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Li J, Fan Y, Li N, Guo Y, Wang W, Feng K, He W, Li F, Huang J, Xu Y, Xiao L, Feng Y. Comparative genomics analysis reveals sequence characteristics potentially related to host preference in Cryptosporidium xiaoi. Int J Parasitol 2024; 54:379-390. [PMID: 38492779 DOI: 10.1016/j.ijpara.2024.03.004] [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: 10/25/2023] [Revised: 02/26/2024] [Accepted: 03/12/2024] [Indexed: 03/18/2024]
Abstract
Cryptosporidium spp. are important diarrhea-associated pathogens in humans and livestock. Among the known species, Cryptosporidium xiaoi, which causes cryptosporidiosis in sheep and goats, was previously recognized as a genotype of the bovine-specific Cryptosporidium bovis based on their high sequence identity in the ssrRNA gene. However, the lack of genomic data has limited characterization of the genetic differences between the two closely related species. In this study, we sequenced the genomes of two C. xiaoi isolates and performed comparative genomic analysis to identify the sequence uniqueness of this ovine-adapted species compared with other Cryptosporidium spp. Our results showed that C. xiaoi is genetically related to C. bovis as shown by their 95.8% genomic identity and similar gene content. Consistent with this, both C. xiaoi and C. bovis appear to have fewer genes encoding mitochondrial metabolic enzymes and invasion-related protein families. However, they appear to possess several species-specific genes. Further analysis indicates that the sequence differences between these two Cryptosporidium spp. are mainly in 24 highly polymorphic genes, half of which are located in the subtelomeric regions. Some of these subtelomeric genes encode secretory proteins that have undergone positive selection. In addition, the genomes of two C. xiaoi isolates, identified as subtypes XXIIIf and XXIIIh, share 99.9% nucleotide sequence identity, with six highly divergent genes encoding putative secretory proteins. Therefore, these species-specific genes and sequence polymorphism in subtelomeric genes probably contribute to the different host preference of C. xiaoi and C. bovis.
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Affiliation(s)
- Jiayu Li
- State Key Laboratory for Animal Disease Control and Prevention, South China Agricultural University, Guangzhou 510642, China
| | - Yingying Fan
- State Key Laboratory for Animal Disease Control and Prevention, South China Agricultural University, Guangzhou 510642, China
| | - Na Li
- State Key Laboratory for Animal Disease Control and Prevention, South China Agricultural University, Guangzhou 510642, China
| | - Yaqiong Guo
- State Key Laboratory for Animal Disease Control and Prevention, South China Agricultural University, Guangzhou 510642, China
| | - Weijian Wang
- State Key Laboratory for Animal Disease Control and Prevention, South China Agricultural University, Guangzhou 510642, China
| | - Kangli Feng
- State Key Laboratory for Animal Disease Control and Prevention, South China Agricultural University, Guangzhou 510642, China
| | - Wei He
- State Key Laboratory for Animal Disease Control and Prevention, South China Agricultural University, Guangzhou 510642, China
| | - Falei Li
- State Key Laboratory for Animal Disease Control and Prevention, South China Agricultural University, Guangzhou 510642, China
| | - Jianbo Huang
- State Key Laboratory for Animal Disease Control and Prevention, South China Agricultural University, Guangzhou 510642, China
| | - Yanhua Xu
- State Key Laboratory for Animal Disease Control and Prevention, South China Agricultural University, Guangzhou 510642, China
| | - Lihua Xiao
- State Key Laboratory for Animal Disease Control and Prevention, South China Agricultural University, Guangzhou 510642, China.
| | - Yaoyu Feng
- State Key Laboratory for Animal Disease Control and Prevention, South China Agricultural University, Guangzhou 510642, China.
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Guttery DS, Zeeshan M, Holder AA, Tewari R. The molecular mechanisms driving Plasmodium cell division. Biochem Soc Trans 2024; 52:593-602. [PMID: 38563493 PMCID: PMC11088906 DOI: 10.1042/bst20230403] [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: 10/02/2023] [Revised: 03/15/2024] [Accepted: 03/18/2024] [Indexed: 04/04/2024]
Abstract
Malaria, a vector borne disease, is a major global health and socioeconomic problem caused by the apicomplexan protozoan parasite Plasmodium. The parasite alternates between mosquito vector and vertebrate host, with meiosis in the mosquito and proliferative mitotic cell division in both hosts. In the canonical eukaryotic model, cell division is either by open or closed mitosis and karyokinesis is followed by cytokinesis; whereas in Plasmodium closed mitosis is not directly accompanied by concomitant cell division. Key molecular players and regulatory mechanisms of this process have been identified, but the pivotal role of certain protein complexes and the post-translational modifications that modulate their actions are still to be deciphered. Here, we discuss recent evidence for the function of known proteins in Plasmodium cell division and processes that are potential novel targets for therapeutic intervention. We also identify key questions to open new and exciting research to understand divergent Plasmodium cell division.
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Affiliation(s)
- David S. Guttery
- School of Life Sciences, Queen's Medical Centre, University of Nottingham, Nottingham, U.K
- Department of Genetics and Genome Biology, College of Life Sciences, University of Leicester, Leicester, U.K
| | - Mohammad Zeeshan
- School of Life Sciences, Queen's Medical Centre, University of Nottingham, Nottingham, U.K
| | - Anthony A. Holder
- Malaria Parasitology Laboratory, The Francis Crick Institute, London, U.K
| | - Rita Tewari
- School of Life Sciences, Queen's Medical Centre, University of Nottingham, Nottingham, U.K
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Li J, Li N, Roellig DM, Zhao W, Guo Y, Feng Y, Xiao L. High subtelomeric GC content in the genome of a zoonotic Cryptosporidium species. Microb Genom 2023; 9:mgen001052. [PMID: 37399068 PMCID: PMC10438818 DOI: 10.1099/mgen.0.001052] [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: 01/06/2023] [Accepted: 05/24/2023] [Indexed: 07/04/2023] Open
Abstract
Cryptosporidium canis is a zoonotic species causing cryptosporidiosis in humans in addition to its natural hosts dogs and other fur animals. To understand the genetic basis for host adaptation, we sequenced the genomes of C. canis from dogs, minks, and foxes and conducted a comparative genomics analysis. While the genomes of C. canis have similar gene contents and organisations, they (~41.0 %) and C. felis (39.6 %) have GC content much higher than other Cryptosporidium spp. (24.3-32.9 %) sequenced to date. The high GC content is mostly restricted to subtelomeric regions of the eight chromosomes. Most of these GC-balanced genes encode Cryptosporidium-specific proteins that have intrinsically disordered regions and are involved in host-parasite interactions. Natural selection appears to play a more important role in the evolution of codon usage in GC-balanced C. canis, and most of the GC-balanced genes have undergone positive selection. While the identity in whole genome sequences between the mink- and dog-derived isolates is 99.9 % (9365 SNVs), it is only 96.0 % (362 894 SNVs) between them and the fox-derived isolate. In agreement with this, the fox-derived isolate possesses more subtelomeric genes encoding invasion-related protein families. Therefore, the change in subtelomeric GC content appears to be responsible for the more GC-balanced C. canis genomes, and the fox-derived isolate could represent a new Cryptosporidium species.
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Affiliation(s)
- Jiayu Li
- State Key Laboratory for Animal Disease Control and Prevention, South China Agricultural University, Guangzhou 510642, PR China
| | - Na Li
- State Key Laboratory for Animal Disease Control and Prevention, South China Agricultural University, Guangzhou 510642, PR China
| | - Dawn M. Roellig
- Division of Foodborne, Waterborne, and Environmental Diseases, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA
| | - Wentao Zhao
- State Key Laboratory for Animal Disease Control and Prevention, South China Agricultural University, Guangzhou 510642, PR China
| | - Yaqiong Guo
- State Key Laboratory for Animal Disease Control and Prevention, South China Agricultural University, Guangzhou 510642, PR China
| | - Yaoyu Feng
- State Key Laboratory for Animal Disease Control and Prevention, South China Agricultural University, Guangzhou 510642, PR China
| | - Lihua Xiao
- State Key Laboratory for Animal Disease Control and Prevention, South China Agricultural University, Guangzhou 510642, PR China
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Zhao M, Yang Y, Shi Y, Chen X, Yang Y, Pan L, Du Z, Sun H, Yao C, Ma G, Du A. PP2Acα-B'/PR61 Holoenzyme of Toxoplasma gondii Is Required for the Amylopectin Metabolism and Proliferation of Tachyzoites. Microbiol Spectr 2023; 11:e0010423. [PMID: 37199633 PMCID: PMC10269777 DOI: 10.1128/spectrum.00104-23] [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: 01/08/2023] [Accepted: 04/26/2023] [Indexed: 05/19/2023] Open
Abstract
Here, we report that the inhibition of the PP2A subfamily by okadaic acid results in an accumulation of polysaccharides in the acute infection stage (tachyzoites) of Toxoplasma gondii, which is a protozoan of global zoonotic importance and a model for the apicomplexan parasites. The loss of the catalytic subunit α of PP2A (ΔPP2Acα) in RHΔku80 leads to the polysaccharide accumulation phenotype in the base of tachyzoites as well as residual bodies and significantly compromises the intracellular growth in vitro and the virulence in vivo. A metabolomic analysis revealed that the accumulated polysaccharides in ΔPP2Acα are derived from interrupted glucose metabolism, which affects the production of ATP and energy homeostasis in the T. gondii knockout. The assembly of the PP2Acα holoenzyme complex involved in the amylopectin metabolism in tachyzoites is possibly not regulated by LCMT1 or PME1, and this finding contributes to the identification of the regulatory B subunit (B'/PR61). The loss of B'/PR61 results in the accumulation of polysaccharide granules in the tachyzoites as well as reduced plaque formation ability, exactly the same as ΔPP2Acα. Taken together, we have identified a PP2Acα-B'/PR61 holoenzyme complex that plays a crucial role in the carbohydrate metabolism and viability in T. gondii, and its deficiency in function remarkably suppresses the growth and virulence of this important zoonotic parasite both in vitro and in vivo. Hence, rendering the PP2Acα-B'/PR61 holoenzyme functionless should be a promising strategy for the intervention of Toxoplasma acute infection and toxoplasmosis. IMPORTANCE Toxoplasma gondii switches back and forth between acute and chronic infections, mainly in response to host immunologic status, which is characterized by flexible but specific energy metabolism. Polysaccharide granules are accumulated in the acute infection stage of T. gondii that have been exposed to a chemical inhibitor of the PP2A subfamily. The genetic depletion of the catalytic subunit α of PP2A leads to this phenotype and significantly affects the cell metabolism, energy production, and viability. Further, a regulatory B subunit PR61 is necessary for the PP2A holoenzyme to function in glucose metabolism and in the intracellular growth of T. gondii tachyzoites. A deficiency of this PP2A holoenzyme complex (PP2Acα-B'/PR61) in T. gondii knockouts results in the abnormal accumulation of polysaccharides and the disruption of energy metabolism, suppressing their growth and virulence. These findings provide novel insights into cell metabolism and identify a potential target for an intervention against a T. gondii acute infection.
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Affiliation(s)
- Mingxiu Zhao
- Institute of Preventive Veterinary Medicine, Zhejiang Provincial Key Laboratory of Preventive Veterinary Medicine, College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang Province, China
| | - Yi Yang
- Institute of Preventive Veterinary Medicine, Zhejiang Provincial Key Laboratory of Preventive Veterinary Medicine, College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang Province, China
| | - Yue Shi
- Institute of Preventive Veterinary Medicine, Zhejiang Provincial Key Laboratory of Preventive Veterinary Medicine, College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang Province, China
- Hainan Institute, Zhejiang University, Yazhou Bay Sci-Tech City, Sanya, China
| | - Xueqiu Chen
- Institute of Preventive Veterinary Medicine, Zhejiang Provincial Key Laboratory of Preventive Veterinary Medicine, College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang Province, China
| | - Yimin Yang
- Institute of Preventive Veterinary Medicine, Zhejiang Provincial Key Laboratory of Preventive Veterinary Medicine, College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang Province, China
| | - Lingtao Pan
- Institute of Preventive Veterinary Medicine, Zhejiang Provincial Key Laboratory of Preventive Veterinary Medicine, College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang Province, China
| | - Zhendong Du
- Institute of Preventive Veterinary Medicine, Zhejiang Provincial Key Laboratory of Preventive Veterinary Medicine, College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang Province, China
| | - Hongchao Sun
- Department of Animal Parasitology, Institute of Animal Husbandry and Veterinary Medicine, Zhejiang Academy of Agricultural Science, Hangzhou, Zhejiang Province, China
| | - Chaoqun Yao
- Department of Biomedical Sciences and One Health Center for Zoonoses and Tropical Veterinary Medicine, Ross University School of Veterinary Medicine, Basseterre, St. Kitts and Nevis
| | - Guangxu Ma
- Institute of Preventive Veterinary Medicine, Zhejiang Provincial Key Laboratory of Preventive Veterinary Medicine, College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang Province, China
- Department of Veterinary Biosciences, Melbourne Veterinary School, The University of Melbourne, Parkville, Victoria, Australia
| | - Aifang Du
- Institute of Preventive Veterinary Medicine, Zhejiang Provincial Key Laboratory of Preventive Veterinary Medicine, College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang Province, China
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Walsh D, Katris NJ, Sheiner L, Botté CY. Toxoplasma metabolic flexibility in different growth conditions. Trends Parasitol 2022; 38:775-790. [PMID: 35718642 PMCID: PMC10506913 DOI: 10.1016/j.pt.2022.06.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 05/31/2022] [Accepted: 06/01/2022] [Indexed: 10/18/2022]
Abstract
Apicomplexan parasites have complex metabolic networks that coordinate acquisition of metabolites by de novo synthesis and by scavenging from the host. Toxoplasma gondii has a wide host range and may rely on the flexibility of this metabolic network. Currently, the literature categorizes genes as essential or dispensable according to their dispensability for parasite survival under nutrient-replete in vitro conditions. However, recent studies revealed correlations between medium composition and gene essentiality. Therefore, nutrient availability in the host environment likely determines the requirement of metabolic pathways, which may redefine priorities for drug target identification in a clinical setting. Here we review the recent work characterizing some of the major Toxoplasma metabolic pathways and their functional adaptation to host nutrient content.
