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Oberstaller J, Otto TD, Rayner JC, Adams JH. Essential Genes of the Parasitic Apicomplexa. Trends Parasitol 2021; 37:304-316. [PMID: 33419671 DOI: 10.1016/j.pt.2020.11.007] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Revised: 11/11/2020] [Accepted: 11/16/2020] [Indexed: 12/29/2022]
Abstract
Genome-scale mutagenesis screens for genes essential for apicomplexan parasite survival have been completed in three species: Plasmodium falciparum, the major human malaria parasite, Plasmodium berghei, a model rodent malaria parasite, and the more distantly related Toxoplasma gondii, the causative agent of toxoplasmosis. These three species share 2606 single-copy orthologs, 1500 of which have essentiality data in all three screens. In this review, we explore the overlap between these datasets to define the core essential genes of the phylum Apicomplexa. We further discuss the implications of these groundbreaking studies for understanding apicomplexan parasite biology, and we identify promising areas of focus for developing new pan-apicomplexan parasite interventions.
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Affiliation(s)
- Jenna Oberstaller
- Center for Global Health and Infectious Diseases and USF Genomics Program, College of Public Health, University of South Florida, 3720 Spectrum Boulevard, Suite 404, Tampa, FL 33612, USA
| | - Thomas D Otto
- Centre of Immunobiology, Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - Julian C Rayner
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge Biomedical Campus, The Keith Peters Building, Hills Road, Cambridge, Cambridgeshire, CB2 0XY, UK
| | - John H Adams
- Center for Global Health and Infectious Diseases and USF Genomics Program, College of Public Health, University of South Florida, 3720 Spectrum Boulevard, Suite 404, Tampa, FL 33612, USA.
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Rojas-Pirela M, Andrade-Alviárez D, Rojas V, Kemmerling U, Cáceres AJ, Michels PA, Concepción JL, Quiñones W. Phosphoglycerate kinase: structural aspects and functions, with special emphasis on the enzyme from Kinetoplastea. Open Biol 2020; 10:200302. [PMID: 33234025 PMCID: PMC7729029 DOI: 10.1098/rsob.200302] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Phosphoglycerate kinase (PGK) is a glycolytic enzyme that is well conserved among the three domains of life. PGK is usually a monomeric enzyme of about 45 kDa that catalyses one of the two ATP-producing reactions in the glycolytic pathway, through the conversion of 1,3-bisphosphoglycerate (1,3BPGA) to 3-phosphoglycerate (3PGA). It also participates in gluconeogenesis, catalysing the opposite reaction to produce 1,3BPGA and ADP. Like most other glycolytic enzymes, PGK has also been catalogued as a moonlighting protein, due to its involvement in different functions not associated with energy metabolism, which include pathogenesis, interaction with nucleic acids, tumorigenesis progression, cell death and viral replication. In this review, we have highlighted the overall aspects of this enzyme, such as its structure, reaction kinetics, activity regulation and possible moonlighting functions in different protistan organisms, especially both free-living and parasitic Kinetoplastea. Our analysis of the genomes of different kinetoplastids revealed the presence of open-reading frames (ORFs) for multiple PGK isoforms in several species. Some of these ORFs code for unusually large PGKs. The products appear to contain additional structural domains fused to the PGK domain. A striking aspect is that some of these PGK isoforms are predicted to be catalytically inactive enzymes or ‘dead’ enzymes. The roles of PGKs in kinetoplastid parasites are analysed, and the apparent significance of the PGK gene duplication that gave rise to the different isoforms and their expression in Trypanosoma cruzi is discussed.
