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Murphy RD, Troublefield CA, Miracle JS, Young LEA, Brizzee CO, Dhara A, Sun RC, Vander Kooi CW, Gentry MS, Sinai AP. TgLaforin, a glucan phosphatase, reveals the dynamic role of storage polysaccharides in Toxoplasma gondii tachyzoites and bradyzoites. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.29.560185. [PMID: 37808860 PMCID: PMC10557770 DOI: 10.1101/2023.09.29.560185] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/10/2023]
Abstract
The asexual stages of Toxoplasma gondii are defined by the rapidly growing tachyzoite during the acute infection and by the slow growing bradyzoite housed within tissue cysts during the chronic infection. These stages represent unique physiological states, each with distinct glucans reflecting differing metabolic needs. A defining feature of T. gondii bradyzoites is the presence of insoluble storage glucans known as amylopectin granules (AGs) that are believed to play a role in reactivation, but their functions during the chronic infection remain largely unexplored. More recently, the presence of storage glucans has been recognized in tachyzoites where their precise function and architecture have yet to be fully defined. Importantly, the T. gondii genome encodes activities needed for glucan turnover: a glucan phosphatase (TgLaforin; TGME49_205290) and a glucan kinase (TgGWD; TGME49_214260) that catalyze a cycle of reversible glucan phosphorylation required for glucan degradation by amylases. The expression of these enzymes in tachyzoites supports the existence of a storage glucan, evidence that is corroborated by specific labeling with the anti-glycogen antibody IV58B6. Disruption of reversible glucan phosphorylation via a CRISPR/Cas9 knockout (KO) of TgLaforin revealed no growth defects under nutrient-replete conditions in tachyzoites. However, the growth of TgLaforin-KO tachyzoites was severely stunted when starved of glutamine, even under glucose replete conditions. The loss of TgLaforin also resulted in the attenuation of acute virulence in mice accompanied by a lower cyst burden. Defective cyst formation due to profound changes in AG morphology was also observed in TgLaforin-KO parasites, both in vitro and in vivo. Together, these data demonstrate the importance of glucan turnover across the T. gondii asexual cycle. These findings, alongside our previously identified class of small molecules that inhibit TgLaforin, implicate reversible glucan phosphorylation as a legitimate target for the development of new drugs against chronic T. gondii infections.
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Affiliation(s)
- Robert D Murphy
- Department of Microbiology, Immunology, and Molecular Genetics, College of Medicine, University of Kentucky
- Department of Molecular and Cellular Biochemistry, College of Medicine, University of Kentucky
| | - Cortni A Troublefield
- Department of Microbiology, Immunology, and Molecular Genetics, College of Medicine, University of Kentucky
| | - Joy S Miracle
- Department of Microbiology, Immunology, and Molecular Genetics, College of Medicine, University of Kentucky
| | - Lyndsay E A Young
- Department of Molecular and Cellular Biochemistry, College of Medicine, University of Kentucky
| | - Corey O Brizzee
- Department of Molecular and Cellular Biochemistry, College of Medicine, University of Kentucky
| | - Animesh Dhara
- Department of Microbiology, Immunology, and Molecular Genetics, College of Medicine, University of Kentucky
| | - Ramon C Sun
- Department of Molecular and Cellular Biochemistry, College of Medicine, University of Kentucky
| | - Craig W Vander Kooi
- Department of Molecular and Cellular Biochemistry, College of Medicine, University of Kentucky
| | - Matthew S Gentry
- Department of Molecular and Cellular Biochemistry, College of Medicine, University of Kentucky
| | - Anthony P Sinai
- Department of Molecular and Cellular Biochemistry, College of Medicine, University of Kentucky
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2
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dos Santos DA, Souza HFS, Silber AM, de Souza TDACB, Ávila AR. Protein kinases on carbon metabolism: potential targets for alternative chemotherapies against toxoplasmosis. Front Cell Infect Microbiol 2023; 13:1175409. [PMID: 37287468 PMCID: PMC10242022 DOI: 10.3389/fcimb.2023.1175409] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Accepted: 05/02/2023] [Indexed: 06/09/2023] Open
Abstract
The apicomplexan parasite Toxoplasma gondii is the causative agent of toxoplasmosis, a global disease that significantly impacts human health. The clinical manifestations are mainly observed in immunocompromised patients, including ocular damage and neuronal alterations leading to psychiatric disorders. The congenital infection leads to miscarriage or severe alterations in the development of newborns. The conventional treatment is limited to the acute phase of illness, without effects in latent parasites; consequently, a cure is not available yet. Furthermore, considerable toxic effects and long-term therapy contribute to high treatment abandonment rates. The investigation of exclusive parasite pathways would provide new drug targets for more effective therapies, eliminating or reducing the side effects of conventional pharmacological approaches. Protein kinases (PKs) have emerged as promising targets for developing specific inhibitors with high selectivity and efficiency against diseases. Studies in T. gondii have indicated the presence of exclusive PKs without homologs in human cells, which could become important targets for developing new drugs. Knockout of specific kinases linked to energy metabolism have shown to impair the parasite development, reinforcing the essentiality of these enzymes in parasite metabolism. In addition, the specificities found in the PKs that regulate the energy metabolism in this parasite could bring new perspectives for safer and more efficient therapies for treating toxoplasmosis. Therefore, this review provides an overview of the limitations for reaching an efficient treatment and explores the role of PKs in regulating carbon metabolism in Toxoplasma, discussing their potential as targets for more applied and efficient pharmacological approaches.