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Affiliation(s)
- Daniel Walsh
- Wellcome Centre for Integrative Parasitology, University of Glasgow, Glasgow, UK
| | - Nicholas J Katris
- ApicoLipid Team, Institute for Advanced Biosciences, CNRS UMR5309, Université Grenoble Alpes, INSERM U1209, Grenoble, France
| | - Lilach Sheiner
- Wellcome Centre for Integrative Parasitology, University of Glasgow, Glasgow, UK.
| | - Cyrille Y Botté
- ApicoLipid Team, Institute for Advanced Biosciences, CNRS UMR5309, Université Grenoble Alpes, INSERM U1209, Grenoble, France.
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Lunghi M, Kloehn J, Krishnan A, Varesio E, Vadas O, Soldati-Favre D. Pantothenate biosynthesis is critical for chronic infection by the neurotropic parasite Toxoplasma gondii. Nat Commun 2022; 13:345. [PMID: 35039477 PMCID: PMC8764084 DOI: 10.1038/s41467-022-27996-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2021] [Accepted: 01/03/2022] [Indexed: 11/16/2022] Open
Abstract
Coenzyme A (CoA) is an essential molecule acting in metabolism, post-translational modification, and regulation of gene expression. While all organisms synthesize CoA, many, including humans, are unable to produce its precursor, pantothenate. Intriguingly, like most plants, fungi and bacteria, parasites of the coccidian subgroup of Apicomplexa, including the human pathogen Toxoplasma gondii, possess all the enzymes required for de novo synthesis of pantothenate. Here, the importance of CoA and pantothenate biosynthesis for the acute and chronic stages of T. gondii infection is dissected through genetic, biochemical and metabolomic approaches, revealing that CoA synthesis is essential for T. gondii tachyzoites, due to the parasite's inability to salvage CoA or intermediates of the pathway. In contrast, pantothenate synthesis is only partially active in T. gondii tachyzoites, making the parasite reliant on its uptake. However, pantothenate synthesis is crucial for the establishment of chronic infection, offering a promising target for intervention against the persistent stage of T. gondii.
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Affiliation(s)
- Matteo Lunghi
- Department of Microbiology and Molecular Medicine, University of Geneva, CMU, Rue Michel-Servet 1, 1211, Geneva, Switzerland
| | - Joachim Kloehn
- Department of Microbiology and Molecular Medicine, University of Geneva, CMU, Rue Michel-Servet 1, 1211, Geneva, Switzerland
| | - Aarti Krishnan
- Department of Microbiology and Molecular Medicine, University of Geneva, CMU, Rue Michel-Servet 1, 1211, Geneva, Switzerland
| | - Emmanuel Varesio
- Institute of Pharmaceutical Sciences of Western Switzerland (ISPSO), University of Geneva, CMU, Rue Michel-Servet 1, 1211, Geneva, Switzerland
- Mass Spectrometry Core Facility (MZ 2.0), University of Geneva, 1211, Geneva, Switzerland
| | - Oscar Vadas
- Department of Microbiology and Molecular Medicine, University of Geneva, CMU, Rue Michel-Servet 1, 1211, Geneva, Switzerland
- Protein and peptide purification platform, University of Geneva, CMU, Rue Michel-Servet 1, 1211, Geneva, Switzerland
| | - Dominique Soldati-Favre
- Department of Microbiology and Molecular Medicine, University of Geneva, CMU, Rue Michel-Servet 1, 1211, Geneva, Switzerland.
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The Oesophageal Squamous Cell Carcinoma Cell Line COLO-680N Fails to Support Sustained Cryptosporidium parvum Proliferation. Pathogens 2021; 11:pathogens11010049. [PMID: 35055997 PMCID: PMC8778297 DOI: 10.3390/pathogens11010049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 12/28/2021] [Accepted: 12/30/2021] [Indexed: 11/16/2022] Open
Abstract
Cryptosporidium parvum is an important diarrhoea-associated protozoan, which is difficult to propagate in vitro. In 2017, a report described a continuous culture of C. parvum Moredun strain, in the oesophageal squamous cell carcinoma cell line COLO-680N, as an easy-to-use system for C. parvum propagation and continuous production of oocysts. Here, we report that—using the Köllitsch strain of C. parvum—even though COLO-680N cells, indeed, allowed parasite invasion and early asexual parasite replication, C. parvum proliferation decreased after the second day post infection. Considering recurring studies, reporting on successful production of newly generated Cryptosporidium oocysts in the past, and the subsequent replication failure by other research groups, the current data stand as a reminder of the importance of reproducibility of in vitro systems in cryptosporidiosis research. This is of special importance since it will only be possible to develop promising strategies to fight cryptosporidiosis and its ominous consequences for both human and animal health by a continuous and reliable methodological progress.
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Li J, Guo Y, Roellig DM, Li N, Feng Y, Xiao L. Cryptosporidium felis differs from other Cryptosporidium spp. in codon usage. Microb Genom 2021; 7. [PMID: 34907893 PMCID: PMC8767354 DOI: 10.1099/mgen.0.000711] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
Abstract
Cryptosporidium spp. are important enteric pathogens in a wide range of vertebrates including humans. Previous comparative analysis revealed conservation in genome composition, gene content, and gene organization among Cryptosporidium spp., with a progressive reductive evolution in metabolic pathways and invasion-related proteins. In this study, we sequenced the genome of zoonotic pathogen Cryptosporidium felis and conducted a comparative genomic analysis. While most intestinal Cryptosporidium species have similar genomic characteristics and almost complete genome synteny, fewer protein-coding genes and some sequence inversions and translocations were found in the C. felis genome. The C. felis genome exhibits much higher GC content (39.6 %) than other Cryptosporidium species (24.3–32.9 %), especially at the third codon position (GC3) of protein-coding genes. Thus, C. felis has a different codon usage, which increases the use of less energy costly amino acids (Gly and Ala) encoded by GC-rich codons. While the tRNA usage is conserved among Cryptosporidium species, consistent with its higher GC content, C. felis uses a unique tRNA for GTG for valine instead of GTA in other Cryptosporidium species. Both mutational pressures and natural selection are associated with the evolution of the codon usage in Cryptosporidium spp., while natural selection seems to drive the codon usage in C. felis. Other unique features of the C. felis genome include the loss of the entire traditional and alternative electron transport systems and several invasion-related proteins. Thus, the preference for the use of some less energy costly amino acids in C. felis may lead to a more harmonious parasite–host interaction, and the strengthened host-adaptation is reflected by the further reductive evolution of metabolism and host invasion-related proteins.
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Affiliation(s)
- Jiayu Li
- Center for Emerging and Zoonotic Diseases, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, PR China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, PR China
| | - Yaqiong Guo
- Center for Emerging and Zoonotic Diseases, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, PR China
| | - Dawn M. Roellig
- Division of Foodborne, Waterborne and Environmental Diseases, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA
| | - Na Li
- Center for Emerging and Zoonotic Diseases, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, PR China
| | - Yaoyu Feng
- Center for Emerging and Zoonotic Diseases, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, PR China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, PR China
- *Correspondence: Yaoyu Feng,
| | - Lihua Xiao
- Center for Emerging and Zoonotic Diseases, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, PR China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, PR China
- *Correspondence: Lihua Xiao,
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Hajialiani F, Shahbazzadeh D, Maleki F, Elmi T, Tabatabaie F, Zamani Z. The Metabolomic Profiles of Sera of Mice Infected with Plasmodium berghei and Treated by Effective Fraction of Naja naja oxiana Using 1H Nuclear Magnetic Resonance Spectroscopy. Acta Parasitol 2021; 66:1517-1527. [PMID: 34357584 DOI: 10.1007/s11686-021-00456-7] [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: 10/05/2020] [Accepted: 07/08/2021] [Indexed: 10/20/2022]
Abstract
BACKGROUND The use of venom fractions from the Iranian cobra could be useful adjunct treatments of malaria with chloroquine. A metabolomic investigation with 1HNMR spectroscopy was conducted on an effective fraction tested earlier using Plasmodium berghei as an experimental murine model. PURPOSE We sought to ascertain both safety and anti-parasitic effects of experimental therapies. METHODS After purification of the venom fractions, 25 mice were infected, then treated for 4 days with 0.2 ml of 5 mg/kg, 2.5 mg/kg and 1 mg/kg of the effective fraction, chloroquine, and a drug vehicle. An ED50 was obtained using Giemsa staining and real-time PCR analysis. The toxicity tests inspecting both liver and kidney tissues were performed. RESULTS A clear inhibitory effect on parasitaemia was observed (with 75% inhibition with 5 mg/kg and 50% reduction when 2.5 mg/kg dosage used). ED50 obtained 2.5 mg/kg. The metabolomics were identified as differentiation of aminoacyl-t-RNA biosynthesis, valine, leucine, isoleucine biosynthesis and degradation pathways were observed. CONCLUSION Upon therapeutic effects of cobra venom fraction, further optimization of dose-dependent response of pharmacokinetics would be worthwhile for further exploration in adjunct experimental venom therapies.
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Pamukcu S, Cerutti A, Bordat Y, Hem S, Rofidal V, Besteiro S. Differential contribution of two organelles of endosymbiotic origin to iron-sulfur cluster synthesis and overall fitness in Toxoplasma. PLoS Pathog 2021; 17:e1010096. [PMID: 34793583 PMCID: PMC8639094 DOI: 10.1371/journal.ppat.1010096] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Revised: 12/02/2021] [Accepted: 11/05/2021] [Indexed: 11/21/2022] Open
Abstract
Iron-sulfur (Fe-S) clusters are one of the most ancient and ubiquitous prosthetic groups, and they are required by a variety of proteins involved in important metabolic processes. Apicomplexan parasites have inherited different plastidic and mitochondrial Fe-S clusters biosynthesis pathways through endosymbiosis. We have investigated the relative contributions of these pathways to the fitness of Toxoplasma gondii, an apicomplexan parasite causing disease in humans, by generating specific mutants. Phenotypic analysis and quantitative proteomics allowed us to highlight notable differences in these mutants. Both Fe-S cluster synthesis pathways are necessary for optimal parasite growth in vitro, but their disruption leads to markedly different fates: impairment of the plastidic pathway leads to a loss of the organelle and to parasite death, while disruption of the mitochondrial pathway trigger differentiation into a stress resistance stage. This highlights that otherwise similar biochemical pathways hosted by different sub-cellular compartments can have very different contributions to the biology of the parasites, which is something to consider when exploring novel strategies for therapeutic intervention.
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Affiliation(s)
| | - Aude Cerutti
- LPHI, Univ Montpellier, CNRS, Montpellier, France
| | - Yann Bordat
- LPHI, Univ Montpellier, CNRS, Montpellier, France
| | - Sonia Hem
- BPMP, Univ Montpellier, CNRS, INRAE, Institut Agro, Montpellier, France
| | - Valérie Rofidal
- BPMP, Univ Montpellier, CNRS, INRAE, Institut Agro, Montpellier, France
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First Metabolic Insights into Ex Vivo Cryptosporidium parvum-Infected Bovine Small Intestinal Explants Studied under Physioxic Conditions. BIOLOGY 2021; 10:biology10100963. [PMID: 34681062 PMCID: PMC8533177 DOI: 10.3390/biology10100963] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/22/2021] [Revised: 09/14/2021] [Accepted: 09/22/2021] [Indexed: 12/12/2022]
Abstract
Simple Summary As the most relevant zoonotic cause of cryptosporidiosis, C. parvum infects cattle worldwide. In vitro studies on C. parvum are absent on the most important animal host under physiological oxygen conditions of the intestine. The aim of this study was to rectify this lack of knowledge, and to deliver a practical model to study C. parvum–host cell–intestinal microbiome interactions in the metabolic context. The present metabolic analyses of C. parvum-infected bovine small intestinal (BSI)-explants revealed a parasite-dependent reduction in important metabolic activities (e.g., glycolysis, glutaminolysis) at 3 hpi (hours post-infection) followed by striking increases in the same metabolic functions at 6 hpi, thus paralleling previously reported metabolic impacts of C. parvum on humans. In addition, PCA analysis confirmed physiological oxygen concentrations as a driving factor of metabolic responses in infected BSI explants. The present model allows the study of C. parvum-triggered metabolic modulation of intestinal cells. Moreover, this realistic platform offers the possibility to address pending questions regarding C. parvum–host cell–intestinal microbiome interactions. Thus, the present approach may deliver important insights into how to promote the innate immune system–intestinal microbiome alliances, which maintain the epithelial integrity of the gut thereby supporting human and animal health. Abstract The apicomplexan Cryptosporidium parvum causes thousands of human deaths yearly. Since bovines represent the most important reservoir of C. parvum, the analysis of infected bovine small intestinal (BSI) explants cultured under physioxia offers a realistic model to study C. parvum–host cell–microbiome interactions. Here, C. parvum-infected BSI explants and primary bovine small intestinal epithelial cells were analysed for parasite development and metabolic reactions. Metabolic conversion rates in supernatants of BSI explants were measured after infection, documenting an immediate parasite-driven metabolic interference. Given that oxygen concentrations affect cellular metabolism, measurements were performed at both 5% O2 (physiological intestinal conditions) and 21% O2 (commonly used, hyperoxic lab conditions). Overall, analyses of C. parvum-infected BSI explants revealed a downregulation of conversion rates of key metabolites—such as glucose, lactate, pyruvate, alanine, and aspartate—at 3 hpi, followed by a rapid increase in the same conversion rates at 6 hpi. Moreover, PCA revealed physioxia as a driving factor of metabolic responses in C. parvum-infected BSI explants. Overall, the ex vivo model described here may allow scientists to address pending questions as to how host cell–microbiome alliances influence intestinal epithelial integrity and support the development of protective intestinal immune reactions against C. parvum infections in a realistic scenario under physioxic conditions.
