- Department of Biological Sciences and Department of Medicine, University of Alberta, Edmonton, Alberta, Canada
| | - Xun Xu
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, China
- Guangdong Provincial Key Laboratory of Genome Read and Write, BGI-Shenzhen, Shenzhen, China
| | - Xin Liu
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, China
| | - Yves Van de Peer
- Department of Plant Biotechnology and Bioinformatics (Ghent University) and Center for Plant Systems Biology, Ghent, Belgium.
- College of Horticulture, Nanjing Agricultural University, Nanjing, China.
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa.
| | - Michael Melkonian
- Institute for Plant Sciences, Department of Biological Sciences, University of Cologne, Cologne, Germany.
- Central Collection of Algal Cultures, Faculty of Biology, University of Duisburg-Essen, Essen, Germany.
| | - Huan Liu
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, China.
- Department of Biology, University of Copenhagen, Copenhagen, Denmark.
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34
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Furman CM, Elbashir R, Alani E. Expanded roles for the MutL family of DNA mismatch repair proteins. Yeast 2020; 38:39-53. [PMID: 32652606 DOI: 10.1002/yea.3512] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Revised: 07/01/2020] [Accepted: 07/08/2020] [Indexed: 12/31/2022] Open
Abstract
The MutL family of DNA mismatch repair proteins plays a critical role in excising and repairing misincorporation errors during DNA replication. In many eukaryotes, members of this family have evolved to modulate and resolve recombination intermediates into crossovers during meiosis. In these organisms, such functions promote the accurate segregation of chromosomes during the meiosis I division. What alterations occurred in MutL homolog (MLH) family members that enabled them to acquire these new roles? In this review, we present evidence that the yeast Mlh1-Mlh3 and Mlh1-Mlh2 complexes have evolved novel enzymatic and nonenzymatic activities and protein-protein interactions that are critical for their meiotic functions. Curiously, even with these changes, these complexes retain backup and accessory roles in DNA mismatch repair during vegetative growth.
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Affiliation(s)
- Christopher M Furman
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
| | - Ryan Elbashir
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
| | - Eric Alani
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
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35
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Two auxiliary factors promote Dmc1-driven DNA strand exchange via stepwise mechanisms. Proc Natl Acad Sci U S A 2020; 117:12062-12070. [PMID: 32414915 DOI: 10.1073/pnas.1917419117] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Homologous recombination (HR) is a universal mechanism operating in somatic and germ-line cells, where it contributes to the maintenance of genome stability and ensures the faithful distribution of genetic material, respectively. The ability to identify and exchange the strands of two homologous DNA molecules lies at the heart of HR and is mediated by RecA-family recombinases. Dmc1 is a meiosis-specific RecA homolog in eukaryotes, playing a predominant role in meiotic HR. However, Dmc1 cannot function without its two major auxiliary factor complexes, Swi5-Sfr1 and Hop2-Mnd1. Through biochemical reconstitutions, we demonstrate that Swi5-Sfr1 and Hop2-Mnd1 make unique contributions to stimulate Dmc1-driven strand exchange in a synergistic manner. Mechanistically, Swi5-Sfr1 promotes establishment of the Dmc1 nucleoprotein filament, whereas Hop2-Mnd1 defines a critical, rate-limiting step in initiating strand exchange. Following execution of this function, we propose that Swi5-Sfr1 then promotes strand exchange with Hop2-Mnd1. Thus, our findings elucidate distinct yet complementary roles of two auxiliary factors in Dmc1-driven strand exchange, providing mechanistic insights into some of the most critical steps in meiotic HR.
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Li X, Zhang N, Wu N, Li J, Yang J, Yu Y, Zheng J, Li X, Wang X, Gong P, Zhang X. Identification of GdRFC1 as a novel regulator of telomerase in Giardia duodenalis. Parasitol Res 2020; 119:1035-1041. [PMID: 32072328 DOI: 10.1007/s00436-020-06610-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2019] [Accepted: 01/15/2020] [Indexed: 11/25/2022]
Abstract
Telomerase plays a crucial role in ageing and tumourigenesis. However, the regulatory network of its activity is complicated and not fully understood. In the present study, a yeast two-hybrid screen identified a homologue of human replication factor C subunit 1 (RFC1) as a novel interacting protein of Giardia duodenalis GdTRBD (Giardia duodenalis telomerase ribonucleoprotein complex RNA binding domain GdTRBD). This interaction was further verified via GST pull-down in vitro and co-immunoprecipitation (Co-IP) and bimolecular fluorescence complementation (BiFC) in vivo. We also found that GdRFC1 (Giardia duodenalis replication factor C subunit 1) only interacted with GdTRBD in one nucleus in Giardia duodenalis via a proximity ligation assay (PLA). We reasoned that the two nuclei might have significant heterogeneity in their functional activities during the trophozoite stage and that the two molecules might be involved in other unidentified functions in addition to telomerase activity. In addition, knockdown of GdRFC1 decreased telomerase activity. Collectively, our results indicate that GdRFC1 is a novel binding partner and positive regulator of telomerase in Giardia duodenalis.
