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Gray S, Fort C, Wheeler RJ. Intraflagellar transport speed is sensitive to genetic and mechanical perturbations to flagellar beating. J Cell Biol 2024; 223:e202401154. [PMID: 38829962 PMCID: PMC11148470 DOI: 10.1083/jcb.202401154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 05/01/2024] [Accepted: 05/13/2024] [Indexed: 06/05/2024] Open
Abstract
Two sets of motor proteins underpin motile cilia/flagella function. The axoneme-associated inner and outer dynein arms drive sliding of adjacent axoneme microtubule doublets to periodically bend the flagellum for beating, while intraflagellar transport (IFT) kinesins and dyneins carry IFT trains bidirectionally along the axoneme. Despite assembling motile cilia and flagella, IFT train speeds have only previously been quantified in immobilized flagella-mechanical immobilization or genetic paralysis. This has limited investigation of the interaction between IFT and flagellar beating. Here, in uniflagellate Leishmania parasites, we use high-frequency, dual-color fluorescence microscopy to visualize IFT train movement in beating flagella. We discovered that adhesion of flagella to a microscope slide is detrimental, reducing IFT train speed and increasing train stalling. In flagella free to move, IFT train speed is not strongly dependent on flagella beat type; however, permanent disruption of flagella beating by deletion of genes necessary for formation or regulation of beating showed an inverse correlation of beat frequency and IFT train speed.
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Affiliation(s)
- Sophie Gray
- Nuffield Department of Medicine, Peter Medawar Building for Pathogen Research, University of Oxford, Oxford, UK
| | - Cecile Fort
- Nuffield Department of Medicine, Peter Medawar Building for Pathogen Research, University of Oxford, Oxford, UK
| | - Richard John Wheeler
- Nuffield Department of Medicine, Peter Medawar Building for Pathogen Research, University of Oxford, Oxford, UK
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2
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Abdi Ghavidel A, Aghamiri S, Raee P, Mohammadi-Yeganeh S, Noori E, Bandehpour M, Kazemi B, Jajarmi V. Recent Advances in CRISPR/Cas9-Mediated Genome Editing in Leishmania Strains. Acta Parasitol 2024; 69:121-134. [PMID: 38127288 DOI: 10.1007/s11686-023-00756-0] [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: 06/04/2023] [Accepted: 11/20/2023] [Indexed: 12/23/2023]
Abstract
BACKGROUND Genome manipulation of Leishmania species and the creation of modified strains are widely employed strategies for various purposes, including gene function studies, the development of live attenuated vaccines, and the engineering of host cells for protein production. OBJECTIVE Despite the introduction of novel manipulation approaches like CRISPR/Cas9 technology with significant advancements in recent years, the development of a reliable protocol for efficiently and precisely altering the genes of Leishmania strains remains a challenging endeavor. Following the successful adaptation of the CRISPR/Cas9 system for higher eukaryotic cells, several research groups have endeavored to apply this system to manipulate the genome of Leishmania. RESULTS Despite the substantial differences between Leishmania and higher eukaryotes, the CRISPR/Cas9 system has been effectively tested and applied in Leishmania. CONCLUSION: This comprehensive review summarizes all the CRISPR/Cas9 systems that have been employed in Leishmania, providing details on their methods and the expression systems for Cas9 and gRNA. The review also explores the various applications of the CRISPR system in Leishmania, including the deletion of multicopy gene families, the development of the Leishmania vaccine, complete gene deletions, investigations into chromosomal translocations, protein tagging, gene replacement, large-scale gene knockout, genome editing through cytosine base replacement, and its innovative use in the detection of Leishmania. In addition, the review offers an up-to-date overview of all double-strand break repair mechanisms in Leishmania.
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Affiliation(s)
- Afshin Abdi Ghavidel
- Student Research Committee, Department of Medical Biotechnology, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Shahin Aghamiri
- Cellular and Molecular Biology Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Pourya Raee
- Department of Biology and Anatomical Sciences, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Samira Mohammadi-Yeganeh
- Department of Medical Biotechnology, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Effat Noori
- Department of Medical Parasitology and Mycology, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mojgan Bandehpour
- Cellular and Molecular Biology Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
- Department of Medical Biotechnology, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Bahram Kazemi
- Cellular and Molecular Biology Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
- Department of Medical Biotechnology, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Vahid Jajarmi
- Cellular and Molecular Biology Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
- Department of Medical Biotechnology, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
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3
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Chiurillo MA, Ahmed M, González C, Raja A, Lande N. Gene editing of putative cAMP and Ca 2+ -regulated proteins using an efficient cloning-free CRISPR/Cas9 system in Trypanosoma cruzi. J Eukaryot Microbiol 2023; 70:e12999. [PMID: 37724511 PMCID: PMC10841170 DOI: 10.1111/jeu.12999] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Revised: 08/23/2023] [Accepted: 08/23/2023] [Indexed: 09/20/2023]
Abstract
Trypanosoma cruzi, the agent of Chagas disease, must adapt to a diversity of environmental conditions that it faces during its life cycle. The adaptation to these changes is mediated by signaling pathways that coordinate the cellular responses to the new environmental settings. Cyclic AMP (cAMP) and Calcium (Ca2+ ) signaling pathways regulate critical cellular processes in this parasite, such as differentiation, osmoregulation, host cell invasion and cell bioenergetics. Although the use of CRISPR/Cas9 technology prompted reverse genetics approaches for functional analysis in T. cruzi, it is still necessary to expand the toolbox for genome editing in this parasite, as for example to perform multigene analysis. Here we used an efficient T7RNAP/Cas9 strategy to tag and delete three genes predicted to be involved in cAMP and Ca2+ signaling pathways: a putative Ca2+ /calmodulin-dependent protein kinase (CAMK), Flagellar Member 6 (FLAM6) and Cyclic nucleotide-binding domain/C2 domain-containing protein (CC2CP). We endogenously tagged these three genes and determined the subcellular localization of the tagged proteins. Furthermore, the strategy used to knockout these genes allows us to presume that TcCC2CP is an essential gene in T. cruzi epimastigotes. Our results will open new venues for future research on the role of these proteins in T. cruzi.
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Affiliation(s)
- Miguel A. Chiurillo
- Department of Biological Sciences, University of Cincinnati, Cincinnati, Ohio 45221-006, United States of America
| | - Milad Ahmed
- Department of Biological Sciences, University of Cincinnati, Cincinnati, Ohio 45221-006, United States of America
| | - César González
- Department of Biological Sciences, University of Cincinnati, Cincinnati, Ohio 45221-006, United States of America
- Escuela de Medicina y Ciencias de la Salud. Instituto Tecnológico y de Estudios Superiores de Monterrey. Monterrey, Nuevo Leon, Mexico
| | - Aqsa Raja
- Department of Biological Sciences, University of Cincinnati, Cincinnati, Ohio 45221-006, United States of America
| | - Noelia Lande
- Department of Biological Sciences, University of Cincinnati, Cincinnati, Ohio 45221-006, United States of America
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4
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Ebrahimi S, Khosravi MA, Raz A, Karimipoor M, Parvizi P. CRISPR-Cas Technology as a Revolutionary Genome Editing tool: Mechanisms and Biomedical Applications. IRANIAN BIOMEDICAL JOURNAL 2023; 27:219-46. [PMID: 37873636 PMCID: PMC10707817 DOI: 10.61186/ibj.27.5.219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Accepted: 06/14/2023] [Indexed: 12/17/2023]
Abstract
Programmable nucleases are powerful genomic tools for precise genome editing. These tools precisely recognize, remove, or change DNA at a defined site, thereby, stimulating cellular DNA repair pathways that can cause mutations or accurate replacement or deletion/insertion of a sequence. CRISPR-Cas9 system is the most potent and useful genome editing technique adapted from the defense immune system of certain bacteria and archaea against viruses and phages. In the past decade, this technology made notable progress, and at present, it has largely been used in genome manipulation to make precise gene editing in plants, animals, and human cells. In this review, we aim to explain the basic principle, mechanisms of action, and applications of this system in different areas of medicine, with emphasizing on the detection and treatment of parasitic diseases.