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Affiliation(s)
- Maura Rojas-Pirela
- Instituto de Biología, Facultad de Ciencias, Pontificia Universidad Católica de Valparaiso, Valparaiso 2373223, Chile
| | - Diego Andrade-Alviárez
- Laboratorio de Enzimología de Parásitos, Departamento de Biología, Facultad de Ciencias, Universidad de Los Andes, Mérida 5101, Venezuela
| | - Verónica Rojas
- Instituto de Biología, Facultad de Ciencias, Pontificia Universidad Católica de Valparaiso, Valparaiso 2373223, Chile
| | - Ulrike Kemmerling
- Instituto de Ciencias Biomédicas, Universidad de Chile, Facultad de Medicina, Santiago de Chile 8380453, Santigo de Chile
| | - Ana J Cáceres
- Laboratorio de Enzimología de Parásitos, Departamento de Biología, Facultad de Ciencias, Universidad de Los Andes, Mérida 5101, Venezuela
| | - Paul A Michels
- Centre for Immunity, Infection and Evolution, The King's Buildings, Edinburgh EH9 3FL, UK.,Centre for Translational and Chemical Biology, School of Biological Sciences, The University of Edinburgh, The King's Buildings, Edinburgh EH9 3FL, UK
| | - Juan Luis Concepción
- Laboratorio de Enzimología de Parásitos, Departamento de Biología, Facultad de Ciencias, Universidad de Los Andes, Mérida 5101, Venezuela
| | - Wilfredo Quiñones
- Laboratorio de Enzimología de Parásitos, Departamento de Biología, Facultad de Ciencias, Universidad de Los Andes, Mérida 5101, Venezuela
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Ospina-Villa JD, Tovar-Ayona BJ, López-Camarillo C, Soto-Sánchez J, Ramírez-Moreno E, Castañón-Sánchez CA, Marchat LA. mRNA Polyadenylation Machineries in Intestinal Protozoan Parasites. J Eukaryot Microbiol 2020; 67:306-320. [PMID: 31898347 DOI: 10.1111/jeu.12781] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Revised: 12/16/2019] [Accepted: 12/22/2019] [Indexed: 12/22/2022]
Abstract
In humans, mRNA polyadenylation involves the participation of about 20 factors in four main complexes that recognize specific RNA sequences. Notably, CFIm25, CPSF73, and PAP have essential roles for poly(A) site selection, mRNA cleavage, and adenosine residues polymerization. Besides the relevance of polyadenylation for gene expression, information is scarce in intestinal protozoan parasites that threaten human health. To better understand polyadenylation in Entamoeba histolytica, Giardia lamblia, and Cryptosporidium parvum, which represent leading causes of diarrhea worldwide, genomes were screened for orthologs of human factors. Results showed that Entamoeba histolytica and C. parvum have 16 and 12 proteins out of the 19 human proteins used as queries, respectively, while G. lamblia seems to have the smallest polyadenylation machinery with only six factors. Remarkably, CPSF30, CPSF73, CstF77, PABP2, and PAP, which were found in all parasites, could represent the core polyadenylation machinery. Multiple genes were detected for several proteins in Entamoeba, while gene redundancy is lower in Giardia and Cryptosporidium. Congruently with their relevance in the polyadenylation process, CPSF73 and PAP are present in all parasites, and CFIm25 is only missing in Giardia. They conserve the functional domains and predicted folding of human proteins, suggesting they may have the same roles in polyadenylation.
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Affiliation(s)
- Juan David Ospina-Villa
- Independent Researcher, Transversal 27A Sur # 42-14, C.P. 055421, Envigado, Antioquia, Colombia
| | - Brisna Joana Tovar-Ayona
- Posgrados en Biomedicina Molecular y en Biotecnología, ENMH, Instituto Politécnico Nacional, Av. Guillermo Massieu Helguera 239, Col. La Escalera, Gustavo A. Madero, C.P. 07320, Ciudad de México, Mexico
| | - César López-Camarillo
- Posgrado en Ciencias Genómicas, Universidad Autónoma de la Ciudad de México, San Lorenzo 290, Col. del Valle Sur, Benito Juárez, C.P. 03100, Ciudad de México, Mexico
| | - Jacqueline Soto-Sánchez
- Posgrados en Biomedicina Molecular y en Biotecnología, ENMH, Instituto Politécnico Nacional, Av. Guillermo Massieu Helguera 239, Col. La Escalera, Gustavo A. Madero, C.P. 07320, Ciudad de México, Mexico
