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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: 5] [Impact Index Per Article: 5.0] [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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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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Environmental Conditions May Shape the Patterns of Genomic Variations in Leishmania panamensis. Genes (Basel) 2019; 10:genes10110838. [PMID: 31652919 PMCID: PMC6896075 DOI: 10.3390/genes10110838] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Revised: 10/03/2019] [Accepted: 10/08/2019] [Indexed: 11/23/2022] Open
Abstract
Due to the absence of transcriptional regulation of gene expression in Leishmania parasites, it is now well accepted that several forms of genomic variations modulate the levels of critical proteins through changes in gene dosage. We previously observed many of these variations in our reference laboratory strain of L. panamensis (PSC-1 strain), including chromosomes with an increased somy and the presence of a putative linear minichromosome derived from chromosome 34. Here, we compared the previously described genomic variations with those occurring after exposure of this strain to increasing concentrations of trivalent antimony (SbIII), as well as those present in two geographically unrelated clinical isolates of L. panamensis. We observed changes in the somy of several chromosomes, amplifications of several chromosomal regions, and copy number variations in gene arrays after exposure to SbIII. Occurrence of amplifications potentially beneficial for the Sb-resistant phenotype appears to be associated with the loss of other forms of amplification, such as the linear minichromosome. In contrast, we found no evidence of changes in somy or amplification of relatively large chromosomal regions in the clinical isolates. In these isolates, the predominant amplifications appear to be those that generate genes arrays; however, in many cases, the amplified arrays have a notably higher number of copies than those from the untreated and Sb-treated laboratory samples.
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Patino LH, Muskus C, Ramírez JD. Transcriptional responses of Leishmania (Leishmania) amazonensis in the presence of trivalent sodium stibogluconate. Parasit Vectors 2019; 12:348. [PMID: 31300064 PMCID: PMC6626383 DOI: 10.1186/s13071-019-3603-8] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Accepted: 07/06/2019] [Indexed: 12/13/2022] Open
Abstract
Background In the last decade, resistance to antimonials has become a serious problem due to the emergence of drug-resistant strains. Therefore, understanding the mechanisms used by Leishmania parasites to survive under drug pressure is essential, particularly for species of medical-veterinary importance such as L. amazonensis. Methods Here, we used RNA-seq technology to analyse transcriptome profiles and identify global changes in gene expression between antimony-resistant and -sensitive L. amazonensis promastigotes. Results A total of 723 differentially expressed genes were identified between resistant and sensitive lines. Comparative transcriptomic analysis revealed that genes encoding proteins involved in metabolism (fatty acids) and stress response, as well as those associated with antimony resistance in other Leishmania species, were upregulated in the antimony-resistant line. Most importantly, we observed upregulation of genes encoding autophagy proteins, suggesting that in the presence of trivalent stibogluconate (SbIII) L. amazonensis can activate these genes either as a survival strategy or to induce cell death, as has been observed in other parasites. Conclusions This work identified global transcriptomic changes in an in vitro-adapted strain in response to SbIII. Our results provide relevant information to continue understanding the mechanism used by parasites of the subgenus Leishmania (L. amazonensis) to generate an antimony-resistant phenotype. Electronic supplementary material The online version of this article (10.1186/s13071-019-3603-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Luz H Patino
- Grupo de Investigaciones Microbiológicas-UR (GIMUR), Programa de Biología, Facultad de Ciencias Naturales y Matemáticas, Universidad del Rosario, Bogotá, Colombia
| | - Carlos Muskus
- Programa de Estudio y Control de Enfermedades Tropicales (PECET), Facultad de Medicina, Universidad de Antioquia, Medellín, Colombia
| | - Juan David Ramírez
- Grupo de Investigaciones Microbiológicas-UR (GIMUR), Programa de Biología, Facultad de Ciencias Naturales y Matemáticas, Universidad del Rosario, Bogotá, Colombia.
