Emerging roles of PPR proteins in trypanosomes: switches, blocks, and triggers

Abstract

Mitochondrial genomes of trypanosomes are composed of catenated maxicircles and mini-circles that are densely packed into a nucleoprotein structure called the kinetoplast. Maxicircle DNA (~25 kb long, 20-50 copies) resembles a typical mitochondrial genome bearing rRNA and respiratory complex subunits genes, and also contains 12 cryptogenes whose transcripts require U-insertion/deletion editing to assemble protein-coding sequences. Production of guide RNAs for the editing process remains the only established function of mini-circle DNA (~1 kb, ~10000 copies). Although editing remains the most studied step in mRNA biogenesis, recent investigations illuminated complex nucleolytic processing and pre- and post-editing 3' modification events that ultimately create translation-competent mRNAs. Key mRNA 3' processing enzymes, such as KPAP1 poly(A) polymerase and RET1 TUTase, have been identified but the mechanisms regulating their activities remain poorly understood. Discoveries of multiple pentatricopeptide repeat-containing (PPR) proteins populating polyadenylation complex and ribosomal subunits opened exciting experimental prospects that may ultimately lead to an integrated picture of mitochondrial gene expression.

Keywords: PPR proteins; RNA editing; TUTase; polyadenylation; trypanosoma.

Figure 1. Pentatricopeptide repeat proteins of Trypanosoma brucei. Repeats identified by TPRpred at http://toolkit.tuebingen.mpg.de/tprpred are indicated by red boxes; blue arrows denote mitochondrial targeting peptides as predicted by Mitoprot. PPR proteins were clustered based on normalized total peptide counts obtained by LC-MS/MS analysis of affinity purified polyadenylation complex and ribosomal subunits.^, Dashed lines typify presence KRIPP1 and KRIPP2 in the polyadenylation complex. Dotted lines illustrate detection of KRIPP5 and KRIPP9 in both LSU and polyadenylation complex. Tb927.5.1710 was identified as ATP synthase subunit. PAC, polyadenylation complex; SSU and LSU, small and large ribosomal subunits, respectively.

Figure 2. Protein sequence similarities among PPR proteins. (A) BLAST search of predicted trypanosomal proteins at http://tritrypdb.org/tritrypdb/ with PPR proteins as queries were used to derive e-values for building a similarity network. The thickest line corresponds to e-value of 10⁻¹⁵² while the thinnest corresponds to 6.5 × 10⁻⁵. (B) Tetratricopeptide repeat proteins of Trypanosoma brucei. Repeats are indicated by green boxes; blue arrows denote mitochondrial targeting peptides as predicted by Mitoprot.