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Bharadava K, Upadhyay TK, Kaushal RS, Ahmad I, Alraey Y, Siddiqui S, Saeed M. Genomic Insight of Leishmania Parasite: In-Depth Review of Drug Resistance Mechanisms and Genetic Mutations. ACS OMEGA 2024; 9:12500-12514. [PMID: 38524425 PMCID: PMC10955595 DOI: 10.1021/acsomega.3c09400] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/25/2023] [Revised: 02/07/2024] [Accepted: 02/14/2024] [Indexed: 03/26/2024]
Abstract
Leishmaniasis, which is caused by a parasitic protozoan of the genus Leishmania, is still a major threat to global health, impacting millions of individuals worldwide in endemic areas. Chemotherapy has been the principal method for managing leishmaniasis; nevertheless, the evolution of drug resistance offers a significant obstacle to therapeutic success. Drug-resistant behavior in these parasites is a complex phenomenon including both innate and acquired mechanisms. Resistance is frequently related to changes in drug transportation, drug target alterations, and enhanced efflux of the drug from the pathogen. This review has revealed specific genetic mutations in Leishmania parasites that are associated with resistance to commonly used antileishmanial drugs such as pentavalent antimonials, miltefosine, amphotericin B, and paromomycin, resulting in changes in gene expression along with the functioning of various proteins involved in drug uptake, metabolism, and efflux. Understanding the genetic changes linked to drug resistance in Leishmania parasites is essential for creating approaches for tackling and avoiding the spread of drug-resistant variants. Based on which specific treatments focus on mutations and pathways could potentially improve treatment efficacy and help long-term leishmaniasis control. More study is needed to uncover the complete range of genetic changes generating medication resistance and to develop new therapies based on available information.
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Affiliation(s)
- Krupanshi Bharadava
- Biophysics
& Structural Biology, Research & Development Cell, Parul University, Vadodara, Gujarat 391760, India
| | - Tarun Kumar Upadhyay
- Department
of Life Sciences, Parul Institute of Applied Sciences & Research
and Development Cell, Parul University, Vadodara, Gujarat 391760, India
| | - Radhey Shyam Kaushal
- Biophysics
& Structural Biology, Research & Development Cell, Parul University, Vadodara, Gujarat 391760, India
- Department
of Life Sciences, Parul Institute of Applied Sciences & Research
and Development Cell, Parul University, Vadodara, Gujarat 391760, India
| | - Irfan Ahmad
- Department
of Clinical Laboratory Sciences, College of Applied Medical Sciences, King Khalid University, Abha 61421, Saudi Arabia
| | - Yasser Alraey
- Department
of Clinical Laboratory Sciences, College of Applied Medical Sciences, King Khalid University, Abha 61421, Saudi Arabia
| | - Samra Siddiqui
- Department
of Health Service Management, College of Public Health and Health
Informatics, University of Hail, Hail 55476, Saudi Arabia
| | - Mohd Saeed
- Department
of Biology, College of Science, University
of Hail, Hail 55476, Saudi Arabia
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2
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Girasol MJ, Krasilnikova M, Marques CA, Damasceno JD, Lapsley C, Lemgruber L, Burchmore R, Beraldi D, Carruthers R, Briggs EM, McCulloch R. RAD51-mediated R-loop formation acts to repair transcription-associated DNA breaks driving antigenic variation in Trypanosoma brucei. Proc Natl Acad Sci U S A 2023; 120:e2309306120. [PMID: 37988471 PMCID: PMC10691351 DOI: 10.1073/pnas.2309306120] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Accepted: 09/13/2023] [Indexed: 11/23/2023] Open
Abstract
RNA-DNA hybrids are epigenetic features of all genomes that intersect with many processes, including transcription, telomere homeostasis, and centromere function. Increasing evidence suggests that RNA-DNA hybrids can provide two conflicting roles in the maintenance and transmission of genomes: They can be the triggers of DNA damage, leading to genome change, or can aid the DNA repair processes needed to respond to DNA lesions. Evasion of host immunity by African trypanosomes, such as Trypanosoma brucei, relies on targeted recombination of silent Variant Surface Glycoprotein (VSG) genes into a specialized telomeric locus that directs transcription of just one VSG from thousands. How such VSG recombination is targeted and initiated is unclear. Here, we show that a key enzyme of T. brucei homologous recombination, RAD51, interacts with RNA-DNA hybrids. In addition, we show that RNA-DNA hybrids display a genome-wide colocalization with DNA breaks and that this relationship is impaired by mutation of RAD51. Finally, we show that RAD51 acts to repair highly abundant, localised DNA breaks at the single transcribed VSG and that mutation of RAD51 alters RNA-DNA hybrid abundance at 70 bp repeats both around the transcribed VSG and across the silent VSG archive. This work reveals a widespread, generalised role for RNA-DNA hybrids in directing RAD51 activity during recombination and uncovers a specialised application of this interplay during targeted DNA break repair needed for the critical T. brucei immune evasion reaction of antigenic variation.
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Affiliation(s)
- Mark John Girasol
- College of Medical, Veterinary and Life Sciences, School of Infection and Immunity, Wellcome Centre for Integrative Parasitology, University of Glasgow, GlasgowG12 8TA, United Kingdom
- Faculty of the MD-PhD in Molecular Medicine Program, College of Medicine, University of the Philippines Manila, Manila1000, Philippines
| | - Marija Krasilnikova
- College of Medical, Veterinary and Life Sciences, School of Infection and Immunity, Wellcome Centre for Integrative Parasitology, University of Glasgow, GlasgowG12 8TA, United Kingdom
| | - Catarina A. Marques
- College of Medical, Veterinary and Life Sciences, School of Infection and Immunity, Wellcome Centre for Integrative Parasitology, University of Glasgow, GlasgowG12 8TA, United Kingdom
| | - Jeziel D. Damasceno
- College of Medical, Veterinary and Life Sciences, School of Infection and Immunity, Wellcome Centre for Integrative Parasitology, University of Glasgow, GlasgowG12 8TA, United Kingdom
| | - Craig Lapsley
- College of Medical, Veterinary and Life Sciences, School of Infection and Immunity, Wellcome Centre for Integrative Parasitology, University of Glasgow, GlasgowG12 8TA, United Kingdom
| | - Leandro Lemgruber
- College of Medical, Veterinary and Life Sciences, School of Infection and Immunity, Wellcome Centre for Integrative Parasitology, University of Glasgow, GlasgowG12 8TA, United Kingdom
| | - Richard Burchmore
- College of Medical, Veterinary and Life Sciences, School of Infection and Immunity, Wellcome Centre for Integrative Parasitology, University of Glasgow, GlasgowG12 8TA, United Kingdom
| | - Dario Beraldi
- College of Medical, Veterinary and Life Sciences, School of Infection and Immunity, Wellcome Centre for Integrative Parasitology, University of Glasgow, GlasgowG12 8TA, United Kingdom
| | - Ross Carruthers
- College of Medical, Veterinary and Life Sciences, School of Cancer Sciences, University of Glasgow, GlasgowG12 0YN, United Kingdom
| | - Emma M. Briggs
- College of Medical, Veterinary and Life Sciences, School of Infection and Immunity, Wellcome Centre for Integrative Parasitology, University of Glasgow, GlasgowG12 8TA, United Kingdom
- Institute for Immunology and Infection Research, School of Biological Sciences, University of Edinburgh, EdinburghEH9 3FL, United Kingdom
| | - Richard McCulloch
- College of Medical, Veterinary and Life Sciences, School of Infection and Immunity, Wellcome Centre for Integrative Parasitology, University of Glasgow, GlasgowG12 8TA, United Kingdom
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3
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Kamran M, Bhattacharjee R, Das S, Mukherjee S, Ali N. The paradigm of intracellular parasite survival and drug resistance in leishmanial parasite through genome plasticity and epigenetics: Perception and future perspective. Front Cell Infect Microbiol 2023; 13:1001973. [PMID: 36814446 PMCID: PMC9939536 DOI: 10.3389/fcimb.2023.1001973] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2022] [Accepted: 01/16/2023] [Indexed: 02/09/2023] Open
Abstract
Leishmania is an intracellular, zoonotic, kinetoplastid eukaryote with more than 1.2 million cases all over the world. The leishmanial chromosomes are divided into polymorphic chromosomal ends, conserved central domains, and antigen-encoding genes found in telomere-proximal regions. The genome flexibility of chromosomal ends of the leishmanial parasite is known to cause drug resistance and intracellular survival through the evasion of host defense mechanisms. Therefore, in this review, we discuss the plasticity of Leishmania genome organization which is the primary cause of drug resistance and parasite survival. Moreover, we have not only elucidated the causes of such genome plasticity which includes aneuploidy, epigenetic factors, copy number variation (CNV), and post-translation modification (PTM) but also highlighted their impact on drug resistance and parasite survival.
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Affiliation(s)
| | | | - Sonali Das
- Infectious Diseases and Immunology Division, Indian Institute of Chemical Biology, Kolkata, West Bengal, India
| | - Sohitri Mukherjee
- Infectious Diseases and Immunology Division, Indian Institute of Chemical Biology, Kolkata, West Bengal, India
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4
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Black JA, Reis-Cunha JL, Cruz AK, Tosi LR. Life in plastic, it's fantastic! How Leishmania exploit genome instability to shape gene expression. Front Cell Infect Microbiol 2023; 13:1102462. [PMID: 36779182 PMCID: PMC9910336 DOI: 10.3389/fcimb.2023.1102462] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Accepted: 01/05/2023] [Indexed: 01/27/2023] Open
Abstract
Leishmania are kinetoplastid pathogens that cause leishmaniasis, a debilitating and potentially life-threatening infection if untreated. Unusually, Leishmania regulate their gene expression largely post-transcriptionally due to the arrangement of their coding genes into polycistronic transcription units that may contain 100s of functionally unrelated genes. Yet, Leishmania are capable of rapid and responsive changes in gene expression to challenging environments, often instead correlating with dynamic changes in their genome composition, ranging from chromosome and gene copy number variations to the generation of extrachromosomal DNA and the accumulation of point mutations. Typically, such events indicate genome instability in other eukaryotes, coinciding with genetic abnormalities, but for Leishmania, exploiting these products of genome instability can provide selectable substrates to catalyse necessary gene expression changes by modifying gene copy number. Unorthodox DNA replication, DNA repair, replication stress factors and DNA repeats are recognised in Leishmania as contributors to this intrinsic instability, but how Leishmania regulate genome plasticity to enhance fitness whilst limiting toxic under- or over-expression of co-amplified and co-transcribed genes is unclear. Herein, we focus on fresh, and detailed insights that improve our understanding of genome plasticity in Leishmania. Furthermore, we discuss emerging models and factors that potentially circumvent regulatory issues arising from polycistronic transcription. Lastly, we highlight key gaps in our understanding of Leishmania genome plasticity and discuss future studies to define, in higher resolution, these complex regulatory interactions.
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Affiliation(s)
- Jennifer A. Black
- Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil,The Wellcome Centre for Integrative Parasitology, School of Infection, Immunity, and Inflammation, University of Glasgow, Glasgow, United Kingdom,*Correspondence: Luiz. R.O. Tosi, ; Jennifer A. Black,
| | | | - Angela. K. Cruz
- Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil
| | - Luiz. R.O. Tosi
- Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil,*Correspondence: Luiz. R.O. Tosi, ; Jennifer A. Black,
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5
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da Silva VS, Machado CR. Sex in protists: A new perspective on the reproduction mechanisms of trypanosomatids. Genet Mol Biol 2022; 45:e20220065. [PMID: 36218381 PMCID: PMC9552303 DOI: 10.1590/1678-4685-gmb-2022-0065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 08/07/2022] [Indexed: 11/04/2022] Open
Abstract
The Protist kingdom individuals are the most ancestral representatives of
eukaryotes. They have inhabited Earth since ancient times and are currently
found in the most diverse environments presenting a great heterogeneity of life
forms. The unicellular and multicellular algae, photosynthetic and heterotrophic
organisms, as well as free-living and pathogenic protozoa represents the protist
group. The evolution of sex is directly associated with the origin of eukaryotes
being protists the earliest protagonists of sexual reproduction on earth. In
eukaryotes, the recombination through genetic exchange is a ubiquitous mechanism
that can be stimulated by DNA damage. Scientific evidences support the
hypothesis that reactive oxygen species (ROS) induced DNA damage can promote
sexual recombination in eukaryotes which might have been a decisive factor for
the origin of sex. The fact that some recombination enzymes also participate in
meiotic sex in modern eukaryotes reinforces the idea that sexual reproduction
emerged as consequence of specific mechanisms to cope with mutations and
alterations in genetic material. In this review we will discuss about origin of
sex and different strategies of evolve sexual reproduction in some protists such
that cause human diseases like malaria, toxoplasmosis, sleeping sickness, Chagas
disease, and leishmaniasis.