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Kloehn J, Lacour CE, Soldati-Favre D. The metabolic pathways and transporters of the plastid organelle in Apicomplexa. Curr Opin Microbiol 2021; 63:250-258. [PMID: 34455306 DOI: 10.1016/j.mib.2021.07.016] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 07/19/2021] [Accepted: 07/24/2021] [Indexed: 11/26/2022]
Abstract
The apicoplast is the relict of a plastid organelle found in several disease-causing apicomplexan parasites such as Plasmodium spp. and Toxoplasma gondii. In these organisms, the organelle has lost its photosynthetic capability but harbours several fitness-conferring or essential metabolic pathways. Although maintaining the apicoplast and fuelling the metabolic pathways within requires the challenging constant import and export of numerous metabolites across its four membranes, only few apicoplast transporters have been identified to date, most of which are orphan transporters. Here we review the roles of metabolic pathways within the apicoplast and what is currently known about the few identified apicoplast metabolite transporters. We discuss what metabolites must get in and out of the apicoplast, the many transporters that are yet to be discovered, and what role these might play in parasite metabolism and as putative drug targets.
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Affiliation(s)
- Joachim Kloehn
- Department of Microbiology and Molecular Medicine, University of Geneva, CMU, Rue Michel-Servet 1, 1211 Geneva, Switzerland.
| | - Clément Em Lacour
- Department of Microbiology and Molecular Medicine, University of Geneva, CMU, Rue Michel-Servet 1, 1211 Geneva, Switzerland
| | - Dominique Soldati-Favre
- Department of Microbiology and Molecular Medicine, University of Geneva, CMU, Rue Michel-Servet 1, 1211 Geneva, Switzerland.
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13
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Karpe AV, Hutton ML, Mileto SJ, James ML, Evans C, Shah RM, Ghodke AB, Hillyer KE, Metcalfe SS, Liu JW, Walsh T, Lyras D, Palombo EA, Beale DJ. Cryptosporidiosis Modulates the Gut Microbiome and Metabolism in a Murine Infection Model. Metabolites 2021; 11:metabo11060380. [PMID: 34208228 PMCID: PMC8230837 DOI: 10.3390/metabo11060380] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Revised: 06/01/2021] [Accepted: 06/01/2021] [Indexed: 02/07/2023] Open
Abstract
Cryptosporidiosis is a major human health concern globally. Despite well-established methods, misdiagnosis remains common. Our understanding of the cryptosporidiosis biochemical mechanism remains limited, compounding the difficulty of clinical diagnosis. Here, we used a systems biology approach to investigate the underlying biochemical interactions in C57BL/6J mice infected with Cryptosporidium parvum. Faecal samples were collected daily following infection. Blood, liver tissues and luminal contents were collected 10 days post infection. High-resolution liquid chromatography and low-resolution gas chromatography coupled with mass spectrometry were used to analyse the proteomes and metabolomes of these samples. Faeces and luminal contents were additionally subjected to 16S rRNA gene sequencing. Univariate and multivariate statistical analysis of the acquired data illustrated altered host and microbial energy pathways during infection. Glycolysis/citrate cycle metabolites were depleted, while short-chain fatty acids and D-amino acids accumulated. An increased abundance of bacteria associated with a stressed gut environment was seen. Host proteins involved in energy pathways and Lactobacillus glyceraldehyde-3-phosphate dehydrogenase were upregulated during cryptosporidiosis. Liver oxalate also increased during infection. Microbiome–parasite relationships were observed to be more influential than the host–parasite association in mediating major biochemical changes in the mouse gut during cryptosporidiosis. Defining this parasite–microbiome interaction is the first step towards building a comprehensive cryptosporidiosis model towards biomarker discovery, and rapid and accurate diagnostics.
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Affiliation(s)
- Avinash V. Karpe
- Land and Water, Commonwealth Scientific and Industrial Research Organization, Ecosciences Precinct, Dutton Park, QLD 4102, Australia; (A.V.K.); (R.M.S.); (K.E.H.); (S.S.M.)
| | - Melanie L. Hutton
- Infection and Immunity Program, Monash Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, VIC 3800, Australia; (M.L.H.); (S.J.M.); (M.L.J.); (C.E.); (D.L.)
| | - Steven J. Mileto
- Infection and Immunity Program, Monash Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, VIC 3800, Australia; (M.L.H.); (S.J.M.); (M.L.J.); (C.E.); (D.L.)
| | - Meagan L. James
- Infection and Immunity Program, Monash Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, VIC 3800, Australia; (M.L.H.); (S.J.M.); (M.L.J.); (C.E.); (D.L.)
| | - Chris Evans
- Infection and Immunity Program, Monash Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, VIC 3800, Australia; (M.L.H.); (S.J.M.); (M.L.J.); (C.E.); (D.L.)
| | - Rohan M. Shah
- Land and Water, Commonwealth Scientific and Industrial Research Organization, Ecosciences Precinct, Dutton Park, QLD 4102, Australia; (A.V.K.); (R.M.S.); (K.E.H.); (S.S.M.)
- Department of Chemistry and Biotechnology, Swinburne University of Technology, Hawthorn, VIC 3122, Australia;
| | - Amol B. Ghodke
- Queensland Alliance for Agriculture and Food Innovation, Department of Horticulture, The University of Queensland, St Lucia, QLD 4072, Australia;
- BIO21 Institute, School of Biosciences, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Katie E. Hillyer
- Land and Water, Commonwealth Scientific and Industrial Research Organization, Ecosciences Precinct, Dutton Park, QLD 4102, Australia; (A.V.K.); (R.M.S.); (K.E.H.); (S.S.M.)
| | - Suzanne S. Metcalfe
- Land and Water, Commonwealth Scientific and Industrial Research Organization, Ecosciences Precinct, Dutton Park, QLD 4102, Australia; (A.V.K.); (R.M.S.); (K.E.H.); (S.S.M.)
| | - Jian-Wei Liu
- Land and Water, Commonwealth Scientific and Industrial Research Organization Research and Innovation Park, Acton, ACT 2601, Australia; (J.-W.L.); (T.W.)
| | - Tom Walsh
- Land and Water, Commonwealth Scientific and Industrial Research Organization Research and Innovation Park, Acton, ACT 2601, Australia; (J.-W.L.); (T.W.)
| | - Dena Lyras
- Infection and Immunity Program, Monash Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, VIC 3800, Australia; (M.L.H.); (S.J.M.); (M.L.J.); (C.E.); (D.L.)
| | - Enzo A. Palombo
- Department of Chemistry and Biotechnology, Swinburne University of Technology, Hawthorn, VIC 3122, Australia;
| | - David J. Beale
- Land and Water, Commonwealth Scientific and Industrial Research Organization, Ecosciences Precinct, Dutton Park, QLD 4102, Australia; (A.V.K.); (R.M.S.); (K.E.H.); (S.S.M.)
- Correspondence: ; Tel.: +61-7-3833-5774
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Harding CR, Sidik SM, Petrova B, Gnädig NF, Okombo J, Herneisen AL, Ward KE, Markus BM, Boydston EA, Fidock DA, Lourido S. Genetic screens reveal a central role for heme metabolism in artemisinin susceptibility. Nat Commun 2020; 11:4813. [PMID: 32968076 PMCID: PMC7511413 DOI: 10.1038/s41467-020-18624-0] [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: 09/04/2019] [Accepted: 09/03/2020] [Indexed: 01/26/2023] Open
Abstract
Artemisinins have revolutionized the treatment of Plasmodium falciparum malaria; however, resistance threatens to undermine global control efforts. To broadly explore artemisinin susceptibility in apicomplexan parasites, we employ genome-scale CRISPR screens recently developed for Toxoplasma gondii to discover sensitizing and desensitizing mutations. Using a sublethal concentration of dihydroartemisinin (DHA), we uncover the putative transporter Tmem14c whose disruption increases DHA susceptibility. Screens performed under high doses of DHA provide evidence that mitochondrial metabolism can modulate resistance. We show that disrupting a top candidate from the screens, the mitochondrial protease DegP2, lowers porphyrin levels and decreases DHA susceptibility, without significantly altering parasite fitness in culture. Deleting the homologous gene in P. falciparum, PfDegP, similarly lowers heme levels and DHA susceptibility. These results expose the vulnerability of heme metabolism to genetic perturbations that can lead to increased survival in the presence of DHA.
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Affiliation(s)
- Clare R Harding
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA
- Wellcome Centre for Molecular Parasitology, Institute of Infection, Immunity & Inflammation, University of Glasgow, Glasgow, UK
| | - Saima M Sidik
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA
| | - Boryana Petrova
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA
| | - Nina F Gnädig
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, NY, USA
| | - John Okombo
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, NY, USA
| | | | - Kurt E Ward
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, NY, USA
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | - Benedikt M Markus
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA
- Faculty of Biology, University of Freiburg, Freiburg, Germany
| | | | - David A Fidock
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, NY, USA
- Division of Infectious Diseases, Department of Medicine, Columbia University Irving Medical Center, New York, NY, USA
| | - Sebastian Lourido
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA.
- Biology Department, Massachusetts Institute of Technology, Cambridge, MA, USA.
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15
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Kloehn J, Harding CR, Soldati-Favre D. Supply and demand-heme synthesis, salvage and utilization by Apicomplexa. FEBS J 2020; 288:382-404. [PMID: 32530125 DOI: 10.1111/febs.15445] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2020] [Revised: 05/23/2020] [Accepted: 06/05/2020] [Indexed: 01/05/2023]
Abstract
The Apicomplexa phylum groups important human and animal pathogens that cause severe diseases, encompassing malaria, toxoplasmosis, and cryptosporidiosis. In common with most organisms, apicomplexans rely on heme as cofactor for several enzymes, including cytochromes of the electron transport chain. This heme derives from de novo synthesis and/or the development of uptake mechanisms to scavenge heme from their host. Recent studies have revealed that heme synthesis is essential for Toxoplasma gondii tachyzoites, as well as for the mosquito and liver stages of Plasmodium spp. In contrast, the erythrocytic stages of the malaria parasites rely on scavenging heme from the host red blood cell. The unusual heme synthesis pathway in Apicomplexa spans three cellular compartments and comprises enzymes of distinct ancestral origin, providing promising drug targets. Remarkably given the requirement for heme, T. gondii can tolerate the loss of several heme synthesis enzymes at a high fitness cost, while the ferrochelatase is essential for survival. These findings indicate that T. gondii is capable of salvaging heme precursors from its host. Furthermore, heme is implicated in the activation of the key antimalarial drug artemisinin. Recent findings established that a reduction in heme availability corresponds to decreased sensitivity to artemisinin in T. gondii and Plasmodium falciparum, providing insights into the possible development of combination therapies to tackle apicomplexan parasites. This review describes the microeconomics of heme in Apicomplexa, from supply, either from de novo synthesis or scavenging, to demand by metabolic pathways, including the electron transport chain.
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Affiliation(s)
- Joachim Kloehn
- Department of Microbiology and Molecular Medicine, CMU, University of Geneva, Switzerland
| | - Clare R Harding
- Wellcome Centre for Molecular Parasitology, Institute of Infection, Immunity & Inflammation, University of Glasgow, UK
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16
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Xu Z, Li N, Guo Y, Feng Y, Xiao L. Comparative genomic analysis of three intestinal species reveals reductions in secreted pathogenesis determinants in bovine-specific and non-pathogenic Cryptosporidium species. Microb Genom 2020; 6. [PMID: 32416746 PMCID: PMC7371110 DOI: 10.1099/mgen.0.000379] [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] [Indexed: 01/15/2023] Open
Abstract
The three common intestinal Cryptosporidium species in cattle differ significantly in host range, pathogenicity and public health significance. While Cryptosporidium parvum is pathogenic in pre-weaned calves and has a broad host range, C. bovis and C. ryanae are largely non-pathogenic and bovine-specific species in post-weaned calves. Thus far, only the genome of C. parvum has been sequenced. To improve our understanding of the genetic determinants of biological differences among Cryptosporidium spcies, we sequenced the genomes of C. bovis and C. ryanae and conducted a comparative genomics analysis. The genome of C. bovis has a gene content and organization more similar to C. ryanae than to other Cryptosporidium species sequenced to date; the level of similarity in amino acid and nucleotide sequences between the two species is 75.2 and 69.4 %, respectively. A total of 3723 and 3711 putative protein-encoding genes were identified in the genomes of C. bovis and C. ryanae, respectively, which are fewer than the 3981 in C. parvum. Metabolism is similar among the three species, although energy production pathways are further reduced in C. bovis and C. ryanae. Compared with C. parvum, C. bovis and C. ryanae have lost 14 genes encoding mucin-type glycoproteins and three for insulinase-like proteases. Other gene gains and losses in the two bovine-specific and non-pathogenic species also involve the secretory pathogenesis determinants (SPDs); they have lost all genes encoding MEDLE, FLGN and SKSR proteins, and two of the three genes for NFDQ proteins, but have more genes encoding secreted WYLE proteins, secreted leucine-rich proteins and GPI-anchored adhesin PGA18. The only major difference between C. bovis and C. ryanae is in nucleotide metabolism. In addition, half of the highly divergent genes between C. bovis and C. ryanae encode secreted or membrane-bound proteins. Therefore, C. bovis and C. ryanae have gene organization and metabolic pathways similar to C. parvum, but have lost some invasion-associated mucin glycoproteins, insulinase-like proteases, MEDLE secretory proteins and other SPDs. The multiple gene families under positive selection, such as helicase-associated domains, AMP-binding domains, protein kinases, mucins, insulinases and TRAPs could contribute to differences in host specificity and pathogenicity between C. parvum and C. bovis. Biological studies should be conducted to assess the contribution of these copy number variations to the narrow host range and reduced pathogenicity of C. bovis and C. ryanae.