| | - Esther Ramírez-Moreno
- Posgrados en Biomedicina Molecular y en Biotecnología, ENMH, Instituto Politécnico Nacional, Av. Guillermo Massieu Helguera 239, Col. La Escalera, Gustavo A. Madero, C.P. 07320, Ciudad de México, Mexico
| | - Carlos A Castañón-Sánchez
- Hospital Regional de Alta Especialidad de Oaxaca, Aldama s/n, Col. Centro, C.P. 71256 San Bartolo Coyotepec, Oaxaca, Mexico
| | - Laurence A Marchat
- Posgrados en Biomedicina Molecular y en Biotecnología, ENMH, Instituto Politécnico Nacional, Av. Guillermo Massieu Helguera 239, Col. La Escalera, Gustavo A. Madero, C.P. 07320, Ciudad de México, Mexico
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Hanada K, Tezuka A, Nozawa M, Suzuki Y, Sugano S, Nagano AJ, Ito M, Morinaga SI. Functional divergence of duplicate genes several million years after gene duplication in Arabidopsis. DNA Res 2018; 25:4898128. [PMID: 29481587 PMCID: PMC6014284 DOI: 10.1093/dnares/dsy005] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2017] [Accepted: 02/02/2018] [Indexed: 12/02/2022] Open
Abstract
Lineage-specific duplicated genes likely contribute to the phenotypic divergence in closely related species. However, neither the frequency of duplication events nor the degree of selection pressures immediately after gene duplication is clear in the speciation process. Here, using Illumina DNA-sequencing reads from Arabidopsis halleri, which has multiple closely related species with high-quality genome assemblies (A. thaliana and A. lyrata), we succeeded in generating orthologous gene groups in Brassicaceae. The duplication frequency of retained genes in the Arabidopsis lineage was ∼10 times higher than the duplication frequency inferred by comparative genomics of Arabidopsis, poplar, rice and moss (Physcomitrella patens). The difference of duplication frequencies can be explained by a rapid decay of anciently duplicated genes. To examine the degree of selection pressure on genes duplicated in either the A. halleri-lyrata or the A. halleri lineage, we examined positive and purifying selection in the A. halleri-lyrata and A. halleri lineages throughout the ratios of nonsynonymous to synonymous substitution rates (KA/KS). Duplicate genes tended to have a higher proportion of positive selection compared with non-duplicated genes. Interestingly, we found that functional divergence of duplicated genes was accelerated several million years after gene duplication compared with immediately after gene duplication.
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Affiliation(s)
- Kousuke Hanada
- Department of Bioscience and Bioinformatics, Frontier Research Academy for Young Researchers, Kyusyu Institute of Technology, Iizuka, Fukuoka 820-8502, Japan
- RIKEN Center for Sustainable Resource Science, RIKEN, Yokohama, Kanagawa 230-0045, Japan
- CREST, Japan Science and Technology Agency, Kawaguchi, Saitama 332-0012, Japan
| | - Ayumi Tezuka
- Department of Bioscience and Bioinformatics, Frontier Research Academy for Young Researchers, Kyusyu Institute of Technology, Iizuka, Fukuoka 820-8502, Japan
| | - Masafumi Nozawa
- Center for Information Biology, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
- Department of Genetics, SOKENDAI, Mishima, Shizuoka 411-8540, Japan
- Department of Biological Sciences, Tokyo Metropolitan University, Hachioji, Tokyo 192-0397, Japan
| | - Yutaka Suzuki
- Graduate School of Frontier Science, The University of Tokyo, Kashiwa, Chiba 277-8562, Japan
| | - Sumio Sugano
- Graduate School of Frontier Science, The University of Tokyo, Kashiwa, Chiba 277-8562, Japan
| | - Atsushi J Nagano
- CREST, Japan Science and Technology Agency, Kawaguchi, Saitama 332-0012, Japan
- Center of Ecological Research, Kyoto University, Hirano, Otsu, Shiga 520-2113, Japan
| | - Motomi Ito
- Graduate School of Arts and Sciences, The University of Tokyo, Tokyo 153-8902, Japan
| | - Shin-Ichi Morinaga
- CREST, Japan Science and Technology Agency, Kawaguchi, Saitama 332-0012, Japan
- Graduate School of Arts and Sciences, The University of Tokyo, Tokyo 153-8902, Japan