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Affiliation(s)
| | - Higo Fernando Santos Souza
- Laboratory of Biochemistry of Trypanosomes (LabTryp), Departamento de Parasitologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo, Brazil
| | - Ariel M. Silber
- Laboratory of Biochemistry of Trypanosomes (LabTryp), Departamento de Parasitologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo, Brazil
| | | | - Andréa Rodrigues Ávila
- Laboratório de Pesquisa em Apicomplexa, Instituto Carlos Chagas, Fiocruz, Curitiba, Brazil
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3
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Niu Z, Ye S, Liu J, Lyu M, Xue L, Li M, Lyu C, Zhao J, Shen B. Two apicoplast dwelling glycolytic enzymes provide key substrates for metabolic pathways in the apicoplast and are critical for Toxoplasma growth. PLoS Pathog 2022; 18:e1011009. [PMID: 36449552 PMCID: PMC9744290 DOI: 10.1371/journal.ppat.1011009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Revised: 12/12/2022] [Accepted: 11/20/2022] [Indexed: 12/05/2022] Open
Abstract
Many apicomplexan parasites harbor a non-photosynthetic plastid called the apicoplast, which hosts important metabolic pathways like the methylerythritol 4-phosphate (MEP) pathway that synthesizes isoprenoid precursors. Yet many details in apicoplast metabolism are not well understood. In this study, we examined the physiological roles of four glycolytic enzymes in the apicoplast of Toxoplasma gondii. Many glycolytic enzymes in T. gondii have two or more isoforms. Endogenous tagging each of these enzymes found that four of them were localized to the apicoplast, including pyruvate kinase2 (PYK2), phosphoglycerate kinase 2 (PGK2), triosephosphate isomerase 2 (TPI2) and phosphoglyceraldehyde dehydrogenase 2 (GAPDH2). The ATP generating enzymes PYK2 and PGK2 were thought to be the main energy source of the apicoplast. Surprisingly, deleting PYK2 and PGK2 individually or simultaneously did not cause major defects on parasite growth or virulence. In contrast, TPI2 and GAPDH2 are critical for tachyzoite proliferation. Conditional depletion of TPI2 caused significant reduction in the levels of MEP pathway intermediates and led to parasite growth arrest. Reconstitution of another isoprenoid precursor synthesis pathway called the mevalonate pathway in the TPI2 depletion mutant partially rescued its growth defects. Similarly, knocking down the GAPDH2 enzyme that produces NADPH also reduced isoprenoid precursor synthesis through the MEP pathway and inhibited parasite proliferation. In addition, it reduced de novo fatty acid synthesis in the apicoplast. Together, these data suggest a model that the apicoplast dwelling TPI2 provides carbon source for the synthesis of isoprenoid precursor, whereas GAPDH2 supplies reducing power for pathways like MEP, fatty acid synthesis and ferredoxin redox system in T. gondii. As such, both enzymes are critical for parasite growth and serve as potential targets for anti-toxoplasmic intervention designs. On the other hand, the dispensability of PYK2 and PGK2 suggest additional sources for energy in the apicoplast, which deserves further investigation.