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Affiliation(s)
- Zhixiao Xu
- State Key Laboratory of Bioreactor Engineering, School of Resources and Environmental Engineering, East China University of Science and Technology, Shanghai 200237, PR China
| | - Na Li
- Key Laboratory of Zoonosis of Ministry of Agriculture, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, PR China
| | - Yaqiong Guo
- Key Laboratory of Zoonosis of Ministry of Agriculture, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, PR China
| | - Yaoyu Feng
- State Key Laboratory of Bioreactor Engineering, School of Resources and Environmental Engineering, East China University of Science and Technology, Shanghai 200237, PR China.,Key Laboratory of Zoonosis of Ministry of Agriculture, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, PR China
| | - Lihua Xiao
- Key Laboratory of Zoonosis of Ministry of Agriculture, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, PR China
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17
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Krishnan A, Kloehn J, Lunghi M, Chiappino-Pepe A, Waldman BS, Nicolas D, Varesio E, Hehl A, Lourido S, Hatzimanikatis V, Soldati-Favre D. Functional and Computational Genomics Reveal Unprecedented Flexibility in Stage-Specific Toxoplasma Metabolism. Cell Host Microbe 2020; 27:290-306.e11. [PMID: 31991093 DOI: 10.1016/j.chom.2020.01.002] [Citation(s) in RCA: 73] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Revised: 11/02/2019] [Accepted: 01/03/2020] [Indexed: 12/31/2022]
Abstract
To survive and proliferate in diverse host environments with varying nutrient availability, the obligate intracellular parasite Toxoplasma gondii reprograms its metabolism. We have generated and curated a genome-scale metabolic model (iTgo) for the fast-replicating tachyzoite stage, harmonized with experimentally observed phenotypes. To validate the importance of four metabolic pathways predicted by the model, we have performed in-depth in vitro and in vivo phenotyping of mutant parasites including targeted metabolomics and CRISPR-Cas9 fitness screening of all known metabolic genes. This led to unexpected insights into the remarkable flexibility of the parasite, addressing the dependency on biosynthesis or salvage of fatty acids (FAs), purine nucleotides (AMP and GMP), a vitamin (pyridoxal-5P), and a cofactor (heme) in both the acute and latent stages of infection. Taken together, our experimentally validated metabolic network leads to a deeper understanding of the parasite's biology, opening avenues for the development of therapeutic intervention against apicomplexans.
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Affiliation(s)
- Aarti Krishnan
- Department of Microbiology & Molecular Medicine, Faculty of Medicine, University of Geneva, Geneva 1211, Switzerland
| | - Joachim Kloehn
- Department of Microbiology & Molecular Medicine, Faculty of Medicine, University of Geneva, Geneva 1211, Switzerland
| | - Matteo Lunghi
- Department of Microbiology & Molecular Medicine, Faculty of Medicine, University of Geneva, Geneva 1211, Switzerland
| | - Anush Chiappino-Pepe
- Laboratory of Computational Systems Biotechnology, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne 1015, Switzerland
| | | | - Damien Nicolas
- Department of Microbiology & Molecular Medicine, Faculty of Medicine, University of Geneva, Geneva 1211, Switzerland
| | - Emmanuel Varesio
- School of Pharmaceutical Sciences Geneva-Lausanne (EPGL), Geneva 1211, Switzerland; Mass Spectrometry Core Facility (MZ 2.0), University of Geneva, Geneva 1211, Switzerland
| | - Adrian Hehl
- Institute of Parasitology, University of Zürich, Zürich 8057, Switzerland
| | - Sebastian Lourido
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Vassily Hatzimanikatis
- Laboratory of Computational Systems Biotechnology, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne 1015, Switzerland
| | - Dominique Soldati-Favre
- Department of Microbiology & Molecular Medicine, Faculty of Medicine, University of Geneva, Geneva 1211, Switzerland.
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18
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Abstract
Cryptosporidium has historically been a difficult organism to work with, and molecular genomic data for this important pathogen have typically lagged behind other prominent protist pathogens. CryptoDB ( http://cryptodb.org/ ) was launched in 2004 following the appearance of draft genome sequences for both C. parvum and C. hominis. CryptoDB merged with the EuPathDB Bioinformatics Resource Center family of databases ( https://eupathdb.org ) and has been maintained and updated regularly since its establishment. These resources are freely available, are web-based, and permit users to analyze their own sequence data in the context of reference genome sequences in our user workspaces. Advances in technology have greatly facilitated Cryptosporidium research in the last several years greatly enhancing and extending the data and types of data available for this genus. Currently, 13 genome sequences are available for 9 species of Cryptosporidium as well as the distantly related Gregarina niphandrodes and two free-living alveolate outgroups of the Apicomplexa, Chromera velia and Vitrella brassicaformis. Recent years have seen several new genome sequences for both existing and new Cryptosporidium species as well as transcriptomics, proteomics, SNP, and isolate population surveys. This chapter introduces the extensive data mining and visualization capabilities of the EuPathDB software platform and introduces the data types and tools that are currently available for Cryptosporidium. Key features are demonstrated with Cryptosporidium-relevant examples and explanations.
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Affiliation(s)
- Susanne Warrenfeltz
- Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, GA, USA
| | - Jessica C Kissinger
- Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, GA, USA.
- Institute of Bioinformatics, University of Georgia, Athens, GA, USA.
- Department of Genetics, University of Georgia, Athens, GA, USA.
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Aggrey SE, Milfort MC, Fuller AL, Yuan J, Rekaya R. Effect of host genotype and Eimeria acervulina infection on the metabolome of meat-type chickens. PLoS One 2019; 14:e0223417. [PMID: 31618222 PMCID: PMC6795442 DOI: 10.1371/journal.pone.0223417] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Accepted: 09/20/2019] [Indexed: 11/21/2022] Open
Abstract
Objective A study was conducted to identify metabolic biochemical differences between two chicken genotypes infected with Eimeria acervulina and to ascertain the underlying mechanisms for these metabolic alterations and to further delineate genotype-specific effects during merozoite formation and oocyst shedding. Methods Fourteen day old chicks of an unimproved (ACRB) and improved (COBB) genotype were orally infected with 2.5 x 105 sporulated E. acervulina oocysts. At 4 and 6 day-post infection, 5 birds from each treatment group and their controls were bled for serum. Global metabolomic profiles were assessed using ultra performance liquid chromatography/tandem mass spectrometry (metabolon, Inc.,). Statistical analyses were based on analysis of variance to identify which biochemicals differed significantly between experimental groups. Pathway enrichment analysis was conducted to identify significant pathways associated with response to E. acervulina infection. Results A total of 752 metabolites were identified across genotype, treatment and time post infection. Altered fatty acid (FA) metabolism and β-oxidation were identified as dominant metabolic signatures associated with E. acervulina infection. Key metabolite changes in FA metabolism included stearoylcarnitine, palmitoylcarnitine and linoleoylcarnitine. The infection induced changes in nucleotide metabolism and elicited inflammatory reaction as evidenced by changes in thromboxane B2, 12-HHTrE and itaconate. Conclusions Serum metabolome of two chicken genotypes infected with E. acervulina demonstrated significant changes that were treatment-, time post-infection- and genotype-dependent. Distinct metabolic signatures were identified in fatty acid, nucleotide, inflammation and oxidative stress biochemicals. Significant microbial associated product alterations are likely to be associated with malabsorption of nutrients during infection.
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Affiliation(s)
- Samuel E. Aggrey
- NutriGenomics Laboratory, Department of Poultry Science, University of Georgia, Athens, Georgia, United States of America
- * E-mail:
| | - Marie C. Milfort
- NutriGenomics Laboratory, Department of Poultry Science, University of Georgia, Athens, Georgia, United States of America
| | - Alberta L. Fuller
- NutriGenomics Laboratory, Department of Poultry Science, University of Georgia, Athens, Georgia, United States of America
| | - Jianmin Yuan
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, Peoples Republic of China
| | - Romdhane Rekaya
- Department of Animal and Dairy Science, University of Georgia, Athens, Georgia, United States of America
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20
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Valenciano AL, Fernández-Murga ML, Merino EF, Holderman NR, Butschek GJ, Shaffer KJ, Tyler PC, Cassera MB. Metabolic dependency of chorismate in Plasmodium falciparum suggests an alternative source for the ubiquinone biosynthesis precursor. Sci Rep 2019; 9:13936. [PMID: 31558748 PMCID: PMC6763611 DOI: 10.1038/s41598-019-50319-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Accepted: 09/10/2019] [Indexed: 01/17/2023] Open
Abstract
The shikimate pathway, a metabolic pathway absent in humans, is responsible for the production of chorismate, a branch point metabolite. In the malaria parasite, chorismate is postulated to be a direct precursor in the synthesis of p-aminobenzoic acid (folate biosynthesis), p-hydroxybenzoic acid (ubiquinone biosynthesis), menaquinone, and aromatic amino acids. While the potential value of the shikimate pathway as a drug target is debatable, the metabolic dependency of chorismate in P. falciparum remains unclear. Current evidence suggests that the main role of chorismate is folate biosynthesis despite ubiquinone biosynthesis being active and essential in the malaria parasite. Our goal in the present work was to expand our knowledge of the ubiquinone head group biosynthesis and its potential metabolic dependency on chorismate in P. falciparum. We systematically assessed the development of both asexual and sexual stages of P. falciparum in a defined medium in the absence of an exogenous supply of chorismate end-products and present biochemical evidence suggesting that the benzoquinone ring of ubiquinones in this parasite may be synthesized through a yet unidentified route.
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Affiliation(s)
- Ana Lisa Valenciano
- Department of Biochemistry & Molecular Biology, and Center for Tropical and Emerging Global Diseases (CTEGD), University of Georgia, Athens, Georgia, 30602, United States
| | - Maria L Fernández-Murga
- Laboratory of Experimental Pathology, Health Research Institute Hospital La Fe, Valencia, 46026, Spain
| | - Emilio F Merino
- Department of Biochemistry & Molecular Biology, and Center for Tropical and Emerging Global Diseases (CTEGD), University of Georgia, Athens, Georgia, 30602, United States
| | - Nicole R Holderman
- Department of Biochemistry & Molecular Biology, and Center for Tropical and Emerging Global Diseases (CTEGD), University of Georgia, Athens, Georgia, 30602, United States
| | - Grant J Butschek
- Department of Biochemistry & Molecular Biology, and Center for Tropical and Emerging Global Diseases (CTEGD), University of Georgia, Athens, Georgia, 30602, United States
| | - Karl J Shaffer
- The Ferrier Research Institute, Victoria University of Wellington, Lower Hutt, New Zealand
| | - Peter C Tyler
- The Ferrier Research Institute, Victoria University of Wellington, Lower Hutt, New Zealand
| | - Maria Belen Cassera
- Department of Biochemistry & Molecular Biology, and Center for Tropical and Emerging Global Diseases (CTEGD), University of Georgia, Athens, Georgia, 30602, United States.
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21
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Füssy Z, Faitová T, Oborník M. Subcellular Compartments Interplay for Carbon and Nitrogen Allocation in Chromera velia and Vitrella brassicaformis. Genome Biol Evol 2019; 11:1765-1779. [PMID: 31192348 PMCID: PMC6668581 DOI: 10.1093/gbe/evz123] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/10/2019] [Indexed: 12/20/2022] Open
Abstract
Endosymbioses necessitate functional cooperation of cellular compartments to avoid pathway redundancy and streamline the control of biological processes. To gain insight into the metabolic compartmentation in chromerids, phototrophic relatives to apicomplexan parasites, we prepared a reference set of proteins probably localized to mitochondria, cytosol, and the plastid, taking advantage of available genomic and transcriptomic data. Training of prediction algorithms with the reference set now allows a genome-wide analysis of protein localization in Chromera velia and Vitrella brassicaformis. We confirm that the chromerid plastids house enzymatic pathways needed for their maintenance and photosynthetic activity, but for carbon and nitrogen allocation, metabolite exchange is necessary with the cytosol and mitochondria. This indeed suggests that the regulatory mechanisms operate in the cytosol to control carbon metabolism based on the availability of both light and nutrients. We discuss that this arrangement is largely shared with apicomplexans and dinoflagellates, possibly stemming from a common ancestral metabolic architecture, and supports the mixotrophy of the chromerid algae.
