1
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Jimenéz-Ruiz E, Li W, Meissner M. Where is the EXIT? Phenotypic screens for new egress factors in apicomplexan parasites. Mol Microbiol 2024; 121:359-367. [PMID: 37740453 DOI: 10.1111/mmi.15166] [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: 06/23/2023] [Revised: 08/31/2023] [Accepted: 09/05/2023] [Indexed: 09/24/2023]
Abstract
Apicomplexans, such as Plasmodium and Toxoplasma are obligate intracellular parasites that invade, replicate and finally EXIT their host cell. During replication within a parasitophorous vacuole (PV), the parasites establish an extensive F-actin-containing network that connects individual parasites and is required for material exchange, recycling and the final steps of daughter cell assembly. After multiple rounds of replication, the parasites exit the host cell involving multiple signalling cascades, disassembly of the network, secretion of microneme proteins and activation of the acto-myosin motor. Blocking the host cell EXIT process leads to the formation of large PVs, making the screening for genes involved in exiting the cell relatively straightforward. Given that apicomplexans are highly diverse from other eukaryotes, approximately 30% of all genes are annotated as hypothetical, some apicomplexan-specific factors are likely to be critical during EXIT. This motivated several labs to design and perform forward genetic and phenotypic screens using various approaches, such as random insertion mutagenesis, temperature-sensitive mutants and, more recently, CRISPR/Cas9-mediated targeted editing and conditional mutagenesis. Here we will provide an overview of the technological developments over recent years and the most successful stories that led to the identification of new critical factors in Toxoplasma gondii.
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Affiliation(s)
- Elena Jimenéz-Ruiz
- Experimental Parasitology, Department of Veterinary Sciences, Faculty of Veterinary Medicine, Ludwig-Maximilians-Universität, LMU, Munich, Germany
| | - Wei Li
- Experimental Parasitology, Department of Veterinary Sciences, Faculty of Veterinary Medicine, Ludwig-Maximilians-Universität, LMU, Munich, Germany
| | - Markus Meissner
- Experimental Parasitology, Department of Veterinary Sciences, Faculty of Veterinary Medicine, Ludwig-Maximilians-Universität, LMU, Munich, Germany
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2
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Pal S, Dam S. CRISPR-Cas9: Taming protozoan parasites with bacterial scissor. J Parasit Dis 2022; 46:1204-1212. [PMID: 36457766 PMCID: PMC9606157 DOI: 10.1007/s12639-022-01534-x] [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: 05/30/2022] [Accepted: 09/12/2022] [Indexed: 10/14/2022] Open
Abstract
The invention of CRISPR-Cas9 technology has opened a new era in which genome manipulation has become precise, faster, cheap and more accurate than previous genome editing strategies. Despite the intricacies of the genomes associated with several protozoan parasites, CRISPR-Cas9 has made a substantial contribution to parasitology. The study of functional genomics through CRISPR-Cas9 mediated gene knockout, insertion, deletion and mutation has helped in understanding intrinsic parasite biology. The invention of CRISPR-dCas9 has helped in the programmable control of protozoan gene expression and epigenetic engineering. CRISPR and CRISPR-based alternatives will continue to thrive and may aid in the development of novel anti-protozoan strategies to tame the protozoan parasites in the imminent future.
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Affiliation(s)
- Suchetana Pal
- Department of Microbiology, The University of Burdwan, Burdwan, West Bengal 713104 India
| | - Somasri Dam
- Department of Microbiology, The University of Burdwan, Burdwan, West Bengal 713104 India
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3
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Sending the message: specialized RNA export mechanisms in trypanosomes. Trends Parasitol 2022; 38:854-867. [PMID: 36028415 PMCID: PMC9894534 DOI: 10.1016/j.pt.2022.07.008] [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: 10/19/2021] [Revised: 07/25/2022] [Accepted: 07/25/2022] [Indexed: 02/04/2023]
Abstract
Export of RNA from the nucleus is essential for all eukaryotic cells and has emerged as a major step in the control of gene expression. mRNA molecules are required to complete a complex series of processing events and pass a quality control system to protect the cytoplasm from the translation of aberrant proteins. Many of these events are highly conserved across eukaryotes, reflecting their ancient origin, but significant deviation from a canonical pathway as described from animals and fungi has emerged in the trypanosomatids. With significant implications for the mechanisms that control gene expression and hence differentiation, responses to altered environments and fitness as a parasite, these deviations may also reveal additional, previously unsuspected, mRNA export pathways.
