1
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Dinon A, Fiorani F, Campero LM, Moore DP, Corva PM. The role of genetic variability of the host on the resistance to Neospora caninum infection in cattle. Anim Genet 2024; 55:304-318. [PMID: 38419150 DOI: 10.1111/age.13410] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Revised: 02/15/2024] [Accepted: 02/15/2024] [Indexed: 03/02/2024]
Abstract
Neospora caninum is one of the most frequently diagnosed abortifacient pathogens in cattle. There is abundant genomic information about the parasite itself, but very little is known about the genetic variability of resistance in the most common intermediate host. The aim of this review was to compile all the available information about the genetic variability associated with the resistance to N. caninum both between and within cattle breeds. We systematically searched for published studies that investigated the influence of genetics of the host on the prevalence of N. caninum and risk of abortion. Beyond the potential confounding effects of feeding systems, management and animal density, some lines of evidence suggest that Holstein, the most popular breed for milk production, has a comparatively higher risk of abortion due to infections by N. caninum, whereas some beef breeds from Continental Europe seem to be more resistant. It is still not clear if different genetic mechanisms of resistance are involved in the two known routes of infection: postnatal ingestion of oocysts or transplacental transmission from the infected dam to the fetus. Genomic information associated with susceptibility to infection and risk of abortion in different cattle breeds is still scarce. The information reported here could be useful to identify new research alternatives and to define novel strategies to deal with this major problem of animal production.
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Affiliation(s)
- Anabella Dinon
- Facultad de Ciencias Agrarias, Universidad Nacional de Mar del Plata, Balcarce, Argentina
| | - Franco Fiorani
- Facultad de Ciencias Agrarias, Universidad Nacional de Mar del Plata, Balcarce, Argentina
| | - Lucía María Campero
- Instituto de Innovación para la Producción Agropecuaria y el Desarrollo Sostenible (IPADS Balcarce), Balcarce, Argentina
| | - Dadín Prando Moore
- Facultad de Ciencias Agrarias, Universidad Nacional de Mar del Plata, Balcarce, Argentina
- Instituto de Innovación para la Producción Agropecuaria y el Desarrollo Sostenible (IPADS Balcarce), Balcarce, Argentina
| | - Pablo Marcelo Corva
- Facultad de Ciencias Agrarias, Universidad Nacional de Mar del Plata, Balcarce, Argentina
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2
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Tetzlaff S, Hillebrand A, Drakoulis N, Gluhic Z, Maschmann S, Lyko P, Wicke S, Schmitz-Linneweber C. Small RNAs from mitochondrial genome recombination sites are incorporated into T. gondii mitoribosomes. eLife 2024; 13:e95407. [PMID: 38363119 PMCID: PMC10948144 DOI: 10.7554/elife.95407] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Accepted: 01/23/2024] [Indexed: 02/17/2024] Open
Abstract
The mitochondrial genomes of apicomplexans comprise merely three protein-coding genes, alongside a set of thirty to forty genes encoding small RNAs (sRNAs), many of which exhibit homologies to rRNA from E. coli. The expression status and integration of these short RNAs into ribosomes remains unclear and direct evidence for active ribosomes within apicomplexan mitochondria is still lacking. In this study, we conducted small RNA sequencing on the apicomplexan Toxoplasma gondii to investigate the occurrence and function of mitochondrial sRNAs. To enhance the analysis of sRNA sequencing outcomes, we also re-sequenced the T. gondii mitochondrial genome using an improved organelle enrichment protocol and Nanopore sequencing. It has been established previously that the T. gondii genome comprises 21 sequence blocks that undergo recombination among themselves but that their order is not entirely random. The enhanced coverage of the mitochondrial genome allowed us to characterize block combinations at increased resolution. Employing this refined genome for sRNA mapping, we find that many small RNAs originated from the junction sites between protein-coding blocks and rRNA sequence blocks. Surprisingly, such block border sRNAs were incorporated into polysomes together with canonical rRNA fragments and mRNAs. In conclusion, apicomplexan ribosomes are active within polysomes and are indeed assembled through the integration of sRNAs, including previously undetected sRNAs with merged mRNA-rRNA sequences. Our findings lead to the hypothesis that T. gondii's block-based genome organization enables the dual utilization of mitochondrial sequences as both messenger RNAs and ribosomal RNAs, potentially establishing a link between the regulation of rRNA and mRNA expression.