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Affiliation(s)
- Sahar Ebrahimi
- Molecular Systematics Laboratory, Parasitology Department, Pasteur Institute of Iran, Tehran, Iran
- Molecular Medicine Department, Biotechnology Research Center (BRC), Pasteur Institute of Iran, Tehran, Iran
| | - Mohammad Ali Khosravi
- Molecular Medicine Department, Biotechnology Research Center (BRC), Pasteur Institute of Iran, Tehran, Iran
| | - Abbasali Raz
- Malaria and Vector Research Group (MVRG), Biotechnology Research Center (BRC), Pasteur Institute of Iran, Tehran, Iran
| | - Morteza Karimipoor
- Molecular Medicine Department, Biotechnology Research Center (BRC), Pasteur Institute of Iran, Tehran, Iran
| | - Parviz Parvizi
- Molecular Systematics Laboratory, Parasitology Department, Pasteur Institute of Iran, Tehran, Iran
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5
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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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Kent RS, Briggs EM, Colon BL, Alvarez C, Silva Pereira S, De Niz M. Paving the Way: Contributions of Big Data to Apicomplexan and Kinetoplastid Research. Front Cell Infect Microbiol 2022; 12:900878. [PMID: 35734575 PMCID: PMC9207352 DOI: 10.3389/fcimb.2022.900878] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 05/06/2022] [Indexed: 11/13/2022] Open
Abstract
In the age of big data an important question is how to ensure we make the most out of the resources we generate. In this review, we discuss the major methods used in Apicomplexan and Kinetoplastid research to produce big datasets and advance our understanding of Plasmodium, Toxoplasma, Cryptosporidium, Trypanosoma and Leishmania biology. We debate the benefits and limitations of the current technologies, and propose future advancements that may be key to improving our use of these techniques. Finally, we consider the difficulties the field faces when trying to make the most of the abundance of data that has already been, and will continue to be, generated.
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Affiliation(s)
- Robyn S. Kent
- Department of Microbiology and Molecular Genetics, University of Vermont, Burlington, VT, United States
| | - Emma M. Briggs
- Institute for Immunology and Infection Research, School of Biological Sciences, University Edinburgh, Edinburgh, United Kingdom
- Wellcome Centre for Integrative Parasitology, Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, United Kingdom
| | - Beatrice L. Colon
- Wellcome Centre for Anti-Infectives Research, Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Catalina Alvarez
- de Duve Institute, Université Catholique de Louvain, Brussels, Belgium
| | - Sara Silva Pereira
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina da Universidade de Lisboa, Lisboa, Portugal
| | - Mariana De Niz
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina da Universidade de Lisboa, Lisboa, Portugal
- Institut Pasteur, Paris, France
- *Correspondence: Mariana De Niz,
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7
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Roberts AJ, Ong HB, Clare S, Brandt C, Harcourt K, Franssen SU, Cotton JA, Müller-Sienerth N, Wright GJ. Systematic identification of genes encoding cell surface and secreted proteins that are essential for in vitro growth and infection in Leishmania donovani. PLoS Pathog 2022; 18:e1010364. [PMID: 35202447 PMCID: PMC8903277 DOI: 10.1371/journal.ppat.1010364] [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: 09/02/2021] [Revised: 03/08/2022] [Accepted: 02/11/2022] [Indexed: 11/23/2022] Open
Abstract
Leishmaniasis is an infectious disease caused by protozoan parasites belonging to the genus Leishmania for which there are no approved human vaccines. Infections localise to different tissues in a species-specific manner with the visceral form of the disease caused by Leishmania donovani and L. infantum being the most deadly in humans. Although Leishmania spp. parasites are predominantly intracellular, the visceral disease can be prevented in dogs by vaccinating with a complex mixture of secreted products from cultures of L. infantum promastigotes. With the logic that extracellular parasite proteins make good subunit vaccine candidates because they are directly accessible to vaccine-elicited host antibodies, here we attempt to discover proteins that are essential for in vitro growth and host infection with the goal of identifying subunit vaccine candidates. Using an in silico analysis of the Leishmania donovani genome, we identified 92 genes encoding proteins that are predicted to be secreted or externally anchored to the parasite membrane by a single transmembrane region or a GPI anchor. By selecting a transgenic L. donovani parasite that expresses both luciferase and the Cas9 nuclease, we systematically attempted to target all 92 genes by CRISPR genome editing and identified four that were required for in vitro growth. For fifty-five genes, we infected cohorts of mice with each mutant parasite and by longitudinally quantifying parasitaemia with bioluminescent imaging, showed that nine genes had evidence of an attenuated infection although all ultimately established an infection. Finally, we expressed two genes as full-length soluble recombinant proteins and tested them as subunit vaccine candidates in a murine preclinical infection model. Both proteins elicited significant levels of protection against the uncontrolled development of a splenic infection warranting further investigation as subunit vaccine candidates against this deadly infectious tropical disease. Leishmaniasis is a parasitic infectious disease that is responsible for many tens of thousands of human deaths per year, primarily in impoverished parts of the world. Although there are drugs to treat this parasite infection, resistance is emerging and there are no approved human vaccines. Extracellular parasite proteins can make good vaccine targets because they are directly accessible to host antibodies; however, not all parasite surface proteins can elicit protective immune responses. With the goal of identifying new vaccine targets, we selected over 90 genes that encode parasite cell surface and secreted proteins and used the latest CRISPR gene editing technology to individually target them. Using these mutant parasites, we identified four genes required for parasite growth in the laboratory. We expressed two of the proteins as subunit vaccines and a preclinical infection model was used to determine if they could elicit protective immune responses. We found that two of our candidates were able to confer significant levels of protection in a murine model of visceral leishmaniasis. Our study will contribute to the search for a highly effective vaccine against visceral leishmaniasis to improve the lives of people living in some of the poorest regions on the planet.
