Trypanosoma cruzi mitochondrial maxicircles display species- and strain-specific variation and a conserved element in the non-coding region

Abstract Background The mitochondrial DNA of kinetoplastid flagellates is distinctive in the eukaryotic world due to its massive size, complex form and large sequence content. Comprised of catenated maxicircles that contain rRNA and protein-coding genes and thousands of heterogeneous minicircles encoding small guide RNAs, the kinetoplast network has evolved along with an extreme form of mRNA processing in the form of uridine insertion and deletion RNA editing. Many maxicircle-encoded mRNAs cannot be translated without this post-transcriptional sequence modification. Results We present the complete sequence and annotation of the Trypanosoma cruzi maxicircles for the CL Brener and Esmeraldo strains. Gene order is syntenic with Trypanosoma brucei and Leishmania tarentolae maxicircles. The non-coding components have strain-specific repetitive regions and a variable region that is unique for each strain with the exception of a conserved sequence element that may serve as an origin of replication, but shows no sequence identity with L. tarentolae or T. brucei. Alternative assemblies of the variable region demonstrate intra-strain heterogeneity of the maxicircle population. The extent of mRNA editing required for particular genes approximates that seen in T. brucei. Extensively edited genes were more divergent among the genera than non-edited and rRNA genes. Esmeraldo contains a unique 236-bp deletion that removes the 5'-ends of ND4 and CR4 and the intergenic region. Esmeraldo shows additional insertions and deletions outside of areas edited in other species in ND5, MURF1, and MURF2, while CL Brener has a distinct insertion in MURF2. Conclusion The CL Brener and Esmeraldo maxicircles represent two of three previously defined maxicircle clades and promise utility as taxonomic markers. Restoration of the disrupted reading frames might be accomplished by strain-specific RNA editing. Elements in the non-coding region may be important for replication, transcription, and anchoring of the maxicircle within the kinetoplast network.

We thank all the collaborators on the T. cruzi genome sequencing project generating the dataset upon which this study was based; Larry Simpson for the generation and maintenance of the RNA editing website; Dan Ray, Robert Hitchcock, Sean Thomas, Jesse Zamudio and L.L. Isadora Trejo Martinez for helpful discussions and/or critical reading of the manuscript. Primary sequence data from the T. cruzi CL Brener strain and Esmeraldo strain were obtained from The Institute for Genomic Research website at74. Sequencing of T. cruzi was funded by the National Institute of Allergy and Infectious Disease (NIAID). S.J.W. is a pre-doctoral trainee of the UCLA Bioinformatics Integrative Graduate Education and Research Traineeship program funded by NSF grant DGE9987641.

We thank all the collaborators on the T. cruzi genome sequencing project generating the dataset upon which this study was based; Larry Simpson for the generation and maintenance of the RNA editing website; Dan Ray, Robert Hitchcock, Sean Thomas, Jesse Zamudio and L.L. Isadora Trejo Martinez for helpful discussions and/or critical reading of the manuscript. Primary sequence data from the T. cruzi CL Brener strain and Esmeraldo strain were obtained from The Institute for Genomic Research website at 74 . Sequencing of T. cruzi was funded by the National Institute of Allergy and Infectious Disease (NIAID). S.J.W. is a predoctoral trainee of the UCLA Bioinformatics Integrative Graduate Education and Research Traineeship program funded by NSF grant DGE9987641.