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Affiliation(s)
| | | | | | - Zala Gluhic
- Molecular Genetics, Humboldt University BerlinBerlinGermany
| | | | - Peter Lyko
- Biodiversity and Evolution, Humboldt University BerlinBerlinGermany
| | - Susann Wicke
- Biodiversity and Evolution, Humboldt University BerlinBerlinGermany
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3
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Lamb IM, Okoye IC, Mather MW, Vaidya AB. Unique Properties of Apicomplexan Mitochondria. Annu Rev Microbiol 2023; 77:541-560. [PMID: 37406344 DOI: 10.1146/annurev-micro-032421-120540] [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: 07/07/2023]
Abstract
Apicomplexan parasites constitute more than 6,000 species infecting a wide range of hosts. These include important pathogens such as those causing malaria and toxoplasmosis. Their evolutionary emergence coincided with the dawn of animals. Mitochondrial genomes of apicomplexan parasites have undergone dramatic reduction in their coding capacity, with genes for only three proteins and ribosomal RNA genes present in scrambled fragments originating from both strands. Different branches of the apicomplexans have undergone rearrangements of these genes, with Toxoplasma having massive variations in gene arrangements spread over multiple copies. The vast evolutionary distance between the parasite and the host mitochondria has been exploited for the development of antiparasitic drugs, especially those used to treat malaria, wherein inhibition of the parasite mitochondrial respiratory chain is selectively targeted with little toxicity to the host mitochondria. We describe additional unique characteristics of the parasite mitochondria that are being investigated and provide greater insights into these deep-branching eukaryotic pathogens.
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Affiliation(s)
- Ian M Lamb
- Center for Molecular Parasitology, Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, Pennsylvania, USA;
| | - Ijeoma C Okoye
- Center for Molecular Parasitology, Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, Pennsylvania, USA;
| | - Michael W Mather
- Center for Molecular Parasitology, Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, Pennsylvania, USA;
| | - Akhil B Vaidya
- Center for Molecular Parasitology, Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, Pennsylvania, USA;
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4
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Cabrera A, Berná L, López L, Faral-Tello P, Arevalo AP, Crispo M, Francia ME, Robello C. New insights into phenotype and genotype relationships in Neospora caninum. Front Vet Sci 2023; 10:1214971. [PMID: 37662990 PMCID: PMC10469931 DOI: 10.3389/fvets.2023.1214971] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Accepted: 08/01/2023] [Indexed: 09/05/2023] Open
Abstract
The successful isolation of four new Neospora caninum strains from different regions and with different backgrounds (obtained from an abortion storm or congenitally infected and asymptomatic calves) allowed us previously to characterize natural isolates, finding differences in phenotype and microsatellites. Given the variability observed, we wondered in this work whether these differences had consequences in virulence, invasion and vertical transmission using cell cultures and murine neosporosis models. In addition, we performed the genomic analysis and SNP comparative studies of the NcURU isolates. The results obtained in this work allowed us to establish that NcURU isolates are of low virulence and have unique phenotypic characteristics. Likewise, sequencing their genomes has allowed us to delve into the genetic singularities underlying these phenotypes, as well as the common mutated genes. This work opens a new perspective for diagnostic purposes and formulating possible vaccines based on attenuated strains.
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Affiliation(s)
- Andres Cabrera
- Laboratorio de Interacciones Hospedero-Patógeno -UBM, Institut Pasteur de Montevideo, Montevideo, Uruguay
- Departamento de Parasitología y Micología, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
| | - Luisa Berná
- Laboratorio de Interacciones Hospedero-Patógeno -UBM, Institut Pasteur de Montevideo, Montevideo, Uruguay
- Laboratorio de Genómica Evolutiva, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | - Lucía López
- Laboratorio de Interacciones Hospedero-Patógeno -UBM, Institut Pasteur de Montevideo, Montevideo, Uruguay
| | - Paula Faral-Tello
- Laboratorio de Interacciones Hospedero-Patógeno -UBM, Institut Pasteur de Montevideo, Montevideo, Uruguay
| | - Ana Paula Arevalo
- Laboratory Animals Biotechnology Unit, Institut Pasteur de Montevideo, Montevideo, Uruguay
