Kinetoplast (k) DNA, a specialized form of mitochondrial DNA in trypanosomes, is composed of catenated maxicircles and minicircles, and is essential for the survival of these parasitic protists. In this study, we provide a detailed description of the near-complete minicircle complement of Trypanosoma musculi, a globally distributed, mouse-specific haemoflagellate. We have identified 39 minicircle classes, which can be grouped via their structural organization into five distinct categories. Using RNA-seq, we have reconstructed mitochondrial transcripts of ATP6, RPS12, CYTB, COX2 and COX3, all of which undergo canonical editing that renders them translatable, as well as abnormally edited transcripts of four respiratory Complex I subunits. Additionally, through a combined analysis of the kDNA minicircles, edited mRNAs and small RNAs, we identified 108 guide (g)RNA genes and further categorized their conservation in comparison with Trypanosoma lewisi, an opportunistic human parasite. Moreover, we demonstrate a small respiratory Complex I in T. musculi, highlighting the functional consequences of missing gRNAs. Finally, we propose a model for the evolutionary maintenance of gRNAs, contributing to our understanding of kDNA dynamics in trypanosomes and other kinetoplastid flagellates.

Ecosystems and Environment Research Centre and Biomedical Research Centre School of Science Engineering and Environment University of Salford Salford UK

Faculty of Science University of South Bohemia České Budějovice Czech Republic

Institute of Parasitology Biology Centre Czech Academy of Sciences České Budějovice Czech Republic

MOE Key Laboratory of Gene Function and Regulation State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Aquatic Economic Animals School of Life Sciences Sun Yat Sen University Guangzhou P R China

Zobrazit více v PubMed

Stuart, K. et al. Kinetoplastids: Related protozoan pathogens, different diseases. PubMed DOI PMC

Amodeo, S., Bregy, I. & Ochsenreiter, T. Mitochondrial genome maintenance—the kinetoplast story. PubMed DOI PMC

Robertson, M. Notes on the life-history of DOI

Kay, C., Williams, T. A. & Gibson, W. Mitochondrial DNAs provide insight into trypanosome phylogeny and molecular evolution. PubMed DOI PMC

Simpson, L. The mitochondrial genome of kinetoplastid protozoa: genomic organization, transcription, replication, and evolution. PubMed DOI

Lukeš, J., Wheeler, R., Jirsová, D., David, V. & Archibald, J. M. Massive mitochondrial DNA content in diplonemid and kinetoplastid protists. PubMed DOI PMC

Jensen, R. E. & Englund, P. T. Network news: The replication of kinetoplast DNA. PubMed DOI

Cooper, S. et al. Assembly and annotation of the mitochondrial minicircle genome of a differentiation-competent strain of PubMed DOI PMC

Lukeš, J. et al. Kinetoplast DNA network: evolution of an improbable structure. PubMed DOI PMC

Li, S. J. et al. Novel organization of mitochondrial minicircles and guide RNAs in the zoonotic pathogen PubMed DOI PMC

Callejas-Hernández, F., Herreros-Cabello, A., Del Moral-Salmoral, J., Fresno, M. & Gironès, N. The complete mitochondrial DNA of PubMed DOI PMC

Ray, D. S. Conserved sequence blocks in kinetoplast minicircles from diverse species of trypanosomes. PubMed PMC

Wang, J. F. et al. Novel insertions in the mitochondrial maxicircle of PubMed DOI PMC

Greif, G., Rodriguez, M., Bontempi, I., Robello, C. & Alvarez-Valin, F. Different kinetoplast degradation patterns in American PubMed DOI

Berná, L. et al. Maxicircle architecture and evolutionary insights into PubMed DOI PMC

Benne, R. et al. Major transcript of the frameshifted coxll gene from trypanosome mitochondria contains four nucleotides that are not encoded in the DNA. PubMed DOI

Aphasizheva, I. et al. Lexis and grammar of mitochondrial RNA processing in trypanosomes. PubMed DOI PMC

Read, L. K., Lukeš, J. & Hashimi, H. Trypanosome RNA editing: The complexity of getting U in and taking U out. PubMed DOI PMC

Liu, S. et al. Structural basis of gRNA stabilization and mRNA recognition in trypanosomal RNA editing. PubMed DOI PMC

Koslowsky, D. J., Reifur, L., Yu, L. E. & Chen, W. Evidence for U-tail stabilization of gRNA/mRNA interactions in kinetoplastid RNA editing. PubMed DOI PMC

Gerasimov, E. S. et al. Evolutionary divergent kinetoplast genome structure and RNA editing patterns in the trypanosomatid PubMed DOI PMC

Afonin, D. A. et al. PubMed DOI PMC

Hong, X. K. et al. PCR-based identification of PubMed DOI

Gerasimov, E. S. et al. Common structural patterns in the maxicircle divergent region of Trypanosomatidae. PubMed DOI PMC

Gómez-Palacio, A. et al. High-throughput analysis of the PubMed DOI PMC

Hoare, C. A.