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Affiliation(s)
- Adam J. Roberts
- Cell Surface Signalling Laboratory, Wellcome Sanger Institute, Hinxton, Cambridge, United Kingdom
| | - Han B. Ong
- Cell Surface Signalling Laboratory, Wellcome Sanger Institute, Hinxton, Cambridge, United Kingdom
| | - Simon Clare
- Pathogen Support Team, Wellcome Sanger Institute, Hinxton, Cambridge, United Kingdom
| | - Cordelia Brandt
- Pathogen Support Team, Wellcome Sanger Institute, Hinxton, Cambridge, United Kingdom
| | - Katherine Harcourt
- Pathogen Support Team, Wellcome Sanger Institute, Hinxton, Cambridge, United Kingdom
| | - Susanne U. Franssen
- Parasite Genomics, Wellcome Sanger Institute, Hinxton, Cambridge, United Kingdom
| | - James A. Cotton
- Parasite Genomics, Wellcome Sanger Institute, Hinxton, Cambridge, United Kingdom
| | - Nicole Müller-Sienerth
- Cell Surface Signalling Laboratory, Wellcome Sanger Institute, Hinxton, Cambridge, United Kingdom
| | - Gavin J. Wright
- Cell Surface Signalling Laboratory, Wellcome Sanger Institute, Hinxton, Cambridge, United Kingdom
- Department of Biology, Hull York Medical School, York Biomedical Research Institute, University of York, York, United Kingdom
- * E-mail:
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8
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Cohen A, Azas N. Challenges and Tools for In Vitro Leishmania Exploratory Screening in the Drug Development Process: An Updated Review. Pathogens 2021; 10:1608. [PMID: 34959563 PMCID: PMC8703296 DOI: 10.3390/pathogens10121608] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Revised: 12/03/2021] [Accepted: 12/07/2021] [Indexed: 12/13/2022] Open
Abstract
Leishmaniases are a group of vector-borne diseases caused by infection with the protozoan parasites Leishmania spp. Some of them, such as Mediterranean visceral leishmaniasis, are zoonotic diseases transmitted from vertebrate to vertebrate by a hematophagous insect, the sand fly. As there is an endemic in more than 90 countries worldwide, this complex and major health problem has different clinical forms depending on the parasite species involved, with the visceral form being the most worrying since it is fatal when left untreated. Nevertheless, currently available antileishmanial therapies are significantly limited (low efficacy, toxicity, adverse side effects, drug-resistance, length of treatment, and cost), so there is an urgent need to discover new compounds with antileishmanial activity, which are ideally inexpensive and orally administrable with few side effects and a novel mechanism of action. Therefore, various powerful approaches were recently applied in many interesting antileishmanial drug development programs. The objective of this review is to focus on the very first step in developing a potential drug and to identify the exploratory methods currently used to screen in vitro hit compounds and the challenges involved, particularly in terms of harmonizing the results of work carried out by different research teams. This review also aims to identify innovative screening tools and methods for more extensive use in the drug development process.
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Affiliation(s)
- Anita Cohen
- IHU Méditerranée Infection, Aix Marseille University, IRD (Institut de Recherche pour le Développement), AP-HM (Assistance Publique—Hôpitaux de Marseille), SSA (Service de Santé des Armées), VITROME (Vecteurs—Infections Tropicales et Méditerranéennes), 13005 Marseille, France;
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9
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Espada CR, Quilles JC, Albuquerque-Wendt A, Cruz MC, Beneke T, Lorenzon LB, Gluenz E, Cruz AK, Uliana SRB. Effective Genome Editing in Leishmania ( Viannia) braziliensis Stably Expressing Cas9 and T7 RNA Polymerase. Front Cell Infect Microbiol 2021; 11:772311. [PMID: 34858879 PMCID: PMC8631273 DOI: 10.3389/fcimb.2021.772311] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Accepted: 10/19/2021] [Indexed: 12/15/2022] Open
Abstract
Until 2015, loss-of-function studies to elucidate protein function in Leishmania relied on gene disruption through homologous recombination. Then, the CRISPR/Cas9 revolution reached these protozoan parasites allowing efficient genome editing with one round of transfection. In addition, the development of LeishGEdit, a PCR-based toolkit for generating knockouts and tagged lines using CRISPR/Cas9, allowed a more straightforward and effective genome editing. In this system, the plasmid pTB007 is delivered to Leishmania for episomal expression or integration in the β-tubulin locus and for the stable expression of T7 RNA polymerase and Cas9. In South America, and especially in Brazil, Leishmania (Viannia) braziliensis is the most frequent etiological agent of tegumentary leishmaniasis. The L. braziliensis β-tubulin locus presents significant sequence divergence in comparison with Leishmania major, which precludes the efficient integration of pTB007 and the stable expression of Cas9. To overcome this limitation, the L. major β-tubulin sequences, present in the pTB007, were replaced by a Leishmania (Viannia) β-tubulin conserved sequence generating the pTB007_Viannia plasmid. This modification allowed the successful integration of the pTB007_Viannia cassette in the L. braziliensis M2903 genome, and in silico predictions suggest that this can also be achieved in other Viannia species. The activity of Cas9 was evaluated by knocking out the flagellar protein PF16, which caused a phenotype of immobility in these transfectants. Endogenous PF16 was also successfully tagged with mNeonGreen, and an in-locus complementation strategy was employed to return a C-terminally tagged copy of the PF16 gene to the original locus, which resulted in the recovery of swimming capacity. The modified plasmid pTB007_Viannia allowed the integration and stable expression of both T7 RNA polymerase and Cas9 in L. braziliensis and provided an important tool for the study of the biology of this parasite.
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Affiliation(s)
- Caroline R Espada
- Departamento de Parasitologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo, Brazil.,Departamento de Biologia Celular e Molecular, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo (FMRP-USP), Ribeirão Preto, Brazil
| | - José Carlos Quilles
- Departamento de Biologia Celular e Molecular, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo (FMRP-USP), Ribeirão Preto, Brazil
| | - Andreia Albuquerque-Wendt
- Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom.,Wellcome Centre for Integrative Parasitology, Institute of Infection, Immunity & Inflammation, College of Medical Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom.,Global Health and Tropical Medicine (GHTM), Instituto de Higiene e Medicina Tropical (IHTM), Universidade de Lisboa (UNL), Lisbon, Portugal
| | - Mario C Cruz
- Centro de Facilidades para Apoio à Pesquisa, Universidade de São Paulo (CEFAP-USP), São Paulo, Brazil
| | - Tom Beneke
- Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom
| | - Lucas B Lorenzon
- Departamento de Biologia Celular e Molecular, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo (FMRP-USP), Ribeirão Preto, Brazil
| | - Eva Gluenz
- Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom.,Wellcome Centre for Integrative Parasitology, Institute of Infection, Immunity & Inflammation, College of Medical Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Angela K Cruz
- Departamento de Biologia Celular e Molecular, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo (FMRP-USP), Ribeirão Preto, Brazil
| | - Silvia R B Uliana
- Departamento de Parasitologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo, Brazil
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10
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Ebrahimi S, Kalantari M, Alipour H, Azizi K, Asgari Q, Bahreini MS. In vitro evaluation of CRISPR PX-LmGP63 vector effect on pathogenicity of Leishmania major as a primary step to control leishmaniasis. Microb Pathog 2021; 161:105281. [PMID: 34752910 DOI: 10.1016/j.micpath.2021.105281] [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: 09/26/2021] [Revised: 10/31/2021] [Accepted: 11/02/2021] [Indexed: 01/13/2023]
Abstract
Cutaneous leishmaniasis (CL) is caused by intracellular obligate parasites (Leishmania spp.) carried by the blood-sucking of female sandflies and transmitted between mammalian hosts. Despite the high incidence and prevalence of Leishmania cases in many countries, it has been a neglected tropical disease. The current treatment approaches are limited by the complications such as loss of fertility and drug resistance. It is, therefore, essential to find new medicines to treat leishmaniasis. CRISPR/Cas9 as a powerful genome-editing tool provides the opportunity to create precise genetic manipulation to investigate the molecular basis of different leishmaniasis cases. Therefore, our main goal was to evaluate the CRISPR PX-LmGP63 vector effect on pathogenicity of Leishmania majorin vitroto challenge for using CRISPR/Cas9 as a therapeutic CL through the reduction of L. major pathogenicity by manipulating the GP63 gene. In this study, L. major parasites were transfected with CRISPR/Cas9 vectors constructed by electroporation and then added to macrophage cells on RPMI. The effect of CRISPR/Cas9 constructs on GP63 mutation, viability, and status of L. major was investigated by counting phagocytic parasites into macrophages and DNA sequence analysis. Our data validate that the use of CRISPR/Cas9 in L. major creates a new stop codon and disrupts the frame sheet of the gene by creating a new insertion (thymine), which prevents its expression. In addition, the parasite count was significantly different in the case and control of infected macrophages (P < 0.05). This study shows the successfully targeted manipulation of the L. major GP63 gene via the adaptation of the CRISPR/Cas9 editing tool. The manipulation of GP63 revealed a reduction in the infection load compared to wild-type parasite infection. Therefore, more studies are necessary for this field to help achieve a new method for the prevention and treatment of CL disease.
