Selection for arsenite resistance causes reversible changes in minicircle composition and kinetoplast organization in Leishmania mexicana

Nuclear and mitochondrial genome sequencing of North-African Leishmania infantum isolates from cured and relapsed visceral leishmaniasis patients reveals variations correlating with geography and phenotype

Although several studies have investigated genetic diversity of Leishmania infantum in North Africa, genome-wide analyses are lacking. Here, we conducted comparative analyses of nuclear and mitochondrial genomes of seven L. infantum isolates from Tunisia with the aim to gain insight into factors that drive genomic and phenotypic adaptation. Isolates were from cured (n=4) and recurrent (n=3) visceral leishmaniasis (VL) cases, originating from northern (n=2) and central (n=5) Tunisia, where respectively stable and emerging VL foci are observed. All isolates from relapsed patients were from Kairouan governorate (Centre); one showing resistance to the anti-leishmanial drug Meglumine antimoniate. Nuclear genome diversity of the isolates was analysed by comparison to the L. infantum JPCM5 reference genome. Kinetoplast maxi and minicircle sequences (1 and 59, respectively) were extracted from unmapped reads and identified by blast analysis against public data sets. The genome variation analysis grouped together isolates from the same geographical origins. Strains from the North were very different from the reference showing more than 34 587 specific single nucleotide variants, with one isolate representing a full genetic hybrid as judged by variant frequency. Composition of minicircle classes within isolates corroborated this geographical population structure. Read depth analysis revealed several significant gene copy number variations correlating with either geographical origin (amastin and Hsp33 genes) or relapse (CLN3 gene). However, no specific gene copy number variation was found in the drug-resistant isolate. In contrast, resistance was associated with a specific minicircle pattern suggesting Leishmania mitochondrial DNA as a potential novel source for biomarker discovery.

Analysis of Kinetoplast DNA from Mexican Isolates of Leishmania (L.) mexicana

This study analyzed DNA minicircles of Mexican isolates of L. (Leishmania) mexicana to look for genetic differences between strains isolated from patients with diffuse cutaneous (DCL) and localized (LCL) leishmaniasis. The kDNA was analyzed using polymerase chain reaction (PCR), restriction fragment polymorphism analysis of the PCR products (PCR-RFLP) and the PCR products were sequenced. In the PCR with primers specific for the subgenus Leishmania, the Mexican isolates gave higher amplification products than the other L. mexicana complex strains and with specific primers for the L. mexicana complex they were poorly amplified. In the PCR-RFLP analysis with the Eco RV, Hae III, and Mbo I endonucleases, the Mexican isolates displayed similar restriction patterns, but different from the patterns of the other members of the L. mexicana complex. In the phylogenetic tree constructed, the kDNA sequences of the Mexican clones formed two groups including sequences of LCD or LCL clones, apart from the other L. mexicana complex members. These results suggest that the kDNA minicircles of the Mexican isolates are more polymorphic than the kDNA of other members of the L. mexicana complex and have different recognition sites for the restriction enzymes used in this study.

Two distinct arsenite-resistant variants of Leishmania amazonensis take different routes to achieve resistance as revealed by comparative transcriptomics

Genome-wide search for the genes involved in arsenite resistance in two distinct variants A and A' of Leishmania amazonensis revealed that the two variants used two different mechanisms to achieve resistance, even though these two variants were derived from the same clone and selected against arsenite under the same conditions. In variant A, the variant with DNA amplification, the biochemical pathways for detoxification of oxidative stress, the energy generation system to support the biochemical and physiological needs of the variant for DNA and protein synthesis and the arsenite translocating system to dispose arsenite are among the primary biochemical events that are upregulated under the arsenite stress to gain resistance. In variant A', the variant without DNA amplification, the upregulation of aquaglyceroporin (AQP) gene and the high level of resistance to arsenate point to the direction that the resistance gained by the variant is due to arsenate which is probably oxidized from arsenite in the arsenite solution used for selection and the maintenance of the cell culture. As a result of the AQP upregulation for arsenite disposal, a different set of biochemical pathways for detoxification of oxidative stress, energy generation and cellular signaling are upregulated to sustain the growth of the variant to gain resistance to arsenate. From current evidences, reactive oxygen species (ROS) overproduced by the parasite soon after exposure to arsenite appear to play an instrumental role in both variants to initiate the subsequent biochemical events that allow the same clone of L. amazonensis to take two totally different routes to diverge into two different variants.