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Affiliation(s)
- Verônica Santana da Silva
- Universidade Federal de Minas Gerais, Departamento de Genética,
Ecologia e Evolução, Belo Horizonte, MG, Brazil
| | - Carlos Renato Machado
- Universidade Federal de Minas Gerais, Departamento de Bioquímica e
Imunologia, Belo Horizonte, MG, Brazil
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Ghosh S, Kumar V, Verma A, Sharma T, Pradhan D, Selvapandiyan A, Salotra P, Singh R. Genome-wide analysis reveals allelic variation and chromosome copy number variation in paromomycin-resistant Leishmania donovani. Parasitol Res 2022; 121:3121-3132. [PMID: 36056959 DOI: 10.1007/s00436-022-07645-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Accepted: 08/24/2022] [Indexed: 11/30/2022]
Abstract
In the absence of adequate diagnosis and treatment, leishmaniasis remains a major public health concern on a global scale. Drug resistance remains a key obstacle in controlling and eliminating visceral leishmaniasis. The therapeutic gap due to lack of target-specific medicine and vaccine can be minimized by obtaining parasite's genomic information. This study compared whole-genome sequence of paromomycin-resistant parasite (K133PMM) developed through in vitro adaptation and selection with sensitive Leishmania clinical isolate (K133WT). We found a large number of upstream and intergenic gene variations in K133PMM. There were 259 single nucleotide polymorphisms (SNPs), 187 insertion-deletion (InDels), and 546 copy number variations (CNVs) identified. Most of the genomic variations were found in the gene's upstream and non-coding regions. Ploidy estimation revealed chromosome 5 in tetrasomy and 6, 9, and 12 in trisomy, uniquely in K133PMM. These contain the genes for protein degradation, parasite motility, autophagy, cell cycle maintenance, and drug efflux membrane transporters. Furthermore, we also observed reduction in ploidy of chromosomes 15, 20, and 23, in the resistant parasite containing mostly the genes for hypothetical proteins and membrane transporters. We chronicled correlated genomic conversion and aneuploidy in parasites and hypothesize that this led to rapid evolutionary changes in response to drug induced pressure, which causes them to become resistant.
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Affiliation(s)
- Sushmita Ghosh
- ICMR-National Institute of Pathology, Safdarjung Hospital Campus, New Delhi, 110029, India.,Department of Molecular Medicine, Jamia Hamdard, New Delhi, 110062, India
| | - Vinay Kumar
- ICMR-National Institute of Pathology, Safdarjung Hospital Campus, New Delhi, 110029, India
| | - Aditya Verma
- ICMR-National Institute of Pathology, Safdarjung Hospital Campus, New Delhi, 110029, India
| | - Tanya Sharma
- ICMR-AIIMS Computational Genomics Centre, Indian Council of Medical Research, New Delhi, 110029, India
| | - Dibyabhaba Pradhan
- ICMR-AIIMS Computational Genomics Centre, Indian Council of Medical Research, New Delhi, 110029, India
| | | | - Poonam Salotra
- ICMR-National Institute of Pathology, Safdarjung Hospital Campus, New Delhi, 110029, India
| | - Ruchi Singh
- ICMR-National Institute of Pathology, Safdarjung Hospital Campus, New Delhi, 110029, India.
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7
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Valdivia HO, Roatt BM, Baptista RDP, Ottino J, Coqueiro-dos-Santos A, Sanders MJ, Reis AB, Cotton JA, Bartholomeu DC. Replacement of Leishmania (Leishmania) infantum Populations in an Endemic Focus of Visceral Leishmaniasis in Brazil. Front Cell Infect Microbiol 2022; 12:900084. [PMID: 35811682 PMCID: PMC9263273 DOI: 10.3389/fcimb.2022.900084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2022] [Accepted: 05/30/2022] [Indexed: 11/21/2022] Open
Abstract
Visceral leishmaniasis is an important global health problem with an estimated of 50,000 to 90,000 new cases per year. VL is the most serious form of leishmaniasis as it can be fatal in 95% of the cases if it remains untreated. VL is a particularly acute problem in Brazil which contributed with 97% of all cases reported in 2020 in the Americas. In this country, VL affects mainly the poorest people in both urban and rural areas and continues to have a high mortality rate estimated around 8.15%. Here, we performed a temporal parasite population study using whole genome sequence data from a set of 34 canine isolates sampled in 2008, 2012 and 2015 from a re-emergent focus in Southeastern Brazil. Our study found the presence of two distinct sexual subpopulations that corresponded to two isolation periods. These subpopulations diverged hundreds of years ago with no apparent gene flow between them suggesting a process of rapid replacement during a two-year period. Sequence comparisons and analysis of nucleotide diversity also showed evidence of balancing selection acting on transport-related genes and antigenic families. To our knowledge this is the first population genomic study showing a turn-over of parasite populations in an endemic region for leishmaniasis. The complexity and rapid adaptability of these parasites pose new challenges to control activities and demand more integrated approaches to understand this disease in New World foci.
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Affiliation(s)
- Hugo O. Valdivia
- Departamento de Parasitologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
- U.S. Naval Medical Research Unit Six, Department of Parasitology, Lima, Peru
| | - Bruno M. Roatt
- Núcleo de Pesquisas em Ciências Biológicas/NUPEB, Universidade Federal de Ouro Preto, Ouro Preto, Brazil
| | - Rodrigo de Paula Baptista
- CTEGD- Center for Tropical and Emerging Global Diseases and IOB - Institute of Bioinformatics, University of Georgia, Athens, United States
- Houston Methodist Research Institute, Houston, United States
| | - Jennifer Ottino
- Departamento de Parasitologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Anderson Coqueiro-dos-Santos
- Departamento de Parasitologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | | | - Alexandre B. Reis
- Núcleo de Pesquisas em Ciências Biológicas/NUPEB, Universidade Federal de Ouro Preto, Ouro Preto, Brazil
| | - James A. Cotton
- Wellcome Sanger Institute, Cambridge, United Kingdom
- Institute of Biodiversity, Animal Health and Comparative Medicine, Wellcome Centre for Integrative Parasitology, University of Glasgow, Glasgow, United Kingdom
| | - Daniella C. Bartholomeu
- Departamento de Parasitologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
- *Correspondence: Daniella C. Bartholomeu,
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8
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Sharma R, Avendaño Rangel F, Reis-Cunha JL, Marques LP, Figueira CP, Borba PB, Viana SM, Beneke T, Bartholomeu DC, de Oliveira CI. Targeted Deletion of Centrin in Leishmania braziliensis Using CRISPR-Cas9-Based Editing. Front Cell Infect Microbiol 2022; 11:790418. [PMID: 35252020 PMCID: PMC8892584 DOI: 10.3389/fcimb.2021.790418] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Accepted: 12/22/2021] [Indexed: 12/25/2022] Open
Abstract
Leishmania braziliensis is the main causative agent of Tegumentary Leishmaniasis in the Americas. However, difficulties related to genome manipulation, experimental infection, and parasite growth have so far limited studies with this species. CRISPR-Cas9-based technology has made genome editing more accessible, and here we have successfully employed the LeishGEdit approach to attenuate L. braziliensis. We generated a transgenic cell line expressing Cas9 and T7 RNA polymerase, which was employed for the targeted deletion of centrin, a calcium-binding cytoskeletal protein involved in the centrosome duplication in eukaryotes. Centrin-deficient Leishmania exhibit growth arrest at the amastigote stage. Whole-genome sequencing of centrin-deficient L. braziliensis (LbCen−/−) did not indicate the presence of off-target mutations. In vitro, the growth rates of LbCen−/− and wild-type promastigotes were similar, but axenic and intracellular LbCen−/− amastigotes showed a multinucleated phenotype with impaired survival following macrophage infection. Upon inoculation into BALB/c mice, LbCen−/− were detected at an early time point but failed to induce lesion formation, contrary to control animals, infected with wild-type L. braziliensis. A significantly lower parasite burden was also observed in mice inoculated with LbCen−/−, differently from control mice. Given that centrin-deficient Leishmania sp. have become candidates for vaccine development, we propose that LbCen−/− can be further explored for the purposes of immunoprophylaxis against American Tegumentary Leishmaniasis.
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Affiliation(s)
- Rohit Sharma
- Instituto Gonçalo Moniz, Fiocruz, Salvador, Brazil
| | - Francys Avendaño Rangel
- Instituto Gonçalo Moniz, Fiocruz, Salvador, Brazil
- Programa de Pós-graduação em Ciências da Saúde, Faculdade de Medicina da Bahia, Universidade Federal da Bahia, Salvador, Brazil
| | - João Luís Reis-Cunha
- Departamento de Medicina Veterinária Preventiva, Escola de Veterinária, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | | | | | | | - Sayonara M. Viana
- Instituto Gonçalo Moniz, Fiocruz, Salvador, Brazil
- Programa de Pós-graduação em Ciências da Saúde, Faculdade de Medicina da Bahia, Universidade Federal da Bahia, Salvador, Brazil
| | - Tom Beneke
- Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom
| | | | - Camila I. de Oliveira
- Instituto Gonçalo Moniz, Fiocruz, Salvador, Brazil
- Programa de Pós-graduação em Ciências da Saúde, Faculdade de Medicina da Bahia, Universidade Federal da Bahia, Salvador, Brazil
- INCT—Instituto de Investigação em Doenças Tropicais, Salvador, Brazil
- *Correspondence: Camila I. de Oliveira,
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Lypaczewski P, Thakur L, Jain A, Kumari S, Paulini K, Matlashewski G, Jain M. An intraspecies Leishmania donovani hybrid from the Indian subcontinent is associated with an atypical phenotype of cutaneous disease. iScience 2022; 25:103802. [PMID: 35198868 PMCID: PMC8841885 DOI: 10.1016/j.isci.2022.103802] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Revised: 01/11/2022] [Accepted: 01/20/2022] [Indexed: 11/23/2022] Open
Abstract
Leishmaniasis is a neglected tropical disease endemic in over 90 countries. The disease has two main pathologies; cutaneous leishmaniasis (CL) that generally self-heals, and visceral leishmaniasis (VL) that is fatal if untreated. The majority of VL cases, concentrated on the Indian subcontinent (ISC) and East Africa, are caused by Leishmania donovani. However, recent foci of CL on the ISC have been attributed as an atypical phenotype of L. donovani including a recent outbreak in Himachal Pradesh, India. Whole genome sequencing and phylogenetic analysis was undertaken to investigate the origins and genetic factors leading to this pathology atypical of L. donovani. Here we demonstrate the isolate from Himachal Pradesh is derived from a genetic hybridization between two independent L. donovani parents from the ‘Yeti’ ISC1 divergent clade of parasites, identified in the Nepalese highlands. This reveals that intraspecies L. donovani hybrids can give rise to a novel strain associated with CL. A novel focus of cutaneous Leishmaniasis is emerging in Himachal Pradesh The normally visceral Leishmania donovani parasite is responsible for the focus The isolated parasite is an intraspecies genetic hybrid Extensive genomic hybridization could explain this atypical phenotype
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10
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Santi AMM, Murta SMF. Impact of Genetic Diversity and Genome Plasticity of Leishmania spp. in Treatment and the Search for Novel Chemotherapeutic Targets. Front Cell Infect Microbiol 2022; 12:826287. [PMID: 35141175 PMCID: PMC8819175 DOI: 10.3389/fcimb.2022.826287] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Accepted: 01/04/2022] [Indexed: 11/21/2022] Open
Abstract
Leishmaniasis is one of the major public health concerns in Latin America, Africa, Asia, and Europe. The absence of vaccines for human use and the lack of effective vector control programs make chemotherapy the main strategy to control all forms of the disease. However, the high toxicity of available drugs, limited choice of therapeutic agents, and occurrence of drug-resistant parasite strains are the main challenges related to chemotherapy. Currently, only a small number of drugs are available for leishmaniasis treatment, including pentavalent antimonials (SbV), amphotericin B and its formulations, miltefosine, paromomycin sulphate, and pentamidine isethionate. In addition to drug toxicity, therapeutic failure of leishmaniasis is a serious concern. The occurrence of drug-resistant parasites is one of the causes of therapeutic failure and is closely related to the diversity of parasites in this genus. Owing to the enormous plasticity of the genome, resistance can occur by altering different metabolic pathways, demonstrating that resistance mechanisms are multifactorial and extremely complex. Genetic variability and genome plasticity cause not only the available drugs to have limitations, but also make the search for new drugs challenging. Here, we examined the biological characteristics of parasites that hinder drug discovery.
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11
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Glans H, Lind Karlberg M, Advani R, Bradley M, Alm E, Andersson B, Downing T. High genome plasticity and frequent genetic exchange in Leishmania tropica isolates from Afghanistan, Iran and Syria. PLoS Negl Trop Dis 2021; 15:e0010110. [PMID: 34968388 PMCID: PMC8754299 DOI: 10.1371/journal.pntd.0010110] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Revised: 01/12/2022] [Accepted: 12/17/2021] [Indexed: 11/23/2022] Open
Abstract
Background The kinetoplastid protozoan Leishmania tropica mainly causes cutaneous leishmaniasis in humans in the Middle East, and relapse or treatment failure after treatment are common in this area. L. tropica’s digenic life cycle includes distinct stages in the vector sandfly and the mammalian host. Sexual reproduction and genetic exchange appear to occur more frequently than in other Leishmania species. Understanding these processes is complicated by chromosome instability during cell division that yields aneuploidy, recombination and heterozygosity. This combination of rare recombination and aneuploid permits may reveal signs of hypothetical parasexual mating, where diploid cells fuse to form a transient tetraploid that undergoes chromosomal recombination and gradual chromosomal loss. Methodology/principal findings The genome-wide SNP diversity from 22 L. tropica isolates showed chromosome-specific runs of patchy heterozygosity and extensive chromosome copy number variation. All these isolates were collected during 2007–2017 in Sweden from patients infected in the Middle East and included isolates from a patient possessing two genetically distinct leishmaniasis infections three years apart with no evidence of re-infection. We found differing ancestries on the same chromosome (chr36) across multiple samples: matching the reference genome with few derived alleles, followed by blocks of heterozygous SNPs, and then by clusters of homozygous SNPs with specific recombination breakpoints at an inferred origin of replication. Other chromosomes had similar marked changes in heterozygosity at strand-switch regions separating polycistronic transcriptional units. Conclusion/significance These large-scale intra- and inter-chromosomal changes in diversity driven by recombination and aneuploidy suggest multiple mechanisms of cell reproduction and diversification in L. tropica, including mitotic, meiotic and parasexual processes. It underpins the need for more genomic surveillance of Leishmania, to detect emerging hybrids that could spread more widely and to better understand the association between genetic variation and treatment outcome. Furthering our understanding of Leishmania genome evolution and ancestry will aid better diagnostics and treatment for cutaneous leishmaniasis caused by L.tropica in the Middle East. Cutaneous leishmaniasis is mainly caused by Leishmania tropica in the Middle East, where it is known for treatment failure and a need for prolonged and/or multiple treatments. Several factors affect the clinical presentation and treatment outcome, such as host genetic variability and specific immune response, as well as environmental factors and the vector species. Little is known about the parasite genome and its influence on treatment response. By analysing the genome of 22 isolates of L. tropica, we have revealed extensive genomic variation and a complex population structure with evidence of genetic exchange within and among the isolates, indicating a possible presence of sexual or parasexual mechanisms. Understanding the Leishmania genome better may improve future treatment and better understanding of treatment failure and relapse.
