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Coughlan S, Mulhair P, Sanders M, Schonian G, Cotton JA, Downing T. The genome of Leishmania adleri from a mammalian host highlights chromosome fission in Sauroleishmania. Sci Rep 2017; 7:43747. [PMID: 28256610 PMCID: PMC5335649 DOI: 10.1038/srep43747] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2016] [Accepted: 01/26/2017] [Indexed: 12/30/2022] Open
Abstract
Control of pathogens arising from humans, livestock and wild animals can be enhanced by genome-based investigation. Phylogenetically classifying and optimal construction of these genomes using short sequence reads are key to this process. We examined the mammal-infecting unicellular parasite Leishmania adleri belonging to the lizard-infecting Sauroleishmania subgenus. L. adleri has been associated with cutaneous disease in humans, but can be asymptomatic in wild animals. We sequenced, assembled and investigated the L. adleri genome isolated from an asymptomatic Ethiopian rodent (MARV/ET/75/HO174) and verified it as L. adleri by comparison with other Sauroleishmania species. Chromosome-level scaffolding was achieved by combining reference-guided with de novo assembly followed by extensive improvement steps to produce a final draft genome with contiguity comparable with other references. L. tarentolae and L. major genome annotation was transferred and these gene models were manually verified and improved. This first high-quality draft Leishmania adleri reference genome is also the first Sauroleishmania genome from a non-reptilian host. Comparison of the L. adleri HO174 genome with those of L. tarentolae Parrot-TarII and lizard-infecting L. adleri RLAT/KE/1957/SKINK-7 showed extensive gene amplifications, pervasive aneuploidy, and fission of chromosomes 30 and 36. There was little genetic differentiation between L. adleri extracted from mammals and reptiles, highlighting challenges for leishmaniasis surveillance.
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Affiliation(s)
- Simone Coughlan
- School of Mathematics, Applied Mathematics and Statistics, National University of Ireland, Galway, Ireland
| | - Peter Mulhair
- School of Biotechnology, Dublin City University, Dublin, Ireland
| | | | | | | | - Tim Downing
- School of Mathematics, Applied Mathematics and Statistics, National University of Ireland, Galway, Ireland
- School of Biotechnology, Dublin City University, Dublin, Ireland
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Stiles JK, Hicock PI, Shah PH, Meade JC. Genomic organization, transcription, splicing and gene regulation inLeishmania. ANNALS OF TROPICAL MEDICINE AND PARASITOLOGY 2016. [DOI: 10.1080/00034983.1999.11813485] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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Carnes J, Anupama A, Balmer O, Jackson A, Lewis M, Brown R, Cestari I, Desquesnes M, Gendrin C, Hertz-Fowler C, Imamura H, Ivens A, Kořený L, Lai DH, MacLeod A, McDermott SM, Merritt C, Monnerat S, Moon W, Myler P, Phan I, Ramasamy G, Sivam D, Lun ZR, Lukeš J, Stuart K, Schnaufer A. Genome and phylogenetic analyses of Trypanosoma evansi reveal extensive similarity to T. brucei and multiple independent origins for dyskinetoplasty. PLoS Negl Trop Dis 2015; 9:e3404. [PMID: 25568942 PMCID: PMC4288722 DOI: 10.1371/journal.pntd.0003404] [Citation(s) in RCA: 103] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2014] [Accepted: 11/09/2014] [Indexed: 11/18/2022] Open
Abstract
Two key biological features distinguish Trypanosoma evansi from the T. brucei group: independence from the tsetse fly as obligatory vector, and independence from the need for functional mitochondrial DNA (kinetoplast or kDNA). In an effort to better understand the molecular causes and consequences of these differences, we sequenced the genome of an akinetoplastic T. evansi strain from China and compared it to the T. b. brucei reference strain. The annotated T. evansi genome shows extensive similarity to the reference, with 94.9% of the predicted T. b. brucei coding sequences (CDS) having an ortholog in T. evansi, and 94.6% of the non-repetitive orthologs having a nucleotide identity of 95% or greater. Interestingly, several procyclin-associated genes (PAGs) were disrupted or not found in this T. evansi strain, suggesting a selective loss of function in the absence of the insect life-cycle stage. Surprisingly, orthologous sequences were found in T. evansi for all 978 nuclear CDS predicted to represent the mitochondrial proteome in T. brucei, although a small number of these may have lost functionality. Consistent with previous results, the F1FO-ATP synthase γ subunit was found to have an A281 deletion, which is involved in generation of a mitochondrial membrane potential in the absence of kDNA. Candidates for CDS that are absent from the reference genome were identified in supplementary de novo assemblies of T. evansi reads. Phylogenetic analyses show that the sequenced strain belongs to a dominant group of clonal T. evansi strains with worldwide distribution that also includes isolates classified as T. equiperdum. At least three other types of T. evansi or T. equiperdum have emerged independently. Overall, the elucidation of the T. evansi genome sequence reveals extensive similarity of T. brucei and supports the contention that T. evansi should be classified as a subspecies of T. brucei.
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Affiliation(s)
- Jason Carnes
- Seattle Biomedical Research Institute, Seattle, United States of America
| | - Atashi Anupama
- Seattle Biomedical Research Institute, Seattle, United States of America
| | - Oliver Balmer
- Swiss Tropical and Public Health Institute, Basel, Switzerland
| | - Andrew Jackson
- Department of Infection Biology, Institute of Infection and Global Health, University of Liverpool, Liverpool, United Kingdom
| | - Michael Lewis
- Department of Pathogen Molecular Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Rob Brown
- Seattle Biomedical Research Institute, Seattle, United States of America
| | - Igor Cestari
- Seattle Biomedical Research Institute, Seattle, United States of America
| | - Marc Desquesnes
- CIRAD, UMR-InterTryp, Montpellier, France
- Faculty of Veterinary Medicine, Kasetsart University, Bangkok, Thailand
| | - Claire Gendrin
- Seattle Biomedical Research Institute, Seattle, United States of America
| | - Christiane Hertz-Fowler
- Centre for Genomic Research, Institute of Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Hideo Imamura
- Unit of Molecular Parasitology, Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Alasdair Ivens
- Centre of Immunity, Infection and Evolution, University of Edinburgh, Edinburgh, United Kingdom
| | - Luděk Kořený
- Biology Centre, Institute of Parasitology, Czech Academy of Sciences, České Budějovice (Budweis), Czech Republic
- Faculty of Sciences, University of South Bohemia, Centre, České Budějovice (Budweis), Czech Republic
| | - De-Hua Lai
- Biology Centre, Institute of Parasitology, Czech Academy of Sciences, České Budějovice (Budweis), Czech Republic
- Faculty of Sciences, University of South Bohemia, Centre, České Budějovice (Budweis), Czech Republic
- Center for Parasitic Organisms, State Key Laboratory of Biocontrol, School of Life Sciences, and Key Laboratory of Tropical Disease Control of Ministry of Education, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, People′s Republic of China
| | - Annette MacLeod
- Wellcome Trust Centre for Molecular Parasitology, Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | | | - Chris Merritt
- Seattle Biomedical Research Institute, Seattle, United States of America
| | - Severine Monnerat
- Seattle Biomedical Research Institute, Seattle, United States of America
| | - Wonjong Moon
- Seattle Biomedical Research Institute, Seattle, United States of America
| | - Peter Myler
- Seattle Biomedical Research Institute, Seattle, United States of America
| | - Isabelle Phan
- Seattle Biomedical Research Institute, Seattle, United States of America
| | - Gowthaman Ramasamy
- Seattle Biomedical Research Institute, Seattle, United States of America
| | - Dhileep Sivam
- Seattle Biomedical Research Institute, Seattle, United States of America
| | - Zhao-Rong Lun
- Center for Parasitic Organisms, State Key Laboratory of Biocontrol, School of Life Sciences, and Key Laboratory of Tropical Disease Control of Ministry of Education, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, People′s Republic of China
- * E-mail: (ZRL); (JL); (KS); (AS)
| | - Julius Lukeš
- Biology Centre, Institute of Parasitology, Czech Academy of Sciences, České Budějovice (Budweis), Czech Republic
- Faculty of Sciences, University of South Bohemia, Centre, České Budějovice (Budweis), Czech Republic
- Canadian Institute for Advanced Research, Toronto, Canada
- * E-mail: (ZRL); (JL); (KS); (AS)
| | - Ken Stuart
- Seattle Biomedical Research Institute, Seattle, United States of America
- Department of Global Health, University of Washington, Seattle, United States of America
- * E-mail: (ZRL); (JL); (KS); (AS)
| | - Achim Schnaufer
- Centre of Immunity, Infection and Evolution, University of Edinburgh, Edinburgh, United Kingdom
- Institute of Immunology & Infection Research, University of Edinburgh, Edinburgh, United Kingdom
- * E-mail: (ZRL); (JL); (KS); (AS)