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Affiliation(s)
- Saeedeh Ebrahimi
- Department of Vector Biology and Control of Diseases, School of Health, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Mohsen Kalantari
- Research Center for Health Sciences, Institute of Health, Department of Vector Biology and Control of Diseases, School of Health, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Hamzeh Alipour
- Research Center for Health Sciences, Institute of Health, Department of Vector Biology and Control of Diseases, School of Health, Shiraz University of Medical Sciences, Shiraz, Iran.
| | - Kourosh Azizi
- Research Center for Health Sciences, Institute of Health, Department of Vector Biology and Control of Diseases, School of Health, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Qasem Asgari
- Department of Parasitology and Mycology, School of Health, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Mohammad Saleh Bahreini
- Department of Parasitology and Mycology, School of Health, Shiraz University of Medical Sciences, Shiraz, Iran
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11
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Mohsin M, Li Y, Zhang X, Wang Y, Huang Z, Yin G, Zhang Z. Development of CRISPR-CAS9 based RNA drugs against Eimeria tenella infection. Genomics 2021; 113:4126-4135. [PMID: 34740777 DOI: 10.1016/j.ygeno.2021.10.019] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2021] [Revised: 09/16/2021] [Accepted: 10/31/2021] [Indexed: 11/29/2022]
Abstract
Parasitic diseases are major trouble in many parts of the world. We consider that if a chemical can break a DNA barcode sequence, it might be used to develop a species-specific anti-parasitic agent. To examine this hypothesis, we constructed sgRNAs that target both the control (5.8S rDNA) and a DNA barcode (ITS) sequence in Eimeria tenella. In vitro experiment showed that Cas9 mRNA combined with sgRNAs could reduce the sporulation percentage of oocysts and the survival rate of sporulated oocysts and sporozoites. Quantitative real-time PCR showed that the DNAs of parasites exposed to Cas9 mRNA and sgRNAs were significantly affected, regardless of whether they were exposed to a combination of two sgRNAs or just a single sgRNA. The DNA sequencing also indicated that the experimental group exposed to two sgRNAs mixed with Cas9-induced deletion of large parts and a single sgRNA mixed with Cas9-induced mutation at sgRNA targeted fragments. In vivo trial, the effect of sgRNA and Cas9 RNA on the pathogenicity of E. tenella in chicken showed less lesion score and oocysts score (P < 0.05) in experimental groups than control groups. The results and concepts presented in this research can lead to discovering novel nucleic acid therapeutic drugs for Eimeriasis and other parasitic infections, which provide insights into the development of species-specific anti-parasitic agents.
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Affiliation(s)
- Muhammad Mohsin
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou, Fujian, China; College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China; Department of Parasitology, University of Agriculture, Faisalabad, Pakistan
| | - Yige Li
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou, Fujian, China; College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China; Key Laboratory of Marine Biotechnology of Fujian Province, Institute of Oceanology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Xin Zhang
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou, Fujian, China; College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China; Key Laboratory of Marine Biotechnology of Fujian Province, Institute of Oceanology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yilei Wang
- College of Fisheries, Jimei University, Xiamen, Fujian, China
| | - Zhijian Huang
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Guangwen Yin
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou, Fujian, China.
| | - Ziping Zhang
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou, Fujian, China; College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China; Key Laboratory of Marine Biotechnology of Fujian Province, Institute of Oceanology, Fujian Agriculture and Forestry University, Fuzhou, China.
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12
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Efstathiou A, Smirlis D. Leishmania Protein Kinases: Important Regulators of the Parasite Life Cycle and Molecular Targets for Treating Leishmaniasis. Microorganisms 2021; 9:microorganisms9040691. [PMID: 33801655 PMCID: PMC8066228 DOI: 10.3390/microorganisms9040691] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 03/21/2021] [Accepted: 03/24/2021] [Indexed: 02/07/2023] Open
Abstract
Leishmania is a protozoan parasite of the trypanosomatid family, causing a wide range of diseases with different clinical manifestations including cutaneous, mucocutaneous and visceral leishmaniasis. According to WHO, one billion people are at risk of Leishmania infection as they live in endemic areas while there are 12 million infected people worldwide. Annually, 0.9-1.6 million new infections are reported and 20-50 thousand deaths occur due to Leishmania infection. As current chemotherapy for treating leishmaniasis exhibits numerous drawbacks and due to the lack of effective human vaccine, there is an urgent need to develop new antileishmanial therapy treatment. To this end, eukaryotic protein kinases can be ideal target candidates for rational drug design against leishmaniasis. Eukaryotic protein kinases mediate signal transduction through protein phosphorylation and their inhibition is anticipated to be disease modifying as they regulate all essential processes for Leishmania viability and completion of the parasitic life cycle including cell-cycle progression, differentiation and virulence. This review highlights existing knowledge concerning the exploitation of Leishmania protein kinases as molecular targets to treat leishmaniasis and the current knowledge of their role in the biology of Leishmania spp. and in the regulation of signalling events that promote parasite survival in the insect vector or the mammalian host.
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13
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Kirti A, Sharma M, Rani K, Bansal A. CRISPRing protozoan parasites to better understand the biology of diseases. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2021; 180:21-68. [PMID: 33934837 DOI: 10.1016/bs.pmbts.2021.01.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Precise gene editing techniques are paramount to gain deeper insights into the biological processes such as host-parasite interactions, drug resistance mechanisms, and gene-function relationships. Discovery of CRISPR-Cas9 system has spearheaded mechanistic understanding of protozoan parasite biology as evident from the number of reports in the last decade. Here, we have described the use of CRISPR-Cas9 in understanding the biology of medically important protozoan parasites such as Plasmodium, Leishmania, Trypanosoma, Babesia and Trichomonas. In spite of intrinsic difficulties in genome editing in these protozoan parasites, CRISPR-Cas9 has acted as a catalyst for faster generation of desired transgenic parasites. Modifications in the CRISPR-Cas9 system for improving the efficiency have been useful in better understanding the molecular mechanisms associated with repair of double strand breaks in the parasites. Moreover, improvement in reagents used for CRISPR mediated gene editing have been instrumental in addressing the issue of non-specificity and toxicity for therapeutic use. These application-based modifications may help in further increasing the efficiency of gene editing in protozoan parasites.