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Affiliation(s)
- Hedvig Glans
- Department of Infectious Diseases, Karolinska University Hospital, Stockholm, Sweden
- Division of Dermatology & Venerology, Dept of Medicine Solna, Karolinska Institutet, Stockholm, Sweden
- * E-mail:
| | - Maria Lind Karlberg
- Department of Microbiology, The Public Health Agency of Sweden, Stockholm, Sweden
| | - Reza Advani
- Department of Microbiology, The Public Health Agency of Sweden, Stockholm, Sweden
| | - Maria Bradley
- Division of Dermatology & Venerology, Dept of Medicine Solna, Karolinska Institutet, Stockholm, Sweden
- Department of Dermatology and Venerology, Karolinska University Hospital, Stockholm, Sweden
| | - Erik Alm
- The European Center for Disease Prevention and Control, Stockholm, Sweden
| | - Björn Andersson
- Department of Cell & Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Tim Downing
- School of Biotechnology, Dublin City University, Dublin, Ireland
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12
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Volpedo G, Huston RH, Holcomb EA, Pacheco-Fernandez T, Gannavaram S, Bhattacharya P, Nakhasi HL, Satoskar AR. From infection to vaccination: reviewing the global burden, history of vaccine development, and recurring challenges in global leishmaniasis protection. Expert Rev Vaccines 2021; 20:1431-1446. [PMID: 34511000 DOI: 10.1080/14760584.2021.1969231] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
INTRODUCTION Leishmaniasis is a major public health problem and the second most lethal parasitic disease in the world due to the lack of effective treatments and vaccines. Even when not lethal, leishmaniasis significantly affects individuals and communities through life-long disabilities, psycho-sociological trauma, poverty, and gender disparity in treatment. AREAS COVERED This review discusses the most relevant and recent research available on Pubmed and GoogleScholar highlighting leishmaniasis' global impact, pathogenesis, treatment options, and lack of effective control strategies. An effective vaccine is necessary to prevent morbidity and mortality, lower health care costs, and reduce the economic burden of leishmaniasis for endemic low- and middle-income countries. Since there are several forms of leishmaniasis, a pan-Leishmania vaccine without geographical restrictions is needed. This review also focuses on recent advances and common challenges in developing prophylactic strategies against leishmaniasis. EXPERT OPINION Despite advances in pre-clinical vaccine research, approval of a human leishmaniasis vaccine still faces major challenges - including manufacturing of candidate vaccines under Good Manufacturing Practices, developing well-designed clinical trials suitable in endemic countries, and defined correlates of protection. In addition, there is a need to explore Challenge Human Infection Model to avoid large trials because of fluctuating incidence and prevalence of leishmanasis.
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Affiliation(s)
- Greta Volpedo
- Departments of Pathology and Microbiology, Wexner Medical Center, The Ohio State University, Columbus, OH, USA
| | - Ryan H Huston
- Departments of Pathology and Microbiology, Wexner Medical Center, The Ohio State University, Columbus, OH, USA
| | - Erin A Holcomb
- Departments of Pathology and Microbiology, Wexner Medical Center, The Ohio State University, Columbus, OH, USA
| | - Thalia Pacheco-Fernandez
- Departments of Pathology and Microbiology, Wexner Medical Center, The Ohio State University, Columbus, OH, USA
| | - Sreenivas Gannavaram
- Division of Emerging and Transfusion Transmitted Diseases, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD, USA
| | - Parna Bhattacharya
- Division of Emerging and Transfusion Transmitted Diseases, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD, USA
| | - Hira L Nakhasi
- Division of Emerging and Transfusion Transmitted Diseases, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD, USA
| | - Abhay R Satoskar
- Departments of Pathology and Microbiology, Wexner Medical Center, The Ohio State University, Columbus, OH, USA
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13
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Franssen SU, Takele Y, Adem E, Sanders MJ, Müller I, Kropf P, Cotton JA. Diversity and Within-Host Evolution of Leishmania donovani from Visceral Leishmaniasis Patients with and without HIV Coinfection in Northern Ethiopia. mBio 2021; 12:e0097121. [PMID: 34182785 PMCID: PMC8262925 DOI: 10.1128/mbio.00971-21] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Accepted: 05/16/2021] [Indexed: 12/20/2022] Open
Abstract
Visceral leishmaniasis (VL) is a fatal disease and a growing public health problem in East Africa, where Ethiopia has one of the highest VL burdens. The largest focus of VL in Ethiopia is driven by high prevalence in migrant agricultural workers and associated with a high rate of coinfection with HIV. This coinfection makes VL more difficult to treat successfully and is associated with a high rate of relapse, with VL/HIV patients frequently experiencing many relapses of VL before succumbing to this infection. We present genome-wide data on Leishmania donovani isolates from a longitudinal study of cohorts of VL and VL/HIV patients reporting to a single clinic in Ethiopia. Extensive clinical data allow us to investigate the influence of coinfection and relapse on the populations of parasites infecting these patients. We find that the same parasite population is responsible for both VL and VL/HIV infections and that, in most cases, disease relapse is caused by recrudescence of the population of parasites that caused primary VL. Complex, multiclonal infections are present in both primary and relapse cases, but the infrapopulation of parasites within a patient loses genetic diversity between primary disease presentation and subsequent relapses, presumably due to a population bottleneck induced by treatment. These data suggest that VL/HIV relapses are not caused by genetically distinct parasite infections or by reinfection. Treatment of VL does not lead to sterile cure, and in VL/HIV, the infecting parasites are able to reestablish after clinically successful treatment, leading to repeated relapse of VL. IMPORTANCE Visceral leishmaniasis (VL) is the second largest cause of deaths due to parasite infections and a growing problem in East Africa. In Ethiopia, it is particularly associated with migrant workers moving from regions of nonendemicity for seasonal agricultural work and is frequently found as a coinfection with HIV, which leads to frequent VL relapse following treatment. Insight into the process of relapse in these patients is thus key to controlling the VL epidemic in Ethiopia. We show that there is little genetic differentiation between the parasites infecting HIV-positive and HIV-negative VL patients. Moreover, we provide evidence that relapses are caused by the initially infecting parasite population and that treatment induces a loss of genetic diversity in this population. We propose that restoring functioning immunity and improving antiparasitic treatment may be key in breaking the cycle of relapsing VL in VL/HIV patients.
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Affiliation(s)
| | - Yegnasew Takele
- Leishmaniasis Research and Treatment Centre, University of Gondar, Gondar, Ethiopia
- Department of Infectious Disease, Imperial College London, London, United Kingdom
| | - Emebet Adem
- Leishmaniasis Research and Treatment Centre, University of Gondar, Gondar, Ethiopia
| | | | - Ingrid Müller
- Department of Infectious Disease, Imperial College London, London, United Kingdom
| | - Pascale Kropf
- Department of Infectious Disease, Imperial College London, London, United Kingdom
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14
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Reproduction in Trypanosomatids: Past and Present. BIOLOGY 2021; 10:biology10060471. [PMID: 34071741 PMCID: PMC8230138 DOI: 10.3390/biology10060471] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 05/20/2021] [Accepted: 05/25/2021] [Indexed: 01/07/2023]
Abstract
Simple Summary The reproduction of trypanosomatids is a fundamental issue for host–parasite interaction, and its biological importance lies in knowing how these species acquire new defense mechanisms against the countermeasures imposed by the host, which is consistent with the theory of the endless race or the Red Queen hypothesis for the existence of meiotic sex. Moreover, the way these species re-produce may also be at the origin of novel and more virulent clades and is relevant from a thera-peutic or vaccination point of view, as sex may contribute to increased tolerance and even to the rapid acquisition of drug resistance mechanisms. Kinetoplastids are single-celled organisms, many of them being responsible for important parasitic diseases, globally termed neglected diseases, which are endemic in low-income countries. Leishmaniasis, African (sleeping sickness) and American trypanosomiasis (Chagas disease) caused by trypanosomatids are among the most ne-glected tropical scourges related to poverty and poor health systems. The reproduction of these microorganisms has long been considered to be clonal due to population genetic observations. However, there is increasing evidence of true sex and genetic exchange events under laboratory conditions. We would like to highlight the importance of this topic in the field of host/parasite in-terplay, virulence, and drug resistance. Abstract Diseases caused by trypanosomatids (Sleeping sickness, Chagas disease, and leishmaniasis) are a serious public health concern in low-income endemic countries. These diseases are produced by single-celled parasites with a diploid genome (although aneuploidy is frequent) organized in pairs of non-condensable chromosomes. To explain the way they reproduce through the analysis of natural populations, the theory of strict clonal propagation of these microorganisms was taken as a rule at the beginning of the studies, since it partially justified their genomic stability. However, numerous experimental works provide evidence of sexual reproduction, thus explaining certain naturally occurring events that link the number of meiosis per mitosis and the frequency of mating. Recent techniques have demonstrated genetic exchange between individuals of the same species under laboratory conditions, as well as the expression of meiosis specific genes. The current debate focuses on the frequency of genomic recombination events and its impact on the natural parasite population structure. This paper reviews the results and techniques used to demonstrate the existence of sex in trypanosomatids, the inheritance of kinetoplast DNA (maxi- and minicircles), the impact of genetic exchange in these parasites, and how it can contribute to the phenotypic diversity of natural populations.
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15
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Lypaczewski P, Matlashewski G. Leishmania donovani hybridisation and introgression in nature: a comparative genomic investigation. THE LANCET MICROBE 2021; 2:e250-e258. [DOI: 10.1016/s2666-5247(21)00028-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 01/19/2021] [Accepted: 01/27/2021] [Indexed: 01/17/2023] Open
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16
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Leishmania Sexual Reproductive Strategies as Resolved through Computational Methods Designed for Aneuploid Genomes. Genes (Basel) 2021; 12:genes12020167. [PMID: 33530584 PMCID: PMC7912377 DOI: 10.3390/genes12020167] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 01/21/2021] [Accepted: 01/21/2021] [Indexed: 11/23/2022] Open
Abstract
A cryptic sexual reproductive cycle in Leishmania has been inferred through population genetic studies revealing the presence of hybrid genotypes in natural isolates, with attempts made to decipher sexual strategies by studying complex chromosomal inheritance patterns. A more informative approach is to study the products of controlled, laboratory-based experiments where known strains or species are crossed in the sand fly vector to generate hybrid progeny. These hybrids can be subsequently studied through high resolution sequencing technologies and software suites such as PAINT that disclose inheritance patterns including ploidies, parental chromosome contributions and recombinations, all of which can inform the sexual strategy. In this work, we discuss the computational methods in PAINT that can be used to interpret the sexual strategies adopted specifically by aneuploid organisms and summarize how PAINT has been applied to the analysis of experimental hybrids to reveal meiosis-like sexual recombination in Leishmania.
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17
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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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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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Kröber-Boncardo C, Lorenzen S, Brinker C, Clos J. Casein kinase 1.2 over expression restores stress resistance to Leishmania donovani HSP23 null mutants. Sci Rep 2020; 10:15969. [PMID: 32994468 PMCID: PMC7525241 DOI: 10.1038/s41598-020-72724-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Accepted: 09/04/2020] [Indexed: 01/25/2023] Open
Abstract
Leishmania donovani is a trypanosomatidic parasite and causes the lethal kala-azar fever, a neglected tropical disease. The Trypanosomatida are devoid of transcriptional gene regulation and rely on gene copy number variations and translational control for their adaption to changing conditions. To survive at mammalian tissue temperatures, L. donovani relies on the small heat shock protein HSP23, the loss of which renders the parasites stress sensitive and impairs their proliferation. Here, we analysed a spontaneous escape mutant with wild type-like in vitro growth. Further selection of this escape strains resulted in a complete reversion of the phenotype. Whole genome sequencing revealed a correlation between stress tolerance and the massive amplification of a six-gene cluster on chromosome 35, with further analysis showing over expression of the casein kinase 1.2 gene as responsible. In vitro phosphorylation experiments established both HSP23 and the related P23 co-chaperone as substrates and modulators of casein kinase 1.2, providing evidence for another crucial link between chaperones and signal transduction protein kinases in this early branching eukaryote.
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Affiliation(s)
- Constanze Kröber-Boncardo
- Leishmania Group, Bernhard Nocht Institute for Tropical Medicine, Bernhard Nocht St 74, 20359, Hamburg, Germany
| | - Stephan Lorenzen
- Department of Epidemiology, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - Christine Brinker
- Leishmania Group, Bernhard Nocht Institute for Tropical Medicine, Bernhard Nocht St 74, 20359, Hamburg, Germany
| | - Joachim Clos
- Leishmania Group, Bernhard Nocht Institute for Tropical Medicine, Bernhard Nocht St 74, 20359, Hamburg, Germany.