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Ubeda JM, Raymond F, Mukherjee A, Plourde M, Gingras H, Roy G, Lapointe A, Leprohon P, Papadopoulou B, Corbeil J, Ouellette M. Genome-wide stochastic adaptive DNA amplification at direct and inverted DNA repeats in the parasite Leishmania. PLoS Biol 2014; 12:e1001868. [PMID: 24844805 PMCID: PMC4028189 DOI: 10.1371/journal.pbio.1001868] [Citation(s) in RCA: 99] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2013] [Accepted: 04/11/2014] [Indexed: 12/31/2022] Open
Abstract
The human parasite Leishmania uses adaptive gene rearrangements and amplification involving repeated sequences on a genome-wide scale as one strategy to adapt to a changing environment. Gene amplification of specific loci has been described in all kingdoms of life. In the protozoan parasite Leishmania, the product of amplification is usually part of extrachromosomal circular or linear amplicons that are formed at the level of direct or inverted repeated sequences. A bioinformatics screen revealed that repeated sequences are widely distributed in the Leishmania genome and the repeats are chromosome-specific, conserved among species, and generally present in low copy number. Using sensitive PCR assays, we provide evidence that the Leishmania genome is continuously being rearranged at the level of these repeated sequences, which serve as a functional platform for constitutive and stochastic amplification (and deletion) of genomic segments in the population. This process is adaptive as the copy number of advantageous extrachromosomal circular or linear elements increases upon selective pressure and is reversible when selection is removed. We also provide mechanistic insights on the formation of circular and linear amplicons through RAD51 recombinase-dependent and -independent mechanisms, respectively. The whole genome of Leishmania is thus stochastically rearranged at the level of repeated sequences, and the selection of parasite subpopulations with changes in the copy number of specific loci is used as a strategy to respond to a changing environment. Variations in the copy number of DNA segments account for a substantial amount of genome diversity of most organisms. DNA amplification, a contributor to copy number variation, can occur in response to various stresses or after altered growth conditions, leading to extensive and often reversible genetic variation. DNA amplification in the parasite Leishmania occurs outside the normal chromosomes and arises by DNA rearrangements involving homologous repeated sequences. We show here that such repeated sequences are widespread in the Leishmania genome and that most of the Leishmania genome is subject to stochastic gene rearrangements mediated by these low-copy repeat sequences. Thus, although cells in the population have a common core genome, many individual cells will differ from the rest of the population by carrying one or more distinct extrachromosomal amplicon. Upon selection with either drugs or culture conditions, a subpopulation can emerge where the amplicon copy number per cell increases, and this clone of cells can then expand to dominate the population. We propose that Leishmania uses adaptive gene amplification at a genome-wide scale as one strategy to adapt to a changing environment.
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Affiliation(s)
- Jean-Michel Ubeda
- Centre de Recherche en Infectiologie, Centre de Recherche du CHU de Québec, Québec, Canada
| | - Frédéric Raymond
- Centre de Recherche en Infectiologie, Centre de Recherche du CHU de Québec, Québec, Canada
| | - Angana Mukherjee
- Centre de Recherche en Infectiologie, Centre de Recherche du CHU de Québec, Québec, Canada
| | - Marie Plourde
- Centre de Recherche en Infectiologie, Centre de Recherche du CHU de Québec, Québec, Canada
| | - Hélène Gingras
- Centre de Recherche en Infectiologie, Centre de Recherche du CHU de Québec, Québec, Canada
| | - Gaétan Roy
- Centre de Recherche en Infectiologie, Centre de Recherche du CHU de Québec, Québec, Canada
| | - Andréanne Lapointe
- Centre de Recherche en Infectiologie, Centre de Recherche du CHU de Québec, Québec, Canada
| | - Philippe Leprohon
- Centre de Recherche en Infectiologie, Centre de Recherche du CHU de Québec, Québec, Canada
| | - Barbara Papadopoulou
- Centre de Recherche en Infectiologie, Centre de Recherche du CHU de Québec, Québec, Canada
| | - Jacques Corbeil
- Centre de Recherche en Infectiologie, Centre de Recherche du CHU de Québec, Québec, Canada
| | - Marc Ouellette
- Centre de Recherche en Infectiologie, Centre de Recherche du CHU de Québec, Québec, Canada
- * E-mail:
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Real F, Vidal RO, Carazzolle MF, Mondego JMC, Costa GGL, Herai RH, Würtele M, de Carvalho LM, Carmona e Ferreira R, Mortara RA, Barbiéri CL, Mieczkowski P, da Silveira JF, Briones MRDS, Pereira GAG, Bahia D. The genome sequence of Leishmania (Leishmania) amazonensis: functional annotation and extended analysis of gene models. DNA Res 2013; 20:567-81. [PMID: 23857904 PMCID: PMC3859324 DOI: 10.1093/dnares/dst031] [Citation(s) in RCA: 83] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
We present the sequencing and annotation of the Leishmania (Leishmania) amazonensis genome, an etiological agent of human cutaneous leishmaniasis in the Amazon region of Brazil. L. (L.) amazonensis shares features with Leishmania (L.) mexicana but also exhibits unique characteristics regarding geographical distribution and clinical manifestations of cutaneous lesions (e.g. borderline disseminated cutaneous leishmaniasis). Predicted genes were scored for orthologous gene families and conserved domains in comparison with other human pathogenic Leishmania spp. Carboxypeptidase, aminotransferase, and 3′-nucleotidase genes and ATPase, thioredoxin, and chaperone-related domains were represented more abundantly in L. (L.) amazonensis and L. (L.) mexicana species. Phylogenetic analysis revealed that these two species share groups of amastin surface proteins unique to the genus that could be related to specific features of disease outcomes and host cell interactions. Additionally, we describe a hypothetical hybrid interactome of potentially secreted L. (L.) amazonensis proteins and host proteins under the assumption that parasite factors mimic their mammalian counterparts. The model predicts an interaction between an L. (L.) amazonensis heat-shock protein and mammalian Toll-like receptor 9, which is implicated in important immune responses such as cytokine and nitric oxide production. The analysis presented here represents valuable information for future studies of leishmaniasis pathogenicity and treatment.
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Affiliation(s)
- Fernando Real
- 1Departamento de Microbiologia, Imunologia e Parasitologia, Escola Paulista de Medicina, Universidade Federal de São Paulo - EPM/UNIFESP, Rua Botucatu 862, 6 andar, 04023-062 São Paulo, Brazil
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Lima FM, Souza RT, Santori FR, Santos MF, Cortez DR, Barros RM, Cano MI, Valadares HMS, Macedo AM, Mortara RA, da Silveira JF. Interclonal variations in the molecular karyotype of Trypanosoma cruzi: chromosome rearrangements in a single cell-derived clone of the G strain. PLoS One 2013; 8:e63738. [PMID: 23667668 PMCID: PMC3646811 DOI: 10.1371/journal.pone.0063738] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2012] [Accepted: 04/11/2013] [Indexed: 12/22/2022] Open
Abstract
Trypanosoma cruzi comprises a pool of populations which are genetically diverse in terms of DNA content, growth and infectivity. Inter- and intra-strain karyotype heterogeneities have been reported, suggesting that chromosomal rearrangements occurred during the evolution of this parasite. Clone D11 is a single-cell-derived clone of the T. cruzi G strain selected by the minimal dilution method and by infecting Vero cells with metacyclic trypomastigotes. Here we report that the karyotype of clone D11 differs from that of the G strain in both number and size of chromosomal bands. Large chromosomal rearrangement was observed in the chromosomes carrying the tubulin loci. However, most of the chromosome length polymorphisms were of small amplitude, and the absence of one band in clone D11 in relation to its reference position in the G strain could be correlated to the presence of a novel band migrating above or below this position. Despite the presence of chromosomal polymorphism, large syntenic groups were conserved between the isolates. The appearance of new chromosomal bands in clone D11 could be explained by chromosome fusion followed by a chromosome break or interchromosomal exchange of large DNA segments. Our results also suggest that telomeric regions are involved in this process. The variant represented by clone D11 could have been induced by the stress of the cloning procedure or could, as has been suggested for Leishmania infantum, have emerged from a multiclonal, mosaic parasite population submitted to frequent DNA amplification/deletion events, leading to a 'mosaic' structure with different individuals having differently sized versions of the same chromosomes. If this is the case, the variant represented by clone D11 would be better adapted to survive the stress induced by cloning, which includes intracellular development in the mammalian cell. Karyotype polymorphism could be part of the T. cruzi arsenal for responding to environmental pressure.
