Homogeneous and heterogeneous mini-circle subpopulations in Trypanosoma cruzi kinetoplast DNA

High-throughput analysis of the Trypanosoma cruzi minicirculome (mcDNA) unveils structural variation and functional diversity

Trypanosoma cruzi causes Chagas disease and has a unique extranuclear genome enclosed in a structure called the kinetoplast, which contains circular genomes known as maxi- and minicircles. While the structure and function of maxicircles are well-understood, many aspects of minicircles remain to be discovered. Here, we performed a high-throughput analysis of the minicirculome (mcDNA) in 50 clones isolated from Colombia's diverse T. cruzi I populations. Results indicate that mcDNA comprises four diverse subpopulations with different structures, lengths, and numbers of interspersed semi-conserved (previously termed ultra-conserved regions mHCV) and hypervariable (mHVPs) regions. Analysis of mcDNA ancestry and inter-clone differentiation indicates the interbreeding of minicircle sequence classes is placed along diverse strains and hosts. These results support evidence of the multiclonal dynamics and random bi-parental segregation. Finally, we disclosed the guide RNA repertoire encoded by mcDNA at a clonal scale, and several attributes of its abundance and function are discussed.

Minicircle classes heterogeneity within the TcIII and TcIV discrete typing units of Trypanosoma cruzi

The taxon Trypanosoma cruzi, causative agent of Chagas disease, is composed of several discrete typing units (DTUs) named TcI-TcVI, and Tcbat. The history of the taxon T. cruzi is known, even though several controversial aspects remain as the relationships between TcIII and TcIV. We analyzed cloned T. cruzi stocks pertaining to the seven DTUs by filter hybridization tests of PCR amplicons from minicircle variable regions and kinetoplast DNA probes. Minicircle DNA blots from the cloned stocks and filter hybridization with one TcI, one TcII, one TcV, one TcVI, three TcIII, one TcIV from North America and one TcIV kinetoplast DNA probes from South America revealed minicircle variable region cross-reaction in some T. cruzi DTUs probed. TcIII was heterogeneous in minicircle class composition, even though two TcIII probes revealed that a small fraction of minicircles cross-hybridized with the minicircles from the TcIII, TcV and TcVI DTUs. The minicircles of TcIV from North America cross-reacted only with TcIV from North America but not with TcIV stocks from Brazil and Bolivia. The results on minicircle cross-hybridizations are discussed in the context of RNA editing, mitochondrial function in T. cruzi DTUs.

Evidence that the entire length of a kinetoplast DNA minicircle is transcribed in Trypanosoma cruzi

A 1.3 kb cDNA (cDNA52) was derived from Trypanosoma cruzi trypomastigote mRNA. Using single stranded probes in Northern blots, we identified the putative coding strand of cDNA52. In addition, a minor band was detected in RNA from epimastigotes that was absent in RNA from trypomastigotes. Nucleotide sequence analysis revealed that cDNA52 was highly homologous to T. cruzi kinetoplast DNA minicircle sequences. All four conserved regions of T. cruzi minicircles were identified in cDNA52. Using several criteria, we demonstrated that the hybridization signals were not caused by contaminating minicircle DNA in the RNA preparations. The data provide direct evidence for the unprecedented finding that the entire length of a kDNA minicircle is transcribed in T. cruzi.

Characterization of kinetoplast minicircle DNA in the lower trypanosomatid Crithidia oncopelti

The kinetoplast DNA of the lower trypanosomatid Crithidia oncopelti contains minicircles of four major size classes. Attempts to clone these molecules revealed the unclonability of the full-length minicircles in pUC and M13 vectors. A few clones were obtained using a lambda insertion vector lambda XIII. The nucleotide sequence of a cloned, apparently full-length minicircle has been determined and characterized. This 1848-bp molecule contains a single region corresponding to the 'conserved' minicircle region in other trypanosomatid species and an area with some features of the bent helix. About one-third of the molecule length is occupied by an extremely (T+G) versus (A+C) strand biased region. The role of this region, as well as the significance of the ORFs found and the putative secondary structures potentially formed by the minicircle sequence, remains unknown. The hybridization of kDNA with the different regions of a cloned minicircle shows that there are some segments of DNA specific to a particular class or a group of classes. Such a mode of sequence heterogeneity suggests that the possible functions (if any) of different minicircle classes may differ.

Trypanosoma (Schizotrypanum) cruzi: repetitive DNA sequence evolution in three geographically distinct isolates

1. Middle-repetitive DNA sequences were analyzed by molecular hybridization to determine both the extent of complementarity and time of evolutionary divergence between isolates of Trypanosoma cruzi from Argentina, Mexico, or Venezuela. 2. Although molecular hybridizations showed no significant difference between the middle-repetitive DNAs of the Mexican and Venezuelan isolates, there was a 2.7% base pair mismatch in hybrid molecules formed by association of strands from both the Mexican and Argentine isolates. 3. Using the rates for divergence of middle-repetitive DNA in sea urchins, the Mexican and Argentine isolates were estimated to have diverged approximately 20-25 million years ago. 4. Analysis of the kinetics for the DNA hybridizations indicates that only minor amplifications of specific gene sequences or changes in the complexity of the genomes could have occurred during the divergence of the three isolates studied.