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20
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Imamura H, Monsieurs P, Jara M, Sanders M, Maes I, Vanaerschot M, Berriman M, Cotton JA, Dujardin JC, Domagalska MA. Evaluation of whole genome amplification and bioinformatic methods for the characterization of Leishmania genomes at a single cell level. Sci Rep 2020; 10:15043. [PMID: 32929126 PMCID: PMC7490275 DOI: 10.1038/s41598-020-71882-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Accepted: 08/19/2020] [Indexed: 02/07/2023] Open
Abstract
Here, we report a pilot study paving the way for further single cell genomics studies in Leishmania. First, the performances of two commercially available kits for Whole Genome Amplification (WGA), PicoPLEX and RepliG were compared on small amounts of Leishmania donovani DNA, testing their ability to preserve specific genetic variations, including aneuploidy levels and SNPs. We show here that the choice of WGA method should be determined by the planned downstream genetic analysis, PicoPLEX and RepliG performing better for aneuploidy and SNP calling, respectively. This comparison allowed us to evaluate and optimize corresponding bio-informatic methods. As PicoPLEX was shown to be the preferred method for studying single cell aneuploidy, this method was applied in a second step, on single cells of L. braziliensis, which were sorted by fluorescence activated cell sorting (FACS). Even sequencing depth was achieved in 28 single cells, allowing accurate somy estimation. A dominant karyotype with three aneuploid chromosomes was observed in 25 cells, while two different minor karyotypes were observed in the other cells. Our method thus allowed the detection of aneuploidy mosaicism, and provides a solid basis which can be further refined to concur with higher-throughput single cell genomic methods.
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Affiliation(s)
- Hideo Imamura
- Institute of Tropical Medicine Antwerp, Molecular Parasitology Unit, Antwerp, Belgium
| | - Pieter Monsieurs
- Institute of Tropical Medicine Antwerp, Molecular Parasitology Unit, Antwerp, Belgium
| | - Marlene Jara
- Institute of Tropical Medicine Antwerp, Molecular Parasitology Unit, Antwerp, Belgium
| | | | - Ilse Maes
- Institute of Tropical Medicine Antwerp, Molecular Parasitology Unit, Antwerp, Belgium
| | - Manu Vanaerschot
- Institute of Tropical Medicine Antwerp, Molecular Parasitology Unit, Antwerp, Belgium
| | | | | | - Jean-Claude Dujardin
- Institute of Tropical Medicine Antwerp, Molecular Parasitology Unit, Antwerp, Belgium.
- Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium.
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21
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Cotton JA, Franssen SU. A Way Straight-Forward for Leishmania Genetics. Trends Parasitol 2020; 36:719-721. [PMID: 32741600 DOI: 10.1016/j.pt.2020.07.005] [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: 07/09/2020] [Accepted: 07/13/2020] [Indexed: 11/29/2022]
Abstract
Genetic exchange between Leishmania parasites was demonstrated in sandflies over 10 years ago. Louradour et al. have shown in vitro hybridization of two Leishmania tropica isolates, with the potential to remove a major roadblock to using forward genetics in Leishmania, understanding Leishmania reproductive biology, and analyzing gene flow in natural populations.
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Affiliation(s)
- James A Cotton
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, UK
| | - Susanne U Franssen
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, UK.
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22
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Cotton JA, Durrant C, Franssen SU, Gelanew T, Hailu A, Mateus D, Sanders MJ, Berriman M, Volf P, Miles MA, Yeo M. Genomic analysis of natural intra-specific hybrids among Ethiopian isolates of Leishmania donovani. PLoS Negl Trop Dis 2020; 14:e0007143. [PMID: 32310945 PMCID: PMC7237039 DOI: 10.1371/journal.pntd.0007143] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Revised: 05/19/2020] [Accepted: 12/24/2019] [Indexed: 12/30/2022] Open
Abstract
Parasites of the genus Leishmania (Kinetoplastida: Trypanosomatidae) cause widespread and devastating human diseases. Visceral leishmaniasis due to Leishmania donovani is endemic in Ethiopia where it has also been responsible for major epidemics. The presence of hybrid genotypes has been widely reported in surveys of natural populations, genetic variation reported in a number of Leishmania species, and the extant capacity for genetic exchange demonstrated in laboratory experiments. However, patterns of recombination and the evolutionary history of admixture that produced these hybrid populations remain unclear. Here, we use whole-genome sequence data to investigate Ethiopian L. donovani isolates previously characterized as hybrids by microsatellite and multi-locus sequencing. To date there is only one previous study on a natural population of Leishmania hybrids based on whole-genome sequences. We propose that these hybrids originate from recombination between two different lineages of Ethiopian L. donovani occurring in the same region. Patterns of inheritance are more complex than previously reported with multiple, apparently independent, origins from similar parents that include backcrossing with parental types. Analysis indicates that hybrids are representative of at least three different histories. Furthermore, isolates were highly polysomic at the level of chromosomes with differences between parasites recovered from a recrudescent infection from a previously treated individual. The results demonstrate that recombination is a significant feature of natural populations and contributes to the growing body of data that shows how recombination, and gene flow, shape natural populations of Leishmania.
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Affiliation(s)
| | | | | | - Tesfaye Gelanew
- Faculty of Medicine, Addis Ababa University, Addis Ababa, Ethiopia
| | - Asrat Hailu
- Faculty of Medicine, Addis Ababa University, Addis Ababa, Ethiopia
| | - David Mateus
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | | | | | - Petr Volf
- Department of Parasitology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Michael A. Miles
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Matthew Yeo
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
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23
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Franssen SU, Durrant C, Stark O, Moser B, Downing T, Imamura H, Dujardin JC, Sanders MJ, Mauricio I, Miles MA, Schnur LF, Jaffe CL, Nasereddin A, Schallig H, Yeo M, Bhattacharyya T, Alam MZ, Berriman M, Wirth T, Schönian G, Cotton JA. Global genome diversity of the Leishmania donovani complex. eLife 2020; 9:e51243. [PMID: 32209228 PMCID: PMC7105377 DOI: 10.7554/elife.51243] [Citation(s) in RCA: 62] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Accepted: 02/27/2020] [Indexed: 12/30/2022] Open
Abstract
Protozoan parasites of the Leishmania donovani complex - L. donovani and L. infantum - cause the fatal disease visceral leishmaniasis. We present the first comprehensive genome-wide global study, with 151 cultured field isolates representing most of the geographical distribution. L. donovani isolates separated into five groups that largely coincide with geographical origin but vary greatly in diversity. In contrast, the majority of L. infantum samples fell into one globally-distributed group with little diversity. This picture is complicated by several hybrid lineages. Identified genetic groups vary in heterozygosity and levels of linkage, suggesting different recombination histories. We characterise chromosome-specific patterns of aneuploidy and identified extensive structural variation, including known and suspected drug resistance loci. This study reveals greater genetic diversity than suggested by geographically-focused studies, provides a resource of genomic variation for future work and sets the scene for a new understanding of the evolution and genetics of the Leishmania donovani complex.
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Affiliation(s)
| | - Caroline Durrant
- Wellcome Sanger Institute, Wellcome Genome CampusHinxtonUnited Kingdom
| | | | | | - Tim Downing
- Wellcome Sanger Institute, Wellcome Genome CampusHinxtonUnited Kingdom
- Dublin City UniversityDublinIreland
| | | | - Jean-Claude Dujardin
- Institute of Tropical MedicineAntwerpBelgium
- Department of Biomedical Sciences, University of AntwerpAntwerpBelgium
| | - Mandy J Sanders
- Wellcome Sanger Institute, Wellcome Genome CampusHinxtonUnited Kingdom
| | - Isabel Mauricio
- Universidade Nova de Lisboa Instituto de Higiene e MedicinaLisboaPortugal
| | - Michael A Miles
- London School of Hygiene and Tropical MedicineLondonUnited Kingdom
| | - Lionel F Schnur
- Kuvin Centre for the Study of Infectious and Tropical Diseases, IMRIC, Hebrew University-Hadassah, Medical SchoolJerusalemIsrael
| | - Charles L Jaffe
- Kuvin Centre for the Study of Infectious and Tropical Diseases, IMRIC, Hebrew University-Hadassah, Medical SchoolJerusalemIsrael
| | - Abdelmajeed Nasereddin
- Kuvin Centre for the Study of Infectious and Tropical Diseases, IMRIC, Hebrew University-Hadassah, Medical SchoolJerusalemIsrael
| | - Henk Schallig
- Amsterdam University Medical Centres – Academic Medical Centre at the University of Amsterdam, Department of Medical Microbiology – Experimental ParasitologyAmsterdamNetherlands
| | - Matthew Yeo
- London School of Hygiene and Tropical MedicineLondonUnited Kingdom
| | | | - Mohammad Z Alam
- Department of Parasitology, Bangladesh Agricultural UniversityMymensinghBangladesh
| | - Matthew Berriman
- Wellcome Sanger Institute, Wellcome Genome CampusHinxtonUnited Kingdom
| | - Thierry Wirth
- Institut de Systématique, Evolution, Biodiversité, ISYEB, Muséum national d'Histoire naturelle, CNRS, Sorbonne Université, EPHE, Université des AntillesParisFrance
- École Pratique des Hautes Études (EPHE)Paris Sciences & Lettres (PSL)ParisFrance
| | | | - James A Cotton
- Wellcome Sanger Institute, Wellcome Genome CampusHinxtonUnited Kingdom
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24
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Butenko A, Opperdoes FR, Flegontova O, Horák A, Hampl V, Keeling P, Gawryluk RMR, Tikhonenkov D, Flegontov P, Lukeš J. Evolution of metabolic capabilities and molecular features of diplonemids, kinetoplastids, and euglenids. BMC Biol 2020; 18:23. [PMID: 32122335 PMCID: PMC7052976 DOI: 10.1186/s12915-020-0754-1] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Accepted: 02/17/2020] [Indexed: 12/24/2022] Open
Abstract
Background The Euglenozoa are a protist group with an especially rich history of evolutionary diversity. They include diplonemids, representing arguably the most species-rich clade of marine planktonic eukaryotes; trypanosomatids, which are notorious parasites of medical and veterinary importance; and free-living euglenids. These different lifestyles, and particularly the transition from free-living to parasitic, likely require different metabolic capabilities. We carried out a comparative genomic analysis across euglenozoan diversity to see how changing repertoires of enzymes and structural features correspond to major changes in lifestyles. Results We find a gradual loss of genes encoding enzymes in the evolution of kinetoplastids, rather than a sudden decrease in metabolic capabilities corresponding to the origin of parasitism, while diplonemids and euglenids maintain more metabolic versatility. Distinctive characteristics of molecular machines such as kinetochores and the pre-replication complex that were previously considered specific to parasitic kinetoplastids were also identified in their free-living relatives. Therefore, we argue that they represent an ancestral rather than a derived state, as thought until the present. We also found evidence of ancient redundancy in systems such as NADPH-dependent thiol-redox. Only the genus Euglena possesses the combination of trypanothione-, glutathione-, and thioredoxin-based systems supposedly present in the euglenozoan common ancestor, while other representatives of the phylum have lost one or two of these systems. Lastly, we identified convergent losses of specific metabolic capabilities between free-living kinetoplastids and ciliates. Although this observation requires further examination, it suggests that certain eukaryotic lineages are predisposed to such convergent losses of key enzymes or whole pathways. Conclusions The loss of metabolic capabilities might not be associated with the switch to parasitic lifestyle in kinetoplastids, and the presence of a highly divergent (or unconventional) kinetochore machinery might not be restricted to this protist group. The data derived from the transcriptomes of free-living early branching prokinetoplastids suggests that the pre-replication complex of Trypanosomatidae is a highly divergent version of the conventional machinery. Our findings shed light on trends in the evolution of metabolism in protists in general and open multiple avenues for future research.
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Affiliation(s)
- Anzhelika Butenko
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice (Budweis), Czech Republic.,Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | - Fred R Opperdoes
- de Duve Institute, Université Catholique de Louvain, Brussels, Belgium
| | - Olga Flegontova
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice (Budweis), Czech Republic.,Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | - Aleš Horák
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice (Budweis), Czech Republic.,Faculty of Science, University of South Bohemia, České Budějovice (Budweis), Czech Republic
| | - Vladimír Hampl
- Faculty of Science, Charles University, Biocev, Vestec, Czech Republic
| | - Patrick Keeling
- Department of Botany, University of British Columbia, Vancouver, Canada
| | | | - Denis Tikhonenkov
- Department of Botany, University of British Columbia, Vancouver, Canada.,Papanin Institute for Biology of Inland Waters, Russian Academy of Sciences, Borok, Russia
| | - Pavel Flegontov
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice (Budweis), Czech Republic. .,Faculty of Science, University of Ostrava, Ostrava, Czech Republic. .,Present address: Department of Genetics, Harvard Medical School, Boston, USA.
| | - Julius Lukeš
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice (Budweis), Czech Republic. .,Faculty of Science, University of South Bohemia, České Budějovice (Budweis), Czech Republic.
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25
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Coupling chemical mutagenesis to next generation sequencing for the identification of drug resistance mutations in Leishmania. Nat Commun 2019; 10:5627. [PMID: 31819054 PMCID: PMC6901541 DOI: 10.1038/s41467-019-13344-6] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Accepted: 11/01/2019] [Indexed: 12/16/2022] Open
Abstract
Current genome-wide screens allow system-wide study of drug resistance but detecting small nucleotide variants (SNVs) is challenging. Here, we use chemical mutagenesis, drug selection and next generation sequencing to characterize miltefosine and paromomycin resistant clones of the parasite Leishmania. We highlight several genes involved in drug resistance by sequencing the genomes of 41 resistant clones and by concentrating on recurrent SNVs. We associate genes linked to lipid metabolism or to ribosome/translation functions with miltefosine or paromomycin resistance, respectively. We prove by allelic replacement and CRISPR-Cas9 gene-editing that the essential protein kinase CDPK1 is crucial for paromomycin resistance. We have linked CDPK1 in translation by functional interactome analysis, and provide evidence that CDPK1 contributes to antimonial resistance in the parasite. This screen is powerful in exploring networks of drug resistance in an organism with diploid to mosaic aneuploid genome, hence widening the scope of its applicability. Here, Bhattacharya et al. chemically mutagenize Leishmania and identify genes associated with resistance to miltefosine and paromomycin by next generation sequencing. The study shows that a protein kinase (CDPK1) can mediate resistance to paromomycin by affecting translation.