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Affiliation(s)
- Xianhe Li
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Institute of Zoonosis, Jilin University, Changchun, 130062, China
| | - Nan Zhang
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Institute of Zoonosis, Jilin University, Changchun, 130062, China
- The First Bethune Hospital, Jilin University, Changchun, 130021, China
| | - Na Wu
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Institute of Zoonosis, Jilin University, Changchun, 130062, China
| | - Jianhua Li
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Institute of Zoonosis, Jilin University, Changchun, 130062, China
| | - Ju Yang
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Institute of Zoonosis, Jilin University, Changchun, 130062, China
| | - Yanhui Yu
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Institute of Zoonosis, Jilin University, Changchun, 130062, China
| | - Jingtong Zheng
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Institute of Zoonosis, Jilin University, Changchun, 130062, China
| | - Xin Li
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Institute of Zoonosis, Jilin University, Changchun, 130062, China
| | - Xiaocen Wang
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Institute of Zoonosis, Jilin University, Changchun, 130062, China
| | - Pengtao Gong
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Institute of Zoonosis, Jilin University, Changchun, 130062, China.
| | - Xichen Zhang
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Institute of Zoonosis, Jilin University, Changchun, 130062, China.
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DuBuc TQ, Schnitzler CE, Chrysostomou E, McMahon ET, Febrimarsa, Gahan JM, Buggie T, Gornik SG, Hanley S, Barreira SN, Gonzalez P, Baxevanis AD, Frank U. Transcription factor AP2 controls cnidarian germ cell induction. Science 2020; 367:757-762. [PMID: 32054756 PMCID: PMC7025884 DOI: 10.1126/science.aay6782] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Accepted: 12/06/2019] [Indexed: 12/18/2022]
Abstract
Clonal animals do not sequester a germ line during embryogenesis. Instead, they have adult stem cells that contribute to somatic tissues or gametes. How germ fate is induced in these animals, and whether this process is related to bilaterian embryonic germline induction, is unknown. We show that transcription factor AP2 (Tfap2), a regulator of mammalian germ lines, acts to commit adult stem cells, known as i-cells, to the germ cell fate in the clonal cnidarian Hydractinia symbiolongicarpus Tfap2 mutants lacked germ cells and gonads. Transplanted wild-type cells rescued gonad development but not germ cell induction in Tfap2 mutants. Forced expression of Tfap2 in i-cells converted them to germ cells. Therefore, Tfap2 is a regulator of germ cell commitment across germ line-sequestering and germ line-nonsequestering animals.
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Affiliation(s)
- Timothy Q DuBuc
- Centre for Chromosome Biology, School of Natural Sciences, National University of Ireland Galway, Galway, Ireland
| | - Christine E Schnitzler
- Whitney Laboratory for Marine Bioscience, University of Florida, St. Augustine, FL 32080, USA
- Department of Biology, University of Florida, Gainesville, FL 32611, USA
| | - Eleni Chrysostomou
- Centre for Chromosome Biology, School of Natural Sciences, National University of Ireland Galway, Galway, Ireland
| | - Emma T McMahon
- Centre for Chromosome Biology, School of Natural Sciences, National University of Ireland Galway, Galway, Ireland
| | - Febrimarsa
- Centre for Chromosome Biology, School of Natural Sciences, National University of Ireland Galway, Galway, Ireland
| | - James M Gahan
- Centre for Chromosome Biology, School of Natural Sciences, National University of Ireland Galway, Galway, Ireland
| | - Tara Buggie
- Centre for Chromosome Biology, School of Natural Sciences, National University of Ireland Galway, Galway, Ireland
| | - Sebastian G Gornik
- Centre for Chromosome Biology, School of Natural Sciences, National University of Ireland Galway, Galway, Ireland
| | - Shirley Hanley
- National Centre for Biomedical Engineering Science, National University of Ireland Galway, Galway, Ireland
| | - Sofia N Barreira
- Computational and Statistical Genomics Branch, Division of Intramural Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Paul Gonzalez
- Computational and Statistical Genomics Branch, Division of Intramural Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Andreas D Baxevanis
- Computational and Statistical Genomics Branch, Division of Intramural Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Uri Frank
- Centre for Chromosome Biology, School of Natural Sciences, National University of Ireland Galway, Galway, Ireland.