| | - Martina Crispo
- Laboratory Animals Biotechnology Unit, Institut Pasteur de Montevideo, Montevideo, Uruguay
| | - Maria E. Francia
- Departamento de Parasitología y Micología, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
- Laboratory of Apicomplexan Biology, Institut Pasteur de Montevideo, Montevideo, Uruguay
| | - Carlos Robello
- Laboratorio de Interacciones Hospedero-Patógeno -UBM, Institut Pasteur de Montevideo, Montevideo, Uruguay
- Departamento de Bioquímica, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
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5
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Dissection of Besnoitia besnoiti intermediate host life cycle stages: From morphology to gene expression. PLoS Pathog 2022; 18:e1010955. [DOI: 10.1371/journal.ppat.1010955] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Revised: 12/01/2022] [Accepted: 10/27/2022] [Indexed: 11/18/2022] Open
Abstract
Cyst-forming Apicomplexa (CFA) of the Sarcocystidae have a ubiquitous presence as pathogens of humans and farm animals transmitted through the food chain between hosts with few notable exceptions. The defining hallmark of this family of obligate intracellular protists consists of their ability to remain for very long periods as infectious tissue cysts in chronically infected intermediate hosts. Nevertheless, each closely related species has evolved unique strategies to maintain distinct reservoirs on global scales and ensuring efficient transmission to definitive hosts as well as between intermediate hosts. Here, we present an in-depth comparative mRNA expression analysis of the tachyzoite and bradyzoite stages of Besnoitia besnoiti strain Lisbon14 isolated from an infected farm animal based on its annotated genome sequence. The B. besnoiti genome is highly syntenic with that of other CFA and also retains the capacity to encode a large majority of known and inferred factors essential for completing a sexual cycle in a yet unknown definitive host. This work introduces Besnoitia besnoiti as a new model for comparative biology of coccidian tissue cysts which can be readily obtained in high purity. This model provides a framework for addressing fundamental questions about the evolution of tissue cysts and the biology of this pharmacologically intractable infectious parasite stage.
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6
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Contreras SM, Zambrano Siri RT, Rivera EM, Cristaldi C, Kamenetzky L, Kim K, Clemente M, Ocampo J, Vanagas L, Angel SO. Architecture, Chromatin and Gene Organization of Toxoplasma gondii Subtelomeres. EPIGENOMES 2022; 6:29. [PMID: 36135316 PMCID: PMC9498087 DOI: 10.3390/epigenomes6030029] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 09/05/2022] [Accepted: 09/08/2022] [Indexed: 11/17/2022] Open
Abstract
Subtelomeres (ST) are chromosome regions that separate telomeres from euchromatin and play relevant roles in various biological processes of the cell. While their functions are conserved, ST structure and genetic compositions are unique to each species. This study aims to identify and characterize the subtelomeric regions of the 13 Toxoplasma gondii chromosomes of the Me49 strain. Here, STs were defined at chromosome ends based on poor gene density. The length of STs ranges from 8.1 to 232.4 kbp, with a gene density of 0.049 genes/kbp, lower than the Me49 genome (0.15 kbp). Chromatin organization showed that H3K9me3, H2A.X, and H3.3 are highly enriched near telomeres and the 5' end of silenced genes, decaying in intensity towards euchromatin. H3K4me3 and H2A.Z/H2B.Z are shown to be enriched in the 5' end of the ST genes. Satellite DNA was detected in almost all STs, mainly the sat350 family and a novel satellite named sat240. Beyond the STs, only short dispersed fragments of sat240 and sat350 were found. Within STs, there were 12 functional annotated genes, 59 with unknown functions (Hypothetical proteins), 15 from multigene FamB, and 13 from multigene family FamC. Some genes presented low interstrain synteny associated with the presence of satellite DNA. Orthologues of FamB and FamC were also detected in Neospora caninum and Hammondia hammondi. A re-analysis of previous transcriptomic data indicated that ST gene expression is strongly linked to the adaptation to different situations such as extracellular passage (evolve and resequencing study) and changes in metabolism (lack of acetyl-CoA cofactor). In conclusion, the ST region of the T. gondii chromosomes was defined, the STs genes were determined, and it was possible to associate them with high interstrain plasticity and a role in the adaptability of T. gondii to environmental changes.