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Affiliation(s)
- Fabio Mitsuo Lima
- Departamento de Microbiologia, Imunologia e Parasitologia, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, São Paulo, Brazil
| | - Renata Torres Souza
- Departamento de Microbiologia, Imunologia e Parasitologia, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, São Paulo, Brazil
| | - Fábio Rinaldo Santori
- Skirball Institute of Biomolecular Medicine, New York University Cancer Center, New York University School of Medicine, New York, New York, United States of America
| | - Michele Fernandes Santos
- Departamento de Microbiologia, Imunologia e Parasitologia, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, São Paulo, Brazil
| | - Danielle Rodrigues Cortez
- Departamento de Microbiologia, Imunologia e Parasitologia, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, São Paulo, Brazil
| | - Roberto Moraes Barros
- Departamento de Microbiologia, Imunologia e Parasitologia, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, São Paulo, Brazil
| | - Maria Isabel Cano
- Departamento de Genética, Instituto de Biociências, Universidade Estadual Paulista Júlio de Mesquita Filho, Botucatu, São Paulo, Brazil
| | - Helder Magno Silva Valadares
- Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
- Campus Centro-Oeste Dona Lindu, Universidade Federal de São João del-Rey, Divinópolis, Minas Gerais, Brazil
| | - Andréa Mara Macedo
- Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Renato Arruda Mortara
- Departamento de Microbiologia, Imunologia e Parasitologia, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, São Paulo, Brazil
| | - José Franco da Silveira
- Departamento de Microbiologia, Imunologia e Parasitologia, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, São Paulo, Brazil
- * E-mail:
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Mannaert A, Downing T, Imamura H, Dujardin JC. Adaptive mechanisms in pathogens: universal aneuploidy in Leishmania. Trends Parasitol 2012; 28:370-6. [PMID: 22789456 DOI: 10.1016/j.pt.2012.06.003] [Citation(s) in RCA: 82] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2012] [Revised: 06/14/2012] [Accepted: 06/14/2012] [Indexed: 02/07/2023]
Abstract
Genomic stability and maintenance of the correct chromosome number are assumed to be essential for normal development in eukaryotes. Aneuploidy is usually associated with severe abnormalities and decrease of cell fitness, but some organisms appear to rely on aneuploidy for rapid adaptation to changing environments. This phenomenon is mostly described in pathogenic fungi and cancer cells. However, recent genome studies highlight the importance of Leishmania as a new model for studies on aneuploidy. Several reports revealed extensive variation in chromosome copy number, indicating that aneuploidy is a constitutive feature of this protozoan parasite genus. Aneuploidy appears to be beneficial in organisms that are primarily asexual, unicellular, and that undergo sporadic epidemic expansions, including common pathogens as well as cancer.
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Affiliation(s)
- An Mannaert
- Unit of Molecular Parasitology, Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
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Raymond F, Boisvert S, Roy G, Ritt JF, Légaré D, Isnard A, Stanke M, Olivier M, Tremblay MJ, Papadopoulou B, Ouellette M, Corbeil J. Genome sequencing of the lizard parasite Leishmania tarentolae reveals loss of genes associated to the intracellular stage of human pathogenic species. Nucleic Acids Res 2011; 40:1131-47. [PMID: 21998295 PMCID: PMC3273817 DOI: 10.1093/nar/gkr834] [Citation(s) in RCA: 118] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
The Leishmania tarentolae Parrot-TarII strain genome sequence was resolved to an average 16-fold mean coverage by next-generation DNA sequencing technologies. This is the first non-pathogenic to humans kinetoplastid protozoan genome to be described thus providing an opportunity for comparison with the completed genomes of pathogenic Leishmania species. A high synteny was observed between all sequenced Leishmania species. A limited number of chromosomal regions diverged between L. tarentolae and L. infantum, while remaining syntenic to L. major. Globally, >90% of the L. tarentolae gene content was shared with the other Leishmania species. We identified 95 predicted coding sequences unique to L. tarentolae and 250 genes that were absent from L. tarentolae. Interestingly, many of the latter genes were expressed in the intracellular amastigote stage of pathogenic species. In addition, genes coding for products involved in antioxidant defence or participating in vesicular-mediated protein transport were underrepresented in L. tarentolae. In contrast to other Leishmania genomes, two gene families were expanded in L. tarentolae, namely the zinc metallo-peptidase surface glycoprotein GP63 and the promastigote surface antigen PSA31C. Overall, L. tarentolae's gene content appears better adapted to the promastigote insect stage rather than the amastigote mammalian stage.
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Affiliation(s)
- Frédéric Raymond
- Infectious Disease Research Centre, CHUL Research Centre (CHUQ), Quebec City,Quebec, Canada
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The challenge of Chagas’ disease: Has the human pathogen, Trypanosoma cruzi, learned how to modulate signaling events to subvert host cells? N Biotechnol 2010; 27:837-43. [DOI: 10.1016/j.nbt.2010.02.003] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2009] [Accepted: 02/14/2010] [Indexed: 12/20/2022]
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Matsunaga S, Endo T, Yagita K, Hirukawa Y, Tomino S, Matsugo S, Tsuruhara T. Chromosome size polymorphisms in the genus acanthamoeba electrokaryotype by pulsed-field gel electrophoresis. Protist 2009. [PMID: 23194715 DOI: 10.1016/s1434-4610(98)70039-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Twenty-eight strains from 12 species from the genus Acanthamoeba, including five isolates from amoebic keratitis patients, were subjected to molecular karyotyping by pulsed-field gel electrophoresis. 9 to 21 chromosome-sized DNA bands ranging from 200 kb to 3 Mb in size were detected. Molecular karyotypes also showed a wide multifariousness, i.e. there existed inter- and intraspecific heterogeneity. The five isolates from amoebic keratitis patients did not exhibit characteristic molecular karyotypes distinguishable from environmental isolates. Although karyotypic heterogeneity was observed within group I amoeba, they are distinguishable from those of group II and III. Strains having identical restriction fragment length polymorphism profiles of mtDNA did not have an identical molecular karyotype, i.e. weak correlation was found between molecular karyotypes and mtDNA restriction fragment length polymorphism profiles.
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Affiliation(s)
- S Matsunaga
- Department of Biology, Tokyo Gakugei University, Koganei-shi, Tokyo 184-8501, Japan
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Ubeda JM, Légaré D, Raymond F, Ouameur AA, Boisvert S, Rigault P, Corbeil J, Tremblay MJ, Olivier M, Papadopoulou B, Ouellette M. Modulation of gene expression in drug resistant Leishmania is associated with gene amplification, gene deletion and chromosome aneuploidy. Genome Biol 2008; 9:R115. [PMID: 18638379 PMCID: PMC2530873 DOI: 10.1186/gb-2008-9-7-r115] [Citation(s) in RCA: 130] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2008] [Revised: 06/06/2008] [Accepted: 07/18/2008] [Indexed: 12/02/2022] Open
Abstract
Gene expression and DNA copy number analyses using full genome oligonucleotide microarrays of Leishmania reveal molecular mechanisms of methotrexate resistance. Background Drug resistance can be complex, and several mutations responsible for it can co-exist in a resistant cell. Transcriptional profiling is ideally suited for studying complex resistance genotypes and has the potential to lead to novel discoveries. We generated full genome 70-mer oligonucleotide microarrays for all protein coding genes of the human protozoan parasites Leishmania major and Leishmania infantum. These arrays were used to monitor gene expression in methotrexate resistant parasites. Results Leishmania is a eukaryotic organism with minimal control at the level of transcription initiation and few genes were differentially expressed without concomitant changes in DNA copy number. One exception was found in Leishmania major, where the expression of whole chromosomes was down-regulated. The microarrays highlighted several mechanisms by which the copy number of genes involved in resistance was altered; these include gene deletion, formation of extrachromosomal circular or linear amplicons, and the presence of supernumerary chromosomes. In the case of gene deletion or gene amplification, the rearrangements have occurred at the sites of repeated (direct or inverted) sequences. These repeats appear highly conserved in both species to facilitate the amplification of key genes during environmental changes. When direct or inverted repeats are absent in the vicinity of a gene conferring a selective advantage, Leishmania will resort to supernumerary chromosomes to increase the levels of a gene product. Conclusion Aneuploidy has been suggested as an important cause of drug resistance in several organisms and additional studies should reveal the potential importance of this phenomenon in drug resistance in Leishmania.