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Affiliation(s)
- Apurva Kirti
- School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Manish Sharma
- School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Komal Rani
- School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Abhisheka Bansal
- School of Life Sciences, Jawaharlal Nehru University, New Delhi, India.
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14
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Rachidi N, Knippschild U, Späth GF. Dangerous Duplicity: The Dual Functions of Casein Kinase 1 in Parasite Biology and Host Subversion. Front Cell Infect Microbiol 2021; 11:655700. [PMID: 33869086 PMCID: PMC8044801 DOI: 10.3389/fcimb.2021.655700] [Citation(s) in RCA: 4] [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: 01/19/2021] [Accepted: 03/05/2021] [Indexed: 02/01/2023] Open
Abstract
Casein Kinase 1 (CK1) family members are serine/threonine protein kinases that are involved in many biological processes and highly conserved in eukaryotes from protozoan to humans. Even though pathogens exploit host CK1 signaling pathways to survive, the role of CK1 in infectious diseases and host/pathogen interaction is less well characterized compared to other diseases, such as cancer or neurodegenerative diseases. Here we present the current knowledge on CK1 in protozoan parasites highlighting their essential role for parasite survival and their importance for host-pathogen interactions. We also discuss how the dual requirement of CK1 family members for parasite biological processes and host subversion could be exploited to identify novel antimicrobial interventions.
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Affiliation(s)
- Najma Rachidi
- Unité de Parasitologie moléculaire et Signalisation, Department of Parasites and Insect Vectors, Institut Pasteur and INSERM U1201, Paris, France
| | - Uwe Knippschild
- Department of General and Visceral Surgery, Surgery Centre, Ulm University Hospital, Ulm, Germany
| | - Gerald F. Späth
- Unité de Parasitologie moléculaire et Signalisation, Department of Parasites and Insect Vectors, Institut Pasteur and INSERM U1201, Paris, France
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15
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Baker N, Catta-Preta CMC, Neish R, Sadlova J, Powell B, Alves-Ferreira EVC, Geoghegan V, Carnielli JBT, Newling K, Hughes C, Vojtkova B, Anand J, Mihut A, Walrad PB, Wilson LG, Pitchford JW, Volf P, Mottram JC. Systematic functional analysis of Leishmania protein kinases identifies regulators of differentiation or survival. Nat Commun 2021; 12:1244. [PMID: 33623024 PMCID: PMC7902614 DOI: 10.1038/s41467-021-21360-8] [Citation(s) in RCA: 51] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Accepted: 01/13/2021] [Indexed: 01/31/2023] Open
Abstract
Differentiation between distinct stages is fundamental for the life cycle of intracellular protozoan parasites and for transmission between hosts, requiring stringent spatial and temporal regulation. Here, we apply kinome-wide gene deletion and gene tagging in Leishmania mexicana promastigotes to define protein kinases with life cycle transition roles. Whilst 162 are dispensable, 44 protein kinase genes are refractory to deletion in promastigotes and are likely core genes required for parasite replication. Phenotyping of pooled gene deletion mutants using bar-seq and projection pursuit clustering reveal functional phenotypic groups of protein kinases involved in differentiation from metacyclic promastigote to amastigote, growth and survival in macrophages and mice, colonisation of the sand fly and motility. This unbiased interrogation of protein kinase function in Leishmania allows targeted investigation of organelle-associated signalling pathways required for successful intracellular parasitism.
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Affiliation(s)
- N Baker
- York Biomedical Research Institute, University of York, York, UK
- Department of Biology, University of York, York, UK
| | - C M C Catta-Preta
- York Biomedical Research Institute, University of York, York, UK
- Department of Biology, University of York, York, UK
| | - R Neish
- York Biomedical Research Institute, University of York, York, UK
- Department of Biology, University of York, York, UK
| | - J Sadlova
- Department of Parasitology, Faculty of Science, Charles University, Prague, Czech Republic
| | - B Powell
- Department of Mathematics, University of York, York, UK
| | - E V C Alves-Ferreira
- York Biomedical Research Institute, University of York, York, UK
- Department of Biology, University of York, York, UK
| | - V Geoghegan
- York Biomedical Research Institute, University of York, York, UK
- Department of Biology, University of York, York, UK
| | - J B T Carnielli
- York Biomedical Research Institute, University of York, York, UK
- Department of Biology, University of York, York, UK
| | - K Newling
- Department of Biology, University of York, York, UK
| | - C Hughes
- York Biomedical Research Institute, University of York, York, UK
- Department of Biology, University of York, York, UK
| | - B Vojtkova
- Department of Parasitology, Faculty of Science, Charles University, Prague, Czech Republic
| | - J Anand
- York Biomedical Research Institute, University of York, York, UK
- Department of Biology, University of York, York, UK
| | - A Mihut
- Department of Biology, University of York, York, UK
| | - P B Walrad
- York Biomedical Research Institute, University of York, York, UK
- Department of Biology, University of York, York, UK
| | - L G Wilson
- York Biomedical Research Institute, University of York, York, UK
- Department of Physics, University of York, York, UK
| | - J W Pitchford
- Department of Biology, University of York, York, UK
- Department of Mathematics, University of York, York, UK
| | - P Volf
- Department of Parasitology, Faculty of Science, Charles University, Prague, Czech Republic
| | - J C Mottram
- York Biomedical Research Institute, University of York, York, UK.
- Department of Biology, University of York, York, UK.
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16
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Grünebast J, Clos J. Leishmania: Responding to environmental signals and challenges without regulated transcription. Comput Struct Biotechnol J 2020; 18:4016-4023. [PMID: 33363698 PMCID: PMC7744640 DOI: 10.1016/j.csbj.2020.11.058] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 11/24/2020] [Accepted: 11/28/2020] [Indexed: 02/06/2023] Open
Abstract
Here we describe the non-canonical control of gene expression in Leishmania, a single-cell parasite that is responsible for one of the major neglected tropical diseases. We discuss the lack of regulated RNA synthesis, the post-transcriptional gene regulation including RNA stability and regulated translation. We also show that genetic adaptations such as mosaic aneuploidy, gene copy number variations and DNA sequence polymorphisms are important means for overcoming drug challenge and environmental diversity. These mechanisms are discussed in the context of the unique flow of genetic information found in Leishmania and related protists.
