Trypanosomes are parasitic protozoan hemoflagellates that cause health problems in developing countries. These organisms diverged from other eukaryotes early in evolution and possess many unique RNA processing pathways such as uridine insertion/deletion editing of mitochondrial mRNAs. Studies of the RNA editing and guide RNA maturation processes emphasize RNA uridylylation reactions as crucial for RNA biogenesis in mitochondria of Trypanosoma brucei. We discovered three Terminal Uridylyl Transferases (TUTases), enzymes of unique structures and essential functions. This proposal focuses on: 1) functions of the RET1-catalyzed 3'-uridylylation in processing RNA precursors;2) the mechanism by which RET2 guides U-insertion;and 3) the biological role of MEAT1. We consider this research to be indispensable for the development of TUTase inhibitors as potential trypanocides.
The Specific Aims are: 1. Investigate functions of RET1-catalyzed 3'-uridylylation of small and ribosomal RNAs. The editing is directed by trans-acting guide RNAs which are post-transcriptionally modified by the 3'U -addition. Similar U-tails are also found in ubiquitous gRNA-like molecules and in rRNAs. We propose that uridylylation stabilizes gRNA-like molecules, which direct nucleolytic cleavage of maxicircle- and minicircle-encoded multicistronic transcripts. We will analyze functions, sequence diversity, and stability of short RNAs by next-generation sequencing and biochemical methods. 2. Determine the mechanism of the RET2-mediated U-insertion editing reaction. We propose that the fidelity of the U-insertion editing is determined by RET2's intrinsic selectivity for UTP and RNA substrates while complex association facilitates the editing efficiency. Structure-based predictions will be tested by a novel RNAi-based inducible genetic knock-in system. 3. Establish the function of MEAT1 TUTase. MEAT1 is an exclusively U-specific TUTase which associates with a 20S editosome-like particle and is essential for the parasite's viability. We propose to investigate whether U-insertion editing is accomplished by distinct RET2- and MEAT1-dependent mechanisms. MEAT1-specific U-insertion editing sites and interacting partners will be identified by in vivo crosslinking and quantitative mass spectrometry.
Trypanosomatids are the causative agents of parasitic diseases in developing countries, including areas of substantial American presence. Available treatments are often toxic and ineffective, which further stresses the need for new drugs. Targeting essential parasite-specific enzymes, such as mitochondrial RNA editing terminal uridylyl transferases (TUTases), is a promising approach toward a new generation of trypanocides.
|Suematsu, Takuma; Zhang, Liye; Aphasizheva, Inna et al. (2016) Antisense Transcripts Delimit Exonucleolytic Activity of the Mitochondrial 3' Processome to Generate Guide RNAs. Mol Cell 61:364-78|
|Aphasizheva, Inna; Maslov, Dmitri A; Qian, Yu et al. (2016) Ribosome-associated pentatricopeptide repeat proteins function as translational activators in mitochondria of trypanosomes. Mol Microbiol 99:1043-58|
|Aphasizheva, Inna; Aphasizhev, Ruslan (2016) U-Insertion/Deletion mRNA-Editing Holoenzyme: Definition in Sight. Trends Parasitol 32:144-56|
|Aphasizheva, Inna; Zhang, Liye; Wang, Xiaorong et al. (2014) RNA binding and core complexes constitute the U-insertion/deletion editosome. Mol Cell Biol 34:4329-42|
|Aphasizhev, Ruslan; Aphasizheva, Inna (2014) Mitochondrial RNA editing in trypanosomes: small RNAs in control. Biochimie 100:125-31|
|Aphasizhev, Ruslan; Aphasizheva, Inna (2013) Emerging roles of PPR proteins in trypanosomes: switches, blocks, and triggers. RNA Biol 10:1495-500|
|Aphasizheva, Inna; Maslov, Dmitri A; Aphasizhev, Ruslan (2013) Kinetoplast DNA-encoded ribosomal protein S12: a possible functional link between mitochondrial RNA editing and translation in Trypanosoma brucei. RNA Biol 10:1679-88|
|Aphasizheva, Inna; Maslov, Dmitri; Wang, Xiaorong et al. (2011) Pentatricopeptide repeat proteins stimulate mRNA adenylation/uridylation to activate mitochondrial translation in trypanosomes. Mol Cell 42:106-17|
|Aphasizhev, Ruslan; Aphasizheva, Inna (2011) Mitochondrial RNA processing in trypanosomes. Res Microbiol 162:655-63|
|Aphasizhev, Ruslan; Aphasizheva, Inna (2011) Uridine insertion/deletion editing in trypanosomes: a playground for RNA-guided information transfer. Wiley Interdiscip Rev RNA 2:669-85|