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Affiliation(s)
- Jean-Michel Ubeda
- Université Laval, Division de Microbiologie, Centre de Recherche en Infectiologie, boulevard Laurier, Québec, G1V 4G2, Canada.
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Murta SMF, Krieger MA, Montenegro LR, Campos FFM, Probst CM, Avila AR, Muto NH, de Oliveira RC, Nunes LR, Nirdé P, Bruna-Romero O, Goldenberg S, Romanha AJ. Deletion of copies of the gene encoding old yellow enzyme (TcOYE), a NAD(P)H flavin oxidoreductase, associates with in vitro-induced benznidazole resistance in Trypanosoma cruzi. Mol Biochem Parasitol 2006; 146:151-62. [PMID: 16442642 DOI: 10.1016/j.molbiopara.2005.12.001] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2005] [Revised: 07/27/2005] [Accepted: 12/06/2005] [Indexed: 10/25/2022]
Abstract
Old yellow enzyme (OYE) is a NAD(P)H flavin oxidoreductase that in Trypanosoma cruzi (TcOYE) catalyzes prostaglandin PGF2alpha synthesis and reduction of some trypanocidal drugs. We performed DNA microarray analysis and it revealed that the levels of transcription of the TcOYE gene were six-fold lower in a T. cruzi population with in vitro-induced resistance to benznidazole (BZ) (17LER) than in the wild-type (17WTS). Further we investigated the TcOYE levels in 15 T. cruzi strains and clones that were either susceptible or naturally resistant to BZ and nifurtimox, or had in vivo-selected resistance to BZ. Northern blot and real-time RT-PCR analyses confirmed our finding that TcOYE transcription levels were lower in 17LER than in 17WTS. In contrast, we detected no differences in TcOYE transcription levels between other T. cruzi samples. All T. cruzi strains contained four copies of TcOYE gene, except 17LER that contained only one. A 42kDa TcOYE protein was detected in all T. cruzi strains tested. The expression of this protein was similar for all samples, with the exception of 17LER for which the protein was nearly seven-fold less expressed. The chromosomal location of the TcOYE gene and the polymorphisms detected in TcOYE nucleotide and amino acid sequences of the T. cruzi strains are associated with the zymodeme but not with drug-resistance phenotype. Our data show that one of the mechanisms conferring in vitro-induced BZ resistance to T. cruzi correlates with deletion of copies of the TcOYE gene. In contrast, the in vivo and natural resistance to BZ are mediated by different mechanisms.
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13
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Abstract
The genome of Leishmania is quite plastic. Chromosomal rearrangements and DNA amplifications are common events in all the species of the genus. Gene amplification occurs both as a mechanism of drug resistance and in the absence of drug pressure. The best known spontaneous amplification in Leishmania is the so-called LD1 family of amplicons. In the past few years there have been great advances in our knowledge of LD1 elements; here, Manuel Segovia and Ginés Ortiz review all the available data.
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Affiliation(s)
- M Segovia
- Departamento de Genética y Microbiología, Facultad de Medicina, Universidad de Murcia, Spain.
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14
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Genest PA, ter Riet B, Dumas C, Papadopoulou B, van Luenen HGAM, Borst P. Formation of linear inverted repeat amplicons following targeting of an essential gene in Leishmania. Nucleic Acids Res 2005; 33:1699-709. [PMID: 15781496 PMCID: PMC1069007 DOI: 10.1093/nar/gki304] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Attempts to inactivate an essential gene in the protozoan parasite Leishmania have often led to the generation of extra copies of the wild-type alleles of the gene. In experiments with Leishmania tarentolae set up to disrupt the gene encoding the J-binding protein 1 (JBP1), a protein binding to the unusual base beta-D-glucosyl-hydroxymethyluracil (J) of Leishmania, we obtained JBP1 mutants containing linear DNA elements (amplicons) of approximately 100 kb. These amplicons consist of a long inverted repeat with telomeric repeats at both ends and contain either the two different targeting cassettes used to inactivate JBP1, or one cassette and one JBP1 gene. Each long repeat within the linear amplicons corresponds to sequences covering the JBP1 locus, starting at the telomeres upstream of JBP1 and ending in a approximately 220 bp sequence repeated in an inverted (palindromic) orientation downstream of the JBP1 locus. We propose that these amplicons have arisen by a template switch inside a DNA replication fork involving the inverted DNA repeats and helped by the gene targeting.
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Affiliation(s)
| | | | - Carole Dumas
- Faculty of Medicine, Department of Medical Biology, Laval University, Infectious Disease Research Center, RC709, CHUL Research Center (CHUQ)2705 blvd Laurier, Quebec, Canada G1V 4G2
| | - Barbara Papadopoulou
- Faculty of Medicine, Department of Medical Biology, Laval University, Infectious Disease Research Center, RC709, CHUL Research Center (CHUQ)2705 blvd Laurier, Quebec, Canada G1V 4G2
| | | | - Piet Borst
- To whom correspondence should be addressed. Tel: +31 020 512 2880; Fax: +31 020 669 1383;
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15
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Yu MC, Orlando TC, Sturm NR, Zhou L, Saito RM, Floeter-Winter LM, Campbell DA. Two distinct functional spliced leader RNA gene arrays in Leishmania tarentolae are found in several lizard Leishmania species. Int J Parasitol 2002; 32:1411-22. [PMID: 12350376 DOI: 10.1016/s0020-7519(02)00131-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
A second distinct array of spliced leader RNA genes has been found in several Leishmania species particular to lizards. This is the first report of two non-allelic arrays of spliced leader RNA genes within a species cell line. The arrays are identical to each other in their transcribed spliced leader RNA gene sequences, but variable in their non-transcribed spacer sequences. In the two arrays from Leishmania tarentolae UC strain the promoter regions are similar, but not identical, at positions shown previously to be critical for spliced leader RNA transcription. These arrays contain similar numbers of genes and are both transcribed in L. tarentolae in vitro transcription extract as well as in vivo. The -66/-58 regions of both genes, which contain an element of the spliced leader RNA gene promoter, bind proteins likely to be transcription factors in a specific manner. A survey of lizard Leishmania spp. revealed a second spliced leader RNA gene array in three of four species. Phylogenetic analyses of these sequences with each other and with the spliced leader RNA gene sequences of non-lizard Leishmania spp. and their near-relatives showed that the lizard groups are more closely related to each other than to arrays from other Leishmania spp. As the transcripts of the two arrays are identical, they may co-exist to fulfil the substantial requirement for spliced leader RNA production; however, they have the potential for differential usage modulated by their distinct promoter elements. The presence of two distinct spliced leader RNA gene arrays within a single cell type may represent dissociated evolution of two redundant loci, or a previously unsuspected level of control in the post-transcriptional gene expression within some kinetoplastids.