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4
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Li W, Grech J, Stortz JF, Gow M, Periz J, Meissner M, Jimenez-Ruiz E. A splitCas9 phenotypic screen in Toxoplasma gondii identifies proteins involved in host cell egress and invasion. Nat Microbiol 2022; 7:882-895. [PMID: 35538310 DOI: 10.1038/s41564-022-01114-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Accepted: 03/31/2022] [Indexed: 11/09/2022]
Abstract
Apicomplexan parasites, such as Toxoplasma gondii, have specific adaptations that enable invasion and exit from the host cell. Owing to the phylogenetic distance between apicomplexan parasites and model organisms, comparative genomics has limited capacity to infer gene functions. Further, although CRISPR/Cas9-based screens have assigned roles to some Toxoplasma genes, the functions of encoded proteins have proven difficult to assign. To overcome this problem, we devised a conditional Cas9-system in T. gondii that enables phenotypic screens. Using an indicator strain for F-actin dynamics and apicoplast segregation, we screened 320 genes to identify those required for defined steps in the asexual life cycle. The detailed characterization of two genes identified in our screen, through the generation of conditional knockout parasites using the DiCre-system, revealed that signalling linking factor (SLF) is an integral part of a signalling complex required for early induction of egress, and a novel conoid protein (conoid gliding protein, CGP) functions late during egress and is required for the activation of gliding motility. Establishing different indicator lines and applying our conditional Cas9 screen could enable the identification of genes involved in organellar biogenesis, parasite replication or maintenance of the endosymbiotic organelles in the future.
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Affiliation(s)
- Wei Li
- Experimental Parasitology, Department of Veterinary Sciences, Faculty of Veterinary Medicine, Ludwig-Maximilians-Universität, LMU, Munich, Germany
| | - Janessa Grech
- Experimental Parasitology, Department of Veterinary Sciences, Faculty of Veterinary Medicine, Ludwig-Maximilians-Universität, LMU, Munich, Germany
| | - Johannes Felix Stortz
- Wellcome Centre for Integrative Parasitology, Institute of Infection, Immunity and Inflammation, Glasgow Biomedical Research Centre, University of Glasgow, Glasgow, UK.,Max Planck Institute for Biology of Ageing, Cologne, Germany
| | - Matthew Gow
- Experimental Parasitology, Department of Veterinary Sciences, Faculty of Veterinary Medicine, Ludwig-Maximilians-Universität, LMU, Munich, Germany
| | - Javier Periz
- Experimental Parasitology, Department of Veterinary Sciences, Faculty of Veterinary Medicine, Ludwig-Maximilians-Universität, LMU, Munich, Germany
| | - Markus Meissner
- Experimental Parasitology, Department of Veterinary Sciences, Faculty of Veterinary Medicine, Ludwig-Maximilians-Universität, LMU, Munich, Germany. .,Wellcome Centre for Integrative Parasitology, Institute of Infection, Immunity and Inflammation, Glasgow Biomedical Research Centre, University of Glasgow, Glasgow, UK.
| | - Elena Jimenez-Ruiz
- Experimental Parasitology, Department of Veterinary Sciences, Faculty of Veterinary Medicine, Ludwig-Maximilians-Universität, LMU, Munich, Germany.