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Affiliation(s)
- Zhipeng Niu
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei Province, PR China
| | - Shu Ye
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei Province, PR China
| | - Jiaojiao Liu
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei Province, PR China
| | - Mengyu Lyu
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei Province, PR China
| | - Lilan Xue
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei Province, PR China
| | - Muxiao Li
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei Province, PR China
| | - Congcong Lyu
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei Province, PR China
| | - Junlong Zhao
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei Province, PR China
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, Wuhan, Hubei Province, PR China
| | - Bang Shen
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei Province, PR China
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, Wuhan, Hubei Province, PR China
- Hubei Hongshan Laboratory, Wuhan, Hubei Province, PR China
- Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Shenzhen, Guangdong Province, PR China
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong Province, PR China
- * E-mail:
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4
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Nie LB, Liang QL, Wang M, Du R, Zhang MY, Elsheikha HM, Zhu XQ. Global profiling of protein lysine malonylation in Toxoplasma gondii strains of different virulence and genetic backgrounds. PLoS Negl Trop Dis 2022; 16:e0010431. [PMID: 35576189 PMCID: PMC9135328 DOI: 10.1371/journal.pntd.0010431] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2022] [Revised: 05/26/2022] [Accepted: 04/18/2022] [Indexed: 11/22/2022] Open
Abstract
Lysine malonylation is a post-translational modification (PTM), which regulates many cellular processes. Limited information is available about the level of lysine malonylation variations between Toxoplasma gondii strains of distinct genetic lineages. Yet, insights into such variations are needed to understand the extent to which lysine malonylation contributes to the differences in the virulence and repertoire of virulence factors between T. gondii genotypes. In this study, we profiled lysine malonylation in T. gondii using quantitative liquid chromatography-tandem mass spectrometry (LC-MS/MS) and immuno-affinity purification. This analysis was performed on three T. gondii strains with distinctive pathogenicity in mice, including RH strain (type I), PRU strain (type II), and VEG strain (type III). In total, 111 differentially malonylated proteins and 152 sites were upregulated, and 17 proteins and 17 sites were downregulated in RH strain versus PRU strain; 50 proteins and 59 sites were upregulated, 50 proteins and 53 sites were downregulated in RH strain versus VEG strain; and 72 proteins and 90 sites were upregulated, and 7 proteins and 8 sites were downregulated in VEG strain versus PRU strain. Differentially malonylated proteins were involved in key processes, such as those mediating the regulation of protein metabolism, stress response, glycolysis, and actin cytoskeleton. These results reveal an association between lysine malonylation and intra-species virulence differences in T. gondii and offer a new resource for elucidating the contribution of lysine malonylation to energy metabolism and virulence in T. gondii. Lysine malonylation has been shown to play important roles in various biological processes in Toxoplasma gondii. Here, we used quantitative liquid chromatography-tandem mass spectrometry (LC-MS/MS) and immuno-affinity purification to test the hypothesis that lysine malonylation underpins the inter-genotype differences in the virulence of T. gondii. Several up-regulated and down- regulated malonylated proteins were identified in the tachyzoites of RH (type I) strain, PRU (type II) strain, and VEG (type III) strain. Differentially regulated malonylated proteins were enriched in many biological and metabolic pathways, and were found to contribute T. gondii energy metabolism, stress response, and infectivity, suggesting the role of lysine malonylation in the regulation of T. gondii virulence. These findings expand our knowledge of lysine malonylation in T. gondii and provide more insight into the mechanisms mediating the virulence differences between T. gondii strains of different genotypes.