Divergence of trypanothione-dependent tryparedoxin cascade into cytosolic and mitochondrial pathways in arsenite-resistant variants of Leishmania amazonensis

Evidences are presented in the in vivo study that overexpression of tryparedoxin peroxidases (TXNPxs) diverged into cytosolic pathway in arsenite-resistant variant A and mitochondrial pathway in variant A' of Leishmania amazonensis is due to the upregulation of the corresponding upstream tryparedoxins (TXNs) in the cytosol as well as the mitochondrion respectively. Evidences are also presented that exposure of L. amazonensis to arsenite in the early hours led to the production of reactive oxygen species (ROS), which in turn induced the overexpression of the genes of both cytosolic and mitochondrial trypanothione-dependent tryparedoxin pathway due probably to physiological and functional needs. The sequence of events leading to the upregulation indicates that cytosolic tryparedoxin pathway is upregulated earlier than that of mitochondrial tryparedoxin pathway. Based on the kinetics of gene upregulation of the cytosolic pathway is different from that of mitochondrial pathway, and cTXNPx and mTXNPx differentially detoxify H(2)O(2) and of t-butyl hydroperoxide respectively, it is postulated that during arsenite selection, different ROS species may have been overproduced in either variants A or A', leading to the divergence of the trypanothione-dependent tryparedoxin pathways in these variants.

Induction of apoptosis-like cell death by pentamidine and doxorubicin through differential inhibition of topoisomerase II in arsenite-resistant L. donovani

The current study has been undertaken to investigate the sensitivity of the topoisomerase II (topo II) of wild type (Ld-Wt) and arsenite-resistant (Ld-As20) L. donovani to an anti-leishmanial agent pentamidine and an anti-cancer drug doxorubicin. We demonstrate that the cross resistance to pentamidine and doxorubicin in Ld-As20, was in part implicated through differential inhibition of topo II in Ld-Wt and Ld-As20. Further, the treatment of promastigotes at drug concentrations inhibiting 50% of topo II activity inflicted a regulated cell death sharing several apoptotic features like externalization of phosphatidylserine, loss of mitochondrial membrane potential, cytochrome C release into the cytosol, activation of cellular proteases and DNA fragmentation. The cytotoxic potential of pentamidine and doxorubicin in L. donovani has been shown to be mediated through topoisomerase II inhibition and results in inciting programmed cell death process.

Radically different maxicircle classes within the same kinetoplast: an artefact or a novel feature of the kinetoplast genome?

We discuss here some results which suggest that radically different maxicircle classes coexist within the same kinetoplast. These data, although tentative and incomplete, may provide a new outlook on the kinetoplast genome structure and expression.

The Leishmania major maxicircle divergent region is variable in different isolates and cell types

The maxicircle divergent region (DR) was partially sequenced in several isolates of Leishmania major. The sequence contains various repeated elements: two types of long GC-rich repeats alternating with clusters of short AT-rich repeats. The arrangement of repeats appears to be similar in the studied Leishmania species and their relative Leptomonas seymouri. Furthermore, a conserved sequence containing putative promoters within a palindrome was revealed in the DRs of these species. Unexpectedly, the DR sequence proved to be dissimilar in promastigotes and amastigotes of the same isolate perhaps through selection of parasites with particular maxicircle variants in the course of the promastigote-amastigote differentiation. Different number of repeats and numerous single nucleotide polymorphisms are observed in the compared sequences. We have also investigated the DR structure in 21 L. major isolates by PCR and demonstrated its great variability. We suppose, however, that different variants of the DR structure are generated by combination of several highly conserved domains.

Distinct overexpression of cytosolic and mitochondrial tryparedoxin peroxidases results in preferential detoxification of different oxidants in arsenite-resistant Leishmania amazonensis with and without DNA amplification

A cytosolic (cTXNPx) and a mitochondrial (mTXNPx) tryparedoxin peroxidase genes, cloned from wildtype Leishmania amazonensis clone 2-23 are homologous in nucleic acid and amino acid sequences to the respective genes described for L. infantum and L. chagasi. Surprisingly, as shown in the results of transcription assays, protein determination and fluorescent antibody detection in situ, cTXNPx is distinctly overexpressed in the cytoplasm of arsenite-resistant A variant with DNA amplification, whereas mTXNPx is distinctly overexpressed in the mitochondrion of arsenite-resistant A' variant without DNA amplification, although A and A' are arsenite-resistant variants derived from the same wildtype clone of L. amazonensis, and selected against arsenite under the same conditions. Since the tunicamycin-resistant variant (T) derived from the same W(2-23) clone and the hydroxyurea-resistant (Hu(2-6)) variant derived from clone W(2-6) do not show overexpression of these two genes, it is suggested that the distinct overexpression of cTXNPx and mTXNPx genes in arsenite-resistant A and A' variants is linked to arsenite selection process. These two genes in A and A' variants, and cTXNPx(+) and mTXNPx(+) transfectants are similar to the respective genes described for L. infantum and L. chagasi in terms of antioxidant activities against H2O2 and t-butyl hydroperoxide, in which cTXNPx is more resistant to H2O2, and mTXNPx is more resistant to t-butyl hydroperoxide than the wildtype. Both genes, however, are cross-resistant to NO as compared to the control wildtype. In the transfectants carrying cTXNPx and mTXNPx in inverted orientation, these two genes are expressed in a level lower than that in wildtype. The decreased expression was followed by increased sensitivity of these transfectants to the oxidants. This possibly is due to the formation of antisense mRNA in these transfectants that causes a specific downregulation of the respective genes.

