Assembly and annotation of the mitochondrial minicircle genome of a differentiation-competent strain of Trypanosoma brucei

Abstract

Kinetoplastids are protists defined by one of the most complex mitochondrial genomes in nature, the kinetoplast. In the sleeping sickness parasite Trypanosoma brucei, the kinetoplast is a chain mail-like network of two types of interlocked DNA molecules: a few dozen ∼23-kb maxicircles (homologs of the mitochondrial genome of other eukaryotes) and thousands of ∼1-kb minicircles. Maxicircles encode components of respiratory chain complexes and the mitoribosome. Several maxicircle-encoded mRNAs undergo extensive post-transcriptional RNA editing via addition and deletion of uridines. The process is mediated by hundreds of species of minicircle-encoded guide RNAs (gRNAs), but the precise number of minicircle classes and gRNA genes was unknown. Here we present the first essentially complete assembly and annotation of the kinetoplast genome of T. brucei. We have identified 391 minicircles, encoding not only ∼930 predicted ‘canonical’ gRNA genes that cover nearly all known editing events (accessible via the web at http://hank.bio.ed.ac.uk), but also ∼370 ‘non-canonical’ gRNA genes of unknown function. Small RNA transcriptome data confirmed expression of the majority of both categories of gRNAs. Finally, we have used our data set to refine definitions for minicircle structure and to explore dynamics of minicircle copy numbers.

Ecological divergence and hybridization of Neotropical Leishmania parasites

“…The minicircles encode guide RNA (gRNA) genes that are responsible for directing an elaborate U-indel RNA editing process that generates translatable maxicircle-encoded transcripts (31). Correct RNA editing is essential for parasite viability (32) and depends on a functionally complete set of minicircles (33). Putative guide RNA genes (gRNAs) were identified by aligning minicircle and maxicircle sequences to predicted edited mRNA sequences, allowing for G-U base pairs (34).…”

Common Structural Patterns in the Maxicircle Divergent Region of Trypanosomatidae

“…In contrast, maxicircles are much larger (25-50 kbps) and present in up to 100 copies [9]. It is highly likely that both molecule populations are heterogeneous in the cell [10][11][12][13][14][15][16][17]. Maxicircles are functional equivalents of mitochondrial genome of other eukaryotes.…”

Discovery of new mitochondrial DNA segregation machinery components inTrypanosoma brucei: a comparison of three approaches

“…The gRNAs are encoded on the minicircles of the network. A recent study showed that the T. brucei mitochondrial genome harbors about 400 different minicircle sequences in the network coding for 1300 gRNA genes (Cooper et al 2019) .…”