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Affiliation(s)
- Lan-Bi Nie
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, People’s Republic of China
- College of Animal Science and Technology, Jilin Agricultural University, Changchun, People’s Republic of China
- College of Veterinary Medicine, Shanxi Agricultural University, Taigu, People’s Republic of China
| | - Qin-Li Liang
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, People’s Republic of China
| | - Meng Wang
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, People’s Republic of China
| | - Rui Du
- College of Animal Science and Technology, Jilin Agricultural University, Changchun, People’s Republic of China
| | - Meng-Yuan Zhang
- Jingjie PTM Biolabs (Hangzhou) Co. Ltd., Hangzhou, People’s Republic of China
| | - Hany M. Elsheikha
- Faculty of Medicine and Health Sciences, School of Veterinary Medicine and Science, University of Nottingham, Loughborough, United Kingdom
- * E-mail: (HME); (XQZ)
| | - Xing-Quan Zhu
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, People’s Republic of China
- College of Veterinary Medicine, Shanxi Agricultural University, Taigu, People’s Republic of China
- Key Laboratory of Veterinary Public Health of Yunnan Province, College of Veterinary Medicine, Yunnan Agricultural University, Kunming, People’s Republic of China
- * E-mail: (HME); (XQZ)
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5
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Celebi M, Inan T, Kurkcuoglu O, Akten ED. Potential allosteric sites captured in glycolytic enzymes via residue-based network models: Phosphofructokinase, glyceraldehyde-3-phosphate dehydrogenase and pyruvate kinase. Biophys Chem 2021; 280:106701. [PMID: 34736071 DOI: 10.1016/j.bpc.2021.106701] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Revised: 10/12/2021] [Accepted: 10/19/2021] [Indexed: 01/05/2023]
Abstract
Likelihood of new allosteric sites for glycolytic enzymes, phosphofructokinase (PFK), glyceraldehyde-3-phosphate dehydrogenase (GADPH) and pyruvate kinase (PK) was evaluated for bacterial, parasitic and human species. Allosteric effect of a ligand binding at a site was revealed on the basis of low-frequency normal modes via Cα-harmonic residue network model. In bacterial PFK, perturbation of the proposed allosteric site outperformed the known allosteric one, producing a high amount of stabilization or reduced dynamics, on all catalytic regions. Another proposed allosteric spot at the dimer interface in parasitic PFK exhibited major stabilization effect on catalytic regions. In parasitic GADPH, the most desired allosteric response was observed upon perturbation of its tunnel region which incorporated key residues for functional regulation. Proposed allosteric site in bacterial PK produced a satisfactory allosteric response on all catalytic regions, whereas in human and parasitic PKs, a partial inhibition was observed. Residue network model based solely on contact topology identified the 'hub residues' with high betweenness tracing plausible allosteric communication pathways between distant functional sites. For both bacterial PFK and PK, proposed sites accommodated hub residues twice as much as the known allosteric site. Tunnel region in parasitic GADPH with the strongest allosteric effect among species, incorporated the highest number of hub residues. These results clearly suggest a one-to-one correspondence between the degree of allosteric effect and the number of hub residues in that perturbation site, which increases the likelihood of its allosteric nature.
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Affiliation(s)
- Metehan Celebi
- Graduate Program of Computational Biology and Bioinformatics, Graduate School of Science and Engineering, Kadir Has University, Istanbul, Turkey
| | - Tugce Inan
- Department of Chemical Engineering, Istanbul Technical University, Istanbul, Turkey
| | - Ozge Kurkcuoglu
- Department of Chemical Engineering, Istanbul Technical University, Istanbul, Turkey
| | - Ebru Demet Akten
- Department of Bioinformatics and Genetics, Faculty of Engineering and Natural Sciences, Kadir Has University, Istanbul, Turkey.
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Gubbels MJ, Keroack CD, Dangoudoubiyam S, Worliczek HL, Paul AS, Bauwens C, Elsworth B, Engelberg K, Howe DK, Coppens I, Duraisingh MT. Fussing About Fission: Defining Variety Among Mainstream and Exotic Apicomplexan Cell Division Modes. Front Cell Infect Microbiol 2020; 10:269. [PMID: 32582569 PMCID: PMC7289922 DOI: 10.3389/fcimb.2020.00269] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2020] [Accepted: 05/06/2020] [Indexed: 12/17/2022] Open
Abstract
Cellular reproduction defines life, yet our textbook-level understanding of cell division is limited to a small number of model organisms centered around humans. The horizon on cell division variants is expanded here by advancing insights on the fascinating cell division modes found in the Apicomplexa, a key group of protozoan parasites. The Apicomplexa display remarkable variation in offspring number, whether karyokinesis follows each S/M-phase or not, and whether daughter cells bud in the cytoplasm or bud from the cortex. We find that the terminology used to describe the various manifestations of asexual apicomplexan cell division emphasizes either the number of offspring or site of budding, which are not directly comparable features and has led to confusion in the literature. Division modes have been primarily studied in two human pathogenic Apicomplexa, malaria-causing Plasmodium spp. and Toxoplasma gondii, a major cause of opportunistic infections. Plasmodium spp. divide asexually by schizogony, producing multiple daughters per division round through a cortical budding process, though at several life-cycle nuclear amplifications stages, are not followed by karyokinesis. T. gondii divides by endodyogeny producing two internally budding daughters per division round. Here we add to this diversity in replication mechanisms by considering the cattle parasite Babesia bigemina and the pig parasite Cystoisospora suis. B. bigemina produces two daughters per division round by a “binary fission” mechanism whereas C. suis produces daughters through both endodyogeny and multiple internal budding known as endopolygeny. In addition, we provide new data from the causative agent of equine protozoal myeloencephalitis (EPM), Sarcocystis neurona, which also undergoes endopolygeny but differs from C. suis by maintaining a single multiploid nucleus. Overall, we operationally define two principally different division modes: internal budding found in cyst-forming Coccidia (comprising endodyogeny and two forms of endopolygeny) and external budding found in the other parasites studied (comprising the two forms of schizogony, binary fission and multiple fission). Progressive insights into the principles defining the molecular and cellular requirements for internal vs. external budding, as well as variations encountered in sexual stages are discussed. The evolutionary pressures and mechanisms underlying apicomplexan cell division diversification carries relevance across Eukaryota.