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Takahashi TS, Da Cunha V, Krupovic M, Mayer C, Forterre P, Gadelle D. Expanding the type IIB DNA topoisomerase family: identification of new topoisomerase and topoisomerase-like proteins in mobile genetic elements. NAR Genom Bioinform 2019; 2:lqz021. [PMID: 33575570 PMCID: PMC7671362 DOI: 10.1093/nargab/lqz021] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Revised: 11/12/2019] [Accepted: 12/06/2019] [Indexed: 12/13/2022] Open
Abstract
The control of DNA topology by DNA topoisomerases is essential for virtually all DNA transactions in the cell. These enzymes, present in every organism, exist as several non-homologous families. We previously identified a small group of atypical type IIB topoisomerases, called Topo VIII, mainly encoded by plasmids. Here, taking advantage of the rapid expansion of sequence databases, we identified new putative Topo VIII homologs. Our analyses confirm the exclusivity of the corresponding genes to mobile genetic elements (MGE) and extend their distribution to nine different bacterial phyla and one archaeal superphylum. Notably, we discovered another subfamily of topoisomerases, dubbed ‘Mini-A’, including distant homologs of type IIB topoisomerases and encoded by extrachromosomal and integrated bacterial and archaeal viruses. Interestingly, a short, functionally uncharacterized motif at the C-terminal extremity of type IIB topoisomerases appears sufficient to discriminate between Mini-A, Topo VI and Topo VIII subfamilies. This motif could be a key element for understanding the differences between the three subfamilies. Collectively, this work leads to an updated model for the origin and evolution of the type IIB topoisomerase family and raises questions regarding the role of topoisomerases during replication of MGE in bacteria and archaea.
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Affiliation(s)
- Tomio S Takahashi
- Institut de Biologie Intégrative de la Cellule, CNRS, Université Paris-Saclay, 91198 Gif sur Yvette Cedex, France.,Unité de Microbiologie Structurale, Institut Pasteur, CNRS, F-75015 Paris, France
| | - Violette Da Cunha
- Institut de Biologie Intégrative de la Cellule, CNRS, Université Paris-Saclay, 91198 Gif sur Yvette Cedex, France
| | - Mart Krupovic
- Institut Pasteur, Archaeal Virology Unit, Department of Microbiology, 75015 Paris, France
| | - Claudine Mayer
- Unité de Microbiologie Structurale, Institut Pasteur, CNRS, F-75015 Paris, France.,Université de Paris, Paris Diderot, F-75013 Paris, France
| | - Patrick Forterre
- Institut de Biologie Intégrative de la Cellule, CNRS, Université Paris-Saclay, 91198 Gif sur Yvette Cedex, France.,Institut Pasteur, F-75015 Paris, France
| | - Danièle Gadelle
- Institut de Biologie Intégrative de la Cellule, CNRS, Université Paris-Saclay, 91198 Gif sur Yvette Cedex, France
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39
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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: 1.8] [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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40
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A 'parameiosis' drives depolyploidization and homologous recombination in Candida albicans. Nat Commun 2019; 10:4388. [PMID: 31558727 PMCID: PMC6763455 DOI: 10.1038/s41467-019-12376-2] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Accepted: 08/28/2019] [Indexed: 12/14/2022] Open
Abstract
Meiosis is a conserved tenet of sexual reproduction in eukaryotes, yet this program is seemingly absent from many extant species. In the human fungal pathogen Candida albicans, mating of diploid cells generates tetraploid products that return to the diploid state via a non-meiotic process of depolyploidization known as concerted chromosome loss (CCL). Here, we report that recombination rates are more than three orders of magnitude higher during CCL than during normal mitotic growth. Furthermore, two conserved ‘meiosis-specific’ factors play central roles in CCL as SPO11 mediates DNA double-strand break formation while both SPO11 and REC8 regulate chromosome stability and promote inter-homolog recombination. Unexpectedly, SPO11 also promotes DNA repair and recombination during normal mitotic divisions. These results indicate that C. albicans CCL represents a ‘parameiosis’ that blurs the conventional boundaries between mitosis and meiosis. They also reveal parallels with depolyploidization in mammalian cells and provide potential insights into the evolution of meiosis. Mating of Candida albicans produces tetraploid products that return to the diploid state via a non-meiotic process known as concerted chromosome loss (CCL). Here, Anderson et al. show high recombination rates during CCL and identify factors that are essential for chromosome stability and recombination during CCL.
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41
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Schwabl P, Imamura H, Van den Broeck F, Costales JA, Maiguashca-Sánchez J, Miles MA, Andersson B, Grijalva MJ, Llewellyn MS. Meiotic sex in Chagas disease parasite Trypanosoma cruzi. Nat Commun 2019; 10:3972. [PMID: 31481692 PMCID: PMC6722143 DOI: 10.1038/s41467-019-11771-z] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Accepted: 07/27/2019] [Indexed: 12/11/2022] Open
Abstract
Genetic exchange enables parasites to rapidly transform disease phenotypes and exploit new host populations. Trypanosoma cruzi, the parasitic agent of Chagas disease and a public health concern throughout Latin America, has for decades been presumed to exchange genetic material rarely and without classic meiotic sex. We present compelling evidence from 45 genomes sequenced from southern Ecuador that T. cruzi in fact maintains truly sexual, panmictic groups that can occur alongside others that remain highly clonal after past hybridization events. These groups with divergent reproductive strategies appear genetically isolated despite possible co-occurrence in vectors and hosts. We propose biological explanations for the fine-scale disconnectivity we observe and discuss the epidemiological consequences of flexible reproductive modes. Our study reinvigorates the hunt for the site of genetic exchange in the T. cruzi life cycle, provides tools to define the genetic determinants of parasite virulence, and reforms longstanding theory on clonality in trypanosomatid parasites.