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Affiliation(s)
- Zoltán Füssy
- Faculty of Science, Department of Molecular Biology and Genetics, University of South Bohemia, České Budějovice, Czech Republic
- Department of Evolutionary Protistology, Institute of Parasitology, Biology Centre CAS, České Budějovice, Czech Republic
| | - Tereza Faitová
- Faculty of Science, Department of Molecular Biology and Genetics, University of South Bohemia, České Budějovice, Czech Republic
- Department of Evolutionary Protistology, Institute of Parasitology, Biology Centre CAS, České Budějovice, Czech Republic
- Faculty of Engineering and Natural Sciences, Department of Computer Science, Johannes Kepler University, Linz, Austria
| | - Miroslav Oborník
- Faculty of Science, Department of Molecular Biology and Genetics, University of South Bohemia, České Budějovice, Czech Republic
- Department of Evolutionary Protistology, Institute of Parasitology, Biology Centre CAS, České Budějovice, Czech Republic
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Xu Z, Guo Y, Roellig DM, Feng Y, Xiao L. Comparative analysis reveals conservation in genome organization among intestinal Cryptosporidium species and sequence divergence in potential secreted pathogenesis determinants among major human-infecting species. BMC Genomics 2019; 20:406. [PMID: 31117941 PMCID: PMC6532270 DOI: 10.1186/s12864-019-5788-9] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2019] [Accepted: 05/09/2019] [Indexed: 11/29/2022] Open
Abstract
Background Cryptosporidiosis is a major cause of gastrointestinal diseases in humans and other vertebrates. Previous analyses of invasion-related proteins revealed that Cryptosporidium parvum, Cryptosporidium hominis, and Cryptosporidium ubiquitum mainly differed in copy numbers of secreted MEDLE proteins and insulinase-like proteases and sequences of mucin-type glycoproteins. Recently, Cryptosporidium chipmunk genotype I was identified as a novel zoonotic pathogen in humans. In this study, we sequenced its genome and conducted a comparative genomic analysis. Results The genome of Cryptosporidium chipmunk genotype I has gene content and organization similar to C. parvum and other intestinal Cryptosporidium species sequenced to date. A total of 3783 putative protein-encoding genes were identified in the genome, 3525 of which are shared by Cryptosporidium chipmunk genotype I and three major human-pathogenic Cryptosporidium species, C. parvum, C. hominis, and Cryptosporidium meleagridis. The metabolic pathways are almost identical among these four Cryptosporidium species. Compared with C. parvum, a major reduction in gene content in Cryptosporidium chipmunk genotype I is in the number of telomeric genes encoding MEDLE proteins (two instead of six) and insulinase-like proteases (one instead of two). Highly polymorphic genes between the two species are mostly subtelomeric ones encoding secretory proteins, most of which have higher dN/dS ratios and half are members of multiple gene families. In particular, two subtelomeric ABC transporters are under strong positive selection. Conclusions Cryptosporidium chipmunk genotype I possesses genome organization, gene content, metabolic pathways and invasion-related proteins similar to the common human-pathogenic Cryptosporidium species, reaffirming its human-pathogenic nature. The loss of some subtelomeric genes encoding insulinase-like proteases and secreted MEDLE proteins and high sequence divergence in secreted pathogenesis determinants could contribute to the biological differences among human-pathogenic Cryptosporidium species. Electronic supplementary material The online version of this article (10.1186/s12864-019-5788-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Zhixiao Xu
- State Key Laboratory of Bioreactor Engineering, School of Resources and Environmental Engineering, East China University of Science and Technology, Shanghai, 200237, China
| | - Yaqiong Guo
- Key Laboratory of Zoonosis of Ministry of Agriculture, College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, China
| | - Dawn M Roellig
- Division of Foodborne, Waterborne, and Environmental Diseases, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, GA, 30329, 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. .,Key Laboratory of Zoonosis of Ministry of Agriculture, College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, China.
| | - Lihua Xiao
- Key Laboratory of Zoonosis of Ministry of Agriculture, College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, China.
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Magni R, Luchini A, Liotta L, Molestina RE. Analysis of the Babesia microti proteome in infected red blood cells by a combination of nanotechnology and mass spectrometry. Int J Parasitol 2019; 49:139-144. [PMID: 30391228 PMCID: PMC10548858 DOI: 10.1016/j.ijpara.2018.08.004] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Revised: 05/17/2018] [Accepted: 08/13/2018] [Indexed: 11/18/2022]
Abstract
Proteomics of Babesia microti has lagged behind other apicomplexans despite recent genome and transcriptome studies. Here, we used a combination of nanotechnology and mass spectrometry to provide a proteomic profile of B. microti acute infection. We identified ∼500 parasite proteins in blood with functions such as transport, carbohydrate and energy metabolism, proteolysis, DNA and RNA metabolism, signaling, translation, lipid biosynthesis, and motility and invasion. We also identified surface antigens with roles in the immune response to the parasite. This first evaluation of the B. microti proteome in erythrocytes provides information for the study of intracellular survival and development of diagnostic tools using mass spectrometry.
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Affiliation(s)
- Ruben Magni
- Center for Applied Proteomics and Molecular Medicine, George Mason University, Manassas, VA 20110, USA
| | - Alessandra Luchini
- Center for Applied Proteomics and Molecular Medicine, George Mason University, Manassas, VA 20110, USA
| | - Lance Liotta
- Center for Applied Proteomics and Molecular Medicine, George Mason University, Manassas, VA 20110, USA
| | - Robert E Molestina
- Protistology Laboratory, American Type Culture Collection, Manassas, VA 20110, USA.
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Santos HJ, Makiuchi T, Nozaki T. Reinventing an Organelle: The Reduced Mitochondrion in Parasitic Protists. Trends Parasitol 2018; 34:1038-1055. [PMID: 30201278 DOI: 10.1016/j.pt.2018.08.008] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Revised: 08/10/2018] [Accepted: 08/10/2018] [Indexed: 12/18/2022]
Abstract
Mitochondria originated from the endosymbiotic event commencing from the engulfment of an ancestral α-proteobacterium by the first eukaryotic ancestor. Establishment of niches has led to various adaptations among eukaryotes. In anaerobic parasitic protists, the mitochondria have undergone modifications by combining features shared from the aerobic mitochondria with lineage-specific components and mechanisms; a diversified class of organelles emerged and are generally called mitochondrion-related organelles (MROs). In this review we summarize and discuss the recent advances in the knowledge of MROs from parasitic protists, particularly the themes such as metabolic functions, contribution to parasitism, dynamics, protein targeting, and novel lineage- specific proteins, with emphasis on the diversity among these organelles.
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Affiliation(s)
- Herbert J Santos
- Department of Biomedical Chemistry, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Takashi Makiuchi
- Department of Infectious Diseases, Tokai University School of Medicine, 143 Shimokasuya, Isehara, Kanagawa 259-1193, Japan
| | - Tomoyoshi Nozaki
- Department of Biomedical Chemistry, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.
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The effects of nitidine chloride and camptothecin on the growth of Babesia and Theileria parasites. Ticks Tick Borne Dis 2018; 9:1192-1201. [PMID: 29730263 DOI: 10.1016/j.ttbdis.2018.04.019] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Revised: 04/19/2018] [Accepted: 04/26/2018] [Indexed: 01/31/2023]
Abstract
The treatment of bovine and equine piroplasmosis is limited to diminazene aceturate (DA) and imidocarb dipropionate. To address this challenge, we need to explore novel drug compounds and targets. Topoisomerases are potential drug targets because they play a vital role in solving topological errors of DNA strands during replication. This study documented the effectiveness of topoisomerase inhibitors, nitidine chloride (NC) and camptothecin (Cpt), on the growth of Babesia and Theileria parasites. The half maximal inhibitory concentrations (IC50s) against B. bovis, B. bigemina, B. caballi, and T. equi were 1.01 ± 0.2, 5.34 ± 1.0, 0.11 ± 0.03, and 2.05 ± 0.4 μM for NC and 11.67 ± 1.6, 4.00 ± 1.0, 2.07 ± 0.6, and 0.33 ± 0.02 μM for Cpt, respectively. The viability experiment revealed that 4, 10, and 4 μM treatments of NC or 48, 8, and 8 μM treatments of Cpt were sufficient to stop the in vitro regrowth of B. bovis, B. bigemina, and B. caballi, respectively. However, T. equi regrew in all of the concentrations used. Moreover, increasing the concentration of NC and Cpt to 16 μM and 1.2 μM (8 × IC50) did not eliminate T. equi. The micrographs of B. bigemina and B. caballi taken at 24 h and 72 h showed deformed merozoites and remnants of parasites within the red blood cell (RBC), respectively. The treatments of 25 mg/kg DA and 20 mg/kg NC administered intraperitoneally and 20 mg/kg NC given orally showed 93.7, 90.7, and 83.6% inhibition against Babesia microti (B. microti), respectively, compared to the untreated group on day 8. In summary, NC and Cpt were effective against Babesia and Theileria parasites in vitro. Moreover, 20 mg/kg NC administered intraperitoneally was as effective as 25 mg/kg DA against B. microti in mice and showed no toxic symptoms in mice. The results indicate that NC may, after further evaluations, prove to be an alternative drug against bovine and equine piroplasmoses.
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Identification of novel therapeutic candidates in Cryptosporidium parvum: an in silico approach. Parasitology 2018; 145:1907-1916. [PMID: 29692282 DOI: 10.1017/s0031182018000677] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Unavailability of vaccines and effective drugs are primarily responsible for the growing menace of cryptosporidiosis. This study has incorporated a bioinformatics-based screening approach to explore potential vaccine candidates and novel drug targets in Cryptosporidium parvum proteome. A systematic strategy was defined for comparative genomics, orthology with related Cryptosporidium species, prioritization parameters and MHC class I and II binding promiscuity. The approach reported cytoplasmic protein cgd7_1830, a signal peptide protein, as a novel drug target. SWISS-MODEL online server was used to generate the 3D model of the protein and was validated by PROCHECK. The model has been subjected to in silico docking study with screened potent lead compounds from the ZINC database, PubChem and ChEMBL database using Flare software package of Cresset®. Furthermore, the approach reported protein cgd3_1400, as a vaccine candidate. The predicted B- and T-cell epitopes on the proposed vaccine candidate with highest scores were also subjected to docking study with MHC class I and II alleles using ClusPro web server. Results from this study could facilitate selection of proteins which could serve as drug targets and vaccine candidates to efficiently tackle the growing threat of cryptosporidiosis.
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Gazanion E, Vergnes B. Protozoan Parasite Auxotrophies and Metabolic Dependencies. EXPERIENTIA SUPPLEMENTUM (2012) 2018; 109:351-375. [PMID: 30535605 DOI: 10.1007/978-3-319-74932-7_9] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Diseases caused by protozoan parasites have a major impact on world health. These early branching eukaryotes cause significant morbidity and mortality in humans and livestock. During evolution, protozoan parasites have evolved toward complex life cycles in multiple host organisms with different nutritional resources. The conservation of functional metabolic pathways required for these successive environments is therefore a prerequisite for parasitic lifestyle. Nevertheless, parasitism drives genome evolution toward gene loss and metabolic dependencies (including strict auxotrophy), especially for obligatory intracellular parasites. In this chapter, we will compare and contrast how protozoan parasites have perfected this metabolic adaptation by focusing on specific auxotrophic pathways and scavenging strategies used by clinically relevant apicomplexan and trypanosomatid parasites to access host's nutritional resources. We will further see how these metabolic dependencies have in turn been exploited for therapeutic purposes against these human pathogens.
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Affiliation(s)
- Elodie Gazanion
- MIVEGEC, IRD, CNRS, University of Montpellier, Montpellier, France
| | - Baptiste Vergnes
- MIVEGEC, IRD, CNRS, University of Montpellier, Montpellier, France.
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28
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De novo synthesis of thiamine (vitamin B1) is the ancestral state in Plasmodium parasites – evidence from avian haemosporidians. Parasitology 2017; 145:1084-1089. [DOI: 10.1017/s0031182017002219] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
AbstractParasites often have reduced genomes as their own genes become redundant when utilizing their host as a source of metabolites, thus losing their own de novo production of metabolites. Primate malaria parasites can synthesize vitamin B1 (thiamine) de novo but rodent malaria and other genome-sequenced apicomplexans cannot, as the three essential genes responsible for this pathway are absent in their genomes. The unique presence of functional thiamine synthesis genes in primate malaria parasites and their sequence similarities to bacterial orthologues, have led to speculations that this pathway was horizontally acquired from bacteria. Here we show that the genes essential for the de novo synthesis of thiamine are found also in avian Plasmodium species. Importantly, they are also present in species phylogenetically basal to all mammalian and avian Plasmodium parasites, i.e. Haemoproteus. Furthermore, we found that these genes are expressed during the blood stage of the avian malaria infection, indicating that this metabolic pathway is actively transcribed. We conclude that the ability to synthesize thiamine is widespread among haemosporidians, with a recent loss in the rodent malaria species.
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Toxoplasma gondii Requires Glycogen Phosphorylase for Balancing Amylopectin Storage and for Efficient Production of Brain Cysts. mBio 2017; 8:mBio.01289-17. [PMID: 28851850 PMCID: PMC5574715 DOI: 10.1128/mbio.01289-17] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In immunocompromised hosts, latent infection with Toxoplasma gondii can reactivate from tissue cysts, leading to encephalitis. A characteristic of T. gondii bradyzoites in tissue cysts is the presence of amylopectin granules. The regulatory mechanisms and role of amylopectin accumulation in this organism are not fully understood. The T. gondii genome encodes a putative glycogen phosphorylase (TgGP), and mutants were constructed to manipulate the activity of TgGP and to evaluate the function of TgGP in amylopectin storage. Both a stop codon mutant (Pru/TgGPS25stop [expressing a Ser-to-stop codon change at position 25 in TgGP]) and a phosphorylation null mutant (Pru/TgGPS25A [expressing a Ser-to-Ala change at position 25 in TgGp]) mutated at Ser25 displayed amylopectin accumulation, while the phosphorylation-mimetic mutant (Pru/TgGPS25E [expressing a Ser-to-Glu change at position 25 in TgGp]) had minimal amylopectin accumulation under both tachyzoite and bradyzoite growth conditions. The expression of active TgGPS25S or TgGPS25E restored amylopectin catabolism in Pru/TgGPS25A To understand the relation between GP and calcium-dependent protein kinase 2 (CDPK2), which was recently reported to regulate amylopectin consumption, we knocked out CDPK2 in these mutants. PruΔcdpk2/TgGPS25E had minimal amylopectin accumulation, whereas the Δcdpk2 phenotype in the other GP mutants and parental lines displayed amylopectin accumulation. Both the inactive S25A and hyperactive S25E mutant produced brain cysts in infected mice, but the numbers of cysts produced were significantly less than the number produced by the S25S wild-type GP parasite. Complementation that restored amylopectin regulation restored brain cyst production to the control levels seen in infected mice. These data suggest that T. gondii requires tight regulation of amylopectin expression for efficient production of cysts and persistent infections and that GP phosphorylation is a regulatory mechanism involved in amylopectin storage and utilization.IMPORTANCEToxoplasma gondii is an obligate intracellular parasite that causes disease in immune-suppressed individuals, as well as a fetopathy in pregnant women who acquire infection for the first time during pregnancy. This parasite can differentiate between tachyzoites (seen in acute infection) and bradyzoites (seen in latent infection), and this differentiation is associated with disease relapse. A characteristic of bradyzoites is that they contain cytoplasmic amylopectin granules. The regulatory mechanisms and the roles of amylopectin granules during latent infection remain to be elucidated. We have identified a role of T. gondii glycogen phosphorylase (TgGP) in the regulation of starch digestion and a role of posttranslational modification of TgGP, i.e., phosphorylation of Ser25, in the regulation of amylopectin digestion. By manipulating TgGP activity in the parasite with genome editing, we found that the digestion and storage of amylopectin due to TgGP activity are both important for latency in the brain.