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Affiliation(s)
- Marc-Jan Gubbels
- Department of Biology, Boston College, Chestnut Hill, MA, United States
| | - Caroline D Keroack
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Harvard University, Boston, MA, United States
| | - Sriveny Dangoudoubiyam
- Department of Veterinary Science, Gluck Equine Research Center, University of Kentucky, Lexington, KY, United States
| | - Hanna L Worliczek
- Department of Biology, Boston College, Chestnut Hill, MA, United States.,Institute of Parasitology, University of Veterinary Medicine, Vienna, Austria
| | - Aditya S Paul
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Harvard University, Boston, MA, United States
| | - Ciara Bauwens
- Department of Biology, Boston College, Chestnut Hill, MA, United States
| | - Brendan Elsworth
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Harvard University, Boston, MA, United States.,School of Biosciences, University of Melbourne, Melbourne, VIC, Australia
| | - Klemens Engelberg
- Department of Biology, Boston College, Chestnut Hill, MA, United States
| | - Daniel K Howe
- Department of Veterinary Science, Gluck Equine Research Center, University of Kentucky, Lexington, KY, United States
| | - Isabelle Coppens
- Department of Molecular Microbiology and Immunology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, United States
| | - Manoj T Duraisingh
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Harvard University, Boston, MA, United States
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7
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Ayyildiz M, Celiker S, Ozhelvaci F, Akten ED. Identification of Alternative Allosteric Sites in Glycolytic Enzymes for Potential Use as Species-Specific Drug Targets. Front Mol Biosci 2020; 7:88. [PMID: 32478093 PMCID: PMC7240002 DOI: 10.3389/fmolb.2020.00088] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Accepted: 04/16/2020] [Indexed: 12/22/2022] Open
Abstract
Three allosteric glycolytic enzymes, phosphofructokinase, glyceraldehyde-3 phosphate dehydrogenase and pyruvate kinase, associated with bacterial, parasitic and human species, were explored to identify potential allosteric sites that would be used as prime targets for species-specific drug design purposes using a newly developed approach which incorporates solvent mapping, elastic network modeling, sequence and structural alignments. The majority of binding sites detected by solvent mapping overlapped with the interface regions connecting the subunits, thus appeared as promising target sites for allosteric regulation. Each binding site was then evaluated by its ability to alter the global dynamics of the receptor defined by the percentage change in the frequencies of the lowest-frequency modes most significantly and as anticipated, the most effective ones were detected in the vicinity of the well-reported catalytic and allosteric sites. Furthermore, some of our proposed regions intersected with experimentally resolved sites which are known to be critical for activity regulation, which further validated our approach. Despite the high degree of structural conservation encountered between bacterial/parasitic and human glycolytic enzymes, the majority of the newly presented allosteric sites exhibited a low degree of sequence conservation which further increased their likelihood to be used as species-specific target regions for drug design studies.