Lin, R.-H. et al. Analysis of the mitochondrial maxicircle of PubMed DOI PMC

Votýpka, J. et al. Unexpectedly high diversity of trypanosomes in small sub-Saharan mammals. PubMed DOI

Vaux, R. et al. Modulation of the immune response by nematode secreted acetylcholinesterase revealed by heterologous expression in PubMed DOI PMC

Zíková, A., Hampl, V., Paris, Z., Týč, J. & Lukeš, J. Aerobic mitochondria of parasitic protists: Diverse genomes and complex functions. PubMed DOI

Griffith, J., Bleyman, M., Rauch, C. A., Kitchin, P. A. & Englund, P. T. Visualization of the bent helix in kinetoplast DNA by electron microscopy. PubMed DOI

Ochsenreiter, T. & Hajduk, S. L. Alternative editing of cytochrome PubMed DOI PMC

Gerasimov, E. S., Ramirez-Barrios, R., Yurchenko, V. & Zimmer, S. L. PubMed DOI PMC

Doleželová, E. et al. Cell-based and multi-omics profiling reveals dynamic metabolic repurposing of mitochondria to drive developmental progression of PubMed DOI PMC

Zíková, A., Verner, Z., Nenarokova, A., Michels, P. A. M. & Lukeš, J. A paradigm shift: The mitoproteomes of procyclic and bloodstream PubMed DOI PMC

Surve, S., Heestand, M., Panicucci, B., Schnaufer, A. & Parsons, M. Enigmatic presence of mitochondrial complex I in PubMed DOI PMC

Cooper, S., Wadsworth, E. S., Schnaufer, A. & Savill, N. J. Organization of minicircle cassettes and guide RNA genes in PubMed DOI PMC

Vallejo, G. A., Macedo, A. M., Chiari, E. & Pena, S. D. J. Kinetoplast DNA from PubMed DOI

Botero, A. et al. The kinetoplast DNA of the Australian trypanosome, PubMed DOI

Junqueira, A. C., Degrave, W. & Brandão, A. Minicircle organization and diversity in PubMed DOI

Ponzi, M., Birago, C. & Battaglia, P. A. Two identical symmetrical regions in the minicircle structure of PubMed DOI

Birhanu, H., Gebrehiwot, T., Goddeeris, B. M., Büscher, P. & Van Reet, N. New PubMed DOI PMC

Lai, D. H., Hashimi, H., Lun, Z. R., Ayala, F. J. & Lukeš, J. Adaptations of PubMed DOI PMC

Sturm, N. R. & Simpson, L. PubMed DOI PMC

Blom, D. et al. Mitochondrial minicircles in the free-living bodonid PubMed DOI PMC

Simpson, A. G. B., Lukeš, J. & Roger, A. J. The evolutionary history of kinetoplastids and their kinetoplasts. PubMed DOI

Guerrero-Castillo, S. et al. The assembly pathway of mitochondrial respiratory chain Complex I. PubMed DOI

Nehls, U., Friedrich, T., Schmiede, A., Ohnishi, T. & Weiss, H. Characterization of assembly intermediates of NADH: Ubiquinone oxidoreductase (complex I) accumulated in PubMed DOI

Hirst, J. Mitochondrial Complex I. PubMed DOI

Barker, C. D., Reda, T. & Hirst, J. The flavoprotein subcomplex of Complex I (NADH:Ubiquinone Oxidoreductase) from bovine heart mitochondria:  Insights into the mechanisms of NADH oxidation and NAD+ reduction from protein film voltammetry. PubMed DOI

Sled, V. D. & Vinogradov, A. D. Kinetics of the mitochondrial NADH-ubiquinone oxidoreductase interaction with hexammineruthenium(III). PubMed DOI

Thiemann, O. H., Maslov, D. A. & Simpson, L. Disruption of RNA editing in PubMed DOI PMC