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Mello LV, Tregilgas L, Cowley G, Gupta A, Makki F, Jhutty A, Shanmugasundram A. 'Students-as-partners' scheme enhances postgraduate students' employability skills while addressing gaps in bioinformatics education. HIGHER EDUCATION PEDAGOGIES 2017; 2:43-57. [PMID: 29098185 PMCID: PMC5632996 DOI: 10.1080/23752696.2017.1339287] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Revised: 05/29/2017] [Accepted: 06/04/2017] [Indexed: 06/07/2023]
Abstract
Teaching bioinformatics is a longstanding challenge for educators who need to demonstrate to students how skills developed in the classroom may be applied to real world research. This study employed an action research methodology which utilised student-staff partnership and peer-learning. It was centred on the experiences of peer-facilitators, students who had previously taken a postgraduate bioinformatics module, and had applied knowledge and skills gained from it to their own research. It aimed to demonstrate to peer-receivers, current students, how bioinformatics could be used in their own research while developing peer-facilitators' teaching and mentoring skills. This student-centred approach was well received by the peer-receivers, who claimed to have gained improved understanding of bioinformatics and its relevance to research. Equally, peer-facilitators also developed a better understanding of the subject and appreciated that the activity was a rare and invaluable opportunity to develop their teaching and mentoring skills, enhancing their employability.
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Affiliation(s)
| | - Luke Tregilgas
- Arthritis Research UK Centre for Integrated Research into Musculoskeletal Ageing (CIMA), Department of Musculoskeletal Biology, Institute of Ageing and Chronic Disease, University of Liverpool, Liverpool, UK
| | - Gwen Cowley
- Institute of Integrative Biology, University of Liverpool, Liverpool, UK
| | - Anshul Gupta
- Institute of Integrative Biology, University of Liverpool, Liverpool, UK
| | - Fatima Makki
- Institute of Integrative Biology, University of Liverpool, Liverpool, UK
| | - Anjeet Jhutty
- Institute of Integrative Biology, University of Liverpool, Liverpool, UK
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Abstract
The increasing prevalence of infections involving intracellular apicomplexan parasites such as Plasmodium, Toxoplasma, and Cryptosporidium (the causative agents of malaria, toxoplasmosis, and cryptosporidiosis, respectively) represent a significant global healthcare burden. Despite their significance, few treatments are available; a situation that is likely to deteriorate with the emergence of new resistant strains of parasites. To lay the foundation for programs of drug discovery and vaccine development, genome sequences for many of these organisms have been generated, together with large-scale expression and proteomic datasets. Comparative analyses of these datasets are beginning to identify the molecular innovations supporting both conserved processes mediating fundamental roles in parasite survival and persistence, as well as lineage-specific adaptations associated with divergent life-cycle strategies. The challenge is how best to exploit these data to derive insights into parasite virulence and identify those genes representing the most amenable targets. In this review, we outline genomic datasets currently available for apicomplexans and discuss biological insights that have emerged as a consequence of their analysis. Of particular interest are systems-based resources, focusing on areas of metabolism and host invasion that are opening up opportunities for discovering new therapeutic targets.
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Affiliation(s)
| | - John Parkinson
- a Program in Molecular Structure and Function , Hospital for Sick Children , Toronto , Ontario , Canada
- b Departments of Biochemistry, Molecular Genetics and Computer Science , University of Toronto , Toronto , Ontario , Canada
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32
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Liu S, Roellig DM, Guo Y, Li N, Frace MA, Tang K, Zhang L, Feng Y, Xiao L. Evolution of mitosome metabolism and invasion-related proteins in Cryptosporidium. BMC Genomics 2016; 17:1006. [PMID: 27931183 PMCID: PMC5146892 DOI: 10.1186/s12864-016-3343-5] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2016] [Accepted: 11/25/2016] [Indexed: 11/10/2022] Open
Abstract
Background The switch from photosynthetic or predatory to parasitic life strategies by apicomplexans is accompanied with a reductive evolution of genomes and losses of metabolic capabilities. Cryptosporidium is an extreme example of reductive evolution among apicomplexans, with losses of both the mitosome genome and many metabolic pathways. Previous observations on reductive evolution were largely based on comparative studies of various groups of apicomplexans. In this study, we sequenced two divergent Cryptosporidium species and conducted a comparative genomic analysis to infer the reductive evolution of metabolic pathways and differential evolution of invasion-related proteins within the Cryptosporidium lineage. Results In energy metabolism, Cryptosporidium species differ from each other mostly in mitosome metabolic pathways. Compared with C. parvum and C. hominis, C. andersoni possesses more aerobic metabolism and a conventional electron transport chain, whereas C. ubiquitum has further reductions in ubiquinone and polyisprenoid biosynthesis and has lost both the conventional and alternative electron transport systems. For invasion-associated proteins, similar to C. hominis, a reduction in the number of genes encoding secreted MEDLE and insulinase-like proteins in the subtelomeric regions of chromosomes 5 and 6 was also observed in C. ubiquitum and C. andersoni, whereas mucin-type glycoproteins are highly divergent between the gastric C. andersoni and intestinal Cryptosporidium species. Conclusions Results of the study suggest that rapidly evolving mitosome metabolism and secreted invasion-related proteins could be involved in tissue tropism and host specificity in Cryptosporidium spp. The finding of progressive reduction in mitosome metabolism among Cryptosporidium species improves our knowledge of organelle evolution within apicomplexans. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-3343-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Shiyou Liu
- 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, 30329, USA
| | - Dawn M Roellig
- Division of Foodborne, Waterborne, and Environmental Diseases, Centers for Disease Control and Prevention, Atlanta, GA, 30329, USA
| | - 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, 30329, 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.,Division of Foodborne, Waterborne, and Environmental Diseases, Centers for Disease Control and Prevention, Atlanta, GA, 30329, USA
| | - Michael A Frace
- Division of Scientific Resources, Centers for Disease Control and Prevention, Atlanta, GA, 30329, USA
| | - Kevin Tang
- Division of Scientific Resources, Centers for Disease Control and Prevention, Atlanta, GA, 30329, USA
| | - Longxian Zhang
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450002, China
| | - 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, 30329, USA.
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Liu S, Wang L, Zheng H, Xu Z, Roellig DM, Li N, Frace MA, Tang K, Arrowood MJ, Moss DM, Zhang L, Feng Y, Xiao L. Comparative genomics reveals Cyclospora cayetanensis possesses coccidia-like metabolism and invasion components but unique surface antigens. BMC Genomics 2016; 17:316. [PMID: 27129308 PMCID: PMC4851813 DOI: 10.1186/s12864-016-2632-3] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2015] [Accepted: 04/20/2016] [Indexed: 01/24/2023] Open
Abstract
Background Cyclospora cayetanensis is an apicomplexan that causes diarrhea in humans. The investigation of foodborne outbreaks of cyclosporiasis has been hampered by a lack of genetic data and poor understanding of pathogen biology. In this study we sequenced the genome of C. cayetanensis and inferred its metabolism and invasion components based on comparative genomic analysis. Results The genome organization, metabolic capabilities and potential invasion mechanism of C. cayetanensis are very similar to those of Eimeria tenella. Propanoyl-CoA degradation, GPI anchor biosynthesis, and N-glycosylation are some apparent metabolic differences between C. cayetanensis and E. tenella. Unlike Eimeria spp., there are no active LTR-retrotransposons identified in C. cayetanensis. The similar repertoire of host cell invasion-related proteins possessed by all coccidia suggests that C. cayetanensis has an invasion process similar to the one in T. gondii and E. tenella. However, the significant reduction in the number of identifiable rhoptry protein kinases, phosphatases and serine protease inhibitors indicates that monoxenous coccidia, especially C. cayetanensis, have limited capabilities or use a different system to regulate host cell nuclear activities. C. cayetanensis does not possess any cluster of genes encoding the TA4-type SAG surface antigens seen in E. tenella, and may use a different family of surface antigens in initial host cell interactions. Conclusions Our findings indicate that C. cayetanensis possesses coccidia-like metabolism and invasion components but unique surface antigens. Amino acid metabolism and post-translation modifications of proteins are some major differences between C. cayetanensis and other apicomplexans. The whole genome sequence data of C. cayetanensis improve our understanding of the biology and evolution of this major foodborne pathogen and facilitate the development of intervention measures and advanced diagnostic tools. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-2632-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Shiyou Liu
- 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
| | - Lin Wang
- State Key Laboratory of Bioreactor Engineering, School of Resources and Environmental Engineering, East China University of Science and Technology, Shanghai, 200237, China
| | - Huajun Zheng
- Shanghai-Ministry of Science and Technology Key Laboratory of Health and Disease Genomics, Chinese National Human Genome Center at Shanghai, 250 Bibo Road, Shanghai, 201203, China
| | - Zhixiao Xu
- 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
| | - Na Li
- 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
| | - Michael A Frace
- Division of Scientific Resources, 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
| | - Michael J Arrowood
- Division of Foodborne, Waterborne, and Environmental Diseases, Centers for Disease Control and Prevention, Atlanta, GA, 30333, USA
| | - Delynn M Moss
- Division of Foodborne, Waterborne, and Environmental Diseases, Centers for Disease Control and Prevention, Atlanta, GA, 30333, USA
| | - Longxian Zhang
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450002, China
| | - 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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Pirtskhalava M, Gabrielian A, Cruz P, Griggs HL, Squires RB, Hurt DE, Grigolava M, Chubinidze M, Gogoladze G, Vishnepolsky B, Alekseyev V, Rosenthal A, Tartakovsky M. DBAASP v.2: an enhanced database of structure and antimicrobial/cytotoxic activity of natural and synthetic peptides. Nucleic Acids Res 2015; 44:D1104-12. [PMID: 26578581 PMCID: PMC4702840 DOI: 10.1093/nar/gkv1174] [Citation(s) in RCA: 124] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2015] [Accepted: 10/22/2015] [Indexed: 01/26/2023] Open
Abstract
Antimicrobial peptides (AMPs) are anti-infectives that may represent a novel and untapped class of biotherapeutics. Increasing interest in AMPs means that new peptides (natural and synthetic) are discovered faster than ever before. We describe herein a new version of the Database of Antimicrobial Activity and Structure of Peptides (DBAASPv.2, which is freely accessible at http://dbaasp.org). This iteration of the database reports chemical structures and empirically-determined activities (MICs, IC50, etc.) against more than 4200 specific target microbes for more than 2000 ribosomal, 80 non-ribosomal and 5700 synthetic peptides. Of these, the vast majority are monomeric, but nearly 200 of these peptides are found as homo- or heterodimers. More than 6100 of the peptides are linear, but about 515 are cyclic and more than 1300 have other intra-chain covalent bonds. More than half of the entries in the database were added after the resource was initially described, which reflects the recent sharp uptick of interest in AMPs. New features of DBAASPv.2 include: (i) user-friendly utilities and reporting functions, (ii) a ‘Ranking Search’ function to query the database by target species and return a ranked list of peptides with activity against that target and (iii) structural descriptions of the peptides derived from empirical data or calculated by molecular dynamics (MD) simulations. The three-dimensional structural data are critical components for understanding structure–activity relationships and for design of new antimicrobial drugs. We created more than 300 high-throughput MD simulations specifically for inclusion in DBAASP. The resulting structures are described in the database by novel trajectory analysis plots and movies. Another 200+ DBAASP entries have links to the Protein DataBank. All of the structures are easily visualized directly in the web browser.
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Affiliation(s)
- Malak Pirtskhalava
- Ivane Beritashvili Center of Experimental Biomedicine, Tbilisi 0160, Georgia
| | - Andrei Gabrielian
- Office of Cyber Infrastructure and Computational Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Phillip Cruz
- Office of Cyber Infrastructure and Computational Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Hannah L Griggs
- Office of Cyber Infrastructure and Computational Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - R Burke Squires
- Office of Cyber Infrastructure and Computational Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Darrell E Hurt
- Office of Cyber Infrastructure and Computational Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Maia Grigolava
- Ivane Beritashvili Center of Experimental Biomedicine, Tbilisi 0160, Georgia
| | - Mindia Chubinidze
- Ivane Beritashvili Center of Experimental Biomedicine, Tbilisi 0160, Georgia
| | - George Gogoladze
- Ivane Beritashvili Center of Experimental Biomedicine, Tbilisi 0160, Georgia
| | - Boris Vishnepolsky
- Ivane Beritashvili Center of Experimental Biomedicine, Tbilisi 0160, Georgia
| | - Vsevolod Alekseyev
- Office of Cyber Infrastructure and Computational Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Alex Rosenthal
- Office of Cyber Infrastructure and Computational Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Michael Tartakovsky
- Office of Cyber Infrastructure and Computational Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
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Dogga SK, Bartošová-Sojková P, Lukeš J, Soldati-Favre D. Phylogeny, Morphology, and Metabolic and Invasive Capabilities of Epicellular Fish Coccidium Goussia janae. Protist 2015; 166:659-76. [PMID: 26599727 DOI: 10.1016/j.protis.2015.09.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2015] [Revised: 09/13/2015] [Accepted: 09/15/2015] [Indexed: 01/08/2023]
Abstract
To fill the knowledge gap on the biology of the fish coccidian Goussia janae, RNA extracted from exogenously sporulated oocysts was sequenced. Analysis by Trinity and Trinotate pipelines showed that 84.6% of assembled transcripts share the highest similarity with Toxoplasma gondii and Neospora caninum. Phylogenetic and interpretive analyses from RNA-seq data provide novel insight into the metabolic capabilities, composition of the invasive machinery and the phylogenetic relationships of this parasite of cold-blooded vertebrates with other coccidians. This allows re-evaluation of the phylogenetic position of G. janae and sheds light on the emergence of the highly successful obligatory intracellularity of apicomplexan parasites. G. janae possesses a partial glideosome and along with it, the metabolic capabilities and adaptions of G. janae might provide cues as to how apicomplexans adjusted to extra- or intra-cytoplasmic niches and also to become obligate intracellular parasites. Unlike the similarly localized epicellular Cryptosporidium spp., G. janae lacks the feeder organelle necessary for directly scavenging nutrients from the host. Transcriptome analysis indicates that G. janae possesses metabolic capabilities comparable to T. gondii. Additionally, this enteric coccidium might also access host cell nutrients given the presence of a recently identified gene encoding the molecular sieve at the parasitophorous vacuole membrane.