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Affiliation(s)
- Susana M. Contreras
- Laboratorio de Parasitología Molecular, Instituto Tecnológico Chascomús (INTECH), Universidad Nacional de General San Martín (UNSAM), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Chascomús 7130, Argentina
| | - Romina T. Zambrano Siri
- Instituto de Investigaciones en Ingeniería Genética y Biología Molecular “Dr. Héctor N. Torres” (INGEBI-CONICET), Buenos Aires C1428ADN, Argentina
| | - Elías M. Rivera
- Laboratorio de Parasitología Molecular, Instituto Tecnológico Chascomús (INTECH), Universidad Nacional de General San Martín (UNSAM), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Chascomús 7130, Argentina
| | - Constanza Cristaldi
- Laboratorio de Parasitología Molecular, Instituto Tecnológico Chascomús (INTECH), Universidad Nacional de General San Martín (UNSAM), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Chascomús 7130, Argentina
| | - Laura Kamenetzky
- Laboratorio de Genómica y Bioinformática de Patógenos, iB3|Instituto de Biociencias, Biotecnología y Biología traslacional, Departamento de Fisiología y Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires C1428EHA, Argentina
| | - Kami Kim
- Department of Internal Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL 33602, USA
| | - Marina Clemente
- Laboratorio de Molecular Farming y Vacunas, Instituto Tecnológico Chascomús (INTECH), Universidad Nacional de General San Martín (UNSAM), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Chascomús 7130, Argentina
| | - Josefina Ocampo
- Instituto de Investigaciones en Ingeniería Genética y Biología Molecular “Dr. Héctor N. Torres” (INGEBI-CONICET), Buenos Aires C1428ADN, Argentina
| | - Laura Vanagas
- Laboratorio de Parasitología Molecular, Instituto Tecnológico Chascomús (INTECH), Universidad Nacional de General San Martín (UNSAM), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Chascomús 7130, Argentina
| | - Sergio O. Angel
- Laboratorio de Parasitología Molecular, Instituto Tecnológico Chascomús (INTECH), Universidad Nacional de General San Martín (UNSAM), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Chascomús 7130, Argentina
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7
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Goodswen SJ, Kennedy PJ, Ellis JT. Compilation of parasitic immunogenic proteins from 30 years of published research using machine learning and natural language processing. Sci Rep 2022; 12:10349. [PMID: 35725870 PMCID: PMC9208253 DOI: 10.1038/s41598-022-13790-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Accepted: 05/18/2022] [Indexed: 12/02/2022] Open
Abstract
The World Health Organisation reported in 2020 that six of the top 10 sources of death in low-income countries are parasites. Parasites are microorganisms in a relationship with a larger organism, the host. They acquire all benefits at the host’s expense. A disease develops if the parasitic infection disrupts normal functioning of the host. This disruption can range from mild to severe, including death. Humans and livestock continue to be challenged by established and emerging infectious disease threats. Vaccination is the most efficient tool for preventing current and future threats. Immunogenic proteins sourced from the disease-causing parasite are worthwhile vaccine components (subunits) due to reliable safety and manufacturing capacity. Publications with ‘subunit vaccine’ in their title have accumulated to thousands over the last three decades. However, there are possibly thousands more reporting immunogenicity results without mentioning ‘subunit’ and/or ‘vaccine’. The exact number is unclear given the non-standardised keywords in publications. The study aim is to identify parasite proteins that induce a protective response in an animal model as reported in the scientific literature within the last 30 years using machine learning and natural language processing. Source code to fulfil this aim and the vaccine candidate list obtained is made available.
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Affiliation(s)
- Stephen J Goodswen
- School of Life Sciences, University of Technology Sydney, 15 Broadway, Ultimo, NSW, 2007, Australia
| | - Paul J Kennedy
- School of Computer Science, Faculty of Engineering and Information Technology and the Australian Artificial Intelligence Institute, University of Technology Sydney, 15 Broadway, Ultimo, NSW, 2007, Australia
| | - John T Ellis
- School of Life Sciences, University of Technology Sydney, 15 Broadway, Ultimo, NSW, 2007, Australia.
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8
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Kent RS, Briggs EM, Colon BL, Alvarez C, Silva Pereira S, De Niz M. Paving the Way: Contributions of Big Data to Apicomplexan and Kinetoplastid Research. Front Cell Infect Microbiol 2022; 12:900878. [PMID: 35734575 PMCID: PMC9207352 DOI: 10.3389/fcimb.2022.900878] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 05/06/2022] [Indexed: 11/13/2022] Open
Abstract
In the age of big data an important question is how to ensure we make the most out of the resources we generate. In this review, we discuss the major methods used in Apicomplexan and Kinetoplastid research to produce big datasets and advance our understanding of Plasmodium, Toxoplasma, Cryptosporidium, Trypanosoma and Leishmania biology. We debate the benefits and limitations of the current technologies, and propose future advancements that may be key to improving our use of these techniques. Finally, we consider the difficulties the field faces when trying to make the most of the abundance of data that has already been, and will continue to be, generated.