Verner, Z. et al. Alternative NADH dehydrogenase (NDH2): Intermembrane-space-facing counterpart of mitochondrial complex I in the procyclic PubMed DOI

Sturm, N. R., Maslov, D. A., Blum, B. & Simpson, L. Generation of unexpected editing patterns in PubMed DOI

Smith, J. T. Jr. et al. Developmental regulation of edited CYb and COIII mitochondrial mRNAs is achieved by distinct mechanisms in PubMed DOI PMC

Gerasimov, E. S. et al. Complete minicircle genome of PubMed DOI PMC

Tylec, B. L. et al. Intrinsic and regulated properties of minimally edited trypanosome mRNAs. PubMed DOI PMC

Rusman, F., Floridia-Yapur, N., Ragone, P. G., Diosque, P. & Tomasini, N. Evidence of hybridization, mitochondrial introgression and biparental inheritance of the kDNA minicircles in PubMed DOI PMC

Simpson, L., Douglass, S. M., Lake, J. A., Pellegrini, M. & Li, F. Comparison of the mitochondrial genomes and steady state transcriptomes of two strains of the Trypanosomatid parasite, PubMed DOI PMC

Simpson, L., Thiemann, O. H., Savill, N. J., Alfonzo, J. D. & Maslov, D. A. Evolution of RNA editing in trypanosome mitochondria. PubMed DOI PMC

Zhao, X. et al. Comparative mitochondrial genome and transcriptome analyses reveal strain-specific features of RNA editing in PubMed DOI PMC

Gerasimov, E. S. et al. Mitochondrial RNA editing in PubMed DOI PMC

Speijer, D. Is kinetoplastid pan-editing the result of an evolutionary balancing act. PubMed DOI

Brun, R., Hecker, H. & Lun, Z. R. PubMed DOI

Lukeš, J., Kachale, A., Votýpka, J., Butenko, A. & Field, M. C. African trypanosome strategies for conquering new hosts and territories: the end of monophyly? PubMed DOI

Lun, Z. R. et al. Cancer in the parasitic protozoans PubMed DOI PMC

Krampitz, H. E. Geographical distribution, host-parasite relationship and multiplication of Sicilian strains of PubMed

Zhang, X. et al. The effect of normal human serum on the mouse trypanosome PubMed DOI

Pérez-Morga, D. & Englund, P. T. The structure of replicating kinetoplast DNA networks. PubMed DOI PMC

Chen, S., Zhou, Y., Chen, Y. & Gu, J. fastp: An ultra-fast all-in-one FASTQ preprocessor. PubMed DOI PMC

Gerasimov, E. S. et al. Trypanosomatid mitochondrial RNA editing: dramatically complex transcript repertoires revealed with a dedicated mapping tool. PubMed DOI PMC

Prjibelski, A., Antipov, D., Meleshko, D., Lapidus, A. & Korobeynikov, A. Using SPAdes de novo assembler. PubMed DOI

Peng, Y., Leung, H. C. M., Yiu, S. M. & Chin, F. Y. L. IDBA-UD: A de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth. PubMed DOI

Koren, S. et al. Canu: Scalable and accurate long-read assembly via adaptive PubMed DOI PMC

Kumar, S., Stecher, G. & Tamura, K. MEGA7: Molecular evolutionary genetics analysis version 7.0 for bigger datasets. PubMed DOI PMC

Crooks, G. E., Hon, G., Chandonia, J.-M. & Brenner, S. E. WebLogo: A sequence logo generator. PubMed DOI PMC

Stamatakis, A. RAxML version 8: A tool for phylogenetic analysis and post-analysis of large phylogenies. PubMed DOI PMC

Krzywinski, M. et al. Circos: An information aesthetic for comparative genomics. PubMed DOI PMC

Wang, J.-F. Custom code for RNA editing analysis in Trypanosomes.

Kim, D., Langmead, B. & Salzberg, S. L. HISAT: A fast spliced aligner with low memory requirements. PubMed DOI PMC

Pertea, M., Kim, D., Pertea, G. M., Leek, J. T. & Salzberg, S. L. Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and Ballgown. PubMed DOI PMC

Horváth, A. et al. Downregulation of the nuclear-encoded subunits of the complexes III and IV disrupts their respective complexes but not complex I in procyclic PubMed DOI

Wittig, I., Karas, M. & Schägger, H. High resolution clear native electrophoresis for in-gel functional assays and fluorescence studies of membrane protein complexes. PubMed DOI