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Affiliation(s)
- Sunil Kumar Dogga
- Department of Microbiology and Molecular Medicine, University of Geneva. CMU, 1 Rue Michel-Servet, CH-1211 Geneva 4, Switzerland
| | - Pavla Bartošová-Sojková
- Institute of Parasitology, Biology Centre, Branišovská 31, České Budějovice (Budweis), Czech Republic
| | - Julius Lukeš
- Institute of Parasitology, Biology Centre, Branišovská 31, České Budějovice (Budweis), Czech Republic; Faculty of Science, University of South Bohemia, Branišovská 1645/31A, České Budějovice (Budweis), Czech Republic; Canadian Institute for Advanced Research, 180 Dundas St W, Toronto, ON M5G 1Z8, Canada
| | - Dominique Soldati-Favre
- Department of Microbiology and Molecular Medicine, University of Geneva. CMU, 1 Rue Michel-Servet, CH-1211 Geneva 4, Switzerland.
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Tymoshenko S, Oppenheim RD, Agren R, Nielsen J, Soldati-Favre D, Hatzimanikatis V. Metabolic Needs and Capabilities of Toxoplasma gondii through Combined Computational and Experimental Analysis. PLoS Comput Biol 2015; 11:e1004261. [PMID: 26001086 PMCID: PMC4441489 DOI: 10.1371/journal.pcbi.1004261] [Citation(s) in RCA: 82] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2015] [Accepted: 03/31/2015] [Indexed: 11/18/2022] Open
Abstract
Toxoplasma gondii is a human pathogen prevalent worldwide that poses a challenging and unmet need for novel treatment of toxoplasmosis. Using a semi-automated reconstruction algorithm, we reconstructed a genome-scale metabolic model, ToxoNet1. The reconstruction process and flux-balance analysis of the model offer a systematic overview of the metabolic capabilities of this parasite. Using ToxoNet1 we have identified significant gaps in the current knowledge of Toxoplasma metabolic pathways and have clarified its minimal nutritional requirements for replication. By probing the model via metabolic tasks, we have further defined sets of alternative precursors necessary for parasite growth. Within a human host cell environment, ToxoNet1 predicts a minimal set of 53 enzyme-coding genes and 76 reactions to be essential for parasite replication. Double-gene-essentiality analysis identified 20 pairs of genes for which simultaneous deletion is deleterious. To validate several predictions of ToxoNet1 we have performed experimental analyses of cytosolic acetyl-CoA biosynthesis. ATP-citrate lyase and acetyl-CoA synthase were localised and their corresponding genes disrupted, establishing that each of these enzymes is dispensable for the growth of T. gondii, however together they make a synthetic lethal pair.
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Affiliation(s)
- Stepan Tymoshenko
- Laboratory of Computational Systems Biotechnology, École Polytechnique Fédérale de Lausanne, EPFL, Lausanne, Switzerland
- Department of Microbiology and Molecular Medicine, Faculty of Medicine, University of Geneva, CMU, Geneva, Switzerland
- Swiss Institute of Bioinformatics, Quartier Sorge, Batiment Genopode, Lausanne, Switzerland
| | - Rebecca D. Oppenheim
- Department of Microbiology and Molecular Medicine, Faculty of Medicine, University of Geneva, CMU, Geneva, Switzerland
| | - Rasmus Agren
- Department of Chemical and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Jens Nielsen
- Department of Chemical and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Dominique Soldati-Favre
- Department of Microbiology and Molecular Medicine, Faculty of Medicine, University of Geneva, CMU, Geneva, Switzerland
| | - Vassily Hatzimanikatis
- Department of Microbiology and Molecular Medicine, Faculty of Medicine, University of Geneva, CMU, Geneva, Switzerland
- Swiss Institute of Bioinformatics, Quartier Sorge, Batiment Genopode, Lausanne, Switzerland
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Endosymbiosis undone by stepwise elimination of the plastid in a parasitic dinoflagellate. Proc Natl Acad Sci U S A 2015; 112:5767-72. [PMID: 25902514 DOI: 10.1073/pnas.1423400112] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Organelle gain through endosymbiosis has been integral to the origin and diversification of eukaryotes, and, once gained, plastids and mitochondria seem seldom lost. Indeed, discovery of nonphotosynthetic plastids in many eukaryotes--notably, the apicoplast in apicomplexan parasites such as the malaria pathogen Plasmodium--highlights the essential metabolic functions performed by plastids beyond photosynthesis. Once a cell becomes reliant on these ancillary functions, organelle dependence is apparently difficult to overcome. Previous examples of endosymbiotic organelle loss (either mitochondria or plastids), which have been invoked to explain the origin of eukaryotic diversity, have subsequently been recognized as organelle reduction to cryptic forms, such as mitosomes and apicoplasts. Integration of these ancient symbionts with their hosts has been too well developed to reverse. Here, we provide evidence that the dinoflagellate Hematodinium sp., a marine parasite of crustaceans, represents a rare case of endosymbiotic organelle loss by the elimination of the plastid. Extensive RNA and genomic sequencing data provide no evidence for a plastid organelle, but, rather, reveal a metabolic decoupling from known plastid functions that typically impede organelle loss. This independence has been achieved through retention of ancestral anabolic pathways, enzyme relocation from the plastid to the cytosol, and metabolic scavenging from the parasite's host. Hematodinium sp. thus represents a further dimension of endosymbiosis--life after the organelle.
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Croken MM, Ma Y, Markillie LM, Taylor RC, Orr G, Weiss LM, Kim K. Distinct Strains of Toxoplasma gondii Feature Divergent Transcriptomes Regardless of Developmental Stage. PLoS One 2014; 9:e111297. [PMID: 25393307 PMCID: PMC4230917 DOI: 10.1371/journal.pone.0111297] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2014] [Accepted: 09/19/2014] [Indexed: 11/18/2022] Open
Affiliation(s)
- Matthew McKnight Croken
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, New York, United States of America
| | - Yanfen Ma
- Department of Pathology, Albert Einstein College of Medicine, Bronx, New York, United States of America
| | - Lye Meng Markillie
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington, United States of America
| | - Ronald C. Taylor
- Computational Biology and Bioinformatics Group, Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, United States of America
| | - Galya Orr
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington, United States of America
| | - Louis M. Weiss
- Department of Pathology, Albert Einstein College of Medicine, Bronx, New York, United States of America
- Department of Medicine, Albert Einstein College of Medicine, Bronx, New York, United States of America
- * E-mail: (LMW); (KK)
| | - Kami Kim
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, New York, United States of America
- Department of Pathology, Albert Einstein College of Medicine, Bronx, New York, United States of America
- Department of Medicine, Albert Einstein College of Medicine, Bronx, New York, United States of America
- * E-mail: (LMW); (KK)
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Shameer S, Logan-Klumpler FJ, Vinson F, Cottret L, Merlet B, Achcar F, Boshart M, Berriman M, Breitling R, Bringaud F, Bütikofer P, Cattanach AM, Bannerman-Chukualim B, Creek DJ, Crouch K, de Koning HP, Denise H, Ebikeme C, Fairlamb AH, Ferguson MAJ, Ginger ML, Hertz-Fowler C, Kerkhoven EJ, Mäser P, Michels PAM, Nayak A, Nes DW, Nolan DP, Olsen C, Silva-Franco F, Smith TK, Taylor MC, Tielens AGM, Urbaniak MD, van Hellemond JJ, Vincent IM, Wilkinson SR, Wyllie S, Opperdoes FR, Barrett MP, Jourdan F. TrypanoCyc: a community-led biochemical pathways database for Trypanosoma brucei. Nucleic Acids Res 2014; 43:D637-44. [PMID: 25300491 PMCID: PMC4384016 DOI: 10.1093/nar/gku944] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
The metabolic network of a cell represents the catabolic and anabolic reactions that interconvert small molecules (metabolites) through the activity of enzymes, transporters and non-catalyzed chemical reactions. Our understanding of individual metabolic networks is increasing as we learn more about the enzymes that are active in particular cells under particular conditions and as technologies advance to allow detailed measurements of the cellular metabolome. Metabolic network databases are of increasing importance in allowing us to contextualise data sets emerging from transcriptomic, proteomic and metabolomic experiments. Here we present a dynamic database, TrypanoCyc (http://www.metexplore.fr/trypanocyc/), which describes the generic and condition-specific metabolic network of Trypanosoma brucei, a parasitic protozoan responsible for human and animal African trypanosomiasis. In addition to enabling navigation through the BioCyc-based TrypanoCyc interface, we have also implemented a network-based representation of the information through MetExplore, yielding a novel environment in which to visualise the metabolism of this important parasite.
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Affiliation(s)
- Sanu Shameer
- Institut National de la Recherche Agronomique (INRA), UMR1331, TOXALIM (Research Centre in Food Toxicology), Université de Toulouse, Toulouse, France
| | | | - Florence Vinson
- Institut National de la Recherche Agronomique (INRA), UMR1331, TOXALIM (Research Centre in Food Toxicology), Université de Toulouse, Toulouse, France
| | - Ludovic Cottret
- Institut National de la Recherche Agronomique (INRA), UMR441, Laboratoire des Interactions Plantes-Microorganismes (LIPM), Auzeville, France
| | - Benjamin Merlet
- Institut National de la Recherche Agronomique (INRA), UMR1331, TOXALIM (Research Centre in Food Toxicology), Université de Toulouse, Toulouse, France
| | - Fiona Achcar
- University of Glasgow, Glasgow, Scotland, G12 8QQ, UK
| | - Michael Boshart
- Ludwig-Maximilians-Universität München, Biocenter, 82152-Martinsried, Germany
| | - Matthew Berriman
- The Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
| | - Rainer Breitling
- Manchester Institute of Biotechnology, Faculty of Life Sciences, University of Manchester, Manchester, UK
| | | | | | | | | | - Darren J Creek
- Monash Institute of Pharmaceutical Sciences, Monash University, Parkville 3052, Australia
| | | | | | - Hubert Denise
- European Bioinformatics Institute (EMBL-EBI), Hinxton, Cambridge, CB10 1SD, UK
| | | | | | | | - Michael L Ginger
- Divisionof Biomedical and Life Sciences, Lancaster University, Bailrigg, Lancaster, LA1 4YG, UK
| | | | - Eduard J Kerkhoven
- Chalmers University of Technology, Kemivägen 10, 412 96, Göteborg, Sweden
| | - Pascal Mäser
- Swiss Tropical and Public Health Institute, Socinstr. 57, Basel 4051, Switzerland
| | | | - Archana Nayak
- University of Glasgow, Glasgow, Scotland, G12 8QQ, UK
| | | | | | | | | | - Terry K Smith
- University of St Andrews, St Andrews, Scotland, KY16 9ST, UK
| | | | - Aloysius G M Tielens
- Utrecht University, Utrecht, 3508 TD, The Netherlands Erasmus University Medical Center, Rotterdam, 3015 CE, The Netherlands
| | - Michael D Urbaniak
- Divisionof Biomedical and Life Sciences, Lancaster University, Bailrigg, Lancaster, LA1 4YG, UK
| | | | | | | | - Susan Wyllie
- University of Dundee, Dundee, Scotland, DD1 4HN, UK
| | | | | | - Fabien Jourdan
- Institut National de la Recherche Agronomique (INRA), UMR1331, TOXALIM (Research Centre in Food Toxicology), Université de Toulouse, Toulouse, France
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Heitlinger E, Spork S, Lucius R, Dieterich C. The genome of Eimeria falciformis--reduction and specialization in a single host apicomplexan parasite. BMC Genomics 2014; 15:696. [PMID: 25142335 PMCID: PMC4287421 DOI: 10.1186/1471-2164-15-696] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2014] [Accepted: 07/19/2014] [Indexed: 01/28/2023] Open
Abstract
BACKGROUND The phylum Apicomplexa comprises important unicellular human parasites such as Toxoplasma and Plasmodium. Eimeria is the largest and most diverse genus of apicomplexan parasites and some species of the genus are the causative agent of coccidiosis, a disease economically devastating in poultry. We report a complete genome sequence of the mouse parasite Eimeria falciformis. We assembled and annotated the genome sequence to study host-parasite interactions in this understudied genus in a model organism host. RESULTS The genome of E. falciformis is 44 Mb in size and contains 5,879 predicted protein coding genes. Comparative analysis of E. falciformis with Toxoplasma gondii shows an emergence and diversification of gene families associated with motility and invasion mainly at the level of the Coccidia. Many rhoptry kinases, among them important virulence factors in T. gondii, are absent from the E. falciformis genome. Surface antigens are divergent between Eimeria species. Comparisons with T. gondii showed differences between genes involved in metabolism, N-glycan and GPI-anchor synthesis. E. falciformis possesses a reduced set of transmembrane transporters and we suggest an altered mode of iron uptake in the genus Eimeria. CONCLUSIONS Reduced diversity of genes required for host-parasite interaction and transmembrane transport allow hypotheses on host adaptation and specialization of a single host parasite. The E. falciformis genome sequence sheds light on the evolution of the Coccidia and helps to identify determinants of host-parasite interaction critical for drug and vaccine development.