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Affiliation(s)
- Merve Ayyildiz
- Graduate Program of Computational Biology and Bioinformatics, Graduate School of Science and Engineering, Kadir Has University, Istanbul, Turkey
| | - Serkan Celiker
- Graduate Program of Computational Biology and Bioinformatics, Graduate School of Science and Engineering, Kadir Has University, Istanbul, Turkey
| | - Fatih Ozhelvaci
- Graduate Program of Computational Science and Engineering, Graduate School of Science and Engineering, Bogazici University, Istanbul, Turkey
| | - E. Demet Akten
- Department of Bioinformatics and Genetics, Faculty of Engineering and Natural Sciences, Kadir Has University, Istanbul, Turkey
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8
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Nie LB, Liang QL, Du R, Elsheikha HM, Han NJ, Li FC, Zhu XQ. Global Proteomic Analysis of Lysine Malonylation in Toxoplasma gondii. Front Microbiol 2020; 11:776. [PMID: 32411114 PMCID: PMC7198775 DOI: 10.3389/fmicb.2020.00776] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Accepted: 03/31/2020] [Indexed: 11/17/2022] Open
Abstract
Lysine malonylation (Kmal) is a new post-translational modification (PTM), which has been reported in several prokaryotic and eukaryotic species. Although Kmal can regulate many and diverse biological processes in various organisms, knowledge about this important PTM in the apicomplexan parasite Toxoplasma gondii is limited. In this study, we performed the first global profiling of malonylated proteins in T. gondii tachyzoites using affinity enrichment and Liquid chromatography-tandem mass spectrometry (LC-MS/MS) analysis. Three experiments performed in tandem revealed 294, 345, 352 Kmal sites on 203, 236, 230 malonylated proteins, respectively. Computational analysis showed the identified malonylated proteins to be localized in various subcellular compartments and involved in many cellular functions, particularly mitochondrial function. Additionally, one conserved Kmal motif with a strong bias for cysteine was detected. Taken together, these findings provide the first report of Kmal profile in T. gondii and should be an important resource for studying the physiological roles of Kmal in this parasite.
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Affiliation(s)
- Lan-Bi Nie
- College of Animal Science and Technology, Jilin Agricultural University, Changchun, China.,State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Qin-Li Liang
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Rui Du
- College of Animal Science and Technology, Jilin Agricultural University, Changchun, China
| | - Hany M Elsheikha
- Faculty of Medicine and Health Sciences, School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington Campus, Loughborough, United Kingdom
| | - Nai-Jian Han
- Jingjie PTM Biolabs (Hangzhou) Co. Ltd., Hangzhou, China
| | - Fa-Cai Li
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Xing-Quan Zhu
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China
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9
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Baptista CG, Lis A, Deng B, Gas-Pascual E, Dittmar A, Sigurdson W, West CM, Blader IJ. Toxoplasma F-box protein 1 is required for daughter cell scaffold function during parasite replication. PLoS Pathog 2019; 15:e1007946. [PMID: 31348812 PMCID: PMC6685633 DOI: 10.1371/journal.ppat.1007946] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Revised: 08/07/2019] [Accepted: 06/27/2019] [Indexed: 01/06/2023] Open
Abstract
By binding to the adaptor protein SKP1 and serving as substrate receptors for the SKP1 Cullin, F-box E3 ubiquitin ligase complex, F-box proteins regulate critical cellular processes including cell cycle progression and membrane trafficking. While F-box proteins are conserved throughout eukaryotes and are well studied in yeast, plants, and animals, studies in parasitic protozoa are lagging. We have identified eighteen putative F-box proteins in the Toxoplasma genome of which four have predicted homologs in Plasmodium. Two of the conserved F-box proteins were demonstrated to be important for Toxoplasma fitness and here we focus on an F-box protein, named TgFBXO1, because it is the most highly expressed by replicative tachyzoites and was also identified in an interactome screen as a Toxoplasma SKP1 binding protein. TgFBXO1 interacts with Toxoplasma SKP1 confirming it as a bona fide F-box protein. In interphase parasites, TgFBXO1 is a component of the Inner Membrane Complex (IMC), which is an organelle that underlies the plasma membrane. Early during replication, TgFBXO1 localizes to the developing daughter cell scaffold, which is the site where the daughter cell IMC and microtubules form and extend from. TgFBXO1 localization to the daughter cell scaffold required centrosome duplication but before kinetochore separation was completed. Daughter cell scaffold localization required TgFBXO1 N-myristoylation and was dependent on the small molecular weight GTPase, TgRab11b. Finally, we demonstrate that TgFBXO1 is required for parasite growth due to its function as a daughter cell scaffold effector. TgFBXO1 is the first F-box protein to be studied in apicomplexan parasites and represents the first protein demonstrated to be important for daughter cell scaffold function.