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Major changes in chromosomal somy, gene expression and gene dosage driven by Sb III in Leishmania braziliensis and Leishmania panamensis. Sci Rep 2019; 9:9485. [PMID: 31263131 PMCID: PMC6603004 DOI: 10.1038/s41598-019-45538-9] [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: 02/08/2019] [Accepted: 06/06/2019] [Indexed: 12/17/2022] Open
Abstract
Leishmania braziliensis and Leishmania panamensis are two species clinically and epidemiologically important, among others because of their relative resistance to first-line drugs (antimonials). The precise mechanism underlying the ability of these species to survive antimony treatment remains unknown. Therefore, elucidating the pathways mediating drug resistance is essential. We herein experimentally selected resistance to trivalent antimony (SbIII) in the reference strains of L. braziliensis (MHOM/BR75/M2904) and L. panamensis (MHOM/COL/81L13) and compared whole genome and transcriptome alterations in the culture promastigote stage. The results allowed us to identify differences in somy, copy number variations in some genes related to antimony resistance and large-scale copy number variations (deletions and duplications) in chromosomes with no somy changes. We found mainly in L. braziliensis, a direct relation between the chromosomal/local copy number variation and the gene expression. We identified differentially expressed genes in the resistant lines that are involved in antimony resistance, virulence, and vital biological processes in parasites. The results of this study may be useful for characterizing the genetic mechanisms of these Leishmania species under antimonial pressure, and for clarifying why the parasites are resistant to first-line drug treatments.
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Da Silva BJM, Hage AAP, Silva EO, Rodrigues APD. Medicinal plants from the Brazilian Amazonian region and their antileishmanial activity: a review. JOURNAL OF INTEGRATIVE MEDICINE-JIM 2018; 16:211-222. [DOI: 10.1016/j.joim.2018.04.004] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Accepted: 04/07/2018] [Indexed: 12/15/2022]
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Monte-Neto R, Laffitte MCN, Leprohon P, Reis P, Frézard F, Ouellette M. Intrachromosomal amplification, locus deletion and point mutation in the aquaglyceroporin AQP1 gene in antimony resistant Leishmania (Viannia) guyanensis. PLoS Negl Trop Dis 2015; 9:e0003476. [PMID: 25679388 PMCID: PMC4332685 DOI: 10.1371/journal.pntd.0003476] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2014] [Accepted: 12/14/2014] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Antimony resistance complicates the treatment of infections caused by the parasite Leishmania. METHODOLOGY/PRINCIPAL FINDINGS Using next generation sequencing, we sequenced the genome of four independent Leishmania guyanensis antimony-resistant (SbR) mutants and found different chromosomal alterations including aneuploidy, intrachromosomal gene amplification and gene deletion. A segment covering 30 genes on chromosome 19 was amplified intrachromosomally in three of the four mutants. The gene coding for the multidrug resistance associated protein A involved in antimony resistance was also amplified in the four mutants, most likely through chromosomal translocation. All mutants also displayed a reduced accumulation of antimony mainly due to genomic alterations at the level of the subtelomeric region of chromosome 31 harboring the gene coding for the aquaglyceroporin 1 (LgAQP1). Resistance involved the loss of LgAQP1 through subtelomeric deletions in three mutants. Interestingly, the fourth mutant harbored a single G133D point mutation in LgAQP1 whose role in resistance was functionality confirmed through drug sensitivity and antimony accumulation assays. In contrast to the Leishmania subspecies that resort to extrachromosomal amplification, the Viannia strains studied here used intrachromosomal amplification and locus deletion. CONCLUSIONS/SIGNIFICANCE This is the first report of a naturally occurred point mutation in AQP1 in antimony resistant parasites.
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Affiliation(s)
- Rubens Monte-Neto
- 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
| | - 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
| | - Priscila Reis
- Departamento de Fisiologia e Biofísica, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brasil
| | - Frédéric Frézard
- Departamento de Fisiologia e Biofísica, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brasil
| | - 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
- * E-mail:
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Moreira DS, Monte Neto RL, Andrade JM, Santi AMM, Reis PG, Frézard F, Murta SM. Molecular characterization of the MRPA transporter and antimony uptake in four New World Leishmania spp. susceptible and resistant to antimony. INTERNATIONAL JOURNAL FOR PARASITOLOGY-DRUGS AND DRUG RESISTANCE 2013; 3:143-53. [PMID: 24533304 PMCID: PMC3862441 DOI: 10.1016/j.ijpddr.2013.08.001] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/29/2012] [Revised: 08/20/2013] [Accepted: 08/21/2013] [Indexed: 11/25/2022]
Abstract
Level of expression of Pgp is increased in the SbIII-resistant L. guyanensis and L. amazonensis lines. Incorporation of antimony was reduced in the SbIII-resistant L. guyanensis, L. amazonensis and L. braziliensis lines. Down-regulation of AQP1 protein was observed in the SbIII-resistant L. guyanensis and L. amazonensis lines. Rates of SbIII efflux are higher in the SbIII-resistant lines of L. guyanensis and L. braziliensis. Mechanisms of antimony-resistance of the MRPA gene are different among species of Leishmania analyzed.