Study on genetic polymorphism of Leishmania infantum through the analysis of restriction enzyme digestion patterns of kinetoplast DNA

Twenty-nine Leishmania infantum strains characterized by different host source, tropism and belonging to 6 zymodemes, were examined by restriction enzyme analysis of kinetoplast DNA (kDNA) using 15 endonucleases. The enzymes which produced only one fragment revealed full identity between all the strains examined, while those producing many bands gave different electrophoretic patterns. They were interpreted with the aid of numerical analyses (cluster and multifactorial analysis). The results show a cline of genetic variability among the strains, the highest similarity being observed between most of the viscerotropic strains isolated from man, dog, black rat and sandflies. The strain agents of human cutaneous leishmaniasis show a varying degree of genetic divergence from this group, which appears more evident when characters from isoenzymes are considered.

Sequence diversity in the kinetoplast DNA minicircles of Trypanosoma cruzi

Minicircles are the most abundant component of the mitochondrially located kinetoplast DNA in the members of the order Kinetoplastida. Minicircle sequences differ among most trypanosomatid species. To learn about the molecular mechanisms that give rise to this diversity, we sequenced a complete minicircle (pTckAWP-2) and two homologous but polymorphic minicircle fragments isolated from different Trypanosoma cruzi clones. Comparison of these sequences revealed 23 point mutations, 19 of which were transitions. A single base pair insertion was also detected in one of the two minicircle fragments sequenced. Analysis of pTckAWP-2 sequence showed the following features: the presence of four internal 118 base pairs conserved regions with 80% or higher homology; the fact that these four conserved regions also differed mainly by point mutations, although in this case a bias in favor of transversions was observed; the existence in each of these four regions of the highly conserved 13 bp sequence 5'GGGGTTGGTGTAA3', detected in all trypanosomatid minicircles, which is thought to be the origin of replication; and the presence of several direct and inverted repeat sequences of 8 base pairs or longer, scattered throughout the minicircle molecule. Comparison of the T. cruzi conserved minicircle region with that of other trypanosomatids showed a higher homology of T. cruzi with T. lewisi, another stercorarian trypanosome, than with African trypanosomes or Leishmania.

Identification of visceral Leishmania species with cloned sequences of kinetoplast DNA

Several efforts have been made in order to develop more precise and sensitive methods in the identification of Leishmania parasites. We report here the identification of cloned subfragments of minicircle kinetoplast DNA (kDNA) isolated from L. donovani, WR352, which show different taxonomic specificities. Analysis of these fragments demonstrates a significant sequence diversity within the kDNA minicircle. For example, one cloned fragment was found to be present in all visceral Leishmania species tested, but was not present in any of the cutaneous Leishmania species. Another cloned fragment was only found in the strain from which it had been derived, and was not present in any of the other strains tested. In similar experiments with the New World visceral leishmanias (L. chagasi, WR518) several different cloned kDNA fragments were found to react with all of isolates of the L. chagasi tested, but not with any cutaneous Leishmania species, either from the Old World or the New World. It is of interest to note that these cloned L. chagasi kDNA fragments reacted with isolates of African visceral Leishmania species but not with isolates from India.

Polymorphisms within minicircle sequence classes in the kinetoplast DNA of Trypanosoma cruzi clones

Four minicircle classes were analyzed using cloned minicircles as probes and single-cell cloned Trypanosoma cruzi parasites. The hybridization conditions used allowed identification of minicircle classes within kinetoplast DNA that were non-homologous to each other. Two of these minicircle classes, detected with probes pTckAWP-2 and -3, were present together in several of the CA 1 and Miranda clones, in spite of the fact that either pTckAWP-2 or both minicircle classes were undetectable in other isolates and clones of the parasite. The other two minicircle classes (pTckM-84 and -88) were located in some Miranda cloned parasites which were characterized by the simple restriction endonuclease pattern of their minicircles. Both pTckM-84 and -88 minicircle classes represented 52-71% of the kinetoplast DNA in the latter group of trypanosomes. Restriction endonuclease mapping allowed the identification of polymorphic minicircles in two of the four minicircle classes analyzed (pTckAWP-2 and pTckM-88). The polymorphisms were observed in part of the molecules of one minicircle class within a single trypanosome clone, as well as when different clones or even some of those obtained from the same isolate were compared. In addition, a different proportion of pTckM-88 type of minicircle sequence class was observed in the kinetoplast DNA from two of the Miranda clones analyzed. These observations demonstrated that similar molecules may evolve independently in sequence in each parasite. The polymorphic minicircles detected may arise from sequence variations before expansion of a future homogeneous minicircle sequence class.