- College of Bioresource Sciences, Nihon University, Fujisawa, Kanagawa 252-0880, Japan
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Shabardina V, Kischka T, Kmita H, Suzuki Y, Makałowski W. Environmental adaptation of Acanthamoeba castellanii and Entamoeba histolytica at genome level as seen by comparative genomic analysis. Int J Biol Sci 2018; 14:306-320. [PMID: 29559848 PMCID: PMC5859476 DOI: 10.7150/ijbs.23869] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Accepted: 12/30/2017] [Indexed: 11/17/2022] Open
Abstract
Amoebozoans are in many aspects interesting research objects, as they combine features of single-cell organisms with complex signaling and defense systems, comparable to multicellular organisms. Acanthamoeba castellanii is a cosmopolitan species and developed diverged feeding abilities and strong anti-bacterial resistance; Entamoeba histolytica is a parasitic amoeba, who underwent massive gene loss and its genome is almost twice smaller than that of A. castellanii. Nevertheless, both species prosper, demonstrating fitness to their specific environments. Here we compare transcriptomes of A. castellanii and E. histolytica with application of orthologs' search and gene ontology to learn how different life strategies influence genome evolution and restructuring of physiology. A. castellanii demonstrates great metabolic activity and plasticity, while E. histolytica reveals several interesting features in its translational machinery, cytoskeleton, antioxidant protection, and nutritional behavior. In addition, we suggest new features in E. histolytica physiology that may explain its successful colonization of human colon and may facilitate medical research.
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Affiliation(s)
- Victoria Shabardina
- Institute of Bioinformatics, University Münster, Niels-Stensen Strasse 14, Münster 48149, Germany
| | - Tabea Kischka
- Institute of Bioinformatics, University Münster, Niels-Stensen Strasse 14, Münster 48149, Germany
| | - Hanna Kmita
- Laboratory of Bioenergetics, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University
| | - Yutaka Suzuki
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8562, Japan
| | - Wojciech Makałowski
- Institute of Bioinformatics, University Münster, Niels-Stensen Strasse 14, Münster 48149, Germany
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Bondarenko NI, Bondarenko AS, Smirnov AV. Lineage-Specific and Highly Derived Gene Sequences Among Amoebozoa, Revealed by the Comparative Analysis of Transcriptomes from Twelve Amoebozoan Species. J Eukaryot Microbiol 2017; 64:622-631. [PMID: 28166371 DOI: 10.1111/jeu.12397] [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: 12/03/2016] [Revised: 01/11/2017] [Accepted: 01/19/2017] [Indexed: 11/28/2022]
Abstract
Amoebozoa represent a difficult group for traditional morphology-based taxonomy. Molecular approaches, such as gene sequencing and DNA barcoding have greatly enhanced our knowledge of the diversity of these organisms. However, metagenomic studies of Amoebozoa still did not provide as impressive results as they did among some other groups of protists. In environmental DNA surveys done on fragments of SSU rDNA gene and other traditional DNA barcodes, Amoebozoa genes normally constitute a minor part of the total gene diversity and represent only the most abundant lineages. A potential way to resolve this problem is the usage of DNA barcodes based on genes, which are unique or highly derived in this group of organisms. In the present study, we attempted to find such genes and gene families with a low level of paralogy, potentially appropriate as Amoebozoa-specific DNA barcodes. For this we re-assembled transcriptomes of 12 amoebozoan species available from the public databases and performed gene annotation and identification of orthologous genes. In our analysis Amoebozoa-specific and highly derived sequences formed 53,182 clusters of orthologs, containing from 2 to 299 proteins each. Some of these genes may be a potential target for DNA barcoding of Amoebozoa.