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Affiliation(s)
- Janne Grünebast
- Leishmaniasis Group, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - Joachim Clos
- Leishmaniasis Group, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
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17
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Testing the CRISPR-Cas9 and glmS ribozyme systems in Leishmania tarentolae. Mol Biochem Parasitol 2020; 241:111336. [PMID: 33166572 DOI: 10.1016/j.molbiopara.2020.111336] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Revised: 09/25/2020] [Accepted: 10/28/2020] [Indexed: 02/03/2023]
Abstract
Leishmania parasites include important pathogens and model organisms and are even used for the production of recombinant proteins. However, functional genomics and the characterization of essential genes are often limited in Leishmania because of low-throughput technologies for gene disruption or tagging and the absence of components for RNA interference. Here, we tested the T7 RNA polymerase-dependent CRISPR-Cas9 system by Beneke et al. and the glmS ribozyme-based knock-down system in the model parasite Leishmania tarentolae. We successfully deleted two reference genes encoding the flagellar motility factor Pf16 and the salvage-pathway enzyme adenine phosphoribosyltransferase, resulting in immotile and drug-resistant parasites, respectively. In contrast, we were unable to disrupt the gene encoding the mitochondrial flavoprotein Erv. Cultivation of L. tarentolae in standard BHI medium resulted in a constitutive down-regulation of an episomal mCherry-glmS reporter by 40 to 60%. For inducible knock-downs, we evaluated the growth of L. tarentolae in alternative media and identified supplemented MEM, IMDM and McCoy's 5A medium as candidates. Cultivation in supplemented MEM allowed an inducible, glucosamine concentration-dependent down-regulation of the episomal mCherry-glmS reporter by more than 70%. However, chromosomal glmS-tagging of the genes encoding Pf16, adenine phosphoribosyltransferase or Erv did not reveal a knock-down phenotype. Our data demonstrate the suitability of the CRISPR-Cas9 system for the disruption and tagging of genes in L. tarentolae as well as the limitations of the glmS system, which was restricted to moderate efficiencies for episomal knock-downs and caused no detectable phenotype for chromosomal knock-downs.
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18
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Application of CRISPR/Cas9-Based Reverse Genetics in Leishmania braziliensis: Conserved Roles for HSP100 and HSP23. Genes (Basel) 2020; 11:genes11101159. [PMID: 33007987 PMCID: PMC7601497 DOI: 10.3390/genes11101159] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Revised: 09/23/2020] [Accepted: 09/25/2020] [Indexed: 01/18/2023] Open
Abstract
The protozoan parasite Leishmania (Viannia) braziliensis (L. braziliensis) is the main cause of human tegumentary leishmaniasis in the New World, a disease affecting the skin and/or mucosal tissues. Despite its importance, the study of the unique biology of L. braziliensis through reverse genetics analyses has so far lagged behind in comparison with Old World Leishmania spp. In this study, we successfully applied a cloning-free, PCR-based CRISPR–Cas9 technology in L. braziliensis that was previously developed for Old World Leishmania major and New World L. mexicana species. As proof of principle, we demonstrate the targeted replacement of a transgene (eGFP) and two L. braziliensis single-copy genes (HSP23 and HSP100). We obtained homozygous Cas9-free HSP23- and HSP100-null mutants in L. braziliensis that matched the phenotypes reported previously for the respective L. donovani null mutants. The function of HSP23 is indeed conserved throughout the Trypanosomatida as L. majorHSP23 null mutants could be complemented phenotypically with transgenes from a range of trypanosomatids. In summary, the feasibility of genetic manipulation of L. braziliensis by CRISPR–Cas9-mediated gene editing sets the stage for testing the role of specific genes in that parasite’s biology, including functional studies of virulence factors in relevant animal models to reveal novel therapeutic targets to combat American tegumentary leishmaniasis.
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19
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Yagoubat A, Corrales RM, Bastien P, Lévêque MF, Sterkers Y. Gene Editing in Trypanosomatids: Tips and Tricks in the CRISPR-Cas9 Era. Trends Parasitol 2020; 36:745-760. [DOI: 10.1016/j.pt.2020.06.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Revised: 06/19/2020] [Accepted: 06/30/2020] [Indexed: 12/22/2022]
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20
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Jesus-Santos FH, Lobo-Silva J, Ramos PIP, Descoteaux A, Lima JB, Borges VM, Farias LP. LPG2 Gene Duplication in Leishmania infantum: A Case for CRISPR-Cas9 Gene Editing. Front Cell Infect Microbiol 2020; 10:408. [PMID: 32903718 PMCID: PMC7438834 DOI: 10.3389/fcimb.2020.00408] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Accepted: 07/02/2020] [Indexed: 12/20/2022] Open
Abstract
On the surface of the Leishmania promastigote, phosphoglycans (PG) such as lipophosphoglycan (LPG), proteophosphoglycan (PPG), free phosphoglycan polymers (PGs), and acid phosphatases (sAP), are dominant and contribute to the invasion and survival of Leishmania within the host cell by modulating macrophage signaling and intracellular trafficking. Phosphoglycan synthesis depends on the Golgi GDP-mannose transporter encoded by the LPG2 gene. Aiming to investigate the role of PG-containing molecules in Leishmania infantum infection process, herein we describe the generation and characterization of L. infantum LPG2-deficient parasites. This gene was unexpectedly identified as duplicated in the L. infantum genome, which impaired gene targeting using the conventional homologous recombination approach. This limitation was circumvented by the use of CRISPR/Cas9 technology. Knockout parasites were selected by agglutination assays using CA7AE antibodies followed by a lectin (RCA 120). Five clones were isolated and molecularly characterized, all revealing the expected edited genome, as well as the complete absence of LPG and PG-containing molecule expression. Finally, the deletion of LPG2 was found to impair the outcome of infection in human neutrophils, as demonstrated by a pronounced reduction (~83%) in intracellular load compared to wild-type parasite infection. The results obtained herein reinforce the importance of LPG and other PGs as virulence factors in host-parasite interactions.