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26
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White MA, Azeroglu B, Lopez-Vernaza MA, Hasan AMM, Leach DRF. RecBCD coordinates repair of two ends at a DNA double-strand break, preventing aberrant chromosome amplification. Nucleic Acids Res 2019; 46:6670-6682. [PMID: 29901759 PMCID: PMC6061781 DOI: 10.1093/nar/gky463] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Accepted: 06/08/2018] [Indexed: 12/23/2022] Open
Abstract
DNA double-strand break (DSB) repair is critical for cell survival. A diverse range of organisms from bacteria to humans rely on homologous recombination for accurate DSB repair. This requires both coordinate action of the two ends of a DSB and stringent control of the resultant DNA replication to prevent unwarranted DNA amplification and aneuploidy. In Escherichia coli, RecBCD enzyme is responsible for the initial steps of homologous recombination. Previous work has revealed recD mutants to be nuclease defective but recombination proficient. Despite this proficiency, we show here that a recD null mutant is defective for the repair of a two-ended DSB and that this defect is associated with unregulated chromosome amplification and defective chromosome segregation. Our results demonstrate that RecBCD plays an important role in avoiding this amplification by coordinating the two recombining ends in a manner that prevents divergent replication forks progressing away from the DSB site.
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Affiliation(s)
- Martin A White
- Institute of Cell Biology, School of Biological Sciences, University of Edinburgh, King's Buildings, Mayfield Road, Edinburgh EH9 3FF, UK
| | - Benura Azeroglu
- Institute of Cell Biology, School of Biological Sciences, University of Edinburgh, King's Buildings, Mayfield Road, Edinburgh EH9 3FF, UK
| | - Manuel A Lopez-Vernaza
- Institute of Cell Biology, School of Biological Sciences, University of Edinburgh, King's Buildings, Mayfield Road, Edinburgh EH9 3FF, UK
| | - A M Mahedi Hasan
- Institute of Cell Biology, School of Biological Sciences, University of Edinburgh, King's Buildings, Mayfield Road, Edinburgh EH9 3FF, UK
| | - David R F Leach
- Institute of Cell Biology, School of Biological Sciences, University of Edinburgh, King's Buildings, Mayfield Road, Edinburgh EH9 3FF, UK
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27
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S. L. Figueiredo de Sá B, Rezende AM, de Melo Neto OP, de Brito MEF, Brandão Filho SP. Identification of divergent Leishmania (Viannia) braziliensis ecotypes derived from a geographically restricted area through whole genome analysis. PLoS Negl Trop Dis 2019; 13:e0007382. [PMID: 31170148 PMCID: PMC6581274 DOI: 10.1371/journal.pntd.0007382] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Revised: 06/18/2019] [Accepted: 04/10/2019] [Indexed: 01/22/2023] Open
Abstract
Leishmania braziliensis, the main etiological agent of cutaneous leishmaniasis (CL) in Latin America, is characterized by major differences in basic biology in comparison with better-known Leishmania species. It is also associated with a high phenotypic and possibly genetic diversity that need to be more adequately defined. Here we used whole genome sequences to evaluate the genetic diversity of ten L. braziliensis isolates from a CL endemic area from Northeastern Brazil, previously classified by Multi Locus Enzyme Electrophoresis (MLEE) into ten distinct zymodemes. These sequences were first mapped using the L. braziliensis M2904 reference genome followed by identification of Single Nucleotide Polymorphisms (SNPs). A substantial level of diversity was observed when compared with the reference genome, with SNP counts ranging from ~95,000 to ~131,000 for the different isolates. When the genome data was used to infer relationship between isolates, those belonging to zymodemes Z72/Z75, recovered from forested environments, were found to cluster separately from the others, generally associated with more urban environments. Among the remaining isolates, those from zymodemes Z74/Z106 were also found to form a separate group. Phylogenetic analyses were also performed using Multi-Locus Sequence Analysis from genes coding for four metabolic enzymes used for MLEE as well as the gene sequence coding for the Hsp70 heat shock protein. All 10 isolates were firmly identified as L. braziliensis, including the zymodeme Z26 isolate previously classified as Leishmania shawi, with the clustering into three groups confirmed. Aneuploidy was also investigated but found in general restricted to chromosome 31, with a single isolate, from zymodeme Z27, characterized by extra copies for other chromosomes. Noteworthy, both Z72 and Z75 isolates are characterized by a much reduced heterozygosity. Our data is consistent with the existence of distinct evolutionary groups in the restricted area sampled and a substantial genetic diversity within L. braziliensis. Leishmania braziliensis is the main etiological agent of cutaneous leishmaniasis (CL) in Latin America. In the Pernambuco state, a highly endemic area for CL in Northeastern Brazil, ten zymodemes have been previously described, identified through the detection of variations in the mobility of selected enzymes on gel electrophoresis (MLEE). Here we used next-generation genome sequencing to reevaluate the genetic diversity and relatedness between isolates representing these zymodemes. The genetic analysis clustered these isolates into three distinct phylogenetic groups, with those circulating in forested environments more related to each other (Z72 and Z75) and separated from the other eight isolates from more urbanized environments, but nevertheless forming two further groups. All ten isolates were definitely identified as L. braziliensis, including one from zymodeme Z26, previously identified as L. shawi through MLEE. Chromosome copy number variation was observed in all isolates studied, but restricted mainly to chromosome 31, with a single isolate (from zymodeme Z27) showing more than two copies of other chromosomes. A low heterozygosity observed only for both Z72/Z75 isolates also confirm differences associated with them. Our findings confirm that MLEE, despite still being considered the gold standard for characterization of Leishmania spp., does not reflect relevant information on intra-specific variations. It also highlights the substantial diversity observed between L. braziliensis isolates.
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Affiliation(s)
- Bruna S. L. Figueiredo de Sá
- Department of Microbiology, Aggeu Magalhães Institute/FIOCRUZ, Recife, Pernambuco, Brazil
- * E-mail: (BSLFdS); (SPBF)
| | - Antonio M. Rezende
- Department of Microbiology, Aggeu Magalhães Institute/FIOCRUZ, Recife, Pernambuco, Brazil
| | | | | | - Sinval P. Brandão Filho
- Department of Immunology, Aggeu Magalhães Institute -FIOCRUZ, Recife, Pernambuco, Brazil
- * E-mail: (BSLFdS); (SPBF)
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Inbar E, Shaik J, Iantorno SA, Romano A, Nzelu CO, Owens K, Sanders MJ, Dobson D, Cotton JA, Grigg ME, Beverley SM, Sacks D. Whole genome sequencing of experimental hybrids supports meiosis-like sexual recombination in Leishmania. PLoS Genet 2019; 15:e1008042. [PMID: 31091230 PMCID: PMC6519804 DOI: 10.1371/journal.pgen.1008042] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Accepted: 02/21/2019] [Indexed: 11/29/2022] Open
Abstract
Hybrid genotypes have been repeatedly described among natural isolates of Leishmania, and the recovery of experimental hybrids from sand flies co-infected with different strains or species of Leishmania has formally demonstrated that members of the genus possess the machinery for genetic exchange. As neither gamete stages nor cell fusion events have been directly observed during parasite development in the vector, we have relied on a classical genetic analysis to determine if Leishmania has a true sexual cycle. Here, we used whole genome sequencing to follow the chromosomal inheritance patterns of experimental hybrids generated within and between different strains of L. major and L. infantum. We also generated and sequenced the first experimental hybrids in L. tropica. We found that in each case the parental somy and allele contributions matched the inheritance patterns expected under meiosis 97–99% of the time. The hybrids were equivalent to F1 progeny, heterozygous throughout most of the genome for the markers that were homozygous and different between the parents. Rare, non-Mendelian patterns of chromosomal inheritance were observed, including a gain or loss of somy, and loss of heterozygosity, that likely arose during meiosis or during mitotic divisions of the progeny clones in the fly or culture. While the interspecies hybrids appeared to be sterile, the intraspecies hybrids were able to produce backcross and outcross progeny. Analysis of 5 backcross and outcross progeny clones generated from an L. major F1 hybrid, as well as 17 progeny clones generated from backcrosses involving a natural hybrid of L. tropica, revealed genome wide patterns of recombination, demonstrating that classical crossing over occurs at meiosis, and allowed us to construct the first physical and genetic maps in Leishmania. Altogether, the findings provide strong evidence for meiosis-like sexual recombination in Leishmania, presenting clear opportunities for forward genetic analysis and positional cloning of important genes. Leishmania promastigotes are able to undergo genetic exchange during their growth and development in the sand fly vector, however, it is still not known if they have a true sexual cycle involving meiosis. Here, we used whole genome sequencing to follow the chromosomal inheritance patterns of 44 experimental hybrids generated between different strains of L. major, L. infantum, and L. tropica. In almost every case the number of chromosomes and the allele contributions from each parent matched the inheritance patterns expected under meiosis. Rare instances of hybrid chromosomes that did not fit Mendelian expectations were observed, including gain or loss of somy, and loss of heterozygosity. Strong evidence for a meiotic-like process was also obtained from the genome wide patterns of recombination observed in the offspring generated from backcrosses involving an experimental or natural hybrid, consistent with crossing over occurring between homologous chromosomes during meiosis. The frequency and position of the recombination breakpoints observed on each chromosome allowed us to construct the first physical and genetic maps in Leishmania. The results demonstrate that forward genetic approaches are possible for positional cloning of important genes.
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Affiliation(s)
- Ehud Inbar
- Laboratory of Parasitic Diseases, National Institutes of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Jahangheer Shaik
- Laboratory of Parasitic Diseases, National Institutes of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
- Department of Molecular Microbiology, Washington University School of Medicine in St Louis, St Louis, Missouri, United States of America
| | - Stefano A. Iantorno
- Laboratory of Parasitic Diseases, National Institutes of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Audrey Romano
- Laboratory of Parasitic Diseases, National Institutes of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Chukwunonso O. Nzelu
- Laboratory of Parasitic Diseases, National Institutes of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Katherine Owens
- Department of Molecular Microbiology, Washington University School of Medicine in St Louis, St Louis, Missouri, United States of America
| | - Mandy J. Sanders
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Deborah Dobson
- Department of Molecular Microbiology, Washington University School of Medicine in St Louis, St Louis, Missouri, United States of America
| | - James A. Cotton
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Michael E. Grigg
- Laboratory of Parasitic Diseases, National Institutes of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Stephen M. Beverley
- Department of Molecular Microbiology, Washington University School of Medicine in St Louis, St Louis, Missouri, United States of America
| | - David Sacks
- Laboratory of Parasitic Diseases, National Institutes of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
- * E-mail: ,
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29
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Reis-Cunha JL, Bartholomeu DC. Trypanosoma cruzi Genome Assemblies: Challenges and Milestones of Assembling a Highly Repetitive and Complex Genome. Methods Mol Biol 2019; 1955:1-22. [PMID: 30868515 DOI: 10.1007/978-1-4939-9148-8_1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Trypanosoma cruzi present one of the most complex parasite genomes sequenced to date. Among its features are 600-kb-long repetitive multigene families' clusters, hybrid strains, and aneuploidies, which hampered genome assembly completeness and contiguity. Several approaches, such as Sanger sequencing in 2005, next-generation sequencing in 2011 and third-generation sequencing in 2018, were used to improve draft assemblies of different strains of this parasite. Hence, the study of T. cruzi genome assemblies' history is an excellent way to describe the evolution of genome sequencing methodologies and compare their efficiency and limitations to assembly complex genomes. In this book chapter, we summarize the principal findings and methodologies of T. cruzi genome assembly projects to date, highlighting the improvements and limitations of each approach.
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Affiliation(s)
- João Luís Reis-Cunha
- Departamento de Parasitologia, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Daniella C Bartholomeu
- Departamento de Parasitologia, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil.
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30
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Briggs E, Crouch K, Lemgruber L, Lapsley C, McCulloch R. Ribonuclease H1-targeted R-loops in surface antigen gene expression sites can direct trypanosome immune evasion. PLoS Genet 2018; 14:e1007729. [PMID: 30543624 PMCID: PMC6292569 DOI: 10.1371/journal.pgen.1007729] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Accepted: 10/01/2018] [Indexed: 11/19/2022] Open
Abstract
Switching of the Variant Surface Glycoprotein (VSG) in Trypanosoma brucei provides a crucial host immune evasion strategy that is catalysed both by transcription and recombination reactions, each operating within specialised telomeric VSG expression sites (ES). VSG switching is likely triggered by events focused on the single actively transcribed ES, from a repertoire of around 15, but the nature of such events is unclear. Here we show that RNA-DNA hybrids, called R-loops, form preferentially within sequences termed the 70 bp repeats in the actively transcribed ES, but spread throughout the active and inactive ES, in the absence of RNase H1, which degrades R-loops. Loss of RNase H1 also leads to increased levels of VSG coat switching and replication-associated genome damage, some of which accumulates within the active ES. This work indicates VSG ES architecture elicits R-loop formation, and that these RNA-DNA hybrids connect T. brucei immune evasion by transcription and recombination.
