Plasticity of the Leishmania genome leading to gene copy number variations and drug resistance [version 1; referees: 5 approved]

Leishmania has a plastic genome, and drug pressure can select for gene copy number variation (CNV). CNVs can apply either to whole chromosomes, leading to aneuploidy, or to specific genomic regions. For the latter, the amplification of chromosomal regions occurs at the level of homologous direct or inverted repeated sequences leading to extrachromosomal circular or linear amplified DNAs. This ability of Leishmania to respond to drug pressure by CNVs has led to the development of genomic screens such as Cos-Seq, which has the potential of expediting the discovery of drug targets for novel promising drug candidates

Formation of Linear Amplicons with Inverted Duplications in <i>Leishmania</i> Requires the MRE11 Nuclease

<div><p>Extrachromosomal DNA amplification is frequent in the protozoan parasite <i>Leishmania</i> selected for drug resistance. The extrachromosomal amplified DNA is either circular or linear, and is formed at the level of direct or inverted homologous repeated sequences that abound in the <i>Leishmania</i> genome. The RAD51 recombinase plays an important role in circular amplicons formation, but the mechanism by which linear amplicons are formed is unknown. We hypothesized that the <i>Leishmania infantum</i> DNA repair protein MRE11 is required for linear amplicons following rearrangements at the level of inverted repeats. The purified LiMRE11 protein showed both DNA binding and exonuclease activities. Inactivation of the <i>LiMRE11</i> gene led to parasites with enhanced sensitivity to DNA damaging agents. The MRE11^−/− parasites had a reduced capacity to form linear amplicons after drug selection, and the reintroduction of an <i>MRE11</i> allele led to parasites regaining their capacity to generate linear amplicons, but only when MRE11 had an active nuclease activity. These results highlight a novel MRE11-dependent pathway used by <i>Leishmania</i> to amplify portions of its genome to respond to a changing environment.</p></div

Detection of gene rearrangements leading to <i>PTR1</i> containing amplicons using PCR assays.

<p>(<b>A</b>) Schematic representation of inverted repeated sequences (arrows depicted as A, A′, B, B′, C, C′, D, D′, E, E′) and direct repeats (F, F′) at the <i>PTR1</i> chromosomal locus on chromosome 23. Arrowheads (depicted as a, a′, b, b′, c, c′, d, d′, e, e′, f and f′) indicate position and orientation of PCR primers that were used to detect amplicon junctions. (<b>B–E</b>) PCR amplification of newly formed amplicon junctions in ten MTX-resistant clones derived either from WT (<b>B</b>), <i>HYG/NEO MRE11^−/−</i> (<b>C</b>), <i>HYG/PUR-MRE11</i>^WT (<b>D</b>) and <i>HYG/PUR-MRE11</i>^H210Y (<b>E</b>).</p

Purification and DNA binding of the <i>L. infantum</i> MRE11 protein.

<p>(<b>A</b>) Alignment of <i>L. infantum</i> and human MRE11 proteins showing the conserved catalytic residue (H) that has been mutated in LiMRE11 (H210Y) to generate the LiMRE11^H210Y mutated version and purification of LiMRE11^WT and LiMRE11^H210Y followed by SDS–PAGE separation. Purified proteins (150 ng) were loaded on an 8% SDS-PAGE, run then stained with Coomassie blue (GE Healthcare). Lane 1: molecular weight markers (Bio-Rad Laboratories); lane 2: purified LiMRE11^WT; lane 3: purified LiMRE11^H210Y. (<b>B</b>) LiMRE11^WT and mutant H210Y can bind various DNA structures. Competition electrophoretic mobility shift assays were performed with LiMRE11^WT (lanes 2–4) and LiMRE11^H210Y (lanes 5–7) and 25 nM of ssDNA (SS), dsDNA (DS) and splayed arm (SA) substrates with increasing concentration of the proteins (0, 5, 10, 15 nM). (<b>C</b>) Quantification of the DNA binding signals of panel <b>B</b>.</p

<i>MRE11</i> gene inactivation in <i>L. infantum</i> and phenotypic analysis.

<p>(<b>A</b>) Schematic representation of the <i>MRE11</i> locus in <i>L. infantum</i> before and after integration of the inactivation cassettes neomycin phosphotransferase (5′-<i>NEO-3′</i>) and hygromycin phosphotransferase B (5′-<i>HYG-3′</i>) generating the double knockout strain <i>HYG/NEO MRE11^−/−</i>. A revertant was obtained by the integration of the re-expressing <i>MRE11</i>^WT or <i>MRE11</i>^H210Y puromycin cassettes (5′-<i>MRE11</i>^WT-α-<i>PUR-3′</i> and <i>5′-MRE11</i>^H210Y-<i>α-PUR-3′</i>) to replace the <i>NEO</i> allele, given respectively strains <i>HYG/PUR-MRE11</i>^WT and <i>HYG/PUR-MRE11</i>^H210Y. X, XhoI restriction sites. (<b>B</b>) Southern blot analysis with genomic DNAs digested with XhoI from the <i>L. infantum</i> WT strain (lanes 1 and 5) and recombinant clones of the double knockout <i>HYG/NEO MRE11^−/−</i> (lanes 2 and 6), <i>HYG/PUR-MRE11</i>^WT (lanes 3 and 7) and <i>HYG/PUR-MRE11</i>^H210Y parasites (lanes 4 and 8). Hybridizations with a probe covering either the 5′ or 3′ flanking region of <i>LiMRE11</i> are shown. (<b>C</b>) Growth retardation of promastigotes <i>MRE11</i> null mutants. <i>L. infantum</i> WT (white circles), <i>HYG/NEO MRE11^−/−</i> (black squares), <i>HYG/PUR-MRE11</i>^WT (black triangles), <i>HYG/PUR-MRE11</i>^H210Y (inverted white triangles). (<b>D</b>) Susceptibility to methylmethane sulfonate (MMS). <i>L. infantum</i> WT (white circles), <i>HYG/NEO MRE11^−/−</i> (black squares), <i>HYG/PUR-MRE11</i>^WT (black triangles), <i>HYG/PUR-MRE11</i>^H210Y (inverted white triangles).</p

<i>PTR1</i> gene amplification of <i>L. infantum</i> methotrexate (MTX) resistant cells.