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Affiliation(s)
- Natalya I Bondarenko
- Department of Invertebrate Zoology, Faculty of Biology, Saint-Petersburg State University, Universitetskaja nab. 7/9, St. Petersburg, 199034, Russia
| | - Anton S Bondarenko
- Faculty of Physics, St. Petersburg State University, St. Petersburg, 199034, Russia
| | - Alexey V Smirnov
- Department of Invertebrate Zoology, Faculty of Biology, Saint-Petersburg State University, Universitetskaja nab. 7/9, St. Petersburg, 199034, Russia
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Guo Y, Tang K, Rowe LA, Li N, Roellig DM, Knipe K, Frace M, Yang C, Feng Y, Xiao L. Comparative genomic analysis reveals occurrence of genetic recombination in virulent Cryptosporidium hominis subtypes and telomeric gene duplications in Cryptosporidium parvum. BMC Genomics 2015; 16:320. [PMID: 25903370 PMCID: PMC4407392 DOI: 10.1186/s12864-015-1517-1] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2014] [Accepted: 04/10/2015] [Indexed: 11/17/2022] Open
Abstract
Background Cryptosporidium hominis is a dominant species for human cryptosporidiosis. Within the species, IbA10G2 is the most virulent subtype responsible for all C. hominis–associated outbreaks in Europe and Australia, and is a dominant outbreak subtype in the United States. In recent yearsIaA28R4 is becoming a major new subtype in the United States. In this study, we sequenced the genomes of two field specimens from each of the two subtypes and conducted a comparative genomic analysis of the obtained sequences with those from the only fully sequenced Cryptosporidium parvum genome. Results Altogether, 8.59-9.05 Mb of Cryptosporidium sequences in 45–767 assembled contigs were obtained from the four specimens, representing 94.36-99.47% coverage of the expected genome. These genomes had complete synteny in gene organization and 96.86-97.0% and 99.72-99.83% nucleotide sequence similarities to the published genomes of C. parvum and C. hominis, respectively. Several major insertions and deletions were seen between C. hominis and C. parvum genomes, involving mostly members of multicopy gene families near telomeres. The four C. hominis genomes were highly similar to each other and divergent from the reference IaA25R3 genome in some highly polymorphic regions. Major sequence differences among the four specimens sequenced in this study were in the 5′ and 3′ ends of chromosome 6 and the gp60 region, largely the result of genetic recombination. Conclusions The sequence similarity among specimens of the two dominant outbreak subtypes and genetic recombination in chromosome 6, especially around the putative virulence determinant gp60 region, suggest that genetic recombination plays a potential role in the emergence of hyper-transmissible C. hominis subtypes. The high sequence conservation between C. parvum and C. hominis genomes and significant differences in copy numbers of MEDLE family secreted proteins and insulinase-like proteases indicate that telomeric gene duplications could potentially contribute to host expansion in C. parvum. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1517-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yaqiong Guo
- State Key Laboratory of Bioreactor Engineering, School of Resources and Environmental Engineering, East China University of Science and Technology, Shanghai, 200237, China. .,Division of Foodborne, Waterborne, and Environmental Diseases, Centers for Disease Control and Prevention, Atlanta, GA, 30333, USA.
| | - Kevin Tang
- Division of Scientific Resources, Centers for Disease Control and Prevention, Atlanta, GA, 30333, USA.
| | - Lori A Rowe
- Division of Scientific Resources, Centers for Disease Control and Prevention, Atlanta, GA, 30333, USA.
| | - Na Li
- State Key Laboratory of Bioreactor Engineering, School of Resources and Environmental Engineering, East China University of Science and Technology, Shanghai, 200237, China.
| | - Dawn M Roellig
- Division of Foodborne, Waterborne, and Environmental Diseases, Centers for Disease Control and Prevention, Atlanta, GA, 30333, USA.
| | - Kristine Knipe
- Division of Scientific Resources, Centers for Disease Control and Prevention, Atlanta, GA, 30333, USA.
| | - Michael Frace
- Division of Scientific Resources, Centers for Disease Control and Prevention, Atlanta, GA, 30333, USA.
| | - Chunfu Yang
- Division of Global HIV/AIDS, Centers for Disease Control and Prevention, Atlanta, GA, 30333, USA.
| | - Yaoyu Feng
- State Key Laboratory of Bioreactor Engineering, School of Resources and Environmental Engineering, East China University of Science and Technology, Shanghai, 200237, China.
| | - Lihua Xiao
- Division of Foodborne, Waterborne, and Environmental Diseases, Centers for Disease Control and Prevention, Atlanta, GA, 30333, USA.
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