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Affiliation(s)
- Carlos Gustavo Baptista
- Department of Microbiology and Immunology, University at Buffalo School of Medicine, Buffalo, New York, United States of America
| | - Agnieszka Lis
- Department of Microbiology and Immunology, University at Buffalo School of Medicine, Buffalo, New York, United States of America
| | - Bowen Deng
- Department of Biochemistry & Molecular Biology, University of Georgia, Athens, Georgia, United States of America
| | - Elisabet Gas-Pascual
- Department of Biochemistry & Molecular Biology, University of Georgia, Athens, Georgia, United States of America
| | - Ashley Dittmar
- Department of Microbiology and Immunology, University at Buffalo School of Medicine, Buffalo, New York, United States of America
| | - Wade Sigurdson
- Department of Physiology and Biophysics, University at Buffalo School of Medicine, Buffalo, New York, United States of America
| | - Christopher M. West
- Department of Biochemistry & Molecular Biology, University of Georgia, Athens, Georgia, United States of America
| | - Ira J. Blader
- Department of Microbiology and Immunology, University at Buffalo School of Medicine, Buffalo, New York, United States of America
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10
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Lykins JD, Filippova EV, Halavaty AS, Minasov G, Zhou Y, Dubrovska I, Flores KJ, Shuvalova LA, Ruan J, El Bissati K, Dovgin S, Roberts CW, Woods S, Moulton JD, Moulton H, McPhillie MJ, Muench SP, Fishwick CWG, Sabini E, Shanmugam D, Roos DS, McLeod R, Anderson WF, Ngô HM. CSGID Solves Structures and Identifies Phenotypes for Five Enzymes in Toxoplasma gondii. Front Cell Infect Microbiol 2018; 8:352. [PMID: 30345257 PMCID: PMC6182094 DOI: 10.3389/fcimb.2018.00352] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Accepted: 09/14/2018] [Indexed: 12/23/2022] Open
Abstract
Toxoplasma gondii, an Apicomplexan parasite, causes significant morbidity and mortality, including severe disease in immunocompromised hosts and devastating congenital disease, with no effective treatment for the bradyzoite stage. To address this, we used the Tropical Disease Research database, crystallography, molecular modeling, and antisense to identify and characterize a range of potential therapeutic targets for toxoplasmosis. Phosphoglycerate mutase II (PGMII), nucleoside diphosphate kinase (NDK), ribulose phosphate 3-epimerase (RPE), ribose-5-phosphate isomerase (RPI), and ornithine aminotransferase (OAT) were structurally characterized. Crystallography revealed insights into the overall structure, protein oligomeric states and molecular details of active sites important for ligand recognition. Literature and molecular modeling suggested potential inhibitors and druggability. The targets were further studied with vivoPMO to interrupt enzyme synthesis, identifying the targets as potentially important to parasitic replication and, therefore, of therapeutic interest. Targeted vivoPMO resulted in statistically significant perturbation of parasite replication without concomitant host cell toxicity, consistent with a previous CRISPR/Cas9 screen showing PGM, RPE, and RPI contribute to parasite fitness. PGM, RPE, and RPI have the greatest promise for affecting replication in tachyzoites. These targets are shared between other medically important parasites and may have wider therapeutic potential.