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Affiliation(s)
- Michael C Yu
- Department of Microbiology, Immunology and Molecular Genetics, School of Medicine, 10833 Le Conte Avenue, University of California, Los Angeles, CA 90095-1747, USA
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16
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Murta SM, dos Santos WG, Anacleto C, Nirdé P, Moreira ES, Romanha AJ. Drug resistance in Trypanosoma cruzi is not associated with amplification or overexpression of P-glycoprotein (PGP) genes. Mol Biochem Parasitol 2001; 117:223-8. [PMID: 11606233 DOI: 10.1016/s0166-6851(01)00350-4] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Affiliation(s)
- S M Murta
- 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
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17
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Sunkin SM, McDonagh P, Cunningham ML, Beverley SM, Stuart K, Myler PJ. Conservation of the LD1 region in Leishmania includes DNA implicated in LD1 amplification. Mol Biochem Parasitol 2001; 113:315-21. [PMID: 11295186 DOI: 10.1016/s0166-6851(01)00215-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Affiliation(s)
- S M Sunkin
- Seattle Biomedical Research Institute, 4 Nickerson Street, Seattle 98109-1651, USA
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18
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Kapushoc ST, Alfonzo JD, Rubio MA, Simpson L. End processing precedes mitochondrial importation and editing of tRNAs in Leishmania tarentolae. J Biol Chem 2000; 275:37907-14. [PMID: 10993905 DOI: 10.1074/jbc.m007838200] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
All mitochondrial tRNAs in Leishmania tarentolae are encoded in the nuclear genome and imported into the mitochondrion from the cytosol. One imported tRNA (tRNA(Trp)) is edited by a C to U modification at the first position of the anticodon. To determine the in vivo substrates for mitochondrial tRNA importation as well as tRNA editing, we examined the subcellular localization and extent of 5'- and 3'-end maturation of tRNA(Trp)(CCA), tRNA(Ile)(UAU), tRNA(Gln)(CUG), tRNA(Lys)(UUU), and tRNA(Val)(CAC). Nuclear, cytosolic, and mitochondrial fractions were obtained with little cross-contamination, as determined by Northern analysis of specific marker RNAs. tRNA(Gln) was mainly cytosolic in localization; tRNA(Ile) and tRNA(Lys) were mainly mitochondrial; and tRNA(Trp) and tRNA(Val) were shared between the two compartments. 5'- and 3'-extended precursors of all five tRNAs were present only in the nuclear fraction, suggesting that the mature tRNAs represent the in vivo substrates for importation into the mitochondrion. Consistent with this model, T7-transcribed mature tRNA(Ile) underwent importation in vitro into isolated mitochondria more efficiently than 5'-extended precursor tRNA(Ile). 5'-Extended precursor tRNA(Trp) was found to be unedited, which is consistent with a mitochondrial localization of this editing reaction. T7-transcribed unedited tRNA(Trp) was imported in vitro more efficiently than edited tRNA(Trp), suggesting the presence of importation determinants in the anticodon.
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Affiliation(s)
- S T Kapushoc
- Departments of Molecular, Cell, and Developmental Biology and Microbiology, Immunology, and Molecular Genetics and the Howard Hughes Medical Institute, University of California, Los Angeles, California 90095, USA
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19
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Sunkin SM, Kiser P, Myler PJ, Stuart K. The size difference between leishmania major friedlin chromosome one homologues is localized to sub-telomeric repeats at one chromosomal end. Mol Biochem Parasitol 2000; 109:1-15. [PMID: 10924752 DOI: 10.1016/s0166-6851(00)00215-2] [Citation(s) in RCA: 41] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Leishmania species are members of the evolutionarily ancient protozoan order Kinetoplastidae and are important human pathogens. The Leishmania genome is relatively small (approximately 34 Mbp) and is distributed among 36 chromosome pairs, ranging in size from 0.3 to 2.5 Mbp. The smallest chromosome of Leishmania major Friedlin, chrl, consists of three homologues which differ in size by approximately 29 kb. Previous sequence and Southern analyses of all three homologues reveal a conserved chromosomal core, consisting of coding and adjacent 'non-informational' sequence. Here we show the size difference between homologues is largely restricted to variation in both the number and content of several sub-telomeric repetitive elements localized on one chromosomal end. These repetitive elements also occur on other chromosomes, but some are more dispersed in the Leishmania genome than others.
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Affiliation(s)
- S M Sunkin
- Seattle Biomedical Research Institute, WA 98109-1651, USA
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20
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Lemley C, Yan S, Dole VS, Madhubala R, Cunningham ML, Beverley SM, Myler PJ, Stuart KD. The Leishmania donovani LD1 locus gene ORFG encodes a biopterin transporter (BT1). Mol Biochem Parasitol 1999; 104:93-105. [PMID: 10589984 DOI: 10.1016/s0166-6851(99)00132-2] [Citation(s) in RCA: 56] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
We have previously described two genes, ORFF and ORFG, from the LD1 locus near one telomere of chromosome 35, which are frequently amplified in Leishmania isolates. In Leishmania donovani LSB-51.1, gene conversion of the rRNA gene locus on chromosome 27 with these two genes resulted in their over-expression, because of their transcription by the RNA polymerase I-mediated rRNA promoter. The predicted ORFG protein has substantial sequence homology to the ESAG10 gene product from the Trypanosoma brucei VSG expression site and both are putative membrane proteins. Using successive rounds of gene replacement of the three ORFG genes in L. donovani LSB-51.1, ORFG null mutants were obtained. These mutant cell lines show a direct relationship between ORFG mRNA, protein expression levels and active transport of biopterin into the cells. Transformation of the null mutant with a plasmid containing ORFG restores biopterin transport activity. In addition, the null mutants are unable to grow in the absence of supplemental biopterin. Thus, ORFG encodes a biopterin transporter and has been renamed BTI.
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Affiliation(s)
- C Lemley
- Seattle Biomedical Research Institute, WA, USA
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21
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Yurchenko V, Hobza R, Benada O, Lukes J. Trypanosoma avium: large minicircles in the kinetoplast DNA. Exp Parasitol 1999; 92:215-8. [PMID: 10403763 DOI: 10.1006/expr.1999.4418] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Affiliation(s)
- V Yurchenko
- Institute of Parasitology, Czech Academy of Sciences, Czech Republic
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22
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Grondin K, Kündig C, Roy G, Ouellette M. Linear amplicons as precursors of amplified circles in methotrexate-resistant Leishmania tarentolae. Nucleic Acids Res 1998; 26:3372-8. [PMID: 9649621 PMCID: PMC147699 DOI: 10.1093/nar/26.14.3372] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Gene amplification is frequently observed in Leishmania cells selected for drug resistance. By gene targeting we have tagged both alleles of the H locus of Leishmania tarentolae with the neomycin and hygromycin phosphotransferase genes ( neo and hyg ). Selection of these recombinant parasites for low level methotrexate resistance led to amplification of the H locus as part of linear amplicons. The availability of tags has permitted us to determine that both alleles can be amplified in the same cell and that chromosomal deletions are frequent. When methotrexate concentration was increased in subsequent selection steps, circles were observed in several mutants. We have introduced a hyg marker into linear amplicons to test whether the circles originated from linear amplicons. After selection with a high methotrexate concentration, circles with the hyg marker were observed, showing that circles can indeed be formed from linear amplicons. The tagging of H locus alleles permits appreciation of the extent of genetic rearrangements leading to amplicon formation in Leishmania cells selected for drug resistance.
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Affiliation(s)
- K Grondin
- Centre de Recherche en Infectiologie du CHUL and Département de Biologie Médicale, Division de Microbiologie, Faculté de Médecine, Université Laval, Québec, Canada
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23
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Grondin K, Kundig C, Roy G, Ouellette M. Linear amplicons as precursors of amplified circles in methotrexate-resistant Leishmania tarentolae. Nucleic Acids Res 1998. [DOI: 10.1093/nar/26.14.3370] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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24
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Lukescaron J, Jirkû M, Avliyakulov N, Benada O. Pankinetoplast DNA structure in a primitive bodonid flagellate, Cryptobia helicis. EMBO J 1998; 17:838-46. [PMID: 9451008 PMCID: PMC1170432 DOI: 10.1093/emboj/17.3.838] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The mitochondrial DNA (mtDNA) of a primitive kinetoplastid flagellate Cryptobia helicis is composed of 4.2 kb minicircles and 43 kb maxicircles. 85% and 6% of the minicircles are in the form of supercoiled (SC) and relaxed (OC) monomers, respectively. The remaining minicircles (9%) constitute catenated oligomers composed of both the SC and OC molecules. Minicircles contain bent helix and sequences homologous to the minicircle conserved sequence blocks. Maxicircles encode typical mitochondrial genes and are not catenated. The mtDNA, which we describe with the term 'pankinetoplast DNA', is spread throughout the mitochondrial lumen, where it is associated with multiple electron-lucent loci. There are approximately 8400 minicircles per pankinetoplast-mitochondrion, with the pan-kDNA representing approximately 36% of the total cellular DNA. Based on the similarity of the C.helicis minicircles to plasmids, we present a theory on the formation of the kDNA network.
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Affiliation(s)
- J Lukescaron
- Institute of Parasitology, Czech Academy of Sciences, Czech Republic.