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Affiliation(s)
- Flávio Henrique Jesus-Santos
- Laboratory of Inflammation and Biomarkers, Instituto Gonçalo Moniz, Fundação Oswaldo Cruz (FIOCRUZ), Salvador, Brazil.,Faculdade de Medicina da Bahia, Federal University of Bahia (UFBA), Salvador, Brazil
| | - Jéssica Lobo-Silva
- Laboratory of Inflammation and Biomarkers, Instituto Gonçalo Moniz, Fundação Oswaldo Cruz (FIOCRUZ), Salvador, Brazil
| | - Pablo Ivan Pereira Ramos
- Center for Data and Knowledge Integration for Health (CIDACS), Instituto Gonçalo Moniz, Fundação Oswaldo Cruz, Salvador, Brazil
| | - Albert Descoteaux
- Institut National de la Recherche Scientifique-Centre Armand-Frappier Santé Biotechnologie, Laval, QC, Canada
| | - Jonilson Berlink Lima
- Center of Biological Sciences and Health, Federal University of Western of Bahia (UFOB), Barreiras, Brazil
| | - Valéria Matos Borges
- Laboratory of Inflammation and Biomarkers, Instituto Gonçalo Moniz, Fundação Oswaldo Cruz (FIOCRUZ), Salvador, Brazil.,Faculdade de Medicina da Bahia, Federal University of Bahia (UFBA), Salvador, Brazil
| | - Leonardo Paiva Farias
- Laboratory of Inflammation and Biomarkers, Instituto Gonçalo Moniz, Fundação Oswaldo Cruz (FIOCRUZ), Salvador, Brazil.,Faculdade de Medicina da Bahia, Federal University of Bahia (UFBA), Salvador, Brazil
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21
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Pan Y, Sun Y, Wang Y, Zhang Z. Barcode sequence could be a good target for developing a species-specific anti-parasite agent based on CRISPR-Cas9. FASEB J 2020; 34:9393-9404. [PMID: 32474999 DOI: 10.1096/fj.202000118rr] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Revised: 04/22/2020] [Accepted: 05/04/2020] [Indexed: 12/20/2022]
Abstract
Parasitic infections are a severe issue in many regions of the world. We assume that if a chemical can destroy a DNA barcode sequence, then this chemical could be developed as a species-specific parasiticidal agent. To test this hypothesis, we designed sgRNAs that target the sequences of both a DNA barcode (ITS-2) and a control (5.8S rDNA) in Cryptocaryon irritans. In in vivo tests, we found that exposure to Cas9 mRNA mixed with sgRNAs was able to significantly reduce the hatching rate of tomont and the survival rate of theront. Quantitative Real-time PCR demonstrated that the DNAs of tomont and theront exposed to sgRNAs and Cas9 mRNA were significantly disrupted, no matter whether they were exposed to a single sgRNA or a mixture of two sgRNAs. DNA sequencing also suggested the test group that was exposed to a single sgRNA mixed with Cas9-induced mutation at sgRNA targeted fragments and the test group exposed to two sgRNAs combined with Cas9-induced deletion of large pieces. The findings and principles provided by this study contribute to the development of novel nucleic acid therapeutic drugs for cryptocaryoniasis and other parasitic diseases and provide insight into the development of species-specific parasiticidal agents.
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Affiliation(s)
- Yinlai Pan
- College of Animal Science, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of Marine Biotechnology of Fujian Province, Institute of Oceanology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yulong Sun
- College of Animal Science, Fujian Agriculture and Forestry University, Fuzhou, China
- College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yilei Wang
- College of Fisheries, Jimei University, Xiamen, China
- State Key Laboratory of Large Yellow Croaker Breeding, Ningde, China
| | - Ziping Zhang
- College of Animal Science, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of Marine Biotechnology of Fujian Province, Institute of Oceanology, Fujian Agriculture and Forestry University, Fuzhou, China
- State Key Laboratory of Large Yellow Croaker Breeding, Ningde, China
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22
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Bhattacharya A, Corbeil A, do Monte-Neto RL, Fernandez-Prada C. Of Drugs and Trypanosomatids: New Tools and Knowledge to Reduce Bottlenecks in Drug Discovery. Genes (Basel) 2020; 11:genes11070722. [PMID: 32610603 PMCID: PMC7397081 DOI: 10.3390/genes11070722] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Revised: 06/23/2020] [Accepted: 06/26/2020] [Indexed: 12/15/2022] Open
Abstract
Leishmaniasis (Leishmania species), sleeping sickness (Trypanosoma brucei), and Chagas disease (Trypanosoma cruzi) are devastating and globally spread diseases caused by trypanosomatid parasites. At present, drugs for treating trypanosomatid diseases are far from ideal due to host toxicity, elevated cost, limited access, and increasing rates of drug resistance. Technological advances in parasitology, chemistry, and genomics have unlocked new possibilities for novel drug concepts and compound screening technologies that were previously inaccessible. In this perspective, we discuss current models used in drug-discovery cascades targeting trypanosomatids (from in vitro to in vivo approaches), their use and limitations in a biological context, as well as different examples of recently discovered lead compounds.
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Affiliation(s)
- Arijit Bhattacharya
- Department of Microbiology, Adamas University, Kolkata, West Bengal 700 126, India;
| | - Audrey Corbeil
- Department of Pathology and Microbiology, Faculty of Veterinary Medicine, Université de Montréal, Saint-Hyacinthe, QC J2S 2M2, Canada;
| | | | - Christopher Fernandez-Prada
- Department of Pathology and Microbiology, Faculty of Veterinary Medicine, Université de Montréal, Saint-Hyacinthe, QC J2S 2M2, Canada;
- Correspondence: ; Tel.: +1-450-773-8521 (ext. 32802)
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23
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Yagoubat A, Crobu L, Berry L, Kuk N, Lefebvre M, Sarrazin A, Bastien P, Sterkers Y. Universal highly efficient conditional knockout system in
Leishmania
, with a focus on untranscribed region preservation. Cell Microbiol 2020; 22:e13159. [DOI: 10.1111/cmi.13159] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Revised: 12/24/2019] [Accepted: 12/27/2019] [Indexed: 12/13/2022]
Affiliation(s)
- Akila Yagoubat
- MiVEGECUniversity of Montpellier, CNRS, IRD, CHU Montpellier France
| | - Lucien Crobu
- MiVEGECUniversity of Montpellier, CNRS, IRD, CHU Montpellier France
| | - Laurence Berry
- Laboratory of Pathogen Host Interactions, Microscopie Electronique et Analytique, CNRSUniversity of Montpellier Montpellier France
| | - Nada Kuk
- MiVEGECUniversity of Montpellier, CNRS, IRD, CHU Montpellier France
| | - Michèle Lefebvre
- MiVEGECUniversity of Montpellier, CNRS, IRD, CHU Montpellier France
| | - Amélie Sarrazin
- Montpellier RIO Imaging Facility, Montpellier BIOCAMPUSUniversity of Montpellier, Arnaud de Villeneuve Campus Imaging Facility‐Institut de Génétique Humaine‐CNRS Montpellier France
| | - Patrick Bastien
- MiVEGECUniversity of Montpellier, CNRS, IRD, CHU Montpellier France
| | - Yvon Sterkers
- MiVEGECUniversity of Montpellier, CNRS, IRD, CHU Montpellier France
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24
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Xu P, Ianes C, Gärtner F, Liu C, Burster T, Bakulev V, Rachidi N, Knippschild U, Bischof J. Structure, regulation, and (patho-)physiological functions of the stress-induced protein kinase CK1 delta (CSNK1D). Gene 2019; 715:144005. [PMID: 31376410 DOI: 10.1016/j.gene.2019.144005] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Revised: 07/19/2019] [Accepted: 07/23/2019] [Indexed: 12/11/2022]
Abstract
Members of the highly conserved pleiotropic CK1 family of serine/threonine-specific kinases are tightly regulated in the cell and play crucial regulatory roles in multiple cellular processes from protozoa to human. Since their dysregulation as well as mutations within their coding regions contribute to the development of various different pathologies, including cancer and neurodegenerative diseases, they have become interesting new drug targets within the last decade. However, to develop optimized CK1 isoform-specific therapeutics in personalized therapy concepts, a detailed knowledge of the regulation and functions of the different CK1 isoforms, their various splice variants and orthologs is mandatory. In this review we will focus on the stress-induced CK1 isoform delta (CK1δ), thereby addressing its regulation, physiological functions, the consequences of its deregulation for the development and progression of diseases, and its potential as therapeutic drug target.