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Affiliation(s)
- Philipp Schwabl
- Institute of Biodiversity, Animal Health & Comparative Medicine, University of Glasgow, Glasgow, G12 8QQ, UK
| | - Hideo Imamura
- Unit of Molecular Parasitology, Institute of Tropical Medicine Antwerp, 155 Nationalestraat, 2000, Antwerp, Belgium
| | - Frederik Van den Broeck
- Unit of Molecular Parasitology, Institute of Tropical Medicine Antwerp, 155 Nationalestraat, 2000, Antwerp, Belgium
| | - Jaime A Costales
- Center for Research on Health in Latin America, School of Biological Sciences, Pontifical Catholic University of Ecuador, Quito, Ecuador
| | - Jalil Maiguashca-Sánchez
- Center for Research on Health in Latin America, School of Biological Sciences, Pontifical Catholic University of Ecuador, Quito, Ecuador
| | - Michael A Miles
- London School of Hygiene & Tropical Medicine, Keppel Street, London, WC1E 7HT, UK
| | - Bjorn Andersson
- Department of Cell and Molecular Biology, Science for Life Laboratory, Karolinska Institutet, Biomedicum 9C, 171 77, Stockholm, Sweden
| | - Mario J Grijalva
- Center for Research on Health in Latin America, School of Biological Sciences, Pontifical Catholic University of Ecuador, Quito, Ecuador
- Infectious and Tropical Disease Institute, Biomedical Sciences Department, Heritage College of Osteopathic Medicine, Ohio University, 45701, Athens, OH, USA
| | - Martin S Llewellyn
- Institute of Biodiversity, Animal Health & Comparative Medicine, University of Glasgow, Glasgow, G12 8QQ, UK.
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42
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Steinfeld JB, Beláň O, Kwon Y, Terakawa T, Al-Zain A, Smith MJ, Crickard JB, Qi Z, Zhao W, Rothstein R, Symington LS, Sung P, Boulton SJ, Greene EC. Defining the influence of Rad51 and Dmc1 lineage-specific amino acids on genetic recombination. Genes Dev 2019; 33:1191-1207. [PMID: 31371435 PMCID: PMC6719624 DOI: 10.1101/gad.328062.119] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Accepted: 07/01/2019] [Indexed: 02/06/2023]
Abstract
The vast majority of eukaryotes possess two DNA recombinases: Rad51, which is ubiquitously expressed, and Dmc1, which is meiosis-specific. The evolutionary origins of this two-recombinase system remain poorly understood. Interestingly, Dmc1 can stabilize mismatch-containing base triplets, whereas Rad51 cannot. Here, we demonstrate that this difference can be attributed to three amino acids conserved only within the Dmc1 lineage of the Rad51/RecA family. Chimeric Rad51 mutants harboring Dmc1-specific amino acids gain the ability to stabilize heteroduplex DNA joints with mismatch-containing base triplets, whereas Dmc1 mutants with Rad51-specific amino acids lose this ability. Remarkably, RAD-51 from Caenorhabditis elegans, an organism without Dmc1, has acquired "Dmc1-like" amino acids. Chimeric C. elegans RAD-51 harboring "canonical" Rad51 amino acids gives rise to toxic recombination intermediates, which must be actively dismantled to permit normal meiotic progression. We propose that Dmc1 lineage-specific amino acids involved in the stabilization of heteroduplex DNA joints with mismatch-containing base triplets may contribute to normal meiotic recombination.