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5
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Niikura M, Fukutomi T, Mitobe J, Kobayashi F. Roles and Cellular Localization of GBP2 and NAB2 During the Blood Stage of Malaria Parasites. Front Cell Infect Microbiol 2021; 11:737457. [PMID: 34604117 PMCID: PMC8479154 DOI: 10.3389/fcimb.2021.737457] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Accepted: 08/24/2021] [Indexed: 12/03/2022] Open
Abstract
The quality control and export of mRNA by RNA-binding proteins are necessary for the survival of malaria parasites, which have complex life cycles. Nuclear poly(A) binding protein 2 (NAB2), THO complex subunit 4 (THO4), nucleolar protein 3 (NPL3), G-strand binding protein 2 (GBP2) and serine/arginine-rich splicing factor 1 (SR1) are involved in nuclear mRNA export in malaria parasites. However, their roles in asexual and sexual development, and in cellular localization, are not fully understood. In this study using the rodent malaria parasite, Plasmodium berghei, we found that NAB2 and SR1, but not THO4, NPL3 or GBP2, played essential roles in the asexual development of malaria parasites. By contrast, GBP2 but not NPL3 was involved in male and female gametocyte production. THO4 was involved in female gametocyte production, but had a lower impact than GBP2. In this study, we focused on GBP2 and NAB2, which play important roles in the sexual and asexual development of malaria parasites, respectively, and examined their cellular localization. GBP2 localized to both the nucleus and cytoplasm of malaria parasites. Using immunoprecipitation coupled to mass spectrometry (IP-MS), GBP2 interacted with the proteins ALBA4, DOZI, and CITH, which play roles in translational repression. IP-MS also revealed that phosphorylated adapter RNA export protein (PHAX) domain-containing protein, an adaptor protein for exportin-1, also interacted with GBP2, implying that mRNA export occurs via the PHAX domain-containing protein pathway in malaria parasites. Live-cell fluorescence imaging revealed that NAB2 localized at the nuclear periphery. Moreover, IP-MS indicated that NAB2 interacted with transportin. RNA immunoprecipitation coupled to RNA sequencing revealed that NAB2 bound directly to 143 mRNAs, including those encoding 40S and 60S ribosomal proteins. Our findings imply that malaria parasites use an evolutionarily ancient mechanism conserved throughout eukaryotic evolution.
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Affiliation(s)
- Mamoru Niikura
- Department of Infectious Diseases, Kyorin University School of Medicine, Tokyo, Japan
| | - Toshiyuki Fukutomi
- Department of Pharmacology and Toxicology, Kyorin University School of Medicine, Tokyo, Japan
| | - Jiro Mitobe
- Department of Infectious Diseases, Kyorin University School of Medicine, Tokyo, Japan
| | - Fumie Kobayashi
- Department of Environmental Science, School of Life and Environmental Science, Azabu University, Kanagawa, Japan
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Briquet S, Gissot M, Silvie O. A toolbox for conditional control of gene expression in apicomplexan parasites. Mol Microbiol 2021; 117:618-631. [PMID: 34564906 PMCID: PMC9293482 DOI: 10.1111/mmi.14821] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Accepted: 09/23/2021] [Indexed: 01/29/2023]
Abstract
Apicomplexan parasites encompass diverse pathogens for humans and animals, including the causative agents of malaria and toxoplasmosis, Plasmodium spp. and Toxoplasma gondii. Genetic manipulation of these parasites has become central to explore parasite biology, unravel gene function and identify new targets for therapeutic strategies. Tremendous progress has been achieved over the past years with the advent of next generation sequencing and powerful genome editing methods. In particular, various methods for conditional gene expression have been developed in both Plasmodium and Toxoplasma to knockout or knockdown essential genes, or for inducible expression of master developmental regulators or mutant versions of proteins. Conditional gene expression can be achieved at three distinct levels. At the DNA level, inducible site‐specific recombinases allow conditional genome editing. At the RNA level, regulation can be achieved during transcription, using stage‐specific or regulatable promoters, or post‐transcriptionally through alteration of mRNA stability or translation. At the protein level, several systems have been developed for inducible degradation or displacement of a protein of interest. In this review, we provide an overview of current systems for conditional control of gene expression in Plasmodium and Toxoplasma parasites, highlighting the advantages and limitations of each approach.
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Affiliation(s)
- Sylvie Briquet
- INSERM, CNRS, Centre d'Immunologie et des Maladies Infectieuses, Sorbonne Université, Paris, France
| | - Mathieu Gissot
- CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, Center for Infection and Immunity of Lille, CIIL, Univ. Lille, Lille, France
| | - Olivier Silvie
- INSERM, CNRS, Centre d'Immunologie et des Maladies Infectieuses, Sorbonne Université, Paris, France
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7
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Evolution and diversification of the nuclear pore complex. Biochem Soc Trans 2021; 49:1601-1619. [PMID: 34282823 PMCID: PMC8421043 DOI: 10.1042/bst20200570] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 06/18/2021] [Accepted: 06/21/2021] [Indexed: 12/21/2022]
Abstract
The nuclear pore complex (NPC) is responsible for transport between the cytoplasm and nucleoplasm and one of the more intricate structures of eukaryotic cells. Typically composed of over 300 polypeptides, the NPC shares evolutionary origins with endo-membrane and intraflagellar transport system complexes. The modern NPC was fully established by the time of the last eukaryotic common ancestor and, hence, prior to eukaryote diversification. Despite the complexity, the NPC structure is surprisingly flexible with considerable variation between lineages. Here, we review diversification of the NPC in major taxa in view of recent advances in genomic and structural characterisation of plant, protist and nucleomorph NPCs and discuss the implications for NPC evolution. Furthermore, we highlight these changes in the context of mRNA export and consider how this process may have influenced NPC diversity. We reveal the NPC as a platform for continual evolution and adaptation.