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Affiliation(s)
- Emanuel Heitlinger
- />Department of Molecular Parasitology, Humboldt University, Philippstraße 13, 10115 Berlin, Germany
| | - Simone Spork
- />Department of Molecular Parasitology, Humboldt University, Philippstraße 13, 10115 Berlin, Germany
| | - Richard Lucius
- />Department of Molecular Parasitology, Humboldt University, Philippstraße 13, 10115 Berlin, Germany
| | - Christoph Dieterich
- />Computational RNA Biology and Ageing, Max Plank Institute for Biology of Ageing, Joseph-Stelzmann Straße 9b, 50913 Cologne, Germany
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Pantothenic acid biosynthesis in the parasite Toxoplasma gondii: a target for chemotherapy. Antimicrob Agents Chemother 2014; 58:6345-53. [PMID: 25049241 DOI: 10.1128/aac.02640-14] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Toxoplasma gondii is a major food pathogen and neglected parasitic infection that causes eye disease, birth defects, and fetal abortion and plays a role as an opportunistic infection in AIDS. In this study, we investigated pantothenic acid (vitamin B5) biosynthesis in T. gondii. Genes encoding the full repertoire of enzymes for pantothenate synthesis and subsequent metabolism to coenzyme A were identified and are expressed in T. gondii. A panel of inhibitors developed to target Mycobacterium tuberculosis pantothenate synthetase were tested and found to exhibit a range of values for inhibition of T. gondii growth. Two inhibitors exhibited lower effective concentrations than the currently used toxoplasmosis drug pyrimethamine. The inhibition was specific for the pantothenate pathway, as the effect of the pantothenate synthetase inhibitors was abrogated by supplementation with pantothenate. Hence, T. gondii encodes and expresses the enzymes for pantothenate synthesis, and this pathway is essential for parasite growth. These promising findings increase our understanding of growth and metabolism in this important parasite and highlight pantothenate synthetase as a new drug target.
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Croken MM, Qiu W, White MW, Kim K. Gene Set Enrichment Analysis (GSEA) of Toxoplasma gondii expression datasets links cell cycle progression and the bradyzoite developmental program. BMC Genomics 2014; 15:515. [PMID: 24962434 PMCID: PMC4092224 DOI: 10.1186/1471-2164-15-515] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2014] [Accepted: 06/17/2014] [Indexed: 11/10/2022] Open
Abstract
Background Large amounts of microarray expression data have been generated for the Apicomplexan parasite Toxoplasma gondii in an effort to identify genes critical for virulence or developmental transitions. However, researchers’ ability to analyze this data is limited by the large number of unannotated genes, including many that appear to be conserved hypothetical proteins restricted to Apicomplexa. Further, differential expression of individual genes is not always informative and often relies on investigators to draw big-picture inferences without the benefit of context. We hypothesized that customization of gene set enrichment analysis (GSEA) to T. gondii would enable us to rigorously test whether groups of genes serving a common biological function are co-regulated during the developmental transition to the latent bradyzoite form. Results Using publicly available T. gondii expression microarray data, we created Toxoplasma gene sets related to bradyzoite differentiation, oocyst sporulation, and the cell cycle. We supplemented these with lists of genes derived from community annotation efforts that identified contents of the parasite-specific organelles, rhoptries, micronemes, dense granules, and the apicoplast. Finally, we created gene sets based on metabolic pathways annotated in the KEGG database and Gene Ontology terms associated with gene annotations available at http://www.toxodb.org. These gene sets were used to perform GSEA analysis using two sets of published T. gondii expression data that characterized T. gondii stress response and differentiation to the latent bradyzoite form. Conclusions GSEA provides evidence that cell cycle regulation and bradyzoite differentiation are coupled. Δgcn5A mutants unable to induce bradyzoite-associated genes in response to alkaline stress have different patterns of cell cycle and bradyzoite gene expression from stressed wild-type parasites. Extracellular tachyzoites resemble a transitional state that differs in gene expression from both replicating intracellular tachyzoites and in vitro bradyzoites by expressing genes that are enriched in bradyzoites as well as genes that are associated with the G1 phase of the cell cycle. The gene sets we have created are readily modified to reflect ongoing research and will aid researchers’ ability to use a knowledge-based approach to data analysis facilitating the development of new insights into the intricate biology of Toxoplasma gondii. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-515) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | | | | | - Kami Kim
- Departments of Medicine, Microbiology & Immunology and Pathology, Albert Einstein College of Medicine, 1300 Morris Park Avenue, 10461 Bronx, NY, USA.
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Monney T, Hemphill A. Vaccines against neosporosis: what can we learn from the past studies? Exp Parasitol 2014; 140:52-70. [PMID: 24602874 DOI: 10.1016/j.exppara.2014.02.015] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2013] [Revised: 02/09/2014] [Accepted: 02/18/2014] [Indexed: 10/25/2022]
Abstract
Neospora caninum is an intracellular apicomplexan parasite, which is a leading cause of abortion in cattle; thus neosporosis represents an important veterinary health problem and is of high economic significance. The parasite can infect cattle via trans-placental transmission from an infected cow to its fetus (vertical transmission), or through the oral route via ingestion of food or water contaminated with oocysts that were previously shed with the feces of a canid definitive host (horizontal transmission). Although vaccination was considered a rational strategy to prevent bovine neosporosis, the only commercialized vaccine (Neoguard®) produced ambiguous results with relatively low efficacy, and was recently removed from the market. Therefore, there is a need to develop an efficient vaccine capable of preventing both, the horizontal transmission through infected food or water to a naïve animal as well as the vertical transmission from infected but clinically asymptomatic dams to the fetus. Different vaccine strategies have been investigated, including the use of live attenuated vaccines, killed parasite lysates, total antigens or antigen fractions from killed parasites, and subunit vaccines. The vast majority of experimental studies were performed in mice, and to a certain extent in gerbils, but there is also a large number of investigations that were conducted in cattle and sheep. However, it is difficult to directly compare these studies due to the high variability of the parameters employed. In this review, we will summarize the recent advances made in vaccine development against N. caninum in cattle and in mice and highlight the most important factors, which are likely to influence the degree of protection mediated by vaccination.
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Affiliation(s)
- Thierry Monney
- Institute of Parasitology, Vetsuisse Faculty, University of Berne, Länggass-Strasse 122, CH-3012 Berne, Switzerland
| | - Andrew Hemphill
- Institute of Parasitology, Vetsuisse Faculty, University of Berne, Länggass-Strasse 122, CH-3012 Berne, Switzerland.
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Exploitation of auxotrophies and metabolic defects in Toxoplasma as therapeutic approaches. Int J Parasitol 2014; 44:109-20. [DOI: 10.1016/j.ijpara.2013.09.003] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2013] [Revised: 09/22/2013] [Accepted: 09/22/2013] [Indexed: 12/30/2022]
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Shanmugasundram A, Gonzalez-Galarza FF, Wastling JM, Vasieva O, Jones AR. An integrated approach to understand apicomplexan metabolism from their genomes. BMC Bioinformatics 2014. [PMCID: PMC4071867 DOI: 10.1186/1471-2105-15-s3-a3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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Okamoto N, Keeling PJ. The 3D structure of the apical complex and association with the flagellar apparatus revealed by serial TEM tomography in Psammosa pacifica, a distant relative of the Apicomplexa. PLoS One 2014; 9:e84653. [PMID: 24392150 PMCID: PMC3879320 DOI: 10.1371/journal.pone.0084653] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2013] [Accepted: 11/17/2013] [Indexed: 11/18/2022] Open
Abstract
The apical complex is one of the defining features of apicomplexan parasites, including the malaria parasite Plasmodium, where it mediates host penetration and invasion. The apical complex is also known in a few related lineages, including several non-parasitic heterotrophs, where it mediates feeding behaviour. The origin of the apical complex is unclear, and one reason for this is that in apicomplexans it exists in only part of the life cycle, and never simultaneously with other major cytoskeletal structures like flagella and basal bodies. Here, we used conventional TEM and serial TEM tomography to reconstruct the three dimensional structure of the apical complex in Psammosa pacifica, a predatory relative of apicomplexans and dinoflagellates that retains the archetype apical complex and the flagellar apparatus simultaneously. The P. pacifica apical complex is associated with the gullet and consists of the pseudoconoid, micronemes, and electron dense vesicles. The pseudoconoid is a convex sheet consisting of eight short microtubules, plus a band made up of microtubules that originate from the flagellar apparatus. The flagellar apparatus consists of three microtubular roots. One of the microtubular roots attached to the posterior basal body is connected to bypassing microtubular strands, which are themselves connected to the extension of the pseudoconoid. These complex connections where the apical complex is an extension of the flagellar apparatus, reflect the ancestral state of both, dating back to the common ancestor of apicaomplexans and dinoflagellates.
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Affiliation(s)
- Noriko Okamoto
- The Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
| | - Patrick J. Keeling
- The Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
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Pollo-Oliveira L, Post H, Acencio ML, Lemke N, van den Toorn H, Tragante V, Heck AJR, Altelaar AFM, Yatsuda AP. Unravelling the Neospora caninum secretome through the secreted fraction (ESA) and quantification of the discharged tachyzoite using high-resolution mass spectrometry-based proteomics. Parasit Vectors 2013; 6:335. [PMID: 24267406 PMCID: PMC4182915 DOI: 10.1186/1756-3305-6-335] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2013] [Accepted: 11/15/2013] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The apicomplexan parasite Neospora caninum causes neosporosis, a disease that leads to abortion or stillbirth in cattle, generating an economic impact on the dairy and beef cattle trade. As an obligatory intracellular parasite, N. caninum needs to invade the host cell in an active manner to survive. The increase in parasite cytosolic Ca2+ upon contact with the host cell mediates critical events, including the exocytosis of phylum-specific secretory organelles and the activation of the parasite invasion motor. Because invasion is considered a requirement for pathogen survival and replication within the host, the identification of secreted proteins (secretome) involved in invasion may be useful to reveal interesting targets for therapeutic intervention. METHODS To chart the currently missing N. caninum secretome, we employed mass spectrometry-based proteomics to identify proteins present in the N. caninum tachyzoite using two different approaches. The first approach was identifying the proteins present in the tachyzoite-secreted fraction (ESA). The second approach was determining the relative quantification through peptide stable isotope labelling of the tachyzoites submitted to an ethanol secretion stimulus (discharged tachyzoite), expecting to identify the secreted proteins among the down-regulated group. RESULTS As a result, 615 proteins were identified at ESA and 2,011 proteins quantified at the discharged tachyzoite. We have analysed the connection between the secreted and the down-regulated proteins and searched for putative regulators of the secretion process among the up-regulated proteins. An interaction network was built by computational prediction involving the up- and down-regulated proteins. The mass spectrometry proteomics data have been deposited to the ProteomeXchange with identifier PXD000424. CONCLUSIONS The comparison between the protein abundances in ESA and their measure in the discharged tachyzoite allowed for a more precise identification of the most likely secreted proteins. Information from the network interaction and up-regulated proteins was important to recognise key proteins potentially involved in the metabolic regulation of secretion. Our results may be helpful to guide the selection of targets to be investigated against Neospora caninum and other Apicomplexan organisms.
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Affiliation(s)
- Letícia Pollo-Oliveira
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto e Núcleo de Apoio à Pesquisa em Produtos Naturais e Sintéticos (NPPNS), Universidade de São Paulo, Av do Café , s/n, Ribeirão Preto, SP 14040-903, Brazil
| | - Harm Post
- Biomolecular Mass Spectrometry and Proteomics, Utrecht Institute for Pharmaceutical Sciences and Bijvoet Centre for Biomolecular Research, Utrecht University, Padualaan 8, Utrecht 3884 CH, The Netherlands
- Netherlands Proteomics Centre, Padualaan 8, Utrecht 3884 CH, The Netherlands
| | - Marcio Luis Acencio
- Botucatu Institute of Biosciences, UNESP - Univ Estadual Paulista, Distrito de Rubião Jr, s/n, Botucatu, São Paulo 18918-970, Brazil
| | - Ney Lemke
- Botucatu Institute of Biosciences, UNESP - Univ Estadual Paulista, Distrito de Rubião Jr, s/n, Botucatu, São Paulo 18918-970, Brazil
| | - Henk van den Toorn
- Biomolecular Mass Spectrometry and Proteomics, Utrecht Institute for Pharmaceutical Sciences and Bijvoet Centre for Biomolecular Research, Utrecht University, Padualaan 8, Utrecht 3884 CH, The Netherlands
- Netherlands Proteomics Centre, Padualaan 8, Utrecht 3884 CH, The Netherlands
| | - Vinicius Tragante
- Division of Heart and Lungs, Department of Cardiology, University Medical Center Utrecht, Utrecht, The Netherlands
- Division of Biomedical Genetics, Department of Medical Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Albert JR Heck
- Biomolecular Mass Spectrometry and Proteomics, Utrecht Institute for Pharmaceutical Sciences and Bijvoet Centre for Biomolecular Research, Utrecht University, Padualaan 8, Utrecht 3884 CH, The Netherlands
- Netherlands Proteomics Centre, Padualaan 8, Utrecht 3884 CH, The Netherlands
| | - AF Maarten Altelaar
- Biomolecular Mass Spectrometry and Proteomics, Utrecht Institute for Pharmaceutical Sciences and Bijvoet Centre for Biomolecular Research, Utrecht University, Padualaan 8, Utrecht 3884 CH, The Netherlands
- Netherlands Proteomics Centre, Padualaan 8, Utrecht 3884 CH, The Netherlands
| | - Ana Patrícia Yatsuda
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto e Núcleo de Apoio à Pesquisa em Produtos Naturais e Sintéticos (NPPNS), Universidade de São Paulo, Av do Café , s/n, Ribeirão Preto, SP 14040-903, Brazil
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