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Affiliation(s)
- Justin B Steinfeld
- Department of Biochemistry and Molecular Biophysics, Columbia University Irving Medical Center, New York, New York 10032, USA
| | - Ondrej Beláň
- DSB Repair Metabolism Laboratory, The Francis Crick Institute, London NW1 1AT, United Kingdom
| | - Youngho Kwon
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, Texas 78229, USA
| | - Tsuyoshi Terakawa
- Department of Biochemistry and Molecular Biophysics, Columbia University Irving Medical Center, New York, New York 10032, USA
| | - Amr Al-Zain
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, New York 10032, USA
| | - Michael J Smith
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, New York 10032, USA
| | - J Brooks Crickard
- Department of Biochemistry and Molecular Biophysics, Columbia University Irving Medical Center, New York, New York 10032, USA
| | - Zhi Qi
- Center for Quantitative Biology, Peking University-Tsinghua University Joint Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
| | - Weixing Zhao
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, Texas 78229, USA
| | - Rodney Rothstein
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, New York 10032, USA
| | - Lorraine S Symington
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, New York 10032, USA
| | - Patrick Sung
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, Texas 78229, USA
| | - Simon J Boulton
- DSB Repair Metabolism Laboratory, The Francis Crick Institute, London NW1 1AT, United Kingdom
| | - Eric C Greene
- Department of Biochemistry and Molecular Biophysics, Columbia University Irving Medical Center, New York, New York 10032, USA
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Genetic and genomic evolution of sexual reproduction: echoes from LECA to the fungal kingdom. Curr Opin Genet Dev 2019; 58-59:70-75. [PMID: 31473482 DOI: 10.1016/j.gde.2019.07.008] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Revised: 06/28/2019] [Accepted: 07/16/2019] [Indexed: 12/30/2022]
Abstract
Sexual reproduction is vastly diverse and yet highly conserved across the eukaryotic domain. This ubiquity suggests that the last eukaryotic common ancestor (LECA) was sexual. It is hypothesized that several critical processes in sexual reproduction, including cell fusion and meiosis, were acquired during the evolution from the first eukaryotic common ancestor (FECA) to the sexual LECA. However, it is challenging to delineate the exact origin and evolution of sexual reproduction given that both FECA and LECA are extinct. Studies of diverse eukaryotes have helped to shed light on this sexual evolutionary trajectory, revealing that a primordial sexual ploidy cycle likely involved endoreplication followed by concerted chromosome loss and that cell-cell fusion, meiosis, and sex determination later arose to shape modern sexual reproduction. Despite the general conservation of sexual reproduction processes throughout eukaryotes, modern sexual cycles are immensely diverse and complex. This diversity and complexity has become readily apparent in the fungal kingdom with the recent rapid expansion of whole-genome sequencing. This abundance of data, the variety of genetic tools available to manipulate and characterize fungi, and the thorough characterization of many fungal sexual cycles make the fungal kingdom an excellent forum, in which to study the conservation and diversification of sexual reproduction.
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Berry ASF, Salazar-Sánchez R, Castillo-Neyra R, Borrini-Mayorí K, Chipana-Ramos C, Vargas-Maquera M, Ancca-Juarez J, Náquira-Velarde C, Levy MZ, Brisson D, the Chagas Disease Working Group in Arequipa. Sexual reproduction in a natural Trypanosoma cruzi population. PLoS Negl Trop Dis 2019; 13:e0007392. [PMID: 31107905 PMCID: PMC6544315 DOI: 10.1371/journal.pntd.0007392] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Revised: 05/31/2019] [Accepted: 04/15/2019] [Indexed: 12/21/2022] Open
Abstract
Background Sexual reproduction provides an evolutionary advantageous mechanism that combines favorable mutations that have arisen in separate lineages into the same individual. This advantage is especially pronounced in microparasites as allelic reassortment among individuals caused by sexual reproduction promotes allelic diversity at immune evasion genes within individuals which is often essential to evade host immune systems. Despite these advantages, many eukaryotic microparasites exhibit highly-clonal population structures suggesting that genetic exchange through sexual reproduction is rare. Evidence supporting clonality is particularly convincing in the causative agent of Chagas disease, Trypanosoma cruzi, despite equally convincing evidence of the capacity to engage in sexual reproduction. Methodology/ Principle Findings In the present study, we investigated two hypotheses that can reconcile the apparent contradiction between the observed clonal population structure and the capacity to engage in sexual reproduction by analyzing the genome sequences of 123 T. cruzi isolates from a natural population in Arequipa, Peru. The distribution of polymorphic markers within and among isolates provides clear evidence of the occurrence of sexual reproduction. Large genetic segments are rearranged among chromosomes due to crossing over during meiosis leading to a decay in the genetic linkage among polymorphic markers compared to the expectations from a purely asexually-reproducing population. Nevertheless, the population structure appears clonal due to a high level of inbreeding during sexual reproduction which increases homozygosity, and thus reduces diversity, within each inbreeding lineage. Conclusions/ Significance These results effectively reconcile the apparent contradiction by demonstrating that the clonal population structure is derived not from infrequent sex in natural populations but from high levels of inbreeding. We discuss epidemiological consequences of this reproductive strategy on genome evolution, population structure, and phenotypic diversity of this medically important parasite. The rearrangement of alleles among individuals in a population during sexual reproduction maintains high allelic diversity within individuals in a population at polymorphic genes. Allelic diversity within individuals can be particularly important for parasites as it enhances their ability to evade host immune systems. Despite the potential benefits of sexual reproduction for parasites, natural populations of the protozoan parasite—and causative agent of human Chagas disease—Trypanosoma cruzi, exhibit clonal population structures indicative of asexual reproduction. This is particularly surprising as T. cruzi has the capacity for sexual reproduction. Here, we resolve this apparent contradiction by sequencing whole genomes of 123 T. cruzi isolates from a natural population in Arequipa, Peru. Evidence of past sexual reproduction and allelic rearrangements are common in this T. cruzi population. However, the majority of sexual reproduction events occur between close relatives resulting in an apparent clonal population structure. Sexual reproduction with distant relatives in areas with greater strain diversity has the potential to affect public health by increasing diversity in immune evasion genes within individuals and enhancing within-host survival, rapidly diversifying antigens that could affect the sensitivity of serological diagnostics, and by generating diversity in pathogenicity or drug resistance.