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8
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Kangussu-Marcolino MM, Morgado P, Manna D, Yee H, Singh U. Development of a CRISPR/Cas9 system in Entamoeba histolytica: proof of concept. Int J Parasitol 2021; 51:193-200. [PMID: 33264648 PMCID: PMC7880892 DOI: 10.1016/j.ijpara.2020.09.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Revised: 09/05/2020] [Accepted: 09/10/2020] [Indexed: 12/24/2022]
Abstract
The protozoan parasite Entamoeba histolytica is an important human pathogen and a leading parasitic cause of death on a global scale. The lack of molecular tools for genome editing hinders the study of important biological functions of this parasite. Due to its versatility, the CRISPR (clustered regularly interspaced short palindromic repeat)-Cas9 system has been successfully used to induce site-specific genomic alterations, including in protozoan parasites. In this study, we optimised CRISPR-Cas9 for use as a genetic tool in E. histolytica. We chose a single plasmid approach containing both guide RNA (gRNA) and Cas9 nuclease expression cassettes. The amebic U6 promoter was used to drive the expression of the gRNA and its expression was confirmed by Northern blot analysis. Stable transfectant cell lines were obtained using a destabilising domain of dihydrofolate reductase fused to myc-tagged Cas9 (ddCas9). With this system, we were able to induce ddCas9 expression 16 h following treatment with the small molecule ligand trimethoprim (TMP). Stable cell lines expressing ddCas9 and Luc-gRNA or non-specific (NS)-gRNA were transiently transfected with a plasmid containing a mutated luciferase gene (pDeadLuc) targeted by Luc-gRNA and another plasmid with a truncated luciferase gene (pDonorLuc) to restore luciferase expression and consequent activity. We observed that luminescence signal increased for the cell line expressing Luc-gRNA, suggesting that homologous recombination was facilitated by Cas9 activity. This evidence is supported by the presence of chimeric DNA detected by PCR and confirmed by sequencing of the resulting repaired DNA obtained by homologous recombination. We believe this represents the first report of a CRISPR/Cas9 system use in Entamoeba and provides evidence that this genome editing approach can be useful for genetic studies in this early branching eukaryote.
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Affiliation(s)
- Monica Mendes Kangussu-Marcolino
- Division of Infectious Diseases, Department of Internal Medicine, Stanford University, Grant Building, S-143, 300 Pasteur Drive, Stanford, CA 94305, United States
| | - Pedro Morgado
- Division of Infectious Diseases, Department of Internal Medicine, Stanford University, Grant Building, S-143, 300 Pasteur Drive, Stanford, CA 94305, United States
| | - Dipak Manna
- Division of Infectious Diseases, Department of Internal Medicine, Stanford University, Grant Building, S-143, 300 Pasteur Drive, Stanford, CA 94305, United States
| | - Heather Yee
- Division of Infectious Diseases, Department of Internal Medicine, Stanford University, Grant Building, S-143, 300 Pasteur Drive, Stanford, CA 94305, United States
| | - Upinder Singh
- Division of Infectious Diseases, Department of Internal Medicine, Stanford University, Grant Building, S-143, 300 Pasteur Drive, Stanford, CA 94305, United States; Department of Microbiology and Immunology, Stanford University, Stanford, CA 94305, United States.