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Affiliation(s)
- Emma Briggs
- The Wellcome Centre for Molecular Parasitology, University of Glasgow, College of Medical, Veterinary and Life Sciences, Institute of Infection, Immunity and Inflammation, Glasgow, United Kingdom
| | - Kathryn Crouch
- The Wellcome Centre for Molecular Parasitology, University of Glasgow, College of Medical, Veterinary and Life Sciences, Institute of Infection, Immunity and Inflammation, Glasgow, United Kingdom
| | - Leandro Lemgruber
- The Wellcome Centre for Molecular Parasitology, University of Glasgow, College of Medical, Veterinary and Life Sciences, Institute of Infection, Immunity and Inflammation, Glasgow, United Kingdom
| | - Craig Lapsley
- The Wellcome Centre for Molecular Parasitology, University of Glasgow, College of Medical, Veterinary and Life Sciences, Institute of Infection, Immunity and Inflammation, Glasgow, United Kingdom
| | - Richard McCulloch
- The Wellcome Centre for Molecular Parasitology, University of Glasgow, College of Medical, Veterinary and Life Sciences, Institute of Infection, Immunity and Inflammation, Glasgow, United Kingdom
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Reis-Cunha JL, Baptista RP, Rodrigues-Luiz GF, Coqueiro-Dos-Santos A, Valdivia HO, de Almeida LV, Cardoso MS, D'Ávila DA, Dias FHC, Fujiwara RT, Galvão LMC, Chiari E, Cerqueira GC, Bartholomeu DC. Whole genome sequencing of Trypanosoma cruzi field isolates reveals extensive genomic variability and complex aneuploidy patterns within TcII DTU. BMC Genomics 2018; 19:816. [PMID: 30424726 PMCID: PMC6234542 DOI: 10.1186/s12864-018-5198-4] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2017] [Accepted: 10/23/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Trypanosoma cruzi, the etiologic agent of Chagas disease, is currently divided into six discrete typing units (DTUs), named TcI-TcVI. TcII is among the major DTUs enrolled in human infections in South America southern cone, where it is associated with severe cardiac and digestive symptoms. Despite the importance of TcII in Chagas disease epidemiology and pathology, so far, no genome-wide comparisons of the mitochondrial and nuclear genomes of TcII field isolates have been performed to track the variability and evolution of this DTU in endemic regions. RESULTS In the present work, we have sequenced and compared the whole nuclear and mitochondrial genomes of seven TcII strains isolated from chagasic patients from the central and northeastern regions of Minas Gerais, Brazil, revealing an extensive genetic variability within this DTU. A comparison of the phylogeny based on the nuclear or mitochondrial genomes revealed that the majority of branches were shared by both sequences. The subtle divergences in the branches are probably consequence of mitochondrial introgression events between TcII strains. Two T. cruzi strains isolated from patients living in the central region of Minas Gerais, S15 and S162a, were clustered in the nuclear and mitochondrial phylogeny analysis. These two strains were isolated from the other five by the Espinhaço Mountains, a geographic barrier that could have restricted the traffic of insect vectors during T. cruzi evolution in the Minas Gerais state. Finally, the presence of aneuploidies was evaluated, revealing that all seven TcII strains have a different pattern of chromosomal duplication/loss. CONCLUSIONS Analysis of genomic variability and aneuploidies suggests that there is significant genomic variability within Minas Gerais TcII strains, which could be exploited by the parasite to allow rapid selection of favorable phenotypes. Also, the aneuploidy patterns vary among T. cruzi strains and does not correlate with the nuclear phylogeny, suggesting that chromosomal duplication/loss are recent and frequent events in the parasite evolution.
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Affiliation(s)
- João Luís Reis-Cunha
- Departamento de Parasitologia, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Rodrigo P Baptista
- Departamento de Parasitologia, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil.,The University of Georgia, Athens, USA
| | - Gabriela F Rodrigues-Luiz
- Departamento de Parasitologia, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil.,Departamento de Microbiologia, Imunologia e Parasitologia, Universidade Federal de Santa Catarina, Florianópolis, Brazil
| | | | - Hugo O Valdivia
- Departamento de Parasitologia, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil.,U.S. Naval Medical Research, Lima, Peru
| | - Laila Viana de Almeida
- Departamento de Parasitologia, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Mariana Santos Cardoso
- Departamento de Parasitologia, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | | | | | | | - Lúcia M C Galvão
- Departamento de Parasitologia, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Egler Chiari
- Departamento de Parasitologia, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | | | - Daniella C Bartholomeu
- Departamento de Parasitologia, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil.
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32
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Almeida LV, Coqueiro-Dos-Santos A, Rodriguez-Luiz GF, McCulloch R, Bartholomeu DC, Reis-Cunha JL. Chromosomal copy number variation analysis by next generation sequencing confirms ploidy stability in Trypanosoma brucei subspecies. Microb Genom 2018; 4. [PMID: 30256189 PMCID: PMC6249438 DOI: 10.1099/mgen.0.000223] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Although aneuploidy usually results in severe abnormalities in multicellular eukaryotes, recent data suggest that it could be beneficial for unicellular eukaryotes, such as yeast and trypanosomatid parasites, providing increased survival under stressful conditions. Among characterized trypanosomatids, Trypanosoma cruzi, Trypanosoma brucei and species from the genus Leishmania stand out due to their importance in public health, infecting around 20 million people worldwide. The presence of aneuploidies in T. cruzi and Leishmania was recently confirmed by analysis based on next generation sequencing (NGS) and fluorescence in situ hybridization, where they have been associated with adaptation during transmission between their insect vectors and mammalian hosts and in promoting drug resistance. Although chromosomal copy number variations (CCNVs) are present in the aforementioned species, PFGE and fluorescence cytophotometry analyses suggest that aneuploidies are absent from T. brucei. A re-evaluation of CCNV in T. b gambiense based on NGS reads confirmed the absence of aneuploidies in this subspecies. However, the presence of aneuploidies in the other two T. brucei subspecies, T. b. brucei and T. b. rhodesiense, has not been evaluated using NGS approaches. In the present work, we tested for aneuploidies in 26 T. brucei isolates, including samples from the three T. brucei subspecies, by both allele frequency and read depth coverage analyses. These analyses showed that none of the T. brucei subspecies presents aneuploidies, which could be related to differences in the mechanisms of DNA replication and recombination in these parasites when compared with Leishmania.
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Affiliation(s)
- Laila Viana Almeida
- 1Departamento de Parasitologia, Universidade Federal de Minas Gerais - Instituto de Ciências Biológicas, Belo Horizonte, Brazil
| | - Anderson Coqueiro-Dos-Santos
- 1Departamento de Parasitologia, Universidade Federal de Minas Gerais - Instituto de Ciências Biológicas, Belo Horizonte, Brazil
| | - Gabriela F Rodriguez-Luiz
- 1Departamento de Parasitologia, Universidade Federal de Minas Gerais - Instituto de Ciências Biológicas, Belo Horizonte, Brazil
| | - Richard McCulloch
- 2University of Glasgow, Wellcome Centre for Molecular Parasitology, Glasgow, UK
| | - Daniella Castanheira Bartholomeu
- 1Departamento de Parasitologia, Universidade Federal de Minas Gerais - Instituto de Ciências Biológicas, Belo Horizonte, Brazil
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Reis-Cunha JL, Valdivia HO, Bartholomeu DC. Gene and Chromosomal Copy Number Variations as an Adaptive Mechanism Towards a Parasitic Lifestyle in Trypanosomatids. Curr Genomics 2018; 19:87-97. [PMID: 29491737 PMCID: PMC5814966 DOI: 10.2174/1389202918666170911161311] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2017] [Revised: 03/14/2017] [Accepted: 04/18/2017] [Indexed: 12/21/2022] Open
Abstract
Trypanosomatids are a group of kinetoplastid parasites including some of great public health importance, causing debilitating and life-long lasting diseases that affect more than 24 million people worldwide. Among the trypanosomatids, Trypanosoma cruzi, Trypanosoma brucei and species from the Leishmania genus are the most well studied parasites, due to their high prevalence in human infections. These parasites have an extreme genomic and phenotypic variability, with a massive expansion in the copy number of species-specific multigene families enrolled in host-parasite interactions that mediate cellular invasion and immune evasion processes. As most trypanosomatids are heteroxenous, and therefore their lifecycles involve the transition between different hosts, these parasites have developed several strategies to ensure a rapid adaptation to changing environments. Among these strategies, a rapid shift in the repertoire of expressed genes, genetic variability and genome plasticity are key mechanisms. Trypanosomatid genomes are organized into large directional gene clusters that are transcribed polycistronically, where genes derived from the same polycistron may have very distinct mRNA levels. This particular mode of transcription implies that the control of gene expression operates mainly at post-transcriptional level. In this sense, gene duplications/losses were already associated with changes in mRNA levels in these parasites. Gene duplications also allow the generation of sequence variability, as the newly formed copy can diverge without loss of function of the original copy. Recently, aneuploidies have been shown to occur in several Leishmania species and T. cruzi strains. Although aneuploidies are usually associated with debilitating phenotypes in superior eukaryotes, recent data shows that it could also provide increased fitness in stress conditions and generate drug resistance in unicellular eukaryotes. In this review, we will focus on gene and chromosomal copy number variations and their relevance to the evolution of trypanosomatid parasites.
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Affiliation(s)
- João Luís Reis-Cunha
- Universidade Federal de Minas Gerais, Laboratório de Imunologia e Genômica de Parasitos, Instituto de Ciências Biológicas, Belo Horizonte, Brazil
| | - Hugo O. Valdivia
- Universidade Federal de Minas Gerais, Laboratório de Imunologia e Genômica de Parasitos, Instituto de Ciências Biológicas, Belo Horizonte, Brazil
- Centro de Investigaciones Tecnológicas, Biomédicas y Medioambientales, Callao, Peru
| | - Daniella Castanheira Bartholomeu
- Universidade Federal de Minas Gerais, Laboratório de Imunologia e Genômica de Parasitos, Instituto de Ciências Biológicas, Belo Horizonte, Brazil
- Centro de Investigaciones Tecnológicas, Biomédicas y Medioambientales, Callao, Peru
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Seco-Hidalgo V, Osuna A, de Pablos LM. Characterizing Cell Heterogeneity Using PCR Fingerprinting of Surface Multigene Families in Protozoan Parasites. Methods Mol Biol 2018; 1745:277-286. [PMID: 29476474 DOI: 10.1007/978-1-4939-7680-5_15] [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] [Indexed: 01/10/2023]
Abstract
Parasites counteract the action of the immune system and other environmental pressures by modulating and changing the composition of their cell surfaces. Surface multigene protein families are defined not only by highly variable regions in length and/or sequence exposed to the outer space but also by conserved sequences codifying for the signal peptide, hydrophobic C-terminal regions necessary for GPI modifications, as well as conserved UTR regions for mRNA regulation. The method here presented exploits these conserved signatures for characterizing variations in the mRNA expression of clonal cell populations of protozoan parasites using a combination of nested PCR amplification and capillary electrophoresis. With this workflow, in silico gels from isolated cell clones can be generated, thus providing an excellent tool for analyzing cellular heterogeneity in protozoan parasites.
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Affiliation(s)
| | - Antonio Osuna
- Departamento de Parasitología, Grupo de Bioquímica y Parasitología Molecular CTS-183, Universidad de Granada, Granada, Spain
| | - Luis Miguel de Pablos
- Departamento de Parasitología, Grupo de Bioquímica y Parasitología Molecular CTS-183, Universidad de Granada, Granada, Spain.
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Ponte-Sucre A, Gamarro F, Dujardin JC, Barrett MP, López-Vélez R, García-Hernández R, Pountain AW, Mwenechanya R, Papadopoulou B. Drug resistance and treatment failure in leishmaniasis: A 21st century challenge. PLoS Negl Trop Dis 2017; 11:e0006052. [PMID: 29240765 PMCID: PMC5730103 DOI: 10.1371/journal.pntd.0006052] [Citation(s) in RCA: 489] [Impact Index Per Article: 69.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Reevaluation of treatment guidelines for Old and New World leishmaniasis is urgently needed on a global basis because treatment failure is an increasing problem. Drug resistance is a fundamental determinant of treatment failure, although other factors also contribute to this phenomenon, including the global HIV/AIDS epidemic with its accompanying impact on the immune system. Pentavalent antimonials have been used successfully worldwide for the treatment of leishmaniasis since the first half of the 20th century, but the last 10 to 20 years have witnessed an increase in clinical resistance, e.g., in North Bihar in India. In this review, we discuss the meaning of “resistance” related to leishmaniasis and discuss its molecular epidemiology, particularly for Leishmania donovani that causes visceral leishmaniasis. We also discuss how resistance can affect drug combination therapies. Molecular mechanisms known to contribute to resistance to antimonials, amphotericin B, and miltefosine are also outlined. Chemotherapy is central to the control and management of leishmaniasis. Antimonials remain the primary drugs against different forms of leishmaniasis in several regions. However, resistance to antimony has necessitated the use of alternative medications, especially in the Indian subcontinent (ISC). Compounds, notably the orally available miltefosine (MIL), parenteral paromomycin, and amphotericin B (AmB), are increasingly used to treat leishmaniasis. Although treatment failure (TF) has been observed in patients treated with most anti-leishmanials, its frequency of appearance may be important in patients treated with MIL, which has replaced antimonials within the kala-azar elimination program in the ISC. AmB is highly efficacious, and the associated toxic effects—when administered in its free deoxycholate form—are somewhat ameliorated in its liposomal formulation. Regrettably, laboratory experimentation has demonstrated a risk of resistance towards AmB as well. The rise of drug resistance impacts treatment outcome, and understanding its causes, spread, and impact will help us manage the risks it imposes. Here, we review the problem of TF in leishmaniasis and the contribution of drug resistance to the problem. Molecular mechanisms causing resistance to anti-leishmanials are discussed along with the appropriate use of additional available drugs, as well as the urgent need to consolidate strategies to monitor drug efficacy, epidemiological surveillance, and local policies. Coordination of these activities in national and international programs against leishmaniasis might represent a successful guide to further research and prevention activities.