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Affiliation(s)
- Alexander S. F. Berry
- Division of Gastroenterology, Hepatology, and Nutrition, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
| | - Renzo Salazar-Sánchez
- Universidad Peruana Cayetano Heredia/University of Pennsylvania Chagas Disease Field Laboratory, Arequipa, Peru
| | - Ricardo Castillo-Neyra
- Universidad Peruana Cayetano Heredia/University of Pennsylvania Chagas Disease Field Laboratory, Arequipa, Peru
- Department of Biostatistics, Epidemiology and Informatics, The Perelman School of Medicine of the University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Katty Borrini-Mayorí
- Universidad Peruana Cayetano Heredia/University of Pennsylvania Chagas Disease Field Laboratory, Arequipa, Peru
| | - Claudia Chipana-Ramos
- Universidad Peruana Cayetano Heredia/University of Pennsylvania Chagas Disease Field Laboratory, Arequipa, Peru
| | - Melina Vargas-Maquera
- Universidad Peruana Cayetano Heredia/University of Pennsylvania Chagas Disease Field Laboratory, Arequipa, Peru
| | - Jenny Ancca-Juarez
- Universidad Peruana Cayetano Heredia/University of Pennsylvania Chagas Disease Field Laboratory, Arequipa, Peru
| | - César Náquira-Velarde
- Universidad Peruana Cayetano Heredia/University of Pennsylvania Chagas Disease Field Laboratory, Arequipa, Peru
| | - Michael Z. Levy
- Universidad Peruana Cayetano Heredia/University of Pennsylvania Chagas Disease Field Laboratory, Arequipa, Peru
- Department of Biostatistics, Epidemiology and Informatics, The Perelman School of Medicine of the University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Dustin Brisson
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- * E-mail:
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Leonard G, Labarre A, Milner DS, Monier A, Soanes D, Wideman JG, Maguire F, Stevens S, Sain D, Grau-Bové X, Sebé-Pedrós A, Stajich JE, Paszkiewicz K, Brown MW, Hall N, Wickstead B, Richards TA. Comparative genomic analysis of the 'pseudofungus' Hyphochytrium catenoides. Open Biol 2019; 8:rsob.170184. [PMID: 29321239 PMCID: PMC5795050 DOI: 10.1098/rsob.170184] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Accepted: 12/01/2017] [Indexed: 12/21/2022] Open
Abstract
Eukaryotic microbes have three primary mechanisms for obtaining nutrients and energy: phagotrophy, photosynthesis and osmotrophy. Traits associated with the latter two functions arose independently multiple times in the eukaryotes. The Fungi successfully coupled osmotrophy with filamentous growth, and similar traits are also manifested in the Pseudofungi (oomycetes and hyphochytriomycetes). Both the Fungi and the Pseudofungi encompass a diversity of plant and animal parasites. Genome-sequencing efforts have focused on host-associated microbes (mutualistic symbionts or parasites), providing limited comparisons with free-living relatives. Here we report the first draft genome sequence of a hyphochytriomycete ‘pseudofungus’; Hyphochytrium catenoides. Using phylogenomic approaches, we identify genes of recent viral ancestry, with related viral derived genes also present on the genomes of oomycetes, suggesting a complex history of viral coevolution and integration across the Pseudofungi. H. catenoides has a complex life cycle involving diverse filamentous structures and a flagellated zoospore with a single anterior tinselate flagellum. We use genome comparisons, drug sensitivity analysis and high-throughput culture arrays to investigate the ancestry of oomycete/pseudofungal characteristics, demonstrating that many of the genetic features associated with parasitic traits evolved specifically within the oomycete radiation. Comparative genomics also identified differences in the repertoire of genes associated with filamentous growth between the Fungi and the Pseudofungi, including differences in vesicle trafficking systems, cell-wall synthesis pathways and motor protein repertoire, demonstrating that unique cellular systems underpinned the convergent evolution of filamentous osmotrophic growth in these two eukaryotic groups.
