Conserved repeats in the kinetoplast maxicircle divergent region of Leishmania sp. and Leptomonas seymouri

Flegontov, Pavel; Qiang, Guo; Ren, Lina; Strelkova, M. V.; Kolesnikov, Alexander

doi:10.1007/s00438-006-0145-5

Cited by 14 publications

(16 citation statements)

References 49 publications

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“…Sequence rearrangements in the 12S-proximal clusters of the Leishmania spp. DRs were investigated previously [34,40] and the current work confirms previous findings, stipulating that the P12 compartment is very dynamic. Of note, differences in the P12 region also determine DR length variation in different isolates of Trypanosoma brucei [22].…”

Section: Discussionsupporting

confidence: 87%

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Common Structural Patterns in the Maxicircle Divergent Region of Trypanosomatidae

et al. 2020

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Maxicircles of all kinetoplastid flagellates are functional analogs of mitochondrial genome of other eukaryotes. They consist of two distinct parts, called the coding region and the divergent region (DR). The DR is composed of highly repetitive sequences and, as such, remains the least explored segment of a trypanosomatid genome. It is extremely difficult to sequence and assemble, that is why very few full length maxicircle sequences were available until now. Using PacBio data, we assembled 17 complete maxicircles from different species of trypanosomatids. Here we present their large-scale comparative analysis and describe common patterns of DR organization in trypanosomatids.

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Section: Discussionsupporting

confidence: 87%

“…Previous studies of sequences, derived from the DRs of Leishmania spp., revealed that they are composed almost exclusively of repeats. These repeats are grouped in arrays or clusters [26,40]. In addition to Leishmania, these were also studies in Strigomonas oncopelti (called then Crithidia oncopelti) [41].…”

Section: Large-scale Divergent Region Architecturementioning

confidence: 99%

Common Structural Patterns in the Maxicircle Divergent Region of Trypanosomatidae

et al. 2020

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“…Due to the absence of larger ORFs, it was proposed that this region may play a structural role and is also required for replication. This notion is based on the presence of a 12 bp-long conserved sequence block (CSB) in the DRs of T. brucei [ 46 ], Crithidia oncopelti [ 47 ] Leptomonas collosoma a nd Leptomonas seymouri [ 48 ]. CSB is a highly conserved replication origin of the kDNA minicircles, and it may fulfill the same role also in the maxicircles [ 14 , 46 ].…”

Section: Discussionmentioning

confidence: 99%

Analysis of the mitochondrial maxicircle of Trypanosoma lewisi, a neglected human pathogen

et al. 2015

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BackgroundThe haemoflagellate Trypanosoma lewisi is a kinetoplastid parasite which, as it has been recently reported to cause human disease, deserves increased attention. Characteristic features of all kinetoplastid flagellates are a uniquely structured mitochondrial DNA or kinetoplast, comprised of a network of catenated DNA circles, and RNA editing of mitochondrial transcripts. The aim of this study was to describe the kinetoplast DNA of T. lewisi.Methods/ResultsIn this study, purified kinetoplast DNA from T. lewisi was sequenced using high-throughput sequencing in combination with sequencing of PCR amplicons. This allowed the assembly of the T. lewisi kinetoplast maxicircle DNA, which is a homologue of the mitochondrial genome in other eukaryotes. The assembly of 23,745 bp comprises the non-coding and coding regions. Comparative analysis of the maxicircle sequence of T. lewisi with Trypanosoma cruzi, Trypanosoma rangeli, Trypanosoma brucei and Leishmania tarentolae revealed that it shares 78 %, 77 %, 74 % and 66 % sequence identity with these parasites, respectively. The high GC content in at least 9 maxicircle genes of T. lewisi (ATPase6; NADH dehydrogenase subunits ND3, ND7, ND8 and ND9; G-rich regions GR3 and GR4; cytochrome oxidase subunit COIII and ribosomal protein RPS12) implies that their products may be extensively edited. A detailed analysis of the non-coding region revealed that it contains numerous repeat motifs and palindromes.ConclusionsWe have sequenced and comprehensively annotated the kinetoplast maxicircle of T. lewisi. Our analysis reveals that T. lewisi is closely related to T. cruzi and T. brucei, and may share similar RNA editing patterns with them rather than with L. tarentolae. These findings provide novel insight into the biological features of this emerging human pathogen.Electronic supplementary materialThe online version of this article (doi:10.1186/s13071-015-1281-8) contains supplementary material, which is available to authorized users.

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“…2 ). Unlike typical trypanosomatid maxicircles, which have a single variable region and a dense protein-coding region ( 43 ), these Perkinsela contigs contain short tandem repeats at their ends. No similarity was found among repetitive sequences flanking the three protein-coding contigs (data not shown).…”

Section: Resultsmentioning

confidence: 99%

Gene Loss and Error-Prone RNA Editing in the Mitochondrion of Perkinsela , an Endosymbiotic Kinetoplastid

David

Flegontov

Gerasimov

et al. 2015

mBio

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Perkinsela is an enigmatic early-branching kinetoplastid protist that lives as an obligate endosymbiont inside Paramoeba (Amoebozoa). We have sequenced the highly reduced mitochondrial genome of Perkinsela, which possesses only six protein-coding genes (cox1, cox2, cox3, cob, atp6, and rps12), despite the fact that the organelle itself contains more DNA than is present in either the host or endosymbiont nuclear genomes. An in silico analysis of two Perkinsela strains showed that mitochondrial RNA editing and processing machineries typical of kinetoplastid flagellates are generally conserved, and all mitochondrial transcripts undergo U-insertion/deletion editing. Canonical kinetoplastid mitochondrial ribosomes are also present. We have developed software tools for accurate and exhaustive mapping of transcriptome sequencing (RNA-seq) reads with extensive U-insertions/deletions, which allows detailed investigation of RNA editing via deep sequencing. With these methods, we show that up to 50% of reads for a given edited region contain errors of the editing system or, less likely, correspond to alternatively edited transcripts.

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Conserved repeats in the kinetoplast maxicircle divergent region of Leishmania sp. and Leptomonas seymouri

Cited by 14 publications

References 49 publications

Common Structural Patterns in the Maxicircle Divergent Region of Trypanosomatidae

Common Structural Patterns in the Maxicircle Divergent Region of Trypanosomatidae

Analysis of the mitochondrial maxicircle of Trypanosoma lewisi, a neglected human pathogen

Gene Loss and Error-Prone RNA Editing in the Mitochondrion of Perkinsela , an Endosymbiotic Kinetoplastid

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