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Affiliation(s)
- Pengfei Xu
- Department of General and Visceral Surgery, Surgery Center, Ulm University Hospital, Albert-Einstein-Allee 23, 89081 Ulm, Germany.
| | - Chiara Ianes
- Department of General and Visceral Surgery, Surgery Center, Ulm University Hospital, Albert-Einstein-Allee 23, 89081 Ulm, Germany.
| | - Fabian Gärtner
- Department of General and Visceral Surgery, Surgery Center, Ulm University Hospital, Albert-Einstein-Allee 23, 89081 Ulm, Germany.
| | - Congxing Liu
- Department of General and Visceral Surgery, Surgery Center, Ulm University Hospital, Albert-Einstein-Allee 23, 89081 Ulm, Germany.
| | - Timo Burster
- Department of Biology, School of Science and Technology, Nazarbayev University, 53 Kabanbay Batyr Ave, Nur-Sultan 020000, Kazakhstan.
| | - Vasiliy Bakulev
- Ural Federal University named after the first President of Russia B. N. Eltsin, Technology for Organic Synthesis Laboratory, 19 Mirastr., 620002 Ekaterinburg, Russia.
| | - Najma Rachidi
- Unité de Parasitologie Moléculaire et Signalisation, Department of Parasites and Insect Vectors, Institut Pasteur and INSERM U1201, 25-28 Rue du Dr Roux, 75015 Paris, France.
| | - Uwe Knippschild
- Department of General and Visceral Surgery, Surgery Center, Ulm University Hospital, Albert-Einstein-Allee 23, 89081 Ulm, Germany.
| | - Joachim Bischof
- Department of General and Visceral Surgery, Surgery Center, Ulm University Hospital, Albert-Einstein-Allee 23, 89081 Ulm, Germany.
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Lander N, Chiurillo MA. State-of-the-art CRISPR/Cas9 Technology for Genome Editing in Trypanosomatids. J Eukaryot Microbiol 2019; 66:981-991. [PMID: 31211904 DOI: 10.1111/jeu.12747] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Revised: 06/12/2019] [Accepted: 06/12/2019] [Indexed: 12/23/2022]
Abstract
CRISPR/Cas9 technology has revolutionized biology. This prokaryotic defense system against foreign DNA has been repurposed for genome editing in a broad range of cell tissues and organisms. Trypanosomatids are flagellated protozoa belonging to the order Kinetoplastida. Some of its most representative members cause important human diseases affecting millions of people worldwide, such as Chagas disease, sleeping sickness and different forms of leishmaniases. Trypanosomatid infections represent an enormous burden for public health and there are no effective treatments for most of the diseases they cause. Since the emergence of the CRISPR/Cas9 technology, the genetic manipulation of these parasites has notably improved. As a consequence, genome editing is now playing a key role in the functional study of proteins, in the characterization of metabolic pathways, in the validation of alternative targets for antiparasitic interventions, and in the study of parasite biology and pathogenesis. In this work we review the different strategies that have been used to adapt the CRISPR/Cas9 system to Trypanosoma cruzi, Trypanosoma brucei, and Leishmania spp., as well as the research progress achieved using these approaches. Thereby, we will present the state-of-the-art molecular tools available for genome editing in trypanosomatids to finally point out the future perspectives in the field.
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Affiliation(s)
- Noelia Lander
- Center for Tropical and Emerging Global Diseases and Department of Cellular Biology, University of Georgia, Athens, Georgia, 30602
| | - Miguel A Chiurillo
- Center for Tropical and Emerging Global Diseases and Department of Cellular Biology, University of Georgia, Athens, Georgia, 30602
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26
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Bryant JM, Baumgarten S, Glover L, Hutchinson S, Rachidi N. CRISPR in Parasitology: Not Exactly Cut and Dried! Trends Parasitol 2019; 35:409-422. [DOI: 10.1016/j.pt.2019.03.004] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Revised: 03/13/2019] [Accepted: 03/14/2019] [Indexed: 12/26/2022]
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Liu Q, Lei J, Kadowaki T. Gene Disruption of Honey Bee Trypanosomatid Parasite, Lotmaria passim, by CRISPR/Cas9 System. Front Cell Infect Microbiol 2019; 9:126. [PMID: 31080782 PMCID: PMC6497781 DOI: 10.3389/fcimb.2019.00126] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2018] [Accepted: 04/10/2019] [Indexed: 11/13/2022] Open
Abstract
Two trypanosomatid species, Lotmaria passim and Crithidia mellificae, have been shown to parasitize honey bees to date. L. passim appears to be more prevalent than C. mellificae and specifically infects the honey bee hindgut. Although the genomic DNA has been sequenced, the effects of infection on honey bee health and colony are poorly understood. To identify the genes that are important for infecting honey bees and to understand their functions, we applied the CRISPR/Cas9 system to establish a method to manipulate L. passim genes. By electroporation of plasmid DNA and subsequent selection by drug, we first established an L. passim clone expressing tdTomato or Cas9. We also successfully disrupted the endogenous miltefosine transporter and tyrosine aminotransferase genes by replacement with drug (hygromycin) resistant gene using the CRISPR/Cas9-induced homology-directed repair pathway. The L. passim clone expressing fluorescent marker, as well as the simple method for editing specific genes, could become useful approaches to understand the underlying mechanisms of honey bee-trypanosomatid parasite interactions.
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Affiliation(s)
| | | | - Tatsuhiko Kadowaki
- Department of Biological Sciences, Xi'an Jiaotong-Liverpool University, Suzhou, China
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28
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Zirpel H, Clos J. Gene Replacement by Homologous Recombination. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2019; 1971:169-188. [PMID: 30980303 DOI: 10.1007/978-1-4939-9210-2_8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
While homologous recombination-based gene replacement is about to be supplanted by more modern approaches, it is still retaining usefulness for genes that prove to be poor targets for CRISPR/cas-based approaches. Homologous recombination has proven to be relatively robust to minor sequence mismatches between GOI-flanking sequences and the gene replacement constructs, and the faithfulness of recombination events is easily verified by whole-genome sequencing. Moreover, the availability of custom synthetic gene production by numerous service providers should allow for a relatively quick generation of null mutants without the need to introduce additional protein-coding genes beyond the selection markers.
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Affiliation(s)
- Henner Zirpel
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - Joachim Clos
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany.
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29
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Abstract
Postgenomic analyses of Leishmania biology benefit from rapid and precise methods for gene manipulation. Traditional methods of gene knockout or tagging by homologous recombination have limitations: they tend to be slow and require successive transfection and selection rounds to knock out multiple alleles of a gene. Clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 systems overcome these limitations. We describe here in detail a simple, rapid, and scalable method for CRISPR-Cas9-mediated gene knockout and tagging in Leishmania. This method details how to use simple PCR to generate (1) templates for single guide RNA (sgRNA) transcription in cells expressing Cas9 and T7 RNA polymerase and (2) drug-selectable editing cassettes, using a modular set of plasmids as templates. pT plasmids allow for amplification of drug resistance genes for knockouts and pPLOT plasmids provide a choice of different tags to generate N- or C-terminally tagged proteins. We describe how to use an online platform ( LeishGEdit.net ) for automated primer design and how to perform PCRs and transfections in small batches or on 96-well plates for large-scale knockout or tagging screens. This method allows generation of knockout mutants or tagged cell lines within 1 week.
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Affiliation(s)
- Tom Beneke
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Eva Gluenz
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK.
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