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9
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Abstract
The passage of mRNAs through the nuclear pores into the cytoplasm is essential in all eukaryotes. For regulation, mRNA export is tightly connected to the full machinery of nuclear mRNA processing, starting at transcription. Export competence of pre-mRNAs gradually increases by both transient and permanent interactions with multiple RNA processing and export factors. mRNA export is best understood in opisthokonts, with limited knowledge in plants and protozoa. Here, I review and compare nuclear mRNA processing and export between opisthokonts and Trypanosoma brucei. The parasite has many unusual features in nuclear mRNA processing, such as polycistronic transcription and trans-splicing. It lacks several nuclear complexes and nuclear-pore-associated proteins that in opisthokonts play major roles in mRNA export. As a consequence, trypanosome mRNA export control is not tight and export can even start co-transcriptionally. Whether trypanosomes regulate mRNA export at all, or whether leakage of immature mRNA to the cytoplasm is kept to a low level by a fast kinetics of mRNA processing remains to be investigated. mRNA export had to be present in the last common ancestor of eukaryotes. Trypanosomes are evolutionary very distant from opisthokonts and a comparison helps understanding the evolution of mRNA export.
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10
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Niikura M, Fukutomi T, Fukui K, Inoue SI, Asahi H, Kobayashi F. G-strand binding protein 2 is involved in asexual and sexual development of Plasmodium berghei. Parasitol Int 2020; 76:102059. [PMID: 31958569 DOI: 10.1016/j.parint.2020.102059] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2019] [Revised: 01/06/2020] [Accepted: 01/14/2020] [Indexed: 02/06/2023]
Abstract
G-strand binding protein 2 (GBP2) is a Ser/Arg-rich (SR) protein involved in mRNA surveillance and nuclear mRNA quality control in yeast. However, the roles of GBP2 in virulence and sexual development in Plasmodium parasites are unclear, although GBP2 is involved in the asexual development of Plasmodium berghei, the rodent malaria parasite. In this study, we investigated the role of GBP2 in virulence and sexual development of P. berghei using gbp2-deleted P. berghei (Δgbp2 parasites). Then, to identify factors affected by gbp2 deletion, we performed a comparative proteomic analysis of the Δgbp2 parasites. We found that GBP2 was not associated with the development of experimental cerebral malaria during infection with P. berghei, but asexual development of the parasite was delayed with deletion of gbp2. However, the development of P. berghei gametocytes was significantly reduced with deletion of gbp2. Comparative proteomic analysis revealed that the levels of adenosine deaminase (ADA), purine nucleoside phosphorylase (PNP), and hypoxanthine-guanine phosphoribosyltransferase (HGPRT) in Δgbp2 parasites were significantly higher than those in wild-type (WT) parasites, suggesting that biosynthesis of purine nucleotides may be involved in function of GBP2. Therefore, we investigated the effect of purine starvation on the sexual development and proteome. In nt1-deleted P. berghei (Δnt1 parasites), the production of male and female gametocytes was significantly reduced compared to that in WT parasites. Moreover, we found that protein levels of GBP2 in Δnt1 parasites were markedly lower than in WT parasites. These findings suggest that GBP2 is primarily involved in the sexual development of malaria parasites, and its function may be suppressed by purine starvation.
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Affiliation(s)
- Mamoru Niikura
- Department of Infectious Diseases, Kyorin University School of Medicine, Tokyo, Japan.
| | - Toshiyuki Fukutomi
- Department of Pharmacology and Toxicology, Kyorin University School of Medicine, Tokyo, Japan
| | - Kana Fukui
- Department of Infectious Diseases, Kyorin University School of Medicine, Tokyo, Japan
| | - Shin-Ichi Inoue
- Division of Immunology, Department of Molecular Microbiology and Immunology, Nagasaki University, Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Hiroko Asahi
- Department of Infectious Diseases, Kyorin University School of Medicine, Tokyo, Japan
| | - Fumie Kobayashi
- Department of Environmental Science, School of Life and Environmental Science, Azabu University, Japan
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11
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Into the basket and beyond: the journey of mRNA through the nuclear pore complex. Biochem J 2020; 477:23-44. [DOI: 10.1042/bcj20190132] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Revised: 11/28/2019] [Accepted: 12/10/2019] [Indexed: 02/06/2023]
Abstract
The genetic information encoded in nuclear mRNA destined to reach the cytoplasm requires the interaction of the mRNA molecule with the nuclear pore complex (NPC) for the process of mRNA export. Numerous proteins have important roles in the transport of mRNA out of the nucleus. The NPC embedded in the nuclear envelope is the port of exit for mRNA and is composed of ∼30 unique proteins, nucleoporins, forming the distinct structures of the nuclear basket, the pore channel and cytoplasmic filaments. Together, they serve as a rather stationary complex engaged in mRNA export, while a variety of soluble protein factors dynamically assemble on the mRNA and mediate the interactions of the mRNA with the NPC. mRNA export factors are recruited to and dissociate from the mRNA at the site of transcription on the gene, during the journey through the nucleoplasm and at the nuclear pore at the final stages of export. In this review, we present the current knowledge derived from biochemical, molecular, structural and imaging studies, to develop a high-resolution picture of the many events that culminate in the successful passage of the mRNA out of the nucleus.