Overexpression and increased DNA topoisomerase II-like enzyme activity in arsenite resistant Leishmania donovani

Western immunoblot analyses of whole cell lysates probed with a human specific monoclonal anti-topoisomerase IIalpha antibody identified a 190 kDa protein over expressed in the arsenite resistant Leishmania donovani strain. The crude nuclear extract of the resistant strain showed higher topoisomerase II-like enzyme activity. suggesting a possible regulatory role of putative topoisomerase II in arsenite resistant Leishmania.

Natural and induced dyskinetoplastic trypanosomatids: how to live without mitochondrial DNA

Salivarian trypanosomes are the causative agents of several diseases of major social and economic impact. The most infamous parasites of this group are the African subspecies of the Trypanosoma brucei group, which cause sleeping sickness in humans and nagana in cattle. In terms of geographical distribution, however, Trypanosoma equiperdum and Trypanosoma evansi have been far more successful, causing disease in livestock in Africa, Asia, and South America. In these latter forms the mitochondrial DNA network, the kinetoplast, is altered or even completely lost. These natural dyskinetoplastic forms can be mimicked in bloodstream form T. brucei by inducing the loss of kinetoplast DNA (kDNA) with intercalating dyes. Dyskinetoplastic T. brucei are incapable of completing their usual developmental cycle in the insect vector, due to their inability to perform oxidative phosphorylation. Nevertheless, they are usually as virulent for their mammalian hosts as parasites with intact kDNA, thus questioning the therapeutic value of attempts to target mitochondrial gene expression with specific drugs. Recent experiments, however, have challenged this view. This review summarises the data available on dyskinetoplasty in trypanosomes and revisits the roles the mitochondrion and its genome play during the life cycle of T. brucei.

A theoretical study of random segregation of minicircles in trypanosomatids

The kinetoplast (k) DNA network of trypanosomatids is made up of approximately 50 maxicircles and the order of 10(4) minicircles. It has been proposed, based on various observations and experiments, that the minicircles are randomly segregated between daughter cells when the parent cell divides. In this paper, this random segregation hypothesis is theoretically tested in a population dynamics model to see if it can account for the observed phenomena. The hypothesis is shown to successfully explain, in Leishmania tarentolae, the observation that there are a few major and many minor minicircle classes, the fluctuations of minicircle class copy numbers over time, the loss of non-essential minicircle classes, the long survival times of a few of these classes and that these classes are likely to be the major classes within the population. Implications of the model are examined for trypanosomatids in general, leading to several predictions. The model predicts variation in network size within a population, variation in the average network size and large-scale changes in class copy number over long time-scales, an evolutionary pressure towards larger network sizes, the selective advantage of non-random over random segregation, very strong selection for the amplified class in Crithidia fasciculata if its minicircles undergo random segregation and that Trypanosoma brucei may use sexual reproduction to maintain its viability.

Modification of kinetoplast DNA minicircle composition in pentamidine-resistant Leishmania

Pentamidine, an antiprotozoal drug, was shown to have various cellular and molecular targets depending on the organism. In Leishmania, ultrastructural modifications of kinetoplast and mitochondria have been observed but no data is available on cellular and molecular events involved in development of pentamidine-resistance. The absence of modification of minicircle DNA in pentamidine treated L. donovani and L. amazonensis promastigotes suggested that topoisomerase II activity is not a target. This result was confirmed by quantitation of the enzyme by immunodetection. Southern blot experiments indicated that the kDNA network was altered in resistant clones. Molecular cloning and sequence analysis of kDNA minicircles showed transkinetoplastidy hitherto reported only for arsenite- and tunicamycin-resistant Leishmania. Comparison of wild-type and resistant sequences showed only 32-51% homology. The AT-rich regions, known as binding sites, of the drug occurred less frequently in the resistant clones and their locations were different. These minicircle sequence modifications leading to decreased binding sites for the drug might contribute to pentamidine-resistance in Leishmania.

Disruption of RNA editing in Leishmania tarentolae by the loss of minicircle-encoded guide RNA genes

RNA editing in kinetoplastids appears to be a labile genetic trait that is affected by prolonged cell culture. The transcripts of the G1-G5 cryptogenes are pan-edited in the recently isolated LEM125 strain of Leishmania tarentolae, but not in the UC strain which has been in culture for 55 years. At least 32 minicircle-encoded guide RNAs (gRNAs) for the editing of G1-G5 transcripts are present in LEM125 and absent in UC. We hypothesize that specific minicircle sequence classes encoding gRNAs for the editing of these transcripts were lost during the long culture history of the UC strain. The protein products, which include components of complex I of the respiratory chain, are probably not required during the culture stage of the Leishmania life cycle.