<p><i>L. infantum</i> cells were selected for MTX resistance, and their chromosomes were separated by pulsed-field gel electrophoresis using a separation range between 150 kb and 1500 kb, transferred on membranes then hybridized with a <i>PTR1</i> probe. MTX-resistant clones resistant to 1600 nM MTX derived from the WT (<b>A</b>), the <i>HYG/NEO MRE11^−/−</i> cells (<b>B</b>), the <i>HYG/PUR-MRE11</i>^WT cells (<b>C</b>) and the <i>HYG/PUR-MRE11</i>^H210Y cells (<b>D</b>). Lanes 0 are parasites without drug selection.</p

Potential mechanisms for the formation of extrachromosomal linear amplicons.

<p>(<b>1</b>) Single-strand hairpin formation (a) or single-strand break (SSB) (near the IRs) during replication followed by annealing of the IRs (b), 3′-5′ exonuclease digestion of the exposed end (c) and DNA synthesis of the upstream region (d) and of the second strand to form an inverted duplication (g). (<b>2</b>) Double-strand break (DSB) near the IRs (e) followed by 3′-5′ exonuclease digestion at the DNA break of one strand (f), annealing of the IRs to form an inverted duplication (d) and synthesis of the second strand to generate linear amplicon (g). The new junction formed during annealing of the IRs can be detected by PCR using specific primers. IRs, inverted repeated sequences; ss, single-strand; SSB, single-strand break; DSB, double-strand break; p1–p2, primer pair used to detect the new junction. White rectangle: telomeric sequences.</p

Fluorescence recovery after photobleaching analysis after DNA damage induction in UV-irradiated cells.

<p>LiMRE11-GFP is recruited to DNA damage sites in human MRE11-deficient cells (ATLD), as the human MRE11-GFP.</p

Chromosomal Translocations in the Parasite <i>Leishmania</i> by a MRE11/RAD50-Independent Microhomology-Mediated End Joining Mechanism

<div><p>The parasite <i>Leishmania</i> often relies on gene rearrangements to survive stressful environments. However, safeguarding a minimum level of genome integrity is important for cell survival. We hypothesized that maintenance of genomic integrity in <i>Leishmania</i> would imply a leading role of the MRE11 and RAD50 proteins considering their role in DNA repair, chromosomal organization and protection of chromosomes ends in other organisms. Attempts to generate <i>RAD50</i> null mutants in a wild-type background failed and we provide evidence that this gene is essential. Remarkably, inactivation of <i>RAD50</i> was possible in a <i>MRE11</i> null mutant that we had previously generated, providing good evidence that <i>RAD50</i> may be dispensable in the absence of <i>MRE11</i>. Inactivation of the <i>MRE11</i> and <i>RAD50</i> genes led to a decreased frequency of homologous recombination and analysis of the null mutants by whole genome sequencing revealed several chromosomal translocations. Sequencing of the junction between translocated chromosomes highlighted microhomology sequences at the level of breakpoint regions. Sequencing data also showed a decreased coverage at subtelomeric locations in many chromosomes in the <i>MRE11</i>^<i>-/-</i><i>RAD50</i>^<i>-/-</i> parasites. This study demonstrates an MRE11-independent microhomology-mediated end-joining mechanism and a prominent role for MRE11 and RAD50 in the maintenance of genomic integrity. Moreover, we suggest the possible involvement of RAD50 in subtelomeric regions stability.</p></div

Intrachromosomal Amplification, Locus Deletion and Point Mutation in the Aquaglyceroporin AQP1 Gene in Antimony Resistant <i>Leishmania (Viannia) guyanensis</i>

<div><p>Background</p><p>Antimony resistance complicates the treatment of infections caused by the parasite <i>Leishmania</i>.</p><p>Methodology/Principal Findings</p><p>Using next generation sequencing, we sequenced the genome of four independent <i>Leishmania guyanensis</i> antimony-resistant (SbR) mutants and found different chromosomal alterations including aneuploidy, intrachromosomal gene amplification and gene deletion. A segment covering 30 genes on chromosome 19 was amplified intrachromosomally in three of the four mutants. The gene coding for the multidrug resistance associated protein A involved in antimony resistance was also amplified in the four mutants, most likely through chromosomal translocation. All mutants also displayed a reduced accumulation of antimony mainly due to genomic alterations at the level of the subtelomeric region of chromosome 31 harboring the gene coding for the aquaglyceroporin 1 (LgAQP1). Resistance involved the loss of <i>LgAQP1</i> through subtelomeric deletions in three mutants. Interestingly, the fourth mutant harbored a single G133D point mutation in LgAQP1 whose role in resistance was functionality confirmed through drug sensitivity and antimony accumulation assays. In contrast to the <i>Leishmania</i> subspecies that resort to extrachromosomal amplification, the <i>Viannia</i> strains studied here used intrachromosomal amplification and locus deletion.</p><p>Conclusions/Significance</p><p>This is the first report of a naturally occurred point mutation in AQP1 in antimony resistant parasites.</p></div