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Affiliation(s)
- Alicia Ponte-Sucre
- Department of Physiological Sciences, Laboratory of Molecular Physiology, Institute of Experimental Medicine, Luis Razetti School of Medicine, Universidad Central de Venezuela, Caracas, Venezuela
- * E-mail: (BP); (APS)
| | - Francisco Gamarro
- Department of Biochemistry and Molecular Pharmacology, Instituto de Parasitología y Biomedicina López-Neyra, Spanish National Research Council (IPBLN-CSIC), Granada, Spain
| | - Jean-Claude Dujardin
- Molecular Parasitology Unit, Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Michael P. Barrett
- Wellcome Centre for Molecular Parasitology, Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, United Kingdom
| | - Rogelio López-Vélez
- Department of Infectious Diseases, National Referral Unit for Tropical Diseases, Ramón y Cajal University Hospital, Madrid, Spain
| | - Raquel García-Hernández
- Department of Biochemistry and Molecular Pharmacology, Instituto de Parasitología y Biomedicina López-Neyra, Spanish National Research Council (IPBLN-CSIC), Granada, Spain
| | - Andrew W. Pountain
- Wellcome Centre for Molecular Parasitology, Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, United Kingdom
| | - Roy Mwenechanya
- Department of Biomedical Sciences, School of Veterinary Medicine, University of Zambia, Lusaka, Zambia
| | - Barbara Papadopoulou
- Research Center in Infectious Diseases, CHU de Quebec Research Center and Department of Microbiology-Infectious Disease and Immunology, University Laval, Quebec, Canada
- * E-mail: (BP); (APS)
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36
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Prieto Barja P, Pescher P, Bussotti G, Dumetz F, Imamura H, Kedra D, Domagalska M, Chaumeau V, Himmelbauer H, Pages M, Sterkers Y, Dujardin JC, Notredame C, Späth GF. Haplotype selection as an adaptive mechanism in the protozoan pathogen Leishmania donovani. Nat Ecol Evol 2017; 1:1961-1969. [DOI: 10.1038/s41559-017-0361-x] [Citation(s) in RCA: 80] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Accepted: 09/26/2017] [Indexed: 11/09/2022]
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Garcia-Silva MR, Sollelis L, MacPherson CR, Stanojcic S, Kuk N, Crobu L, Bringaud F, Bastien P, Pagès M, Scherf A, Sterkers Y. Identification of the centromeres of Leishmania major: revealing the hidden pieces. EMBO Rep 2017; 18:1968-1977. [PMID: 28935715 DOI: 10.15252/embr.201744216] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2017] [Revised: 08/15/2017] [Accepted: 08/28/2017] [Indexed: 01/16/2023] Open
Abstract
Leishmania affects millions of people worldwide. Its genome undergoes constitutive mosaic aneuploidy, a type of genomic plasticity that may serve as an adaptive strategy to survive distinct host environments. We previously found high rates of asymmetric chromosome allotments during mitosis that lead to the generation of such ploidy. However, the underlying molecular events remain elusive. Centromeres and kinetochores most likely play a key role in this process, yet their identification has failed using classical methods. Our analysis of the unconventional kinetochore complex recently discovered in Trypanosoma brucei (KKTs) leads to the identification of a Leishmania KKT gene candidate (LmKKT1). The GFP-tagged LmKKT1 displays "kinetochore-like" dynamics of intranuclear localization throughout the cell cycle. By ChIP-Seq assay, one major peak per chromosome is revealed, covering a region of 4 ±2 kb. We find two largely conserved motifs mapping to 14 of 36 chromosomes while a higher density of retroposons are observed in 27 of 36 centromeres. The identification of centromeres and of a kinetochore component of Leishmania chromosomes opens avenues to explore their role in mosaic aneuploidy.
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Affiliation(s)
- Maria-Rosa Garcia-Silva
- Department of Parasitology-Mycology, Faculty of Medicine, University of Montpellier, Montpellier, France.,CNRS 5290 - IRD 224 - University of Montpellier (UMR "MiVEGEC"), Montpellier, France
| | - Lauriane Sollelis
- Department of Parasitology-Mycology, Faculty of Medicine, University of Montpellier, Montpellier, France.,CNRS 5290 - IRD 224 - University of Montpellier (UMR "MiVEGEC"), Montpellier, France
| | - Cameron Ross MacPherson
- Biology of Host-Parasite Interactions Unit, Institut Pasteur, Paris, France.,CNRS, ERL 9195, Paris, France.,INSERM, Unit U1201, Paris, France
| | - Slavica Stanojcic
- Department of Parasitology-Mycology, Faculty of Medicine, University of Montpellier, Montpellier, France.,CNRS 5290 - IRD 224 - University of Montpellier (UMR "MiVEGEC"), Montpellier, France
| | - Nada Kuk
- Department of Parasitology-Mycology, Faculty of Medicine, University of Montpellier, Montpellier, France.,CNRS 5290 - IRD 224 - University of Montpellier (UMR "MiVEGEC"), Montpellier, France
| | - Lucien Crobu
- CNRS 5290 - IRD 224 - University of Montpellier (UMR "MiVEGEC"), Montpellier, France
| | - Frédéric Bringaud
- Laboratoire de Microbiologie Fondamentale et Pathogénicité (MFP), University of Bordeaux, Bordeaux, France.,CNRS, UMR 5234, Bordeaux, France
| | - Patrick Bastien
- Department of Parasitology-Mycology, Faculty of Medicine, University of Montpellier, Montpellier, France.,CNRS 5290 - IRD 224 - University of Montpellier (UMR "MiVEGEC"), Montpellier, France.,Department of Parasitology-Mycology, University Hospital Centre (CHU), Montpellier, France
| | - Michel Pagès
- CNRS 5290 - IRD 224 - University of Montpellier (UMR "MiVEGEC"), Montpellier, France
| | - Artur Scherf
- Biology of Host-Parasite Interactions Unit, Institut Pasteur, Paris, France.,CNRS, ERL 9195, Paris, France.,INSERM, Unit U1201, Paris, France
| | - Yvon Sterkers
- Department of Parasitology-Mycology, Faculty of Medicine, University of Montpellier, Montpellier, France .,CNRS 5290 - IRD 224 - University of Montpellier (UMR "MiVEGEC"), Montpellier, France.,Department of Parasitology-Mycology, University Hospital Centre (CHU), Montpellier, France
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38
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Duncan SM, Jones NG, Mottram JC. Recent advances in Leishmania reverse genetics: Manipulating a manipulative parasite. Mol Biochem Parasitol 2017. [DOI: 10.1016/j.molbiopara.2017.06.005] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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Rougeron V, De Meeûs T, Bañuls AL. Reproduction in Leishmania: A focus on genetic exchange. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2017; 50:128-132. [PMID: 27769896 DOI: 10.1016/j.meegid.2016.10.013] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2016] [Revised: 10/17/2016] [Accepted: 10/18/2016] [Indexed: 11/26/2022]
Abstract
One key process of the life cycle of pathogens is their mode of reproduction. Indeed, this fundamental biological process conditions the multiplication and the transmission of genes and thus the propagation of diseases in the environment. Reproductive strategies of protozoan parasites have been a subject of debate for many years, principally due to the difficulty in making direct observations of sexual reproduction (i.e. genetic recombination). Traditionally, these parasites were considered as characterized by a preeminent clonal structure. Nevertheless, with the development of elaborate culture experiments, population genetics and evolutionary and population genomics, several studies suggested that most of these pathogens were also characterized by constitutive genetic recombination events. In this opinion, we focused on Leishmania parasites, pathogens responsible of leishmaniases, a major public health issue. We first discuss the evolutionary advantages of a mixed mating reproductive strategy, then we review the evidence of genetic exchange, and finally we detail available tools to detect naturally occurring genetic recombination in Leishmania parasites and more generally in protozoan parasites.
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Affiliation(s)
- V Rougeron
- MIVEGEC (Laboratoire Maladies Infectieuses et Vecteurs: Ecologie, Génétique, Evolution et Contrôle), UMR CNRS 5290-IRD 224-Université de Montpellier, Montpellier, France.
| | - T De Meeûs
- Institut de Recherche pour le Développement (IRD), UMR 177 INTERTRYP IRD-CIRAD, TA A-17/G, Campus International de Baillarguet, 34398 Montpellier Cedex 5, France
| | - A-L Bañuls
- MIVEGEC (Laboratoire Maladies Infectieuses et Vecteurs: Ecologie, Génétique, Evolution et Contrôle), UMR CNRS 5290-IRD 224-Université de Montpellier, Montpellier, France
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40
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Devlin R, Marques CA, McCulloch R. Does DNA replication direct locus-specific recombination during host immune evasion by antigenic variation in the African trypanosome? Curr Genet 2017; 63:441-449. [PMID: 27822899 PMCID: PMC5422504 DOI: 10.1007/s00294-016-0662-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2016] [Revised: 10/26/2016] [Accepted: 10/27/2016] [Indexed: 12/14/2022]
Abstract
All pathogens must survive host immune attack and, amongst the survival strategies that have evolved, antigenic variation is a particularly widespread reaction to thwart adaptive immunity. Though the reactions that underlie antigenic variation are highly varied, recombination by gene conversion is a widespread approach to immune survival in bacterial and eukaryotic pathogens. In the African trypanosome, antigenic variation involves gene conversion-catalysed movement of a huge number of variant surface glycoprotein (VSG) genes into a few telomeric sites for VSG expression, amongst which only a single site is actively transcribed at one time. Genetic evidence indicates VSG gene conversion has co-opted the general genome maintenance reaction of homologous recombination, aligning the reaction strategy with targeted rearrangements found in many organisms. What is less clear is how gene conversion might be initiated within the locality of the VSG expression sites. Here, we discuss three emerging models for VSG switching initiation and ask how these compare with processes for adaptive genome change found in other organisms.
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Affiliation(s)
- Rebecca Devlin
- The Wellcome Trust Centre for Molecular Parasitology, Institute of Infection, Immunity and Inflammation, University of Glasgow, Sir Graeme Davis Building, 120 University Place, Glasgow, G12 8TA, UK
| | - Catarina A Marques
- The Wellcome Trust Centre for Molecular Parasitology, Institute of Infection, Immunity and Inflammation, University of Glasgow, Sir Graeme Davis Building, 120 University Place, Glasgow, G12 8TA, UK
- Division of Biological Chemistry and Drug Discovery, College of Life Sciences, University of Dundee, Dundee, UK
| | - Richard McCulloch
- The Wellcome Trust Centre for Molecular Parasitology, Institute of Infection, Immunity and Inflammation, University of Glasgow, Sir Graeme Davis Building, 120 University Place, Glasgow, G12 8TA, UK.
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41
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Dumetz F, Imamura H, Sanders M, Seblova V, Myskova J, Pescher P, Vanaerschot M, Meehan CJ, Cuypers B, De Muylder G, Späth GF, Bussotti G, Vermeesch JR, Berriman M, Cotton JA, Volf P, Dujardin JC, Domagalska MA. Modulation of Aneuploidy in Leishmania donovani during Adaptation to Different In Vitro and In Vivo Environments and Its Impact on Gene Expression. mBio 2017; 8:e00599-17. [PMID: 28536289 PMCID: PMC5442457 DOI: 10.1128/mbio.00599-17] [Citation(s) in RCA: 117] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Accepted: 05/01/2017] [Indexed: 12/23/2022] Open
Abstract
Aneuploidy is usually deleterious in multicellular organisms but appears to be tolerated and potentially beneficial in unicellular organisms, including pathogens. Leishmania, a major protozoan parasite, is emerging as a new model for aneuploidy, since in vitro-cultivated strains are highly aneuploid, with interstrain diversity and intrastrain mosaicism. The alternation of two life stages in different environments (extracellular promastigotes and intracellular amastigotes) offers a unique opportunity to study the impact of environment on aneuploidy and gene expression. We sequenced the whole genomes and transcriptomes of Leishmania donovani strains throughout their adaptation to in vivo conditions mimicking natural vertebrate and invertebrate host environments. The nucleotide sequences were almost unchanged within a strain, in contrast to highly variable aneuploidy. Although high in promastigotes in vitro, aneuploidy dropped significantly in hamster amastigotes, in a progressive and strain-specific manner, accompanied by the emergence of new polysomies. After a passage through a sand fly, smaller yet consistent karyotype changes were detected. Changes in chromosome copy numbers were correlated with the corresponding transcript levels, but additional aneuploidy-independent regulation of gene expression was observed. This affected stage-specific gene expression, downregulation of the entire chromosome 31, and upregulation of gene arrays on chromosomes 5 and 8. Aneuploidy changes in Leishmania are probably adaptive and exploited to modulate the dosage and expression of specific genes; they are well tolerated, but additional mechanisms may exist to regulate the transcript levels of other genes located on aneuploid chromosomes. Our model should allow studies of the impact of aneuploidy on molecular adaptations and cellular fitness.IMPORTANCE Aneuploidy is usually detrimental in multicellular organisms, but in several microorganisms, it can be tolerated and even beneficial. Leishmania-a protozoan parasite that kills more than 30,000 people each year-is emerging as a new model for aneuploidy studies, as unexpectedly high levels of aneuploidy are found in clinical isolates. Leishmania lacks classical regulation of transcription at initiation through promoters, so aneuploidy could represent a major adaptive strategy of this parasite to modulate gene dosage in response to stressful environments. For the first time, we document the dynamics of aneuploidy throughout the life cycle of the parasite, in vitro and in vivo We show its adaptive impact on transcription and its interaction with regulation. Besides offering a new model for aneuploidy studies, we show that further genomic studies should be done directly in clinical samples without parasite isolation and that adequate methods should be developed for this.