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Affiliation(s)
- Joseph D. Lykins
- Pritzker School of Medicine, University of Chicago, Chicago, IL, United States
| | - Ekaterina V. Filippova
- Center for Structural Genomics of Infectious Diseases and the Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, United States
| | - Andrei S. Halavaty
- Center for Structural Genomics of Infectious Diseases and the Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, United States
| | - George Minasov
- Center for Structural Genomics of Infectious Diseases and the Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, United States
| | - Ying Zhou
- Department of Ophthalmology and Visual Sciences, University of Chicago, Chicago, IL, United States
| | - Ievgeniia Dubrovska
- Center for Structural Genomics of Infectious Diseases and the Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, United States
| | - Kristin J. Flores
- Center for Structural Genomics of Infectious Diseases and the Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, United States
| | - Ludmilla A. Shuvalova
- Center for Structural Genomics of Infectious Diseases and the Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, United States
| | - Jiapeng Ruan
- Center for Structural Genomics of Infectious Diseases and the Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, United States
| | - Kamal El Bissati
- Department of Ophthalmology and Visual Sciences, University of Chicago, Chicago, IL, United States
| | - Sarah Dovgin
- Illinois Math and Science Academy, Aurora, IL, United States
| | - Craig W. Roberts
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, United Kingdom
| | - Stuart Woods
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, United Kingdom
| | | | - Hong Moulton
- Department of Biomedical Sciences, College of Veterinary Medicine, Oregon State University, Corvallis, OR, United States
| | - Martin J. McPhillie
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield, United Kingdom
| | - Stephen P. Muench
- School of Biomedical Sciences, Faculty of Biological Sciences, and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, United Kingdom
| | - Colin W. G. Fishwick
- School of Chemistry and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, United Kingdom
| | - Elisabetta Sabini
- Center for Structural Genomics of Infectious Diseases and the Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, United States
| | | | - David S. Roos
- Department of Biology, University of Pennsylvania, Philadelphia, PA, United States
| | - Rima McLeod
- Department of Ophthalmology and Visual Sciences, University of Chicago, Chicago, IL, United States
- Department of Pediatrics (Infectious Diseases), Institute of Genomics, Genetics, and Systems Biology, Global Health Center, Toxoplasmosis Center, CHeSS, The College, University of Chicago, Chicago, IL, United States
| | - Wayne F. Anderson
- Center for Structural Genomics of Infectious Diseases and the Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, United States
| | - Huân M. Ngô
- Center for Structural Genomics of Infectious Diseases and the Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, United States
- BrainMicro LLC, New Haven, CT, United States
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11
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Two Phosphoglucomutase Paralogs Facilitate Ionophore-Triggered Secretion of the Toxoplasma Micronemes. mSphere 2017; 2:mSphere00521-17. [PMID: 29202046 PMCID: PMC5705807 DOI: 10.1128/msphere.00521-17] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Accepted: 11/05/2017] [Indexed: 12/28/2022] Open
Abstract
Ca2+-dependent exocytosis is essential for the life cycle of apicomplexan parasites. Toxoplasma gondii harbors a phosphoglucomutase (PGM) ortholog, PRP1, previously associated with Ca2+-dependent microneme secretion. Here it is shown that genetic deletion of either PRP1, its PGM2 ortholog, or both genes is dispensable for the parasite’s lytic cycle, including host cell egress and invasion. Depletion of the proteins abrogated high Ca2+-mediated microneme secretion induced by the ionophore A23187; however, the constitutive and phosphatidic acid-mediated release remained unaffected. Secretion mediated by the former pathway is not essential for tachyzoite survival or acute in vivo infection in the mice. Paralogs of the widely prevalent phosphoglucomutase (PGM) protein called parafusin function in calcium (Ca2+)-mediated exocytosis across eukaryotes. In Toxoplasma gondii, the parafusin-related protein 1 (PRP1) has been associated with Ca2+-dependent microneme organelle secretion required for essential processes like host cell invasion and egress. Using reverse genetics, we observed PRP1 to be dispensable for completion of the lytic cycle, including host cell invasion and egress by the parasite. However, the absence of the gene affected increased microneme release triggered by A23187, a Ca2+ ionophore used to raise the cytoplasmic Ca2+ concentration mimicking the physiological role of Ca2+ during invasion and egress. The basal levels of constitutive microneme release in extracellular parasites and phosphatidic acid-triggered microneme secretion were unaffected in the mutant. The phenotype of the deletion mutant of the second PGM-encoding gene in Toxoplasma, PGM2, was similar to the phenotype of the PRP1 deletion mutant. Furthermore, the ability of the tachyzoites to induce acute infection in the mice remained normal in the absence of both PGM paralogs. Our data thus reveal that the microneme secretion upon high Ca2+ flux is facilitated by the Toxoplasma PGM paralogs, PRP1 and PGM2. However, this protein-mediated release is neither essential for lytic cycle completion nor for acute virulence of the parasite. IMPORTANCE Ca2+-dependent exocytosis is essential for the life cycle of apicomplexan parasites. Toxoplasma gondii harbors a phosphoglucomutase (PGM) ortholog, PRP1, previously associated with Ca2+-dependent microneme secretion. Here it is shown that genetic deletion of either PRP1, its PGM2 ortholog, or both genes is dispensable for the parasite’s lytic cycle, including host cell egress and invasion. Depletion of the proteins abrogated high Ca2+-mediated microneme secretion induced by the ionophore A23187; however, the constitutive and phosphatidic acid-mediated release remained unaffected. Secretion mediated by the former pathway is not essential for tachyzoite survival or acute in vivo infection in the mice.
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