ATP-binding cassette (ABC) transporters have been associated with drug resistance in various diseases. The MRPA gene, a transporter of ABCC subfamily, is involved in the resistance by sequestering metal-thiol conjugates in intracellular vesicles of Leishmania parasite. In this study, we performed the molecular characterization of the MRPA transporter, analysis of P-glycoprotein (Pgp) and aquaglyceroporin-1 (AQP1) expression, and determination of antimony level in antimony-susceptible and -resistant lines of L. (V.) guyanensis, L. (L.) amazonensis, L. (V.) braziliensis and L. (L.) infantum. PFGE analysis revealed an association of chromosomal amplification of MRPA gene with the drug resistance phenotype in all SbIII-resistant Leishmania lines analyzed. Levels of mRNA from MRPA gene determined by real-time quantitative RT-PCR showed an increased expression of two fold in SbIII-resistant lines of Leishmania guyanensis, Leishmania amazonensis and Leishmania braziliensis. Western blot analysis revealed that Pgp is increased in the SbIII-resistant L. guyanensis and L. amazonensis lines. The intracellular level of antimony quantified by graphite furnace atomic absorption spectrometry showed a reduction in the accumulation of this element in SbIII-resistant L. guyanensis, L. amazonensis and L. braziliensis lines when compared to their susceptible counterparts. Interestingly, a down-regulation of AQP1 protein was observed in the SbIII-resistant L. guyanensis and L. amazonensis lines, contributing for decreasing of SbIII entry in these lines. In addition, efflux experiments revealed that the rates of SbIII efflux are higher in the SbIII-resistant lines of L. guyanensis and L. braziliensis, that may explain also the low SbIII concentration within of these parasites. The BSO, an inhibitor of γ-glutamylcysteine synthetase enzyme, reversed the SbIII-resistance phenotype of L. braziliensis and caused an increasing in the Sb intracellular level in the LbSbR line. Our data indicate that the mechanisms of antimony-resistance are different among species of Leishmania analyzed in this study.
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Key Words
- AQP1, aquaglyceroporin-1
- Drug resistance
- La, L. (L.) amazonensis
- Lb, L. (V.) braziliensis
- Leishmania spp.
- Lg, L. (V.) guyanensis
- Li, L. (L.) infantum
- MRPA transporter
- MRPA, multidrug-resistance protein A
- Pgp, phosphoglycoprotein
- Potassium antimonyl tartrate
- SbIII, potassium antimonyl tartrate
- SbR, SbIII-resistant
- WTS, Wild-type susceptible
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Affiliation(s)
- Douglas S. Moreira
- Laboratório de Parasitologia Celular e Molecular, Centro de Pesquisas René Rachou – CPqRR/FIOCRUZ, Belo Horizonte 30190-002, Minas Gerais, Brazil
| | - Rubens L. Monte Neto
- Departamento de Fisiologia e Biofísica, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, Minas Gerais, Brazil
- Centre de Recherche en Infectiologie, CHUL, Québec G1V 4G2, QC, Canada
| | - Juvana M. Andrade
- Laboratório de Parasitologia Celular e Molecular, Centro de Pesquisas René Rachou – CPqRR/FIOCRUZ, Belo Horizonte 30190-002, Minas Gerais, Brazil
| | - Ana Maria M. Santi
- Laboratório de Parasitologia Celular e Molecular, Centro de Pesquisas René Rachou – CPqRR/FIOCRUZ, Belo Horizonte 30190-002, Minas Gerais, Brazil
| | - Priscila G. Reis
- Departamento de Fisiologia e Biofísica, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, Minas Gerais, Brazil
| | - Frédéric Frézard
- Departamento de Fisiologia e Biofísica, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, Minas Gerais, Brazil
| | - Silvane M.F. Murta
- Laboratório de Parasitologia Celular e Molecular, Centro de Pesquisas René Rachou – CPqRR/FIOCRUZ, Belo Horizonte 30190-002, Minas Gerais, Brazil
- Corresponding author. Address: Laboratório de Parasitologia Celular e Molecular, Centro de Pesquisas ‘René Rachou’, FIOCRUZ, Av. Augusto de Lima 1715, Caixa Postal 1743, CEP 30190-002 Belo Horizonte, MG, Brazil. Tel.: +55 31 3349 7780; fax: +55 31 32953115.