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25
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Hwang HY, Gilberts T, Jardim A, Shih S, Ullman B. Creation of homozygous mutants of Leishmania donovani with single targeting constructs. J Biol Chem 1996; 271:30840-6. [PMID: 8940067 DOI: 10.1074/jbc.271.48.30840] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Homozygous null mutants of the hypoxanthine-guanine phosphoribosyltransferase (hgprt) and adenine phosphoribosyltransferase (aprt) loci were created in Leishmania donovani in which both alleles were eliminated using only a single targeting construct. Functional heterozygotes were first generated by homologous recombination after transfection with vectors containing 5'- and 3'-flanking regions of either the hgprt or the aprt gene circumscribing drug resistance markers. Homozygous null mutants were then isolated from the heterozygotes by negative selection in media containing subversive substrates of the encoded proteins, i.e. allopurinol for HGPRT and 4-aminopyrazolopyrimidine for APRT. The novel alleles created by homologous recombination were verified by Southern blotting, and the effects of gene replacement upon gene expression in intact parasites were evaluated by direct enzymatic assay and by immunoblotting. All mutant strains were viable under the selection conditions and exhibited appropriate drug resistance phenotypes. The ability to generate homozygous knockouts with single targeting constructs greatly facilitates the genetic dissection and subsequent biochemical investigations of the purine pathway in Leishmania and has important general implications for the genetic manipulation and analysis of the leishmanial genome.
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Affiliation(s)
- H Y Hwang
- Department of Biochemistry and Molecular Biology, Oregon Health Sciences University, Portland, Oregon 97201-3098, USA.
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26
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Gueiros-Filho FJ, Beverley SM. Selection against the dihydrofolate reductase-thymidylate synthase (DHFR-TS) locus as a probe of genetic alterations in Leishmania major. Mol Cell Biol 1996; 16:5655-63. [PMID: 8816478 PMCID: PMC231565 DOI: 10.1128/mcb.16.10.5655] [Citation(s) in RCA: 67] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
The genome of the trypanosomatid protozoan genus Leishmania has been shown to undergo a number of changes relevant to drug resistance and virulence, such as gene amplification, chromosomal rearrangement, and variation in ploidy. Experimental approaches to the study of genomic changes have in some cases been limited by the fact that Leishmania cells are asexual diploids, as are some other trypanosomatids, pathogenic fungi, and cultured mammalian cells. Here we report upon a system which permits the measurement of several types of genomic change occurring at the dihydrofolate reductase-thymidylate synthase (DHFR-TS) locus. First, we show that DHFR-TS can function as a positive/negative marker. We used selection against DHFR-TS on a heterozygous line (+/HYG) to generate colonies exhibiting both loss of heterozygosity and structural mutations in DHFR-TS, permitting the first measurement of mutation frequencies in this parasite. Loss of heterozygosity occurred at a frequency ranging from 10(-4) to 10(-6) and was elevated 24-fold by treatment with gamma-irradiation, while the frequency of other events was less than 10(-6) and was increased more than 1,000-fold by nitrosoguanidine treatment. The frequency of loss of heterozygosity relative to other processes such as mutation and gene replacement has important implications for genetic variability in natural Leishmania populations and the generation of both targeted and random mutations. We also developed a protocol for null targeting of diploid cells, in which transfection of a DHFR-TS deletion construct into Leishmania cells followed by negative selection yielded parasites lacking DHFR-TS or foreign sequences. The null-targeting method can be applied to any diploid cell, at any locus for which a negative selection exists. Such marker-free auxotrophic Leishmania cells show potential as an attenuated vaccine, and the methods developed here provide a new approach for manipulating and characterizing the plasticity of the Leishmania genome.
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Affiliation(s)
- F J Gueiros-Filho
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, USA
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27
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Patnaik PK, Axelrod N, Van der Ploeg LH, Cross GA. Artificial linear mini-chromosomes for Trypanosoma brucei. Nucleic Acids Res 1996; 24:668-75. [PMID: 8604308 PMCID: PMC145704 DOI: 10.1093/nar/24.4.668] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
We have constructed artificial linear mini- chromosomes for the parasitic protozoan Trypanosoma brucei. These chromosomes exist at approx. 2 copies per cell, are indefinitely stable under selection but are lost from 50% of the transformed population in approx. 7 generations when grown in the absence of selective pressure. Consistent with results obtained earlier with natural chromosomes in T.brucei, the telomeres on these artificial chromosomes grow, adding approx. 1- 1.5 telomeric repeats per generation. The activity of a procyclic acidic repetitive protein (parp) gene promoter on these elements is unaffected by its proximity to a telomere, implying the lack of a telomere-proximal position effect (TPE) in procyclic trypanosomes. Among other things, these autonomously replicating dispensable genetic elements will provide a defined system for the study of nuclear DNA replication, karyotypic plasticity and other aspects of chromosomal behavior in this ancient eukaryotic lineage.
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Affiliation(s)
- P K Patnaik
- Laboratory of Molecular Parasitology, The Rockefeller University, New York, NY 10021-6399 USA
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28
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Olmo A, Arrebola R, Bernier V, González-Pacanowska D, Ruiz-Pérez LM. Co-existence of circular and multiple linear amplicons in methotrexate-resistant Leishmania. Nucleic Acids Res 1995; 23:2856-64. [PMID: 7659507 PMCID: PMC307122 DOI: 10.1093/nar/23.15.2856] [Citation(s) in RCA: 25] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Circular and linear amplicons were analyzed in detail in Leishmania tropica cells resistant to methotrexate (MTX). Both types of elements presented sequences related to the H locus and coexisted in resistant cells. The linear amplicons appeared first during the selection process (at 10 microM MTX) and varied with regard to size and structure in cells exposed to increasing concentrations of drug. The circular element was evident at higher concentrations (50 microMs) but was the major amplified DNA in cells resistant to 1000 microM MTX while the level of amplification of the linear elements remained low. The extrachromosomal DNAs were unstable in the absence of drug and their disappearance coincided with an increase in sensitivity to MTX. Mapping of the minichromosomes and the circular element showed that they were all constituted by inverted duplications. The circular amplicon contained an inverted repeat derived from the H locus that encompassed the pteridine reductase gene (PTR1) responsible for MTX resistance. The amplified segment in the linear amplicons was longer and included the pgpB and pgpC genes that encode P-glycoproteins of unknown function previously characterized in different Leishmania species.
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Affiliation(s)
- A Olmo
- Instituto de Parasitología y Biomedicina, Consejo Superior de Investigaciones Científicas, Granada, Spain
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29
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Lanzer M, Fischer K, Le Blancq SM. Parasitism and chromosome dynamics in protozoan parasites: is there a connection? Mol Biochem Parasitol 1995; 70:1-8. [PMID: 7637690 DOI: 10.1016/0166-6851(95)00021-r] [Citation(s) in RCA: 68] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Genomic plasticity is a hallmark of many protozoan parasites, including Plasmodium spp, Trypanosoma spp, Leishmania ssp and Giardia lamblia. Strikingly, there is a common theme regarding the structural basis of this karyotype variability. Chromosomes are compartmentalized into conserved central domains and polymorphic chromosome ends. Since antigen-encoding genes frequently reside in telomere-proximal domains, it is tempting to speculate that the genetic flexibility of chromosome ends has been recruited as a tool in immune evasion strategies by some parasitic protozoa.
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Affiliation(s)
- M Lanzer
- Zentrum für Infektionsforschung, Würzburg, Germany
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30
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RNA editing and mitochondrial genomic organization in the cryptobiid kinetoplastid protozoan Trypanoplasma borreli. Mol Cell Biol 1994. [PMID: 7969154 DOI: 10.1128/mcb.14.12.8174] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The bodonids and cryptobiids represent an early diverged sister group to the trypanosomatids among the kinetoplastid protozoa. The trypanosome type of uridine insertion-deletion RNA editing was found to occur in the cryptobiid fish parasite Trypanoplasma borreli. A pan-edited ribosomal protein, S12, and a novel 3'- and 5'-edited cytochrome b, in addition to an unedited cytochrome oxidase III gene and an apparently unedited 12S rRNA gene, were found in a 6-kb fragment of the 80- to 90-kb mitochondrial genome. The gene order differs from that in trypanosomatids, as does the organization of putative guide RNA genes; guide RNA-like molecules are transcribed from tandemly repeated 1-kb sequences organized in 200- and 170-kb molecules instead of minicircles. The presence of pan-editing in this lineage is consistent with an ancient evolutionary origin of this process.