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Affiliation(s)
- Robyn S. Kent
- Department of Microbiology and Molecular Genetics, University of Vermont, Burlington, VT, United States
| | - Emma M. Briggs
- Institute for Immunology and Infection Research, School of Biological Sciences, University Edinburgh, Edinburgh, United Kingdom
- Wellcome Centre for Integrative Parasitology, Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, United Kingdom
| | - Beatrice L. Colon
- Wellcome Centre for Anti-Infectives Research, Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Catalina Alvarez
- de Duve Institute, Université Catholique de Louvain, Brussels, Belgium
| | - Sara Silva Pereira
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina da Universidade de Lisboa, Lisboa, Portugal
| | - Mariana De Niz
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina da Universidade de Lisboa, Lisboa, Portugal
- Institut Pasteur, Paris, France
- *Correspondence: Mariana De Niz,
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9
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Dubey JP. Invited review: Sarcocystis neurona, Neospora spp. and Toxoplasma gondii infections in horses and equine protozoal myeloencephalitis (EPM): five decades of personal experience, perspectives, and update. Parasitology 2022; 149:1-44. [PMID: 35260209 DOI: 10.1017/s0031182021002055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
AbstractSarcocystis neurona, Neospora spp. and Toxoplasma gondii are related protozoans; they were considered the same parasite until 1970s. Two of these parasites, S. neurona and Neospora spp. are associated with a neurological syndrome in horses, called equine protozoal myeloencephalitis (EPM). The diagnosis and treatment of EPM are difficult. Most cases of EPM are related to S. neurona while only a few are due to Neospora spp. infections. There are two species of Neospora, Neospora caninum that has a wide host range and Neospora hughesi that has been found only in horses. Currently, T. gondii is not considered as a cause of EPM in horses, although it causes neurological illness in many other hosts, including humans. The present review provides an update on history, life cycle, diagnosis and treatment of these three infections in horses.
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Affiliation(s)
- J P Dubey
- United States Department of Agriculture, Agricultural Research Service, Animal Parasitic Diseases Laboratory, Beltsville Agricultural Research Center, Building 1001, Beltsville, MD20705-2350, USA
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10
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Dubey JP, Khan A, Rosenthal BM. Life Cycle and Transmission of Cyclospora cayetanensis: Knowns and Unknowns. Microorganisms 2022; 10:microorganisms10010118. [PMID: 35056567 PMCID: PMC8779055 DOI: 10.3390/microorganisms10010118] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Revised: 12/29/2021] [Accepted: 01/04/2022] [Indexed: 12/04/2022] Open
Abstract
Although infections with Cyclospora cayetanensis are prevalent worldwide, many aspects of this parasite’s life cycle and transmission remain unknown. Humans are the only known hosts of this parasite. Existing information on its endogenous development has been derived from histological examination of only a few biopsy specimens. Its asexual and sexual stages occur in biliary-intestinal epithelium. In histological sections, its stages are less than 10 μm, making definitive identification difficult. Asexual (schizonts) and sexual (gamonts) are located in epithelial cells. Male microgamonts have two flagella; female macrogametes contain wall-forming bodies. Oocysts are excreted in feces unsporulated. Sporulation occurs in the environment, but there are many unanswered questions concerning dissemination and survival of C. cayetanensis oocysts. Biologically and phylogenetically, C. cayetanensis closely resembles Eimeria spp. that parastize chickens; among them, E. acervulina most closely resembles C. cayetanensis in size. Here, we review known and unknown aspects of its life cycle and transmission and discuss the appropriateness of surrogates best capable of hastening progress in understanding its biology and developing mitigating strategies.