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In silico identification of conserved intercoding sequences in Leishmania genomes: Unraveling putative cis-regulatory elements. Mol Biochem Parasitol 2012; 183:140-50. [DOI: 10.1016/j.molbiopara.2012.02.009] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2011] [Revised: 02/16/2012] [Accepted: 02/17/2012] [Indexed: 01/21/2023]
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Antimony resistance in leishmania, focusing on experimental research. J Trop Med 2011; 2011:695382. [PMID: 22174724 PMCID: PMC3235892 DOI: 10.1155/2011/695382] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2011] [Revised: 08/24/2011] [Accepted: 09/05/2011] [Indexed: 12/02/2022] Open
Abstract
Leishmaniases are parasitic diseases that spread in many countries with a prevalence of 12 million cases. There are few available treatments and antimonials are still of major importance in the therapeutic strategies used in most endemic regions. However, resistance toward these compounds has recently emerged in areas where the replacement of these drugs is mainly limited by the cost of alternative molecules. In this paper, we reviewed the studies carried out on antimonial resistance in Leishmania. Several common limitations of these works are presented before prevalent approaches to evidence antimonial resistance are related. Afterwards, phenotypic determination of resistance is described, then confronted to clinical outcome. Finally, we detail molecular mechanisms and targets involved in resistance and already identified in vitro within selected mutant strains or in clinical isolates.
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do Monte-Neto RL, Coelho AC, Raymond F, Légaré D, Corbeil J, Melo MN, Frézard F, Ouellette M. Gene expression profiling and molecular characterization of antimony resistance in Leishmania amazonensis. PLoS Negl Trop Dis 2011; 5:e1167. [PMID: 21629719 PMCID: PMC3101167 DOI: 10.1371/journal.pntd.0001167] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2010] [Accepted: 03/31/2011] [Indexed: 11/21/2022] Open
Abstract
Background Drug resistance is a major problem in leishmaniasis chemotherapy. RNA expression profiling using DNA microarrays is a suitable approach to study simultaneous events leading to a drug-resistance phenotype. Genomic analysis has been performed primarily with Old World Leishmania species and here we investigate molecular alterations in antimony resistance in the New World species L. amazonensis. Methods/Principal Findings We selected populations of L. amazonensis promastigotes for resistance to antimony by step-wise drug pressure. Gene expression of highly resistant mutants was studied using DNA microarrays. RNA expression profiling of antimony-resistant L. amazonensis revealed the overexpression of genes involved in drug resistance including the ABC transporter MRPA and several genes related to thiol metabolism. The MRPA overexpression was validated by quantitative real-time RT-PCR and further analysis revealed that this increased expression was correlated to gene amplification as part of extrachromosomal linear amplicons in some mutants and as part of supernumerary chromosomes in other mutants. The expression of several other genes encoding hypothetical proteins but also nucleobase and glucose transporter encoding genes were found to be modulated. Conclusions/Significance Mechanisms classically found in Old World antimony resistant Leishmania were also highlighted in New World antimony-resistant L. amazonensis. These studies were useful to the identification of resistance molecular markers. Leishmania are unicellular microorganisms that can be transmitted to humans by the bite of sandflies. They cause a spectrum of diseases called leishmaniasis, which are classified as neglected tropical diseases by the World Health Organization. The treatment of leishmaniasis is based on the administration of antimony-containing drugs. These drugs have been used since 1947 and still constitute the mainstay for leishmaniasis treatment in several countries. One of the problems with these compounds is the emergence of resistance. Our work seeks to understand how these parasites become resistant to the drug. We studied antimony-resistant Leishmania amazonensis mutants. We analyzed gene expression at the whole genome level in antimony-resistant parasites and identified mechanisms used by Leishmania for resistance. This work could help us in developing new strategies for treatment in endemic countries where people are unresponsive to antimony-based chemotherapy. The identification of common mechanisms among different species of resistant parasites may also contribute to the development of diagnostic kits to identify and monitor the spread of resistance.