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Affiliation(s)
- F Dumetz
- Molecular Parasitology, Institute of Tropical Medicine, Antwerp, Belgium
| | - H Imamura
- Molecular Parasitology, Institute of Tropical Medicine, Antwerp, Belgium
| | - M Sanders
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, United Kingdom
| | - V Seblova
- Charles University, Prague, Czech Republic
| | - J Myskova
- Charles University, Prague, Czech Republic
| | - P Pescher
- Unité de Parasitologie Moléculaire et Signalisation, INSERM U1201, Institut Pasteur, Paris, France
| | - M Vanaerschot
- Molecular Parasitology, Institute of Tropical Medicine, Antwerp, Belgium
| | - C J Meehan
- Mycobacteriology Unit, Institute of Tropical Medicine, Antwerp, Belgium
| | - B Cuypers
- Molecular Parasitology, Institute of Tropical Medicine, Antwerp, Belgium
- Advanced Database Research and Modelling (ADReM), Department of Mathematics and Computer Science, University of Antwerp, Antwerp, Belgium
| | - G De Muylder
- Molecular Parasitology, Institute of Tropical Medicine, Antwerp, Belgium
| | - G F Späth
- Unité de Parasitologie Moléculaire et Signalisation, INSERM U1201, Institut Pasteur, Paris, France
| | - G Bussotti
- Unité de Parasitologie Moléculaire et Signalisation, INSERM U1201, Institut Pasteur, Paris, France
| | - J R Vermeesch
- Molecular Cytogenetics and Genome Research, Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - M Berriman
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, United Kingdom
| | - J A Cotton
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, United Kingdom
| | - P Volf
- Charles University, Prague, Czech Republic
| | - J C Dujardin
- Molecular Parasitology, Institute of Tropical Medicine, Antwerp, Belgium
- Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
| | - M A Domagalska
- Molecular Parasitology, Institute of Tropical Medicine, Antwerp, Belgium
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42
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Comparative genomics of canine-isolated Leishmania (Leishmania) amazonensis from an endemic focus of visceral leishmaniasis in Governador Valadares, southeastern Brazil. Sci Rep 2017; 7:40804. [PMID: 28091623 PMCID: PMC5238499 DOI: 10.1038/srep40804] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2016] [Accepted: 12/12/2016] [Indexed: 01/12/2023] Open
Abstract
Leishmaniasis is a highly diverse group of diseases caused by kinetoplastid of the genus Leishmania. These parasites are taxonomically diverse, with human pathogenic species separated into two subgenera according to their development site inside the alimentary tract of the sand fly insect vector. The disease encompasses a variable spectrum of clinical manifestations with tegumentary or visceral symptoms. Among the causative species in Brazil, Leishmania (Leishmania) amazonensis is an important etiological agent of human cutaneous leishmaniasis that accounts for more than 8% of all cases in endemic regions. L. (L.) amazonensis is generally found in the north and northeast regions of Brazil. Here, we report the first isolation of L. (L.) amazonensis from dogs with clinical manifestations of visceral leishmaniasis in Governador Valadares, an endemic focus in the southeastern Brazilian State of Minas Gerais where L. (L.) infantum is also endemic. These isolates were characterized in terms of SNPs, chromosome and gene copy number variations, confirming that they are closely related to a previously sequenced isolate obtained in 1973 from the typical Northern range of this species. The results presented in this article will increase our knowledge of L. (L.) amazonensis-specific adaptations to infection, parasite survival and the transmission of this Amazonian species in a new endemic area of Brazil.
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43
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Fotouhi-Ardakani R, Dabiri S, Ajdari S, Alimohammadian MH, AlaeeNovin E, Taleshi N, Parvizi P. Assessment of nuclear and mitochondrial genes in precise identification and analysis of genetic polymorphisms for the evaluation of Leishmania parasites. INFECTION GENETICS AND EVOLUTION 2016; 46:33-41. [DOI: 10.1016/j.meegid.2016.10.011] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2016] [Revised: 09/28/2016] [Accepted: 10/16/2016] [Indexed: 10/20/2022]
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44
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Tibayrenc M, Ayala FJ. Is Predominant Clonal Evolution a Common Evolutionary Adaptation to Parasitism in Pathogenic Parasitic Protozoa, Fungi, Bacteria, and Viruses? ADVANCES IN PARASITOLOGY 2016; 97:243-325. [PMID: 28325372 DOI: 10.1016/bs.apar.2016.08.007] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
We propose that predominant clonal evolution (PCE) in microbial pathogens be defined as restrained recombination on an evolutionary scale, with genetic exchange scarce enough to not break the prevalent pattern of clonal population structure. The main features of PCE are (1) strong linkage disequilibrium, (2) the widespread occurrence of stable genetic clusters blurred by occasional bouts of genetic exchange ('near-clades'), (3) the existence of a "clonality threshold", beyond which recombination is efficiently countered by PCE, and near-clades irreversibly diverge. We hypothesize that the PCE features are not mainly due to natural selection but also chiefly originate from in-built genetic properties of pathogens. We show that the PCE model obtains even in microbes that have been considered as 'highly recombining', such as Neisseria meningitidis, and that some clonality features are observed even in Plasmodium, which has been long described as panmictic. Lastly, we provide evidence that PCE features are also observed in viruses, taking into account their extremely fast genetic turnover. The PCE model provides a convenient population genetic framework for any kind of micropathogen. It makes it possible to describe convenient units of analysis (clones and near-clades) for all applied studies. Due to PCE features, these units of analysis are stable in space and time, and clearly delimited. The PCE model opens up the possibility of revisiting the problem of species definition in these organisms. We hypothesize that PCE constitutes a major evolutionary strategy for protozoa, fungi, bacteria, and viruses to adapt to parasitism.
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Affiliation(s)
- M Tibayrenc
- Institut de Recherche pour le Développement, Montpellier, France
| | - F J Ayala
- University of California at Irvine, United States
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Laffitte MCN, Leprohon P, Papadopoulou B, Ouellette M. Plasticity of the Leishmania genome leading to gene copy number variations and drug resistance. F1000Res 2016; 5:2350. [PMID: 27703673 PMCID: PMC5031125 DOI: 10.12688/f1000research.9218.1] [Citation(s) in RCA: 80] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 09/19/2016] [Indexed: 01/04/2023] Open
Abstract
Leishmania has a plastic genome, and drug pressure can select for gene copy number variation (CNV). CNVs can apply either to whole chromosomes, leading to aneuploidy, or to specific genomic regions. For the latter, the amplification of chromosomal regions occurs at the level of homologous direct or inverted repeated sequences leading to extrachromosomal circular or linear amplified DNAs. This ability of
Leishmania to respond to drug pressure by CNVs has led to the development of genomic screens such as Cos-Seq, which has the potential of expediting the discovery of drug targets for novel promising drug candidates.
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Affiliation(s)
- Marie-Claude N Laffitte
- Centre de Recherche en Infectiologie du Centre de Recherche du CHU Québec, and Département de Microbiologie, Infectiologie et Immunologie, Faculté de Médecine, Université Laval, Québec, Québec, Canada
| | - Philippe Leprohon
- Centre de Recherche en Infectiologie du Centre de Recherche du CHU Québec, and Département de Microbiologie, Infectiologie et Immunologie, Faculté de Médecine, Université Laval, Québec, Québec, Canada
| | - Barbara Papadopoulou
- Centre de Recherche en Infectiologie du Centre de Recherche du CHU Québec, and Département de Microbiologie, Infectiologie et Immunologie, Faculté de Médecine, Université Laval, Québec, Québec, Canada
| | - Marc Ouellette
- Centre de Recherche en Infectiologie du Centre de Recherche du CHU Québec, and Département de Microbiologie, Infectiologie et Immunologie, Faculté de Médecine, Université Laval, Québec, Québec, Canada
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Abstract
Eukaryotic microbial pathogens are major contributors to illness and death globally. Although much of their impact can be controlled by drug therapy as with prokaryotic microorganisms, the emergence of drug resistance has threatened these treatment efforts. Here, we discuss the challenges posed by eukaryotic microbial pathogens and how these are similar to, or differ from, the challenges of prokaryotic antibiotic resistance. The therapies used for several major eukaryotic microorganisms are then detailed, and the mechanisms that they have evolved to overcome these therapies are described. The rapid emergence of resistance and the restricted pipeline of new drug therapies pose considerable risks to global health and are particularly acute in the developing world. Nonetheless, we detail how the integration of new technology, biological understanding, epidemiology and evolutionary analysis can help sustain existing therapies, anticipate the emergence of resistance or optimize the deployment of new therapies.
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Affiliation(s)
- Alan H. Fairlamb
- Dundee Drug Discovery Unit, Biological Chemistry and Drug Discovery, College of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
| | - Neil A. R. Gow
- Aberdeen Fungal Group, Wellcome Trust Strategic Award in Medical Mycology and Fungal Immunology, School of Medical Sciences, Institute of Medical Sciences, Foresterhill, University of Aberdeen, Aberdeen AB25 2ZD, UK
| | - Keith R. Matthews
- Centre for Immunity, Infection and Evolution, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3FL, UK
| | - Andrew P. Waters
- Wellcome Trust Centre for Molecular Parasitology, Institute of Infection, Immunity and Inflammation, College of Medical and Veterinary Life Sciences, University of Glasgow, Glasgow G12 8TA, UK
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Bifeld E, Tejera Nevado P, Bartsch J, Eick J, Clos J. A versatile qPCR assay to quantify trypanosomatidic infections of host cells and tissues. Med Microbiol Immunol 2016; 205:449-58. [PMID: 27283847 DOI: 10.1007/s00430-016-0460-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2016] [Accepted: 05/27/2016] [Indexed: 02/06/2023]
Abstract
The majority of PCR-based detection systems for Leishmania spp. and Trypanosoma cruzi aim at high sensitivity and specificity, rather than an accurate parasite load quantification required for experimental infections in basic research and drug development. Here, we describe the use of a dual-labelled probe qPCR to detect and quantify intracellular Old World Leishmania spp. and T. cruzi amastigotes after in vitro and in vivo infection experiments. We show that quantification of parasite actin gene DNA relative to the host cell actin gene DNA accurately reflects the parasite load relative to the host cells and that qPCR quantification is highly sensible to drug-induced cell death. Furthermore, qPCR allows to determine parasite loads even after host cell detachment and/or rupture, important when comparing untreated versus drug-treated samples. The method is also suitable for the quantification of parasites from infected mouse tissue, making it suitable for drug testing and mutant phenotype analysis.
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Affiliation(s)
- Eugenia Bifeld
- Bernhard Nocht Institute for Tropical Medicine, Bernhard Nocht St 74, 20359, Hamburg, Germany
| | - Paloma Tejera Nevado
- Bernhard Nocht Institute for Tropical Medicine, Bernhard Nocht St 74, 20359, Hamburg, Germany
| | - Janika Bartsch
- Bernhard Nocht Institute for Tropical Medicine, Bernhard Nocht St 74, 20359, Hamburg, Germany.,Beuth Hochschule für Technik, Berlin, Germany
| | - Julia Eick
- Bernhard Nocht Institute for Tropical Medicine, Bernhard Nocht St 74, 20359, Hamburg, Germany
| | - Joachim Clos
- Bernhard Nocht Institute for Tropical Medicine, Bernhard Nocht St 74, 20359, Hamburg, Germany.
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Tibayrenc M, Ayala FJ. Reproductive clonality in protozoan pathogens-truth or artifact? A comment on Ramírez and Llewellyn. Mol Ecol 2015; 24:5778-81. [DOI: 10.1111/mec.13443] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2015] [Revised: 07/07/2015] [Accepted: 07/20/2015] [Indexed: 11/27/2022]
Affiliation(s)
- Michel Tibayrenc
- Maladies Infectieuses et Vecteurs Ecologie, Génétique, Evolution et Contrôle; MIVEGEC (IRD 224-CNRS 5290-UM1-UM2); IRD Center, BP 64501; 34394 Montpellier Cedex 5 France
| | - Francisco J. Ayala
- Department of Ecology and Evolutionary Biology; University of California Irvine; 321 Steinhaus Hall Irvine CA 92697-2525 USA
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Messenger LA, Miles MA. Evidence and importance of genetic exchange among field populations of Trypanosoma cruzi. Acta Trop 2015; 151:150-5. [PMID: 26188331 PMCID: PMC4644990 DOI: 10.1016/j.actatropica.2015.05.007] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2015] [Revised: 04/25/2015] [Accepted: 05/06/2015] [Indexed: 10/31/2022]
Abstract
Many eukaryotic pathogenic microorganisms that were previously assumed to propagate clonally have retained cryptic sexual cycles. The principal reproductive mode of Trypanosoma cruzi, the aetiological agent of Chagas disease, remains a controversial topic. Despite the existence of two recent natural hybrid lineages, a pervasive view is that recombination has been restrained at an evolutionary scale and is of little epidemiological relevance to contemporary parasite populations. This article reviews the growing number of field studies which indicate that natural hybridization in T. cruzi may be frequent, non-obligatory and idiosyncratic; potentially involving independent exchange of kinetoplast and nuclear genetic material as well as canonical meiotic mechanisms. Together these observations now challenge the traditional paradigm of preponderate clonal evolution in T. cruzi and highlight the need for additional, intensive and appropriately sampled field surveys, complemented by high resolution, combined nuclear and mitochondrial population genetics analyses.
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Tibayrenc M, Ayala FJ. The population genetics of Trypanosoma cruzi revisited in the light of the predominant clonal evolution model. Acta Trop 2015; 151:156-65. [PMID: 26188332 PMCID: PMC7117470 DOI: 10.1016/j.actatropica.2015.05.006] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2015] [Revised: 05/02/2015] [Accepted: 05/06/2015] [Indexed: 01/18/2023]
Abstract
Comparing the population structure of Trypanosoma cruzi with that of other pathogens, including parasitic protozoa, fungi, bacteria and viruses, shows that the agent of Chagas disease shares typical traits with many other species, related to a predominant clonal evolution (PCE) pattern: statistically significant linkage disequilibrium, overrepresented multilocus genotypes, near-clades (genetic subdivisions somewhat blurred by occasional genetic exchange/hybridization) and "Russian doll" patterns (PCE is observed, not only at the level of the whole species, but also, within the near-clades). Moreover, T. cruzi population structure exhibits linkage with the diversity of several strongly selected genes, with gene expression profiles, and with some major phenotypic traits. We discuss the evolutionary significance of these results, and their implications in terms of applied research (molecular epidemiology/strain typing, analysis of genes of interest, vaccine and drug design, immunological diagnosis) and of experimental evolution. Lastly, we revisit the long-term debate of describing new species within the T. cruzi taxon.
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