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31
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Maslov DA, Simpson L. RNA editing and mitochondrial genomic organization in the cryptobiid kinetoplastid protozoan Trypanoplasma borreli. Mol Cell Biol 1994; 14:8174-82. [PMID: 7969154 PMCID: PMC359356 DOI: 10.1128/mcb.14.12.8174-8182.1994] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
The bodonids and cryptobiids represent an early diverged sister group to the trypanosomatids among the kinetoplastid protozoa. The trypanosome type of uridine insertion-deletion RNA editing was found to occur in the cryptobiid fish parasite Trypanoplasma borreli. A pan-edited ribosomal protein, S12, and a novel 3'- and 5'-edited cytochrome b, in addition to an unedited cytochrome oxidase III gene and an apparently unedited 12S rRNA gene, were found in a 6-kb fragment of the 80- to 90-kb mitochondrial genome. The gene order differs from that in trypanosomatids, as does the organization of putative guide RNA genes; guide RNA-like molecules are transcribed from tandemly repeated 1-kb sequences organized in 200- and 170-kb molecules instead of minicircles. The presence of pan-editing in this lineage is consistent with an ancient evolutionary origin of this process.
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Affiliation(s)
- D A Maslov
- Department of Biology, University of California, Los Angeles 90024-1606
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32
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Wilson K, Berens RL, Sifri CD, Ullman B. Amplification of the inosinate dehydrogenase gene in Trypanosoma brucei gambiense due to an increase in chromosome copy number. J Biol Chem 1994. [DOI: 10.1016/s0021-9258(19)62002-8] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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33
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Myler PJ, Lodes MJ, Merlin G, de Vos T, Stuart KD. An amplified DNA element in Leishmania encodes potential integral membrane and nucleotide-binding proteins. Mol Biochem Parasitol 1994; 66:11-20. [PMID: 7984172 DOI: 10.1016/0166-6851(94)90031-0] [Citation(s) in RCA: 26] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
LD1 is a 27.5-kb sequence that occurs in an approx. 2.2-Mb chromosome in all species and strains of Leishmania. In Leishmania infantum MHOM/BL/67/ITMAP263, LD1 is also present as an inverted dimeric repeat in multicopy, 55-kb circular molecules. Sequence analysis of a 7873-nt segment derived from the circular DNA reveals 4 open reading frames (ORFs) with potential protein coding function. One ORF predicts a protein with an ATP/GTP binding site motif. Another ORF predicts a protein with 10-12 potential membrane-spanning domains, suggesting that it encodes an integral membrane protein. This protein also has homology with that predicted by the ESAG10 gene of Trypanosoma brucei.
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Affiliation(s)
- P J Myler
- Seattle Biomedical Research Institute, WA 98109-1651
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34
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Alves AM, De Almeida DF, von Krüger WM. Changes in Trypanosoma cruzi kinetoplast DNA minicircles induced by environmental conditions and subcloning. J Eukaryot Microbiol 1994; 41:415-9. [PMID: 8087110 DOI: 10.1111/j.1550-7408.1994.tb06099.x] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Reversible changes in kinetoplast DNA (kDNA) minicircles sequences were observed in clones of Trypanosoma cruzi strain Y, following a number of passages during exponential growth phase or after subcloning in blood-free medium. kDNA restriction patterns of clones were similar to those of the original uncloned strain, while subclones presented distinct kDNA restriction patterns. Homology experiments demonstrated strong hybridization between kDNA with the same electrophoretic mobility patterns while only weak signals were observed with kDNA of different patterns. The changes observed, which are unprecedented in T. cruzi clones, characterize transkinetoplastidy, and seem to be associated with similarly reversible changes both in zymodeme and in infectivity.
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Affiliation(s)
- A M Alves
- Laboratório de Fisiologia Celular, Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Brazil
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35
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Fleischmann J, Campbell DA. Expression of the Leishmania tarentolae ubiquitin-encoding and mini-exon genes. Gene X 1994; 144:45-51. [PMID: 8026757 DOI: 10.1016/0378-1119(94)90201-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
To develop models for transcription and trans-splicing in kinetoplastid protozoa, we have characterized ubiquitin (Ubi) gene organization and mRNA processing in Leishmania tarentolae (Lt). Three ubi loci were characterized: two discrete Ubi-extension protein 52 (EP52)-encoding genes (ubiA and ubiB) and a polymorphic polyubiquitin-encoding gene (ubiC). The three loci resided on chromosomes of 2.05 Mb, 630 kb and 2.9 Mb, respectively. On the basis of upstream flanking gene identity, ubiB appears to be the homologue of the tandemly repeated ubi-EP52/1 and 2 in Trypanosoma brucei (Tb). Similar to Trypanosoma cruzi, Lt did not contain a homologue of the ubi-EP76 that has been found in Saccharomyces cerevisiae and multicellular organisms. All three Lt ubi loci were transcribed. The primary transcripts from the ubi loci were processed at the 5'-end by trans-splicing with the mini-exon. A Lt mini-exon gene (min) that gave rise to a 95-nt primary transcript, which is the second template in the trans-splicing reaction, was also characterized.
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Affiliation(s)
- J Fleischmann
- Department of Microbiology and Immunology, University of California, Los Angeles 90024
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Cappai R, Morris L, Aebischer T, Bacic A, Curtis JM, Kelleher M, McLeod KS, Moody SF, Osborn AH, Handman E. Ricin-resistant mutants of Leishmania major which express modified lipophosphoglycan remain infective for mice. Parasitology 1994; 108 ( Pt 4):397-405. [PMID: 8008453 DOI: 10.1017/s0031182000075946] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Glycosylation variants of the virulent Leishmania major clone V121 were generated by mutagenesis with N-methyl-N-nitroso-N-nitroguanidine and selected using the galactose-specific lectin Ricinus communis II (RCA II). Three mutants, 4B9, 1D1 and 1C12, which failed to bind RCA II, were found to have an altered expression of lipophosphoglycan (LPG), a molecule implicated in the attachment to host macrophages and survival within the phagolysosome. There were differences in the antigenicity, molecular weight and localization of LPG from mutant parasites as compared to V121. Expression of gp63, a surface molecule also implicated in attachment to macrophages, was unaltered. All 3 mutants caused disease when injected into genetically susceptible BALB/c mice but lesions developed at a much slower rate than those caused by the virulent V121 clone. This slow rate of lesion development did not correlate with promastigotes' ability to invade macrophages in vitro. Karyotype analysis showed that there was a reduction in the size of chromosome band number 2 in all 3 mutants. The differences in LPG and chromosome band 2 were retained by mutant clones following passage through mice, suggesting that these phenotypes are stable. Although the mutant parasites were infective and caused lesions, the changed structure of the LPG appeared to influence the virulence of the parasites.
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Affiliation(s)
- R Cappai
- Walter and Eliza Hall Institute of Medical Research, Royal Melbourne Hospital, Victoria, Australia
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37
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Papadopoulou B, Roy G, Ouellette M. Autonomous replication of bacterial DNA plasmid oligomers in Leishmania. Mol Biochem Parasitol 1994; 65:39-49. [PMID: 7935627 DOI: 10.1016/0166-6851(94)90113-9] [Citation(s) in RCA: 72] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Extrachromosomal amplicons are frequently observed in drug-resistant Leishmania. A dominant selectable marker, the neomycin phosphotransferase gene, was introduced by gene targeting in a circular amplicon derived from the H locus of Leishmania in a mutant cell. This recombinant amplicon was isolated and transfected in a wild-type cell. The amplicon was kept in the wild-type cells, provided the selective pressure was maintained, suggesting that it was capable of autonomous replication. Novel Leishmania expression vectors suited for stable transfections were made to isolate, by a high transformation assay, the putative origin of replication in the amplicons. However, these plasmids, which did not contain a single Leishmania nucleotide, were found as extrachromosomal circular oligomers in Leishmania transfectants. Their relative stability, in addition to changes in their methylation pattern, indicated that these plasmids were most likely replicating. No specific sequences seem to be required for replication (and expression) in Leishmania, therefore precluding the isolation of origins of replication by genetic transformation.