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12
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CRISPR-Cas9 system: A new-fangled dawn in gene editing. Life Sci 2019; 232:116636. [DOI: 10.1016/j.lfs.2019.116636] [Citation(s) in RCA: 86] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Revised: 06/30/2019] [Accepted: 07/05/2019] [Indexed: 12/24/2022]
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13
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Lacombe A, Maclean AE, Ovciarikova J, Tottey J, Mühleip A, Fernandes P, Sheiner L. Identification of the
Toxoplasma gondii
mitochondrial ribosome, and characterisation of a protein essential for mitochondrial translation. Mol Microbiol 2019; 112:1235-1252. [PMID: 31339607 PMCID: PMC6851545 DOI: 10.1111/mmi.14357] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/21/2019] [Indexed: 01/20/2023]
Abstract
Apicomplexan parasites cause diseases such as malaria and toxoplasmosis. The apicomplexan mitochondrion shows striking differences from common model organisms, including fundamental processes such as mitochondrial translation. Despite evidence that mitochondrial translation is essential for parasite survival, it is largely understudied. Progress has been restricted by the absence of functional assays to detect apicomplexan mitochondrial translation, a lack of knowledge of proteins involved in the process and the inability to identify and detect mitoribosomes. We report the localization of 12 new mitochondrial proteins, including 6 putative mitoribosomal proteins. We demonstrate the integration of three mitoribosomal proteins in macromolecular complexes, and provide evidence suggesting these are apicomplexan mitoribosomal subunits, detected here for the first time. Finally, a new analytical pipeline detected defects in mitochondrial translation upon depletion of the small subunit protein 35 (TgmS35), while other mitochondrial functions remain unaffected. Our work lays a foundation for the study of apicomplexan mitochondrial translation.
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Affiliation(s)
- Alice Lacombe
- Wellcome Centre for Integrative Parasitology University of Glasgow 120 University Place GlasgowG12 8TAUK
| | - Andrew E. Maclean
- Wellcome Centre for Integrative Parasitology University of Glasgow 120 University Place GlasgowG12 8TAUK
| | - Jana Ovciarikova
- Wellcome Centre for Integrative Parasitology University of Glasgow 120 University Place GlasgowG12 8TAUK
| | - Julie Tottey
- Wellcome Centre for Integrative Parasitology University of Glasgow 120 University Place GlasgowG12 8TAUK
- UMR 1282 ISP INRA‐Université François Rabelais de Tours Nouzilly France
| | - Alexander Mühleip
- Department of Biochemistry and Biophysics Stockholm University Stockholm Sweden
| | - Paula Fernandes
- Wellcome Centre for Integrative Parasitology University of Glasgow 120 University Place GlasgowG12 8TAUK
| | - Lilach Sheiner
- Wellcome Centre for Integrative Parasitology University of Glasgow 120 University Place GlasgowG12 8TAUK
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14
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Grzybek M, Golonko A, Górska A, Szczepaniak K, Strachecka A, Lass A, Lisowski P. The CRISPR/Cas9 system sheds new lights on the biology of protozoan parasites. Appl Microbiol Biotechnol 2018; 102:4629-4640. [PMID: 29626235 PMCID: PMC5954013 DOI: 10.1007/s00253-018-8927-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Accepted: 03/06/2018] [Indexed: 01/04/2023]
Abstract
The CRISPR/Cas9 system, a natural defence system of bacterial organisms, has recently been used to modify genomes of the most important protozoa parasites. Successful genome manipulations with the CRISPR/Cas9 system are changing the present view of genetics in parasitology. The application of this system offers a major chance to overcome the current restriction in culturing, maintaining and analysing protozoan parasites, and allows dynamic analysis of parasite genes functions, leading to a better understanding of pathogenesis. CRISPR/Cas9 system will have a significant influence on the process of developing novel drugs and treatment strategies against protozoa parasites.