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11
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Berná L, Rego N, Francia ME. The Elusive Mitochondrial Genomes of Apicomplexa: Where Are We Now? Front Microbiol 2021; 12:751775. [PMID: 34721355 PMCID: PMC8554336 DOI: 10.3389/fmicb.2021.751775] [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: 08/02/2021] [Accepted: 09/16/2021] [Indexed: 11/16/2022] Open
Abstract
Mitochondria are vital organelles of eukaryotic cells, participating in key metabolic pathways such as cellular respiration, thermogenesis, maintenance of cellular redox potential, calcium homeostasis, cell signaling, and cell death. The phylum Apicomplexa is entirely composed of obligate intracellular parasites, causing a plethora of severe diseases in humans, wild and domestic animals. These pathogens include the causative agents of malaria, cryptosporidiosis, neosporosis, East Coast fever and toxoplasmosis, among others. The mitochondria in Apicomplexa has been put forward as a promising source of undiscovered drug targets, and it has been validated as the target of atovaquone, a drug currently used in the clinic to counter malaria. Apicomplexans present a single tubular mitochondria that varies widely both in structure and in genomic content across the phylum. The organelle is characterized by massive gene migrations to the nucleus, sequence rearrangements and drastic functional reductions in some species. Recent third generation sequencing studies have reignited an interest for elucidating the extensive diversity displayed by the mitochondrial genomes of apicomplexans and their intriguing genomic features. The underlying mechanisms of gene transcription and translation are also ill-understood. In this review, we present the state of the art on mitochondrial genome structure, composition and organization in the apicomplexan phylum revisiting topological and biochemical information gathered through classical techniques. We contextualize this in light of the genomic insight gained by second and, more recently, third generation sequencing technologies. We discuss the mitochondrial genomic and mechanistic features found in evolutionarily related alveolates, and discuss the common and distinct origins of the apicomplexan mitochondria peculiarities.
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Affiliation(s)
- Luisa Berná
- Laboratory of Apicomplexan Biology, Institut Pasteur de Montevideo, Montevideo, Uruguay.,Molecular Biology Unit, Institut Pasteur de Montevideo, Montevideo, Uruguay.,Bioinformatics Unit, Institut Pasteur de Montevideo, Montevideo, Uruguay.,Sección Biomatemática-Laboratorio de Genómica Evolutiva, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | - Natalia Rego
- Bioinformatics Unit, Institut Pasteur de Montevideo, Montevideo, Uruguay
| | - María E Francia
- Laboratory of Apicomplexan Biology, Institut Pasteur de Montevideo, Montevideo, Uruguay.,Departamento de Parasitología y Micología, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
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12
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Xia J, Venkat A, Bainbridge RE, Reese ML, Le Roch KG, Ay F, Boyle JP. Third-generation sequencing revises the molecular karyotype for Toxoplasma gondii and identifies emerging copy number variants in sexual recombinants. Genome Res 2021; 31:834-851. [PMID: 33906962 PMCID: PMC8092015 DOI: 10.1101/gr.262816.120] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Accepted: 02/03/2021] [Indexed: 12/28/2022]
Abstract
Toxoplasma gondii is a useful model for intracellular parasitism given its ease of culture in the laboratory and genomic resources. However, as for many other eukaryotes, the T. gondii genome contains hundreds of sequence gaps owing to repetitive and/or unclonable sequences that disrupt the assembly process. Here, we use the Oxford Nanopore Minion platform to generate near-complete de novo genome assemblies for multiple strains of T. gondii and its near relative, N. caninum. We significantly improved T. gondii genome contiguity (average N50 of ∼6.6 Mb) and added ∼2 Mb of newly assembled sequence. For all of the T. gondii strains that we sequenced (RH, ME49, CTG, II×III progeny clones CL13, S27, S21, S26, and D3X1), the largest contig ranged in size between 11.9 and 12.1 Mb in size, which is larger than any previously reported T. gondii chromosome, and found to be due to a consistent fusion of Chromosomes VIIb and VIII. These data were validated by mapping existing T. gondii ME49 Hi-C data to our assembly, providing parallel lines of evidence that the T. gondii karyotype consists of 13, rather than 14, chromosomes. By using this technology, we also resolved hundreds of tandem repeats of varying lengths, including in well-known host-targeting effector loci like rhoptry protein 5 (ROP5) and ROP38. Finally, when we compared T. gondii with N. caninum, we found that although the 13-chromosome karyotype was conserved, extensive, previously unappreciated chromosome-scale rearrangements had occurred in T. gondii and N. caninum since their most recent common ancestry.
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Affiliation(s)
- Jing Xia
- Department of Biological Sciences, Dietrich School of Arts and Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, USA
| | - Aarthi Venkat
- Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut 06520, USA.,La Jolla Institute for Immunology, La Jolla, California 92037, USA
| | - Rachel E Bainbridge
- Department of Biological Sciences, Dietrich School of Arts and Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, USA
| | | | - Karine G Le Roch
- Department of Molecular, Cell and Systems Biology, College of Agricultural and Life Sciences, University of California-Riverside, Riverside, California 92521, USA
| | - Ferhat Ay
- La Jolla Institute for Immunology, La Jolla, California 92037, USA.,School of Medicine, University of California-San Diego, La Jolla, California 92093, USA
| | - Jon P Boyle
- Department of Biological Sciences, Dietrich School of Arts and Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, USA
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