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Eresh S, Mendoza-Leòn A, Barker DC. A small chromosome of Leishmania (Viannia) braziliensis contains multicopy sequences which are complex specific. Acta Trop 1993; 55:33-46. [PMID: 7903136 DOI: 10.1016/0001-706x(93)90046-e] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Orthogonal Field Alternating Gel Electrophoresis (OFAGE) has been used to show a band of approximately 260 kb which is stained intensely with ethidium bromide in Leishmania (V.) braziliensis stock M2903. This small chromosome (sc-2903), as well as a 50 kb and a 200 kb chromosome seen in L. (L.) mexicana and L. (L.) amazonensis, respectively, are stably maintained and linear. When used as a hybridisation probe, sc-2903 showed homology to large chromosomal DNA bands and to a multiplicity of genomic fragments in all braziliensis stocks tested, indicating either different sequences, different copy numbers or both but no hybridisation to mexicana stocks. It is possible that these sequences are present in all members of the braziliensis complex and are not related to LD1 or any other previously published small chromosome sequences. However, at least one clone isolated from a sc-2903 library recognised genomic DNA of stocks belonging to the braziliensis, mexicana and donovani complexes. Our results suggest that the clone carries sequence(s) that are repeated and shared between stocks of different complexes but with a variable genomic distribution.
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Affiliation(s)
- S Eresh
- MRC Outstation of NIMR, Molteno Laboratories, Department of Pathology, University of Cambridge, UK
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Maslov DA, Elgort MG, Wong S, Pecková H, Lom J, Simpson L, Campbell DA. Organization of mini-exon and 5S rRNA genes in the kinetoplastid Trypanoplasma borreli. Mol Biochem Parasitol 1993; 61:127-35. [PMID: 8259125 DOI: 10.1016/0166-6851(93)90165-t] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Mini-exon gene repeats from Trypanoplasma borreli, which belongs to the Cryptobiidae family of the Bodonina suborder of the Kinetoplastida, were isolated by PCR amplification and cloning. The presence of kinetoplastid-like mini-exon genes in T. borreli is consistent with the taxonomic status of this organism as a kinetoplastid protozoan. Two families of repeats were found: 597 nt (T1) and 794 nt (T2), each of which encodes an approximately 95-nt medRNA transcript. The T1 repeats also contain a complete 5S rRNA gene on the complementary strand. The T2 repeats contain a defective copy of a 5S gene, in which the 5' portion is absent. The intergenic regions between the 5'-ends of the mini-exon genes and the 5S rRNA genes in the T1 and T2 repeats are highly diverged. All or most mini-exon genes and 5S genes are located within either the T1 or the T2 repeats. The T1 repeats were localized to a megabase-size chromosome, while the T2 repeats were localized within at least 4 large chromosomes.
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Affiliation(s)
- D A Maslov
- Department of Biology, University of California, Los Angeles 90024-1662
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40
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Petter R, Rozenblatt S, Schechtman D, Wellems TE, Mirelman D. Electrophoretic karyotype and chromosome assignments for a pathogenic and a nonpathogenic strain of Entamoeba histolytica. Infect Immun 1993; 61:3574-7. [PMID: 8335392 PMCID: PMC281045 DOI: 10.1128/iai.61.8.3574-3577.1993] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
The electrophoretic karyotypes of a pathogenic and a nonpathogenic strain of Entamoeba histolytica were determined by pulsed-field gel electrophoresis. A number of previously isolated genes were assigned to specific chromosomal bands. Significant differences between the chromosomal patterns of these strains as well as in the assignment of most genes were found.
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Affiliation(s)
- R Petter
- MacArthur Center for Molecular Biology of Parasitic Diseases, Weizmann Institute of Science, Rehovot, Israel
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41
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Grondin K, Papadopoulou B, Ouellette M. Homologous recombination between direct repeat sequences yields P-glycoprotein containing amplicons in arsenite resistant Leishmania. Nucleic Acids Res 1993; 21:1895-901. [PMID: 8098523 PMCID: PMC309430 DOI: 10.1093/nar/21.8.1895] [Citation(s) in RCA: 83] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
The protozoan parasite Leishmania often responds to drug pressure by amplifying part of its genome. At least two loci derived from the same 800 kb chromosome were amplified either as extrachromosomal circles or linear fragments after sodium arsenite selection. A 50 kb linear amplicon was detected in six independent arsenite mutants and revertants grown in absence of arsenite rapidly lost the amplicon and part of their resistance. The circular extrachromosomal amplicons, all derived from the H locus of Leishmania, were characterized more extensively. In all cases, direct repeated sequences appeared to be involved in the formation of circular amplicons. Most amplicons were generated after homologous recombination between two linked P-glycoprotein genes. This recombination event was, in two cases, associated with the loss of one allele of the chromosomal copy. A novel rearrangement point was found in a mutant where the amplicon was created by recombination between two 541 bp direct repeats surrounding the P-glycoprotein gene present at the H locus. It is also at one of these repeats that an H circle with large inverted duplications was formed. We propose that the presence of repeated sequences in the H locus facilitates the amplification of the drug resistance genes concentrated in this locus.
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Affiliation(s)
- K Grondin
- Service d'Infectiologie du Centre de Recherche du CHUL, Québec, Canada
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42
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McDaniel JP, Dvorak JA. Identification, isolation, and characterization of naturally-occurring Trypanosoma cruzi variants. Mol Biochem Parasitol 1993; 57:213-22. [PMID: 8433713 DOI: 10.1016/0166-6851(93)90197-6] [Citation(s) in RCA: 50] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Naturally occurring DNA variants of the single-cell-derived Y-02 stock of Trypanosoma cruzi were discovered during a routine assay of the stock. Three DNA variant types were isolated. One type was indistinguishable from the parental Y-02 stock on the basis of total DNA cell-1. The other two types contained approximately 30% and 70% more DNA cell-1 than the parental Y-02 stock. Both the nucleus and kinetoplast were involved in the DNA content differences. The increase in DNA cell-1 was not G-C- or A-T-specific and was unrelated to the developmental stage of the parasite. Epimastigote population doubling times, isoenzymes, and schizodeme analyses could not differentiate the variant stocks. However, marked karyotype polymorphisms were observed by pulse-field gel electrophoresis, and restriction-fragment-length-polymorphisms were detected in hybridizations of some endonuclease-restricted samples to the spliced leader probe. We postulate that the Y-02 variants are genetic homologs. The ability to form viable hybrids or aneuploids provides T. cruzi with a mechanism to survive environmental stress, promote intra-specific heterogeneity and generate the diversity observed in the presentation and course of Chagas' disease.
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Affiliation(s)
- J P McDaniel
- Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892
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Wilson K, Beverley SM, Ullman B. Stable amplification of a linear extrachromosomal DNA in mycophenolic acid-resistant Leishmania donovani. Mol Biochem Parasitol 1992; 55:197-206. [PMID: 1359409 DOI: 10.1016/0166-6851(92)90140-f] [Citation(s) in RCA: 30] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Pulsed field gel electrophoretic analysis of chromosomes of MPA100 cells, a strain of Leishmania donovani that possesses an approx. 15-fold amplified IMP dehydrogenase (IMPDH) gene copy number, revealed a new 280-kb extrachromosomal DNA, IMPDH-280, that was not present in wild type parental cells. Southern blots of these pulsed field gels revealed that the vast majority of the amplified impdh genes were localized on IMPDH-280. In addition to the 700-kb wild type chromosome, the impdh probe also recognized a 740-kb chromosome in the MPA100 genome. The pulse time-dependent relative mobility of IMPDH-280 in pulsed field gels, the failure of limited gamma-irradiation to generate a new discrete DNA fragment, and the susceptibility of IMPDH-280 to lambda-exonuclease digestion, demonstrated that IMPDH-280 was a linear molecule. IMPDH-280 was also recognized by a telomere probe but not by fragments derived from amplified DNAs found in other drug-resistant Leishmania. IMPDH-280 and the drug resistance phenotype remained stable when MPA100 cells were propagated in the absence of drug for 2 years. The appearance of IMPDH-280 in MPA100 cells represents one of the first examples of an amplification of a linear extrachromosomal DNA element mediating drug resistance in Leishmania and the first instance of a linear DNA amplification that is stable in the absence of selective pressure.
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Affiliation(s)
- K Wilson
- Department of Biochemistry and Molecular Biology, Oregon Health Sciences University, Portland 97201-3098
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