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Affiliation(s)
- Maciej Grzybek
- Department of Tropical Parasitology, Medical University of Gdansk, Powstania Styczniowego 9b, 81-519 Gdynia, Poland
| | - Aleksandra Golonko
- Department of Biotechnology, Bialystok University of Technology, Wiejska 45E, 15-351, Bialystok, Poland
| | - Aleksandra Górska
- Faculty of Veterinary Medicine, University of Life Sciences in Lublin, Akademicka 13, 20-950 Lublin, Poland
| | - Klaudiusz Szczepaniak
- Faculty of Veterinary Medicine, University of Life Sciences in Lublin, Akademicka 13, 20-950 Lublin, Poland
| | - Aneta Strachecka
- Faculty of Biology, Animal Sciences and Bioeconomy, University of Life Sciences in Lublin, Akademicka 13, 20-950 Lublin, Poland
| | - Anna Lass
- Department of Tropical Parasitology, Medical University of Gdansk, Powstania Styczniowego 9b, 81-519 Gdynia, Poland
| | - Paweł Lisowski
- Department of Molecular Biology, Institute of Genetics and Animal Breeding PAS, Postepu 36A, 05-552 Jastrzebiec, Poland
- iPS Cell-Based Disease Modeling Group, Max-Delbrück-Center for Molecular Medicine (MDC) in the Helmholtz Association, Robert-Rössle-Str. 10, 13092 Berlin, Germany
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15
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Mina JGM, Denny PW. Everybody needs sphingolipids, right! Mining for new drug targets in protozoan sphingolipid biosynthesis. Parasitology 2018; 145:134-147. [PMID: 28637533 PMCID: PMC5964470 DOI: 10.1017/s0031182017001081] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2017] [Revised: 05/15/2017] [Accepted: 05/18/2017] [Indexed: 12/18/2022]
Abstract
Sphingolipids (SLs) are an integral part of all eukaryotic cellular membranes. In addition, they have indispensable functions as signalling molecules controlling a myriad of cellular events. Disruption of either the de novo synthesis or the degradation pathways has been shown to have detrimental effects. The earlier identification of selective inhibitors of fungal SL biosynthesis promised potent broad-spectrum anti-fungal agents, which later encouraged testing some of those agents against protozoan parasites. In this review we focus on the key enzymes of the SL de novo biosynthetic pathway in protozoan parasites of the Apicomplexa and Kinetoplastidae, outlining the divergence and interconnection between host and pathogen metabolism. The druggability of the SL biosynthesis is considered, alongside recent technology advances that will enable the dissection and analyses of this pathway in the parasitic protozoa. The future impact of these advances for the development of new therapeutics for both globally threatening and neglected infectious diseases is potentially profound.
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Affiliation(s)
- John G M Mina
- Department of Biosciences,Lower Mountjoy,Stockton Road,Durham DH1 3LE,UK
| | - P W Denny
- Department of Biosciences,Lower Mountjoy,Stockton Road,Durham DH1 3LE,UK
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16
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Ávila AR, Cabezas-Cruz A, Gissot M. mRNA export in the apicomplexan parasite Toxoplasma gondii: emerging divergent components of a crucial pathway. Parasit Vectors 2018; 11:62. [PMID: 29370868 PMCID: PMC5785795 DOI: 10.1186/s13071-018-2648-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2017] [Accepted: 01/15/2018] [Indexed: 01/08/2023] Open
Abstract
Control of gene expression is crucial for parasite survival and is the result of a series of processes that are regulated to permit fine-tuning of gene expression in response to biological changes during the life-cycle of apicomplexan parasites. Control of mRNA nuclear export is a key process in eukaryotic cells but is poorly understood in apicomplexan parasites. Here, we review recent knowledge regarding this process with an emphasis on T. gondii. We describe the presence of divergent orthologs and discuss structural and functional differences in export factors between apicomplexans and other eukaryotic lineages. Undoubtedly, the use of the CRISPR/Cas9 system in high throughput screenings associated with the discovery of mRNA nuclear export complexes by proteomic analysis will contribute to identify these divergent factors. Ligand-based or structure-based strategies may be applied to investigate the potential use of these proteins as targets for new antiprotozoal agents.