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Affiliation(s)
- Guy Leonard
- Living Systems Institute, Department of Biosciences, University of Exeter, Exeter EX4 4QD, UK
| | - Aurélie Labarre
- Living Systems Institute, Department of Biosciences, University of Exeter, Exeter EX4 4QD, UK
| | - David S Milner
- Living Systems Institute, Department of Biosciences, University of Exeter, Exeter EX4 4QD, UK
| | - Adam Monier
- Living Systems Institute, Department of Biosciences, University of Exeter, Exeter EX4 4QD, UK
| | - Darren Soanes
- Living Systems Institute, Department of Biosciences, University of Exeter, Exeter EX4 4QD, UK
| | - Jeremy G Wideman
- Living Systems Institute, Department of Biosciences, University of Exeter, Exeter EX4 4QD, UK
| | - Finlay Maguire
- Living Systems Institute, Department of Biosciences, University of Exeter, Exeter EX4 4QD, UK
| | - Sam Stevens
- Living Systems Institute, Department of Biosciences, University of Exeter, Exeter EX4 4QD, UK
| | - Divya Sain
- Department of Plant Pathology and Microbiology, Institute for Integrative Genome Biology, University of California, Riverside, CA 92506, USA
| | - Xavier Grau-Bové
- Institute of Evolutionary Biology, CSIC-UPF, Barcelona, Catalonia, Spain
| | | | - Jason E Stajich
- Department of Plant Pathology and Microbiology, Institute for Integrative Genome Biology, University of California, Riverside, CA 92506, USA
| | - Konrad Paszkiewicz
- Living Systems Institute, Department of Biosciences, University of Exeter, Exeter EX4 4QD, UK
| | - Matthew W Brown
- Department of Biological Sciences, Mississippi State University, Mississippi State, MS 39762, USA.,Institute for Genomics, Biocomputing and Biotechnology, Mississippi State University, Mississippi State, MS 39762, USA
| | - Neil Hall
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK
| | - Bill Wickstead
- School of Life Sciences, University of Nottingham, Nottingham NG7 2UH, UK
| | - Thomas A Richards
- Living Systems Institute, Department of Biosciences, University of Exeter, Exeter EX4 4QD, UK
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46
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Kraus D, Chi J, Boenigk J, Beisser D, Graupner N, Dunthorn M. Putatively asexual chrysophytes have meiotic genes: evidence from transcriptomic data. PeerJ 2019; 6:e5894. [PMID: 30671284 PMCID: PMC6339481 DOI: 10.7717/peerj.5894] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Accepted: 10/08/2018] [Indexed: 01/06/2023] Open
Abstract
Chrysophytes are a large group of heterotrophic, phototrophic, or even mixotrophic protists that are abundant in aquatic as well as terrestrial environments. Although much is known about chrysophyte biology and ecology, it is unknown if they are sexual or not. Here we use available transcriptomes of 18 isolates of 15 putatively asexual species to inventory the presence of genes used in meiosis. Since we were able to detect a set of nine meiosis-specific and 29 meiosis-related genes shared by the chrysophytes, we conclude that they are secretively sexual and therefore should be investigated further using genome sequencing to uncover any missed genes from the transcriptomes.
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Affiliation(s)
- Diana Kraus
- Department of Ecology, University of Kaiserslautern, Kaiserslautern, Germany
| | - Jingyun Chi
- Department of Ecology, University of Kaiserslautern, Kaiserslautern, Germany
| | - Jens Boenigk
- Department of Biodiversity, University of Duisburg-Essen, Essen, Germany
| | - Daniela Beisser
- Department of Biodiversity, University of Duisburg-Essen, Essen, Germany.,Centre for Water and Environmental Research (ZWU), University of Duisburg-Essen, Essen, Germany
| | - Nadine Graupner
- Department of Biodiversity, University of Duisburg-Essen, Essen, Germany
| | - Micah Dunthorn
- Department of Ecology, University of Kaiserslautern, Kaiserslautern, Germany.,Centre for Water and Environmental Research (ZWU), University of Duisburg-Essen, Essen, Germany.,Department of Eukaryotic Microbiology, University of Duisburg-Essen, Essen, Germany
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47
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Gibson W, Peacock L. Fluorescent proteins reveal what trypanosomes get up to inside the tsetse fly. Parasit Vectors 2019; 12:6. [PMID: 30609932 PMCID: PMC6320599 DOI: 10.1186/s13071-018-3204-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Accepted: 11/19/2018] [Indexed: 12/12/2022] Open
Abstract
The discovery and development of fluorescent proteins for the investigation of living cells and whole organisms has been a major advance in biomedical research. This approach was quickly exploited by parasitologists, particularly those studying single-celled protists. Here we describe some of our experiments to illustrate how fluorescent proteins have helped to reveal what trypanosomes get up to inside the tsetse fly. Fluorescent proteins turned the tsetse fly from a "black box" into a bright showcase to track trypanosome migration and development within the insect. Crosses of genetically modified red and green fluorescent trypanosomes produced yellow fluorescent hybrids and established the "when" and "where" of trypanosome sexual reproduction inside the fly. Fluorescent-tagging endogenous proteins enabled us to identify the meiotic division stage and gametes inside the salivary glands of the fly and thus elucidate the mechanism of sexual reproduction in trypanosomes. Without fluorescent proteins we would still be in the "dark ages" of understanding what trypanosomes get up to inside the tsetse fly.