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Affiliation(s)
- Rubens L. do Monte-Neto
- Departamento de Fisiologia e Biofísica, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brasil
- Centre de Recherche en Infectiologie du Centre de Recherche du CHUL and Département de Microbiologie, Immunologie et Infectiologie, Université Laval, Québec, Québec, Canada
| | - Adriano C. Coelho
- Centre de Recherche en Infectiologie du Centre de Recherche du CHUL and Département de Microbiologie, Immunologie et Infectiologie, Université Laval, Québec, Québec, Canada
| | - Frédéric Raymond
- Centre de Recherche en Infectiologie du Centre de Recherche du CHUL and Département de Microbiologie, Immunologie et Infectiologie, Université Laval, Québec, Québec, Canada
- Département de Médecine Moléculaire Faculté de Médecine, Université Laval, Québec, Québec, Canada
| | - Danielle Légaré
- Centre de Recherche en Infectiologie du Centre de Recherche du CHUL and Département de Microbiologie, Immunologie et Infectiologie, Université Laval, Québec, Québec, Canada
| | - Jacques Corbeil
- Centre de Recherche en Infectiologie du Centre de Recherche du CHUL and Département de Microbiologie, Immunologie et Infectiologie, Université Laval, Québec, Québec, Canada
- Département de Médecine Moléculaire Faculté de Médecine, Université Laval, Québec, Québec, Canada
| | - Maria N. Melo
- Departamento de Parasitologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brasil
| | - Frédéric Frézard
- Departamento de Fisiologia e Biofísica, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brasil
| | - Marc Ouellette
- Centre de Recherche en Infectiologie du Centre de Recherche du CHUL and Département de Microbiologie, Immunologie et Infectiologie, Université Laval, Québec, Québec, Canada
- * E-mail:
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Lye LF, Owens K, Shi H, Murta SMF, Vieira AC, Turco SJ, Tschudi C, Ullu E, Beverley SM. Retention and loss of RNA interference pathways in trypanosomatid protozoans. PLoS Pathog 2010; 6:e1001161. [PMID: 21060810 PMCID: PMC2965760 DOI: 10.1371/journal.ppat.1001161] [Citation(s) in RCA: 166] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2010] [Accepted: 09/23/2010] [Indexed: 01/02/2023] Open
Abstract
RNA interference (RNAi) pathways are widespread in metaozoans but the genes required show variable occurrence or activity in eukaryotic microbes, including many pathogens. While some Leishmania lack RNAi activity and Argonaute or Dicer genes, we show that Leishmania braziliensis and other species within the Leishmania subgenus Viannia elaborate active RNAi machinery. Strong attenuation of expression from a variety of reporter and endogenous genes was seen. As expected, RNAi knockdowns of the sole Argonaute gene implicated this protein in RNAi. The potential for functional genetics was established by testing RNAi knockdown lines lacking the paraflagellar rod, a key component of the parasite flagellum. This sets the stage for the systematic manipulation of gene expression through RNAi in these predominantly diploid asexual organisms, and may also allow selective RNAi-based chemotherapy. Functional evolutionary surveys of RNAi genes established that RNAi activity was lost after the separation of the Leishmania subgenus Viannia from the remaining Leishmania species, a divergence associated with profound changes in the parasite infectious cycle and virulence. The genus Leishmania therefore offers an accessible system for testing hypothesis about forces that may select for the loss of RNAi during evolution, such as invasion by viruses, changes in genome plasticity mediated by transposable elements and gene amplification (including those mediating drug resistance), and/or alterations in parasite virulence. RNAi interference pathways play fundamental roles in eukaryotes and provide important methods for the analysis of gene function. Occasionally RNAi has been lost, precluding its use as a tool, as well as raising the question of what forces could lead to loss of such a key pathway. Genomic and functional studies previously showed that within trypanosomatids protozoans RNAi was absent in both Leishmania major and Trypanosoma cruzi. The genome of L. braziliensis, a member of the early diverging Leishmania subgenus Viannia, retained key genes required for RNAi such as an Argonaute. We demonstrated that in fact L. braziliensis shows strong RNAi activity with reporter and endogenous genes affecting flagellar function. These data suggest that RNAi may be productively applied for functional genomic studies in L. braziliensis. We mapped the evolutionary point at which RNAi was lost in lineage leading to Leishmania and Crithidia, and establish that RNAi must have been lost at least twice in the trypanosomatids, once on the lineage leading to T. cruzi and independently following the divergence of the Viannia subgenus from other Leishmania species. Lastly, we discuss hypotheses concerning the forces leading to the loss of RNAi in Leishmania evolution, including viral invasion, increased genome plasticity, and altered virulence.