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Affiliation(s)
- Andréa Rodrigues Ávila
- Instituto Carlos Chagas, FIOCRUZ, Rua Algacyr Munhoz Mader, 3775. CIC, Curitiba, PR, 81350-010, Brazil. .,UMR BIPAR, Animal Health Laboratory, ANSES, INRA, ENVA, Maisons Alfort, Cedex, France.
| | - Alexjandro Cabezas-Cruz
- UMR BIPAR, Animal Health Laboratory, ANSES, INRA, ENVA, Maisons Alfort, Cedex, France.,Institute of Parasitology, Biology Center, Czech Academy of Sciences, České Budějovice, Czech Republic.,Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
| | - Mathieu Gissot
- University of Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019 - UMR 8204 - CIIL - Centre d'Infection et d'Immunité de Lille, F-59000, Lille, France.
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17
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Obado SO, Field MC, Rout MP. Comparative interactomics provides evidence for functional specialization of the nuclear pore complex. Nucleus 2017; 8:340-352. [PMID: 28463551 DOI: 10.1080/19491034.2017.1313936] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022] Open
Abstract
The core architecture of the eukaryotic cell was established well over one billion years ago, and is largely retained in all extant lineages. However, eukaryotic cells also possess lineage-specific features, frequently keyed to specific functional requirements. One quintessential core eukaryotic structure is the nuclear pore complex (NPC), responsible for regulating exchange of macromolecules between the nucleus and cytoplasm as well as acting as a nuclear organizational hub. NPC architecture has been best documented in one eukaryotic supergroup, the Opisthokonts (e.g. Saccharomyces cerevisiae and Homo sapiens), which although compositionally similar, have significant variations in certain NPC subcomplex structures. The variation of NPC structure across other taxa in the eukaryotic kingdom however, remains poorly understood. We explored trypanosomes, highly divergent organisms, and mapped and assigned their NPC proteins to specific substructures to reveal their NPC architecture. We showed that the NPC central structural scaffold is conserved, likely across all eukaryotes, but more peripheral elements can exhibit very significant lineage-specific losses, duplications or other alterations in their components. Amazingly, trypanosomes lack the major components of the mRNA export platform that are asymmetrically localized within yeast and vertebrate NPCs. Concomitant with this, the trypanosome NPC is ALMOST completely symmetric with the nuclear basket being the only major source of asymmetry. We suggest these features point toward a stepwise evolution of the NPC in which a coating scaffold first stabilized the pore after which selective gating emerged and expanded, leading to the addition of peripheral remodeling machineries on the nucleoplasmic and cytoplasmic sides of the pore.
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Affiliation(s)
| | - Mark C Field
- b Wellcome Trust Centre for Anti-Infectives Research, School of Life Sciences , University of Dundee , Dundee , UK
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18
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Bittencourt IDA, Serpeloni M, Hiraiwa PM, de Arruda Campos Brasil de Souza T, Ávila AR. Dissecting biochemical peculiarities of the ATPase activity of TcSub2, a component of the mRNA export pathway in Trypanosoma cruzi. Int J Biol Macromol 2017; 98:793-801. [PMID: 28212935 DOI: 10.1016/j.ijbiomac.2017.02.050] [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] [Received: 10/14/2016] [Revised: 02/10/2017] [Accepted: 02/11/2017] [Indexed: 11/16/2022]
Abstract
The RNA helicase DEAD-box protein Sub2 (yeast)/UAP56 (mammals) is conserved across eukaryotes and is essential for mRNA export in trypanosomes. Despite the high conservation of Sub2 in lower eukaryotes such as Trypanosoma cruzi, the low conservation of other mRNA export factors raises questions regarding whether the mode of action of TcSub2 is similar to that of orthologs from other eukaryotes. Mutation of the conserved K87 residue of TcSub2 abolishes ATPase activity, showing that its ATPase domain is functional. However, the Vmax of TcSub2 was much higher than the Vmax described for the human protein UAP56, which suggests that the TcSub2 enzyme hydrolyzes ATP faster than its human homolog. Furthermore, we demonstrate that RNA association is less important to the activity of TcSub2 compared to UAP56. Our results show differences in activity of this protein, even though the structure of TcSub2 is very similar to UAP56. Functional complementation assays indicate that these differences may be common to other trypanosomatids. Distinct features of RNA influence and ATPase efficiency between UAP56 and TcSub2 may reflect distinct structures for functional sites of TcSub2. For this reason, ligand-based or structure-based methodologies can be applied to investigate the potential of TcSub2 as a target for new drugs.
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