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Affiliation(s)
- Wendy Gibson
- School of Biological Sciences, University of Bristol, Bristol, BS8 1TQ UK
| | - Lori Peacock
- School of Biological Sciences, University of Bristol, Bristol, BS8 1TQ UK
- School of Clinical Veterinary Science, University of Bristol, Langford, Bristol, BS40 7DU UK
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48
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Hörandl E, Speijer D. How oxygen gave rise to eukaryotic sex. Proc Biol Sci 2019; 285:rspb.2017.2706. [PMID: 29436502 PMCID: PMC5829205 DOI: 10.1098/rspb.2017.2706] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Accepted: 01/15/2018] [Indexed: 12/13/2022] Open
Abstract
How did full meiotic eukaryotic sex evolve and what was the immediate advantage allowing it to develop? We propose that the crucial determinant can be found in internal reactive oxygen species (ROS) formation at the start of eukaryotic evolution approximately 2 × 109 years ago. The large amount of ROS coming from a bacterial endosymbiont gave rise to DNA damage and vast increases in host genome mutation rates. Eukaryogenesis and chromosome evolution represent adaptations to oxidative stress. The host, an archaeon, most probably already had repair mechanisms based on DNA pairing and recombination, and possibly some kind of primitive cell fusion mechanism. The detrimental effects of internal ROS formation on host genome integrity set the stage allowing evolution of meiotic sex from these humble beginnings. Basic meiotic mechanisms thus probably evolved in response to endogenous ROS production by the ‘pre-mitochondrion’. This alternative to mitosis is crucial under novel, ROS-producing stress situations, like extensive motility or phagotrophy in heterotrophs and endosymbiontic photosynthesis in autotrophs. In multicellular eukaryotes with a germline–soma differentiation, meiotic sex with diploid–haploid cycles improved efficient purging of deleterious mutations. Constant pressure of endogenous ROS explains the ubiquitous maintenance of meiotic sex in practically all eukaryotic kingdoms. Here, we discuss the relevant observations underpinning this model.
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Affiliation(s)
- Elvira Hörandl
- Department of Systematics, Biodiversity and Evolution of Plants, University of Goettingen, Göttingen, Germany
| | - Dave Speijer
- Department of Medical Biochemistry, Academic Medical Centre (AMC), University of Amsterdam, Amsterdam, The Netherlands
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49
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Hofstatter PG, Brown MW, Lahr DJG. Comparative Genomics Supports Sex and Meiosis in Diverse Amoebozoa. Genome Biol Evol 2018; 10:3118-3128. [PMID: 30380054 PMCID: PMC6263441 DOI: 10.1093/gbe/evy241] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/30/2018] [Indexed: 12/30/2022] Open
Abstract
Sex and reproduction are often treated as a single phenomenon in animals and plants, as in these organisms reproduction implies mixis and meiosis. In contrast, sex and reproduction are independent biological phenomena that may or may not be linked in the majority of other eukaryotes. Current evidence supports a eukaryotic ancestor bearing a mating type system and meiosis, which is a process exclusive to eukaryotes. Even though sex is ancestral, the literature regarding life cycles of amoeboid lineages depicts them as asexual organisms. Why would loss of sex be common in amoebae, if it is rarely lost, if ever, in plants and animals, as well as in fungi? One way to approach the question of meiosis in the "asexuals" is to evaluate the patterns of occurrence of genes for the proteins involved in syngamy and meiosis. We have applied a comparative genomic approach to study the occurrence of the machinery for plasmogamy, karyogamy, and meiosis in Amoebozoa, a major amoeboid supergroup. Our results support a putative occurrence of syngamy and meiotic processes in all major amoebozoan lineages. We conclude that most amoebozoans may perform mixis, recombination, and ploidy reduction through canonical meiotic processes. The present evidence indicates the possibility of sexual cycles in many lineages traditionally held as asexual.
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Affiliation(s)
- Paulo G Hofstatter
- Departamento de Zoologia, Instituto de Biociências, Universidade de São Paulo, Brazil
| | - Matthew W Brown
- Department of Biological Sciences, Mississippi State University
| | - Daniel J G Lahr
- Departamento de Zoologia, Instituto de Biociências, Universidade de São Paulo, Brazil
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50
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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: 19] [Impact Index Per Article: 2.7] [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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