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Affiliation(s)
- Lon-Fye Lye
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Katherine Owens
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Huafang Shi
- Department of Internal Medicine, Yale University Medical School, New Haven, Connecticut, United States of America
| | - Silvane M. F. Murta
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Ana Carolina Vieira
- Department of Biochemistry, University of Kentucky Medical Center, Lexington, Kentucky, United States of America
| | - Salvatore J. Turco
- Department of Biochemistry, University of Kentucky Medical Center, Lexington, Kentucky, United States of America
| | - Christian Tschudi
- Department of Internal Medicine, Yale University Medical School, New Haven, Connecticut, United States of America
- Department of Epidemiology & Public Health, Yale University Medical School, New Haven, Connecticut, United States of America
| | - Elisabetta Ullu
- Department of Internal Medicine, Yale University Medical School, New Haven, Connecticut, United States of America
- Department of Cell Biology, Yale University Medical School, New Haven, Connecticut, United States of America
| | - Stephen M. Beverley
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, United States of America
- * E-mail:
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Comparison of gene expression patterns among Leishmania braziliensis clinical isolates showing a different in vitro susceptibility to pentavalent antimony. Parasitology 2010; 138:183-93. [PMID: 20678296 DOI: 10.1017/s0031182010001095] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
INTRODUCTION Evaluation of Leishmania drug susceptibility depends on in vitro Sb(V) susceptibility assays, which are labour-intensive and may give a biased view of the true parasite resistance. Molecular markers are urgently needed to improve and simplify the monitoring of Sb(V)-resistance. We analysed here the gene expression profile of 21 L. braziliensis clinical isolates in vitro defined as Sb(V)-resistant and -sensitive, in order to identify potential resistance markers. METHODS The differential expression of 13 genes involved in Sb(V) metabolism, oxidative stress or housekeeping functions was analysed during in vitro promastigote growth. RESULTS Expression profiles were up-regulated for 5 genes only, each time affecting a different set of isolates (mosaic picture of gene expression). Two genes, ODC (ornithine decarboxylase) and TRYR (trypanothione reductase), showed a significantly higher expression rate in the group of Sb(V)-resistant compared to the group of Sb(V)-sensitive parasites (P<0.01). However, analysis of individual isolates showed both markers to explain only partially the drug resistance. DISCUSSION Our results might be explained by (i) the occurrence of a pleiotropic molecular mechanism leading to the in vitro Sb(V) resistance and/or (ii) the existence of different epi-phenotypes not revealed by the in vitro Sb(V) susceptibility assays, but interfering with the gene expression patterns.
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14
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Dujardin JC. Structure, dynamics and function of Leishmania genome: Resolving the puzzle of infection, genetics and evolution? INFECTION GENETICS AND EVOLUTION 2009; 9:290-7. [DOI: 10.1016/j.meegid.2008.11.007] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2008] [Revised: 11/25/2008] [Accepted: 11/25/2008] [Indexed: 01/23/2023]
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Coelho AC, Gentil LG, da Silveira JF, Cotrim PC. Characterization of Leishmania (Leishmania) amazonensis promastigotes resistant to pentamidine. Exp Parasitol 2008; 120:98-102. [PMID: 18511047 DOI: 10.1016/j.exppara.2008.03.018] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2007] [Revised: 03/20/2008] [Accepted: 03/27/2008] [Indexed: 11/30/2022]
Abstract
Pentamidine is a second-line agent used in the treatment of leishmaniasis and its mode of action and mechanism of resistance is not well understood. It was previously demonstrated that transfection of promastigotes and amastigotes with the ABC transporter PRP1 gene confers resistance to pentamidine. To further clarify this point, we generated Leishmania amazonensis mutants resistant to pentamidine. Our results indicated that this ABC transporter is not associated with pentamidine resistance in lines generated by drug pressure through amplification or overexpression mechanisms of PRP1 gene.
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Affiliation(s)
- Adriano C Coelho
- Instituto de Medicina Tropical, Departamento Moléstias infecciosas e Parasitárias, Faculdade de Medicina da Universidade de São Paulo, Av. Dr. Enéas de Carvalho Aguiar, 470, 4 degrees andar, 05403-